PDF - Microbiology Society



PDF - Microbiology Society
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W. FordDoolittle
C e n o m e s e q u e n c e d a t a a r e r a i s i n gq u e s t i o n s o v e r t h e
definition of hacterial
After decades of radical reform, protozoan
Taxono m ic parameters
. larnishedgold
M o l e c u l a r s t a n d a r d su s e d t o c h a r a c t e r i z es o e c r e s
are outdated and may require re-definipg.
1 56 Virus systematics:taxonomy
for the tiny
s y s t e m a t i c sr e a c h e sa c o n s e n s u s .
170 Disentangling
the trailsof
SandraL. Baldauf
P h y l o g e n e ttirce e sa r e m a k i n ga n a l y s iosf t h e a b u n d a n c e
o f n e w s e q u e n cd
e a t ap o s s i b l e .
Haenni& Mike Mayo
A host of factors complicate the classificationof viruses.
160 How manyyeasts?
C o mm e n tMicrobiologyBytes
AlanJ. Cann
Whereto startwhen classifying
v e a s ts o e c i e s .
media' the future for microbiology
inrr6,*Lightningstrikinga tree.Mike Agliolo/ Science
,hj!t+r Dr Matt Hutchings
fhe views expressed
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New Editor f or MicrobiologyToday- Matt Hutchings
I am delightedto be taking over from CavinThomas
as Editor of MicrobiologyToday.I have a long-standing
i n t e r e s ti n m i c r o b i o l o g yw h i c h b e g a na s a P h D s t u d e n ti n
t h e B i o c h e m i s t rD
y e p a r t m e nat t S o u t h a m p t o nU n i v e r s i t y .
set up my own laboratoryas an RCUI(fellow in Molecular
My researchis focusedon learningmore about the
speciessenseand respond
waysin which Streptomyces
belongto a
to their environment.The streptomycetes
ln 19981 moved to StephenSpiro'slaboratoryat the
much largergroup of bacteriacalledthe actinomycetes
Universityof EastAngliato investigatenitric oxideand
one of my aims as Editorof MicrobiologyTodayis
t r o d u c et h i s d i v e r s eg r o u p o f b a c t e r i at o a w i d e r
audience.I am also interestedin the effectsthat microbes
postdoctoralpositionin Mark Buttner'slaboratoryat the
h a v eo n o u r l i v e s .T h i si n c l u d e sn o t j u s t b a c t e r i ab u t a l l
J o h n l n n e sC e n t r e .l t w a s h e r et h a t I s t a r t e dw o r k i n gw i t h
Strepto myces coeIi coIor,
t h e m o d e l o r g a n i s mf o r
the genus Streptomyces.
The streptomyceteshave
a c o m p l e xl i f e c y c l ew h i c h
i s u n u s u aal m o n gb a c t e r i a
a n d w h i c h i n c l u d e sh y p h a l
growthand sporulation.
More importantly,they
p r o d u c em o s t o f t h e
l se
a n t i b i o t i c si n c l i n i c a u
today.Earlierthis year
I m a d et h e s h o r tt r i p
backacrossthe Norwich
ResearchParkto UEA to
m i c r o - o r g a n i s mTs h
. o s et h a t l i v e o n o r i n s i d eu s , e i t h e ra s
p a t h o g e no
s r c o m m e n s aol r g a n i s m st ,h o s et h a t p r o d u c e
primaryor secondarymetabolitesthat are used by the
food and agriculturalindustriesand
t h e f r e e - l i v i n gm i c r o b e sw h i c h h a v eb o t h p o s i t i v ea n d
negativeeffectson the ecosystem.Traditionally,we have
s t u d i e do n l y t h o s e m i c r o b e sw h i c h a r e c u l t u r a b l ei n t h e
laboratory,a tiny fractionof the total microbiallife on this
planet.However,recent projectsto sequenceDNA from
t h e s o i l ,t h e o c e a n sa n d t h e a t m o s p h e r eh a v er e v e a l e d
j u s t h o w l i t t l ew e u n d e r s t a n d
a b o u t t h i s d i v e r s em i c r o b i a l
w o r l d . I h o p e t o c o v e rs o m e o f t h e s et o p i c sd u r i n g m y
time as Editor. I also hope we can useMicrobiologyToday
t h e s ei d e a st o a w i d e r a u d i e n c ea n d m a k e
to communicate
p e o p l ea p p r e c i a t e
w h y m i c r o b i o l o g yi s s o i m p o r t a n t .
Newsof members
ProfessorHilary Lappin-Scott,SCM Sci0ntificMeetingsOfficer,has become Presidentof
the lnternationalSocietyfor Microbial Ecology,with effectfrom August2006.
to EducationOfficerDr Sue Assinderon her appointmentas Director
t n i t i n t h e S c h o o lo f E d u c a t i o na t t h e U n i v e r s i t yo f W a l e s ,
o f t h e A c a d e m i cD e v e l o p m e nU
AgencyhasappointedProfessorHarry Flint, Head of the Cut
The Food Standards
Microbiologyand lmmunologyDivisionat the Rowett ResearchInstitute,to its Advisory
Committeeon Novel Foodsand Processes.
As a resultof recent
e l e c t i o n st ,h e f o l l o w i n gh a v e
been welcomedas new
m e m b e r so f t h e C o u n c i lo f
t h e B i o S c i e n c eFse d e r a t i o n :
ProfessorJohn Coggins,
l n s t i t u t eo f B i o m e d i c aal n d
The Societynoteswith regretthe death of Dr Andrew Robinson,HealthProtectionAgency,
PortonDown (member since1973).
N e w C o r p o r a tM
e ember
Dr Pat Coodwin (SCM
member),Head of Pathogens,
Im m u n o l o g ya n d P o p u l a t i o n
Studies,The WellcomeTrust
of syntheticolignucleotides,
Welcometo VH Bio, a manufacturer
s ,l e c t r o p h o r e sei sq u i p m e n ts, e q u e n c i n ag n d P C R
U l ( d i s t r i b u t ofro r s e p s i sP C Rd i a g n o s t i c e
(SCM member), Professor
lvxrrtlilsrLeEoll-insservice stationApproach,
ono suooofi
En w
w; w w w . v h b i o . c o m ) .
N E 1 1O z F( e a h e w i t t @ v h b i o . c o m
of MedicalMycology,
U n i v e r s i t yo f A b e r d e e n .
microbiologytoday n'{}r,'
SCM Council
Ynr rno
J u n eM e e t i n gH i g h l i g h t s
of the Year
S C Mj o u r n a l so p e na c c e sps o l i c y
I t i s n o w a c o n d i t i o no f W e l l c o m eT r u s tg r a n t st h a t p u b l i c a t i o nasr i s i n gf r o m w o r k f u n d e d
b y t h e T r u s tm u s t b e m a d ef r e e l ya v a i l a b l w
e i t h i n 5 m o n t h so f p u b l i c a t i o no, r i m m e d i a t e l y
if an open accesschargehas been paid.The Medical ResearchCouncilhas recentlyagreed
t o f o l l o w a s i m i l a rp o l i c y ,w h i l e o t h e r U l ( R e s e a r c C
h o u n c i l sh a v es e t r a t h e rm o r e r e l a x e d
r e q u i r e m e n t sT. h e p u b l i s h i n gp o l i c i e so f a l l S C M j o u r n a l sh a v eb e e n m o d i f i e dt o i n c l u d e
an open acessoption in exchangefor an author-sidepayment(for detailssee Ron Fraser
and Robin Dunford'sarticlein the August issueof MicrobiologyToday,
p. 1aC4.Further
d e v e l o p m e n to
s n t h i s f r o n t w i l l b e c l o s e l ym o n i t o r e db y S C M a s o p e n a c c e s sp u b l i s h i n gi s
t h e s u b j e c to f i n t e n s ed e b a t ea n d r a p i dc h a n g e .
B u d g e 2t O O 7
T h em a i n b u s i n e s o
s f t h e s u m m e rm e e t i n go f t h e S C M C o u n c i lw a st h e a p p r o v aol f t h e
budget 2007. Thiswas set with either no changesor inflationaryincreases
to membership
s u b s c r i p t i o nasn dj o u r n a l p r i c e s .I n s t i t u t i o n asl u b s c r i p t i o ntso j o u r n a l sw e r e i n c r e a s e d
l i n e w i t h i n f l a t i o nt,h e i n c r e a s ei n t h e s i z eo f t h e j o u r n a l sa n d t h e s m a l la n n u a ld e c l i n ei n
the market. In the caseof the Journalof 1eneral Virology,an allowancewas made for the
i n c o m es t r e a md u e t o t h e n e w a r r a n g e m e n tws i t h o p e n a c c e s sc o n d i t i o n sS
. C Mj o u r n a l s
r e p r e s e net x c e l l e nvt a l u ef o r m o n e y ,g e n e r a l l yb e i n go n e - t h i r dt o o n e - q u a r t eor f t h e p r i c e
p e r p a g eo f j o u r n a l sp u b l i s h e db y c o m m e r c i apl u b l i s h e r s .
I \-/
The York meetingsaw the
f i n a l so f t h e S C M ' ss c i e n c e
c o m m u n i c a t i o cn o n t e s tT. h i s
y e a ra b u m p e rf i e l d o f 1 1
keen postgradsor postdocs,
who had been selected
as finalistsby the Special
I n t e r e sC
t r o u p sa n d l r i s h
B r a n c ho n t h e b a s i so f t h e i r
oral or poster)at recentSCM
m e e t i n g sg, a v e1 0 m i n u t e
talkson their research.
standardwas amazingly
h i g ha n d t h e j u d g e s ,
p r o v i d e df r o m t h e C r o u p
C o m m i t t e e sa n d c h a i r e d
b y J o V e r r a n ,E d u c a t i o n&
The funds availablefor SCM grantshave been increasedfrom approximatelyf.332kto
T r a i n i n gC r o u p C o n v e n e r ,
had a very difficultjob. The
f 3 8 5 k a s a r e s u l to f s i g n i f i c a ni tn c r e a s eisn t h e j o i n t m e e t i n g sa n d t r a v e lf u n d s( s e eb e l o w ) .
w i n n e r sw e r e a n n o u n c e d
C o u n c im
l embers
at the SocietyDinner later
that evening.The first
T h i sw a s t h e l a s tC o u n c i lm e e t i n gf o r H u g h P e n n i n g t o na s S C M P r e s i d e nat n d c h a i r .
C o u n c i lm e m b e r st h a n k e dh i m f o r a l l h i s e f f o r t s ,i n p a r t i c u l afro r h i s i n t e r a c t i o nw i t h t h e
m e d i aw h i c h h a sh e l p e dt o r a i s et h e p r o f i l eo f m i c r o b i o l o g yi n g e n e r a a
l ndthat of the SCM
i n t h e p u b l i ce y e .C o u n c i la l s ow i s h e dh i m w e l l i n h i s r o l e a s C h a i r m a no f a W e l s hA s s e m b l y
l n q u i r yi n t o a r e c e n tE . c o l i 0 1 5 7 o u t b r e a k T
. h e i n c o m i n gP r e s i d e n tR, o b i nW e i s s ,a t t e n d e d
t h e C o u n c i lm e e t i n ga s a n o b s e r v e a
r n d w i l l t a k e o v e r f r o m H u g h i n S e p t e m b e r2 0 0 6 .) e f f
Cole,Jeff Errington,PeterAndrew and Cavin Thomas havealso completedtheir term on
C o u n c i l ,a n d t h e P r e s i d e ntth a n k e dt h e m f o r t h e i r e x p e r ti n p u t a n d e n g a g e m e n t .
S C M C r a n t sa n d F u n d s
T h eS C M C r a n t sa n d F u n d ss c h e m e sh a v eb e e n r e v i s e da, n d t h e o v e r a l fl u n d i n gh a s
been increased(seep. 146 for further information).Detailsof the schemesand extended
e l i g i b i l i t yc r i t e r i aw i l l b e a v a i l a b l e
o n t h e S C M w e b s i t e( w w w . s g m . a c . u ki n) d u e c o u r s e .
U n t i l t h e e n d o f 2 0 0 5 ,t h e p r e s e n tc o n d i t i o n sa p p l y .
UIrich Desselberger,CeneralSecretary
to StaffEditorAshreenaOsman and her husbandJasonon the birth of a
s o nA j a yi n i u n e .
Althoughthe baby appearedon the sceneratherearlierthan expectedand had to stayin
h o s p i t aflo r w h i l e , h e i s n o w a t h o m e w i t h h i s m u m a n d d o i n gw e l l .
mi c r ob i ol o g y
o r i z eo f f 5 0 0 w e n t t o J . D .
Neufeld (Warwick)for his
presentation Methy Iotrop hs
in the spotlight.The second
prizeof f200 was won by
P.A.Rowley (Aberdeen)and
the third prizeof f.100 by
All finalistswill get free 5CM
m e m b e r s h i pi n 2 0 0 7 .
F u r t h e rd e t a i l so f t h e
competitionand an entry
form are availableon the
meetingspageof the SCM
website.Why not enter
by submittingan offered
posteror oral presentation
for the springmeetingat
Manchesternext year?The
closingdate for abstractsis
27 November2006, so get
New Council Officers
With effectfrom 12 September2006, ProfessorRobin
y o l l e g eL o n d o n )c o m m e n c e sh i s 3 - y e a r
W e i s s( U n i v e r s i tC
term as President.A profileof ProfessorWeissappeared
Today.Dr Matt
in the Augustissueof Microbiology
i a)
al socommen ces
H utchi ngs
3-yearterm as Editorof
New electedmembersof Council
The followingwill serveon Councilfor 4 yearsfrom 12 September2005. ProfessorMichael
) , r R i c h a r dM . H a l l ( C l a x o S m i t h l ( l i n ae n) d D r C a t h e r i n e
R . B a r e r( U n i v e r s i t oy f L e i c e s t e r D
O'Reilly (WaterfordInstituteof Technology).
C a t h e r i nO
I a m P r o f e s s oor f C l i n i c a l
Microbiologyat Leicester
U n i v e r s i t yI .t r a i n e di n
M e d i c i n ea n d l m m u n o l o g y
T r i n i t yC o l l e g eD u b l i n i n
1 9 7 8 a n d c o n t i n u e di n t h e
samedepartmentto do my
at UniversityCollege
L o n d o na n d i n C l i n i c a l
Microbiologyat 5t
C e o r g e ' sL, o n d o na n d i n
Newcastle.My principal
researchinterestslie on the
interfacebetween bacterial
physiologyand infectionand most of my current research
i s c o n c e r n e dw i t h t u b e r c u l o s iasn d t h e s t u d yo f b a c t e r i a l
c e l l st h a t a r e d i f f i c u l t o c u l t u r e .| f i r m l yb e l i e v ec l i n i c a l
and practice
m i c r o b i o l o g i s st sh o u l db a s et h e i r r e s e a r c h
g i c r o - o r g a n i s masn d s e e kt o p r o m o t e
o n u n d e r s t a n d i nm
e e t w e e nb a s i cs c i e n c ea n d c l i n i c a l
b e t t e ri n t e r c h a n g b
practicein this area.
I graduatedin Ceneticsat
P h D o n p r o l i n eb i o s y n t h e s i s
typhimuilum.I then
and insertionsequencesin Salmonella
moved to the Max PlanckInstitutein Colognefor 2 years
as an EMBO postdoctoralfellow where I worked on
t r a n s p o s a b leel e m e n t si n m a i z e .F o l l o w i n gt h a t I w o r k e d
as an EU postdoctoralfellow in the Departmentof Botany,
D u r h a m ,w o r k i n go n o p l n e b i o s y n t h e s iisn A g r o b a c t e r i u m
The next 10 yearswere spent at the University
o f S u n d e r l a n dT. h e r eI d e v e l o p e da n i n t e r e s ti n m i c r o b i a l
cyanideand nitrile metabolism.I moved to Waterfordin
1 9 9 6 a n d h a v ec o n t i n u e dt o w o r k o n n i t r i l ea n d c y a n i d e
m e t a b o l i s mC. u r r e n tr e s e a r c hi s m a i n l yf o c u s s e do n t h e
and the use
geneticsof nitrile metabolismin Rhodococcus
of nitrile-hydrolysing enzymesi n biotransformation.
industryfor over
I haveworked in the pharmaceutical
g r o u p l o c a t e dw i t h i n C e n e E x p r e s s i oann d P r o t e i n
B i o c h e m i s t rayt C l a x o S m i t h l ( l i ni en H a r l o w .M y m a i n
interestsare in the expressionand scale-upof recombinant
I remainedin Manchesterand was appointedas a Research
i n c l u d i n gt h e u s eo f m i c r o b i a sl y s t e m st o m i m i c m a m m a l i a n
m e t a b o l i s mC. l a x o S m i t h l ( l i nwea s f o r m e d i n 2 0 0 0 a n d I
m o v e dt o m y p r e s e n tl o c a t i o ni n 2 0 0 1 .
I am marriedwith two daughtersboth at university.
H o b b i e si n c l u d ef i s h i n g f, o o t b a l l( l ' m a l o n g - t i m es u p p o r t e r
of ManchesterCity) and
w a l k i n g( l c o m e f r o m t h e
s e p a r t m e not f C h i l d H e a l t h ,
A s s i s t a ni n
t t h e U n i v e r s i t y 'D
on brain development.
I h a d t h e g o o d f o r t u n et o t h e n j o i n C o l i n R a t l e d g e ' s
g r o u p ( U n i v e r s i toy f H u l l )w o r k i n go n a s p e c t so f i r o n
and was awardedmy PhD
metabolismin mycobacteria
L a k eD i s t r i c ts o i t i s i n t h e
g e n e s l )l.j o i n e d t h e S C M
i n 1 9 8 4( l t h i n k C o l i n
i n 1 9 8 3 . I r e m a i n e da t H u l l f o r a p o s t d o c f, o c u s s i n g
Mycobacteriumleprae(causalorganismof leprosy).
with the Fermentatio&
B i o p r o c e s s i nCgr o u p .I h a v e
l n 1 9 8 5 , l j o i n e d C l a x o ,w o r k i n gi n a n a t u r a lp r o d u c t s
group basedat Creenford.Followingthe mergerwith
where I was
Wellcomein 1995,1 moved to Stevenage,
recentlyoffered my services
t o t h e E d u c a t i o n& T r a i n i n g
g r o u p a n d a m d e l i g h t e dt o
b e j o i n i n gt h e C o u n c i l .
particularlyinvolved in aspectsof biotransformation,
talked me into it) and
have previouslyworked
microbiologytoday l"r**:r
S C M h a sj u s t p u b l i s h e ad
c o l o u r f u lb o o k l e tt o h e l p
c o m m u n i c a t teh e i m p o r t a n c e
o f m i c r o b i o l o g i c ar el s e a r c h .
b o o l < l eits t o a l e r tt h e p u b l i c
to some of the amazing
d i s c o v e r i ebse i n gm a d e b y
m i c r o b i o l o g i s itns t h e U l ( .
M i l l i o n sa r e s p e n te a c hy e a r
T h e b o o k l e ti s t h e
o n r e s e a r c hi n v o l v i n gm i c r o o r g a n i s m sH. o w e v e r t, h e
public can perceiveresearch
o u t p u tf r o m a w o r l c s h o p
on Communicating
M i crobi oIogy or ganized
a s b e i n ge s o t e r i ca n d u n l i l < e l y b y t h e S C M . T e ny o u n g
to havea significantimpact
m i c r o b i o l o g i sjtosi n e d M y c
on their livesA
. tlention
Riggulsford,a professional
t e n d st o b e c o n f i n e dt o
facilitatorwith extensive
c o n t r o v e r s i ai sl s u e s u c h
ef writing
as avian'flu and MMR
s c i e n c ef o r t h e g e n e r a l
p u b l i c ,t o l e a r na b o u t
t h e m i c r o b i o l o g i c ai nl t e r e s t s
s f effective
the principleo
of only a f ractionof U l(
s c i e n t i s t sT.h e i d e ao f t h e
s c i e n c ec o m m u ni c a t i o n .
T h ec h a l l e n g e
for the
N e w c o m m i t t e em e m b e r s e
, l e c t e db y p o s t a lb a l l o tf o r t h e
P h y s i o l o g yB,i o c h e m i s t rayn d M o l e c u l a rC e n e t i c sC r o u p o r
e l e c t e du n o p p o s e d( a l l o t h e r C r o u p s )t o s e r v ef o r 3 y e a r s
f r o m 1 2 S e p t e m be r 2 0 0 6 a r e a s f o l l o w s :
C e l l sa n d C e l lS u r f a c e s
A. Cunningham Universityof Birmingham
J.R. Fitzgerald Universityof Edinburgh
R. Massey Universityof Oxford
C l i n i c aMl i c r o b i o l o g y
5. Lang ClasgowCaledonianUniversity
D. Mack Universityof WalesSwansea
S. Patrick Queen'sIJniversitvBelfast
D. Ready EastmanDental Hospital,London
C l i n i c aVl i r o l o g y
P.Cane Health ProtectionAgency,Porton Down
E. MacMahon St Thomas'Hospital,London
D. Pillay UniversityCollegeLondon
J. Breuer Barts& TheLondon hastaken over as Crouo
Edu cat iona n dT r a i n i n g
W. Ashraf University
of Bradford
S.Bur t on Universityof Exeter
R .Dix on Universityof Lincoln
E n v i r o n m e n tM
a il c r o b i o l o g y
was to then
a p p l yt h e l e s s o n sl e a r n t o
produce a 1 -pagearticle
d e m o n s t r a t teh e n e e d
t o p r o v i d ec o n t i n u e d
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u Le! er n
d e f i n i n o. . ) r_n.d. . . .r.e- ._. .-l g n l z r n g
needs for ldentifica[ion and naming
s n e c i e s F re n a n i m a l a n d
plant speciesaresometrmes
difficult to delimlt. and
philosophers disagreeabout the ontothe word. But
^l "o
b 'p
- * i' c a l r e [ e r e n l so l
nrir-roheq -
seem to pose special problems. Their
smal1 srze and general uncultivability
(only a ver;'small percentagecan grow
in the 1ab)confound efforts to describe
r r r - h i v c.
r, v, /nfe-
nrokarv,rlesrenrodlrcease\uallv and
a r e t h l r s ,i 'n' n
r ' r 'i-n' -c' irn' l e u n a b [ et o e o n [ o r m
1t) Frnst V
' ^v]r' s- r "nr o
. .n. r. r' l"r.r" . \BJi .o5l o. -p*i c a l
S p e c i e sC o n c e p t - ' g r o u p s o J a t t u u l l y o r
" "b"'
rt ,' l, r, i' l, l, i, n6 o
1L v6
c h , r v' c' . . i.nt ] -o .e.n. e^ r. e. l
2 L6l 1l l-l il tI
tt hl l nC tl L
P l a r L L l L A l
a g r e e d - u p t r nb u t p r o r i s i o n a l ( a n d a i
least in some sensearbitrary) speciet
d e f i n i t i o nw. h i l e t h e m o r et h e o r e t i c a l l ;
driven searchfor a unrlyng species
conceptthat would explain patterns
o i m i c r o b i a ld i v e r s i t yi n e c o l o g i c aal n d
population genetic terms could wait
for the accumulation of more data,
e c n e c i , r l l v' - l o e n e
d a t a . O p e r a l i o n a l l ym
. o l e c u l a rd e f i n i tions havewon the da;. and species
a r e l l q l r a l l ve x n e c t e dt o s h a r ea t l e a s t
7 0 o / ob" - -i-n* - -d' b i n s -i-n- s" r a n d a r d i z e D
d NAf \ \ ' 1 L . . L - : - : :l - ^ , : . ^
rJr\11 rry rjrlLlrzdLrurl
and/Of Of ef 97
potentially interbreeding naturctl popu-
o p n p - q e n r r e n r ^ ei d e n t i t i r f n r
lations whtch are reproductittely isolated
somal RNA (rRNA) (see the article by
€>Eberson p. 152).
Thrrc. rni{-rnhinlnois.t
I 6S
t o d a y i ] l r ! , i, , i l
a Lawrence Lawry / Science Photo Library
WhatI S a bacterial
Doolittle d iscusses
how genomed alaare
giving microbiologists
causeto th ink carefully
abouthow to define
the 'species'.
within diversity
As a bonus, molecuiar methods allow
us to identify and enumerate species
in the environment without isolating
and cultivating any organisms - for
instance,using specific PCR primers to
amplify and sequence 165 genes from
unfractionated environmental DNA
preparations. What we often find is
an astonishing number and diversity
of apparent species, with few 165
sequencesassignableat the 97 o/olevel
to any cultivated isolates - including
isolates from the same sampling site.
Moreover, many species, as defined
by the 97 ok 163 identity cut-off, wili
themselvesbe representedby multiple
different but similar indivldual sequencesin any sample (Flg. 1).
Such gene sequence'microdiversity'
is the rule rather than the exception
with environmental sampling of many
genes(in addition to 165), and may be
matched by another kind of variation
at the level of genome composition
(gene content). Martin Polz and coliaborators have used pulsed-field geL
eiectrophoresis to show that Vibno
splendidusisolates (with >99ok 165
sequence identity) from a sample site
on the Massachusettscoast can differ
by as much as a megabase in size,
least a thousand distinct
geno$pes, each occurnng at extremely
Iow enyironmental concentrations bn
averagelessthan oneper millilitre)'.
Gene content diversity has also
emerged as a principal message of
more'traditional' complete genome
sequence studies, based on cultivated
isolates.When such activities began, a
decade ago, the thought was that one
sequence (that of strain K12) would
surely be enough to define Eschenchia
coli, one would do for Bacillus subtilis,
and so forth. Completion of the second
E. coli (O157:H7) gaveus a shock. This
sometimes lethal food contaminant
proved to have I,387 genesnot presenl
in KI2, scatteredin hundreds of small
or large clusters around its genome.
(Reciprocally,Kt2 had 528 genes nol
in Ol57:H7.) The two genomeswere
otherwise (aside from one inversion)
collnear,exhibiting 98o/oaveraqenucleotide identity (ANI) between shared
Now that there are more than three
dozen species with more than one
strain sequenced,results like this seem
to be almost the norm. Strains which
are very close on the basis of the
sequencesof the genes they do share
;..:.' genes
within and
may neverthelessdiffer by ,p to 30 % in gene content, the
differencesbeing attributable to scoresor hundreds of events
of gene gain (mostly by lateral gene transfer) and gene loss
after divergence from a common speciesancestor.Although
many variable sequences are phages or transposable elements, others are genesvitally important in defining a strain's
specificniche. Sometimessuch genesare t{ansferredtogether:
islands' exemplify this, but the phenomenon
is not limited to pathogens. Endosl'rnbiotic nitrogen-fixing
strains of Mesorhizobium,for instance, possessan approxi'qrmbiosis
island' which encodes not only
mately 500 kb
the dozen and more genesneeded to form root nodules, but
most or all genesneeded for nitrogen fixation and the island's
own strain-to-strain transfer.
It has recently become popular to think in terms of
'pangenomes' (Fig.
l), consisting of a core or
genomes' or
backbone of genes shared by all strains and an auxiliary or
flexible gene pool found only in one or some strains. For
some groups, the number of such auxiliary genes abeady
exceedsthe number of genes in the core, and just keeps on
climbing with each new genome sequenced. Core genes in
contrasl get fewer with each new genome. But still there will
be hundreds to thousands of core genes for any group we
might want to call a species, and they will usually comprise
a colinear backbone, within which Iaterally transferred
genes and islands can be seen to be embedded. We might
use concatenated (strung-together) core gene sequences to
define species with greater precision and nuance than either
Fig. 1. Diversityand microdiversity.
T r e e sb a s e d o n 1 6 5 r R N A o r o t h e r
phylogeneticmarker genes sequences
o f t e n s h o w ' m i c r o d i v e r s i t y ' ,e x h i b i t i n g
c l u s t e r so f s e q u e n c e sm o r e c l o s e l y r e l a t e d
than the value accepted as defining
s p e c i e s( v e r t i c a l h a t c h e d r e d l i n e ) . E v e n
i n s p e c i e ss o d e f i n e d , g e n o m e s c a n s h o w
s u b s t a n t i a l( u p t o 3 0 7 o ) v a r i a t i o n i n s i z e
and gene content. A
genome' or
can be imagined to comprise
c o r e g e n e s s h a r e d b y a l l i t s s t r a i n s ,a n d a
s e t o f a u x i l i a r yg e n e s f o u n d o n l y i n s o m e
strains. These two classesof genes may
have different evolutionarv modes and
temoi. W.F. Doolittle
DNA-DNA hybridization or 165 allow. Konstantinidis &
Tiedje noted that an ANI value of greater than 94 o/ofor core
genes characLeizesmost species defined by other means.
We might also use phylogenetic trees of concatenated
core gene sequences to establish lineage relationships of
strains within a species, although for this, homologous
recombination poses a complication. Increasingly, many
bacteria (and some archaea) turn out to avidly indulge in
between-strain homologous recombination. Recombination
means that different genes will have different evolutionary
histories, and there will be no unique phylogeny relating
the genomes of different s[rains of a species. The rate of
recombination in bacteria will of course never approach that
of animals, who must recombine every time they reproduce,
but still it can exceedmutation as a generator of evolutionary
novelty This raises the possibility that the Biological Species
Concept might appropriately be applied to some bacreria
after all, at least in so far as it entails sharing of core genesby
recombination in a common gene pool.
Cettingthe concept
Homologous recombination is one process that confers
genomic coherence (within-species similarity and betweenspeciesdivergence)in prokaryotes,just as it does in animals.
Members of speciesA will more closely resemble each other
than they do members of a sister speciesB, becauseat most
core gene loci they share alleies that have arisen within the A
genepool. Periodic selectionis another coherence-generating
microbiologytoday rre.rv
We will be morelikellrto realizeafult
of microbialdiversification
we acceptthat the word 'species',
fo, all its
utility, may haveno precisereferent.
process, which will also homogenize
gene content. In this mode, favourable
mutations sweep to fixation within
a physically or ecologically bounded
finite asexual population, carrying the
rest of the genome in which they first
occurred (and whatever auxiliary
genes it might bear) along for the
ride. Mutations at other loci than that
under selection may of course occur
along the wa\, and if homologous
recombination is frequent, in the end
only the favoured mutation - not the
genome in which it first appeared wiil achieve fixation. In different
groups and at different times these two
forces will vary in strength to promote
coherence in gene sequence and/or
genecontent, but there is no guarantee
that either will maintain or createsharo
species boundaries. Divergence i"
sequence suppresses recombination,
but recombination with divergent
sequences might often offer more
significant selective advantage. Agents
of genetic exchange (phages and
conjugation systems) have recognition
specificity, but as selfish elements are
under pressureto broaden, not restrict,
and ecological selective forces may
creategroups as genomically coherent
as animal species, but there is no
compelling theoretical argument that
they must always or usually do so, and
so far there are insufficient data to say
that they generaily have.
Lateral gene transfer is no respecter
of species boundaries and disrupts
genomic coherence, however defined
or achieved.More to the point, transfer
is often the source of those geneswhose
microbiologytodayn*v ir{:i
expressionin phenotype most strongly
differentiares closely related taxa,
and concerns us most as practising
microbiologists. So molecular definitions of species based on whole
genomes may be only poorly coupled
to the ecologicaldrivers of the processes
of diversification and adapration we
would like to think of as speciation.
For this reason Konstantinidis &
Tiedje suggesr that microbiologists
might better bring their ideas about
speciesin line with those of zoologists
only strains that show a
>99 % ANI or are less identical at tlte
nucleotidelevel,but sharean overlapping
ecologcal niche...' (emphasis mine).
They are willing ro be flexible about
using overall genomic coherence in
recognizing species,when phenotypic
differences.(which will often be due
to laterally transferred genes) seem
to warrant it. Our current species
definitions and the more genomically
based criteria likely ro be adopted soon
serve thelr practical purposes as well as
we can expect, but there can be no very
precise mapping to arry unitary model
of diversificarion and adaptation. Thar
is, it seemsunlikely that we will soon,
if ever, have a uniform speciesconcept
that will allow us ro give unqualified
(definition-independent) answers to
such questionsashow many prokaryotic
speciesare there at some particular site,
or in the whole world. It's not that there
is no hope for a full understanding of
microbial diversificarion, adaptation
and dispersal - it's just that we will be
more likely to realize rhat hope if we
accept that the word'species', for all its
utility, may have no precise referent.
W. FordDoolittle
of Biochemistry
83H 1X5(. ford6dal.ca)
Hanage, WP, Fraser, C. 6c Spratt,
B.G. (2005).Fuzzy speciesamong
recombinogenic bacrena. BMC Biol3, 6.
Konstanrinidis, T.K. 6l Tiedje, J.M.
(2005). Genomic insights that advance
the speciesdefinition for prokaryotes. proc
N atl Acadsci U 5 A L02, 2567 -2572.
Perna, N.T., Plunkett, G., Burland, V
& others (200f). Genome sequenceof
enterohaemorrhagrcEschenchiacoli O I 5T :
H7 . Nature 4I0, 529-533.
Sogin, M.L., Morrison, H.G., Huber
J.A., Welch, D.M., Huse, S.M., Neal, pR.,
Arrieta,J.M. & Herndl, GJ. (2006).
Microbial diversity in the deep sea and
the underexplored 'rare biosphere'. proc
NatlAcadsci USA 103,12I L5-I}IZO.
Thompson, J.R., Pacocha,S., pharino,
C., Klepac-Ceraj, V, Hunt, D.E., Benoit,
J., Sarma-Rupavtarm,R., Distel, D.L. &
Polz, M.E (2005). Genotypic diversity
within a natural coastal bactenoplankton
307, 131l-1313.
. Exciti
the definition of a pecies'
ith the inclusion
of defined genomic properties in
ards' of
descriptions, molecular data arenow fully acknowledgec
in systematic studies of prokaryotes.
Depending on the rank of a taxon,
these approaches are either mandatory
or optional. At the taxonomic level of
molecular properties serve
two requirements: first, to verify the
chemotaxonomic coherence of strains
by their similarities
of a
(preferably identity) at the genomic
level and, second, to delineate this
taxon from phylogenetically neighbouring species of the genus (Wayne
hereby ffin*<m
new findingsannounced
show that
and Swmas
a 155rRNAgenesequence
above98.7-99o/oshouldbe mandatoryfor
of a novel
testingthe genomicuniqueness
the old valueof
97 o/oand will greatlyfacilitatethe work
et al., l9B7 Rossell6-Mora & Amann,
2001). As the taxon'species'represents
populations that themselves are the
of taxonomists.
microbiologytoday rl*v fr{i
result of different mechanisms and tempi of evolution
(Stackebrandtet al., 2002; Geverset a\.,2005), the degree
of deviation from nearly absolute phenotypic and genomlc
identity (as expected to occur in clones) requires from taxonomists a balanced judgement of evolutionary processesthat
they may possibly not be aware of. In order to facilitate
and harmonrze taxonomic decisions in a field in which the
Biological SpeciesConcept does not apply, an arbitrary and
artificial definition has evolved over a century of bacterial
taxonomy (Staley& Krieg, L9B4; Stackebrandt,2000); today,
is more stringently
the description of [he construct
controlled by recommendations than that of any other taxon.
While in the pre-Approved Lists era, taxonomists were
allowed to follow their own subjectivejudgements, the past
75 yearshave witnessed a more objective and internationally
controlled verification processof
The predictability of the uniqueness of a
has been largely strengthened by the universal applicability
of molecular data. Methods applied, to name a few,
embrace approximate characterization of the chromosome
by determination of the base composition (mol% G+C
content) and degree of reassociationof single-strandedDNA
(DNA-DNA hybridization) as well as comparison of one-
dimensional restriction and PCR patterns (Pukall, 2005);
other methods focus on genesand operons, encodlng rRNA
and proteins, including typing and sequencing. Each of the
methods appiied has its strength in elucidating a defined
range of the 4-billion-year evolution of prokaryotes. Though
several molecular methods have their merits in taxonomy,
two approaches,the
standards', play a dominant role:
DNA-DNA hybridization for'species' delimitation, and 165
rRNA gene sequencesimilarities for unravelling more distant
relationships among strains. DNA-DNA hybridization can
be expressed as percentage reassociationsimilarity or ATof reassociatedDNA strands (Wayne et aL, 1987), but
only the first parame[er is in general use. This judgement
appears objective when browsing through the past 15 or
so volumes of the International Journal oJ Systematicand
Evolutionary Microbiology (USEM) (formerly International
Journal of SystematicBactenologt), the official publication of
the International Union of Microbiological Societies(IUMS).
Almost every species description contains a phylogenetic
analysisof the tlpe strain based on 165 rRNA gene sequence
similarity comparison and many novel speciesare delineated
from their phylogenetic neighbours by DNA-DNA reassociation valuesbelow 70o/o.
4 Cold standards. Digital Vision
microbiology today $$ri iJi;i;
s i m i l a r i t i easn d D N A - D N A r e a s s o c i a t l o n
W F i g . ' i .C o m p a r i s oonf 1 6 5 r R N A g e n es e q u e n c e
s p e c i e sd e s c r i p t i o nfsr o m
v a l u e sD
. a t ah a v eb e e nc o m p i l e df r o m p u b l i c a t i o ncso n t a i n i n g
of reassociation
IJSEM55 (2005).Thedifferentcoloursreferto broad categories
r e d , m i c r o t i t r ep l a t et e c h n i q u ee, . g .E z a kei t a l . ( 1 9 8 9 ) ;d a r kb l u e ,s p e c t r o p h o t o m e t r i c
, e m b r a n ef i l t e rm e t h o d ,e . g .T o u r o v a&
t e c h n i q u ee, . g .D e L e ye t a l . ( 1 9 7 0 ) ;l i g h t - b l u em
a t a | . 2 0 0 5 ) ,o r
, . g .d o t h y b r i d i z a t i o(nA m a k a t e
A n t o n o v( 1 9 8 7 ) ;b l a c k ,o t h e rm e t h o d s e
n o t d e f i n e d .H o r i z o n t arlu l e sb e t w e e ns q u a r e si n d i c a t ed a t ao b t a i n e db y t w o d i f f e r e n t
t ei nda r y1 6 5
. r r o w sp o i n t t o t h e p o s i t i o no f i n s i l i c o - r e c a l c u l a b
r e a s s o c i a t i omne t h o d sA
r R N Ag e n es e q u e n c se i m i l a r i t vy a l u e so f s e q u e n c edse p o s i t e db y A m a k a t ae t a l . ( 2 O O 5 ) . f h e
h o r i z o n t abl l u e b a r i n d i c a t etsh e t h r e s h o l dr a n g ea b o v ew h i c h i t i s n o w r e c o m m e n d etdo
p e r f o r mD N A - D N A r e a s s o c i a t i oenx p e r i m e n t st h; e h o r i z o n t arle d b a r i n d i c a t etsh e t h r e s h o l d
d tC o e b e l , 1 9 9 4 )E
d tJ . E b e r s
. . S t a c k e b r a n&
v a l u e sp u b l i s h e dp r e v i o u s l(yS t a c k e b r a n&
Despite the imporlance of the DNA-DNA reassociation
approach, most microbial taxonomisls are not in a position
to pedorm these studies and need collaboration with
specialized laboratories. Experience is needed in isolation
and purification of DNA and, although one can choose from
a v ariety of differen t hybrrdization metho ds (Rosse1l6
2005), none of these is straightforward to appiy without
thorough training. But these are not the only reasons for
the aversion to this technique: the method of reassociation
of denatured DNA strands of two different slrains unfolds
the homologous genome stretches that are involved in the
reassociation process. in these times of complete genome
sequences and the teaching of sequence techniques to
undergraduates, this failure to examine the mechanisms
behind the process makes DNA-DNA reassociation seem
like a method salvaged from the past. Also, a significant
number of physico-chemical parameters, genome size, the
presence of large plasmids, DNA purity and other factors,
influence the hybridization results; reciprocal values may
differ by rp to 15 o/o.Unlike sequences,which must be
deposited in public databasesfor inspection of quality, no
reviewer of a new speciesdescription is in a position to judge
DNA reassocialion values. Last, but nol least, as the data
are not cumulative, studies on a large number of closely
related species(i.e. in the genera Streptomyces,
Aeromonasor certain groups of Bacillus)may become a search
for the end of the rainbow. However, il must be conceded
that the requirement to provide evidence for overall genomic
and phenetic similarity among members of a species on
the one hand, while proving dissimilarity of characler
traits between members of different species on the other,
works well, and has set the stage for stability in prokaryotic
taxonomy, keeping in mind the artificial definition with
which'species' are described.
At the beginning of the 1990s, with the release of the
avalanche of 165 rRNA gene sequences,il became obvious
that sequence similarities and DNA reassociation values
obtained for the same strain pairs do not show a linear
6sAmann, 2001; Foxet aL,1992',
could be demonstratedon
the basis of a limited dataset that, below a threshold value
of 98.5 o/ogene sequence similarity, the corresponding DNA
reassociationvalues were always lower than 70 o/o.In order
to reduce the workload involved in DNA-DNA reassociation
experiments, it was suggestedthat reassociationexperiments
need onlybe performed for strainsthat shared 165 rRNA gene
sequencesimilarities higher than about 97 .0 o/o(Stackebrandt
& Goebei, 1994). This value was lower than that determined
from the literature, but was suggested from a taxonomically
conservative point of view Having been cited more than
1,350 dmes since 1994, this demarcation value indeed
turned ou[ [o be a guide for researchersand reviewers. In
order to update the correlation between these two taxonomic
parameters,we screenedall articles published in volume 55
of ISEM and are now able to revise the results published
in L994 (Fig. 1). Rather than 97.0 o/o,we now recommend
a 165 rRNA gene sequence similarity threshold range of
98.7-99o/o as the point at which DNA-DNA reassociation
experiments should be mandatory for testing the genomic
uniqueness of a novel isolate(s). The graph compiles 380
data points obtained by al1 major hybridization techniques
performed on representatives of most phyla of prokaryotes
(only values above 96 % similarity areshown in Fig. 1). Only
two studies on three strain pairs revealed that, at 165 rRNA
gene sequencesimilarity lower than 99 o/o,thecorresponding
DNA reassociationvalues were higher than 70o/o.
Our criticism is also directed towards a somewhat careless
handling of 165 rRNA gene sequences. Many sequences
deposited in public databasesappear to be direct downloads
from computer printouts, lacking rigorous inspection of
quality and secondary-structure feasibility. As sequenceerrors
decreaserather than increasesimilarity values, the relatedness
between organisms with erroneous sequences is lowered.
Indeed, there are some sequences of highly related strains
which show deviations from highly conserved secondary
structure features.We have critically analysed the quality and
similarity values of 165 rRNA gene sequences for one data
set that show higher than 70 o/oDNA reassociation values at
165 rRNA gene sequence similarities below 99 % (marked
in black in Fig. 1). Though we had access to neither the
strains nor the original data, in silico corrections of nucleotide
idiosyncrasies meant that the similarity values increased by
microbiologytoday r"i*ritlt$
[email protected]
. ?oa
[email protected]
t /')
[email protected]+t
+ o oo a
DNA-DNA reassociation
up to 0.Bo/o,pushing them over the
99 o/oline'. these values are indicated
by arrows in Fig. l. It appears to be
critically important to check the quality
of sequences according to secondary
features prior to deposition in public
This recommended increaseof about
2.0o/oin 165 rRNA genesequencesimilarity mll significanrly facilirate the
work of taxonomistswithout sacrificing
the quality and precision of a 'species'
description. As indicated above, DNADNA hybridrzanon constiruresthe bottleneck of taxonomic studies among
and taxonomists
should acknowledgethe updated correlation curve and welcome the expected
reduction in workload. As the artificial cut-off value of around 70o/o reassociationmay not have phylogenetic
significance, tare examples may exist
and will arise in the future in which
reassociationvalues around and above
70o/o emerge aL corresponding 165
rRNA genesequencesimilarities around
99.0o/o.in these cases, taxonomists
are reminded of the article of Wayne
et aL (1987), summafiztng an overall
concern of these authors 'that any
based taxonomicschemes
that result must also show pLtenotypic
DS M Z- Deut s c he
S a mml u n g
vo nM ik r oor ganisme
u nnd
t"+49 53 1261
6 3 52;* er k [email protected] m z .d e )
m i c r o b i o l o g yt o d a y r ' i ; r ,
i E. Stackebrandr.
n l
Amakata, D., Matsuo, Y., Shimono, K.,
P a r k , J . K . ,Y u n , C . S . ,M a t s u d a ,H . ,
i Rossello-Mora,
R. & Amann,R. (2001).
Yokota, A. & Kawamukai, M. (2005).
Mitsuana chitosanitabidagen.nov, sp.
nov., an aerobic, chitosanase-producing
member ol the'Betaproteobactena'
. Int J
SystEvolMicrobiol55, 1927*1932.
The speciesconcept for prokaryotes.
FEMS Microbiol Rev25, 39-67.
Stackebrandr, E. (2000). Defining
taxonomic ranks. In The Prolzaryotes.
i An EyolvingElectronicResource the
i MicrobiologlcalCommunity,release3.1.
i Edited by M. Dworkin and orhers. New
De Ley,J., Cattoir, H. & Reynaerts,A.
( 1 9 7 0 ) .T h e q u a n t i t a r i v em e a s u r e m e n t
of DNA hybridization from renaruration
raLes.Eur J Biochem12" 133-142.
i York: Springer. http://link.springer; nycom4inUsenrce/books/IOI25/
Ezaki, T., Hashimoto, Y. & Yabuuchi, E.
( i9B9). Fluorometric deoxyribonucleic
r Stackebrandt,E. & Goebel, B.M. (1994).
; A place for DNA-DNA reassociation
acid-deoxyribonucleic acid hybridi zation
in microdilution wells as an alternative to
and 165 rRNA sequenceanalysisin the
speciesdefinition in bacteriolog;r
t Int I SystBactenol44" 846-849.
membrane filter hybridizaLion in which
radioisotopesare used to determine
geneticrelatednessamong bacLerial
Stackebrandt, E., Frederiksen, W,
strains.Int J SystBacteriol39,224-229.
Fox, G.E., Wisotzkey,J.D. 6l Jurtshuk,
P.,Jr (1992). How closeis close:165
IRNA sequenceidentity may not be
Garrity,G.M. & I0 other authors
(2002). Report oi rhe ad hoc commitree
sufficientto guaranleespeciesidentity.
Int J SystBactenol42, 166-170.
Gevers,D., Cohan, FM., Lawrence,J.G.
& B other authors (2005). Re-evaluating
prokaryotic species.Nat RevMicrobiol3,
for the re-evaluation of the species
r definition in bacteriolo gy. Int J SystEvol
i Microbiol 52, IO43-I052.
Staley,J.T.6r Krieg, N.R. (1984).
r BacterialclassificationI. Classificationo{
i pro.uryotic organisms:an oveMew In
: Bergeys Manual of SystematicBactenologt,
r vo1. 1, pp. 1-4. Edired by N.R. Krieg &
i J G Ho1t. Baltimore: Williams & Wilkins.
Pukall, R. (2005). DNA fingerprinrrng
techniques applied to the identification,
r Tourova, T.P & Anronov, A.S. (1987).
[axonomy and community analysls of
prokaryotes. In Molecularldentification,
and PopulationStructureof
I Identification of microorganlsms by
1 rapid DNA-DNA hybridization. Methods
i Microbiol 19, 333-355.
otes,pp. 52-82. Edired by
E. Stackebrandt.Heidelberg:Springer.
r Wayne, L., Brenner, DJ., Colwell, R.R.
& 9 other authors (1987). Inrernatlonal
; Committee on SystematicBacteriologz
' R"port of the ad hoc committee on
Rossello-Mora, R. (2005). OXeDNA reassociationmethods applied to
microbial taxonomy and therr critical
evaluation. In Molecularldentif.cation,
and PopulationStructureof
i reconciliation of approachesto bacterial
; systematics.Int J SystBacteiol3T ,
| 463-464.
the tlnY
of viruses
fromthoseof classifying
HaenniandMike Mayo describe.
question frequently asked of virologists
by non-viroiogists is - are viruses living?
Perhaps one answer to this chestnut is in
the nature of virus systematics. Although
molecular in scale (circoviruses have -20 nm
diameter virions and -2 kb ssDNA genomes;
viroid genomes consist of ssRNA of only -0.3 kb), viruses
and viroids are replicated by error-prone mechanisms that
result in variations from which natural selection yreids
distinctive forms fitted to particular niches. Thus one can
study and describe virus variation, investigate the causesand
consequences of this variation and manipulate the data to
produce a system of classification. This constitutes a classic
definition of systematics and can be said to describe much of
current virological research activity.
any number of organisms, that allows easier reference to its
components, nomenclature - the construction of a system
of names ard. a formal guide to their use in ta*onomy, and
taxonomy- the process of naming organisms and classifying
them hierarchically to express their mutual relationship in
a simplified way and according to internationally agreed
codes of practice. In virology, these activities are undertaken
by the International Committee on the Taxonomy of Viruses
(ICTV). ICTV consists of a network of some 500 virologists
organued into Study Groups for particular groups of viruses
(e.9. a family) that report to a subcommittee for each of the
major groups of hosts (vertebrates, invertebrates, plants,
prokaryotes, or fungi, protozoa and algae). The Chairs of
these subcommittees form the backbone of the Executive
Committee of ICTV
It is feasible to administer virus taxonomy (including
nomenclature) through such an organization because of
the relatively small number of virus species currently recognized.In contrast to the approximately 17,000 new species
Intrinsic to any biological research are classification - the
production of a logical system of categories, each containing
m i c r o b i o l o g yt o d a yn o v 0 6
Hosts Cenome size (kb)
T a b l e1 . V i r u sf a m i l i e sa n d s o m er e p r e s e n t a t i vper o p e r t i e s
Pro, prokaryotes;
V, vertebrates;l, invertebrates;
P l , p l a n t s ;F ,f u n g i .C o l o u r si n d i c a t em a i n h o s t s g
, r a d i e n t s i g n i f ym o r e
t h a n o n e t y p e o f h o s t .C e n o m es i z e sa r ef o r a r e p r e s e n t a t i vsep e c i e s .
of animals that are described every
year,the virus world consists of a mere
1,950 species. As parasite diversity
surely parallels host diversity, this
number is cleariy a massive underrepresentation,but is probably held in
check because to establish a new virus
speciesis a laborious researchexercise
and only'important'hosts such as man
are studied intensively
Viruses are diverse in genome type
and size and infect hosts in all major
types of organisms. The table shows
the currently recognized virus families
clustered according to genome type.
Taxonomy above the level of families is
at presenl limited to the recognition of
three orders, most families are not
clustered into orders and some genera
microbiologytodayi'r*v {:#
are as yet unassigned to taxa above
the level of genus. This reflects some
of the uncertainties in current vinis
The nomenclature of virus taxa. in
particular species,differs fundamentally
from that of the rest of biologr It is
regulated by the International Code of
Virus Classificationand Nomenclature,
which is published on the ICTV
website (www. danforthcenter. or$kab/
ICTVnet/asp/_MainPage.asp) and in
reports such as the current 8th ICTV
Report. This article is concerned only
with the classificationaspectsof ICWs
work, in particular the factors that
complicate virus classification: the intrinsicpropefiies ofviruses and the probable evolutionary origins of viruses.
of viruses
As for many microbes, morphological
charactersare of limited use (although
the advent of electron microscopy did
lead to significant taxonomic advances)
and small genetic changes can resuh
in substantial changes in pathological
impact. Virus genomes are small (see
Table l) and can often vary rapidly
However, it is now possible to obtain
nucleotide sequences very quickly,
sometimes without isolating the virus
from its host. By using appropriate
software, evolutionary distances between sequencescan be deduced and
phylogenetic trees obtained. This
assumesthat the sequencesare derived
from a single ancestral sequence and
bination between gene blocks has
happenedduring the evolutionof these
viruses (Fig. 1). Expecting sequence
comparisonsand the resulting trees
to produce a durable classification
is thus, at least in some instances,a
naive approachto virus classification.
Whereasit works for somevirus taxa,
for othersa more arbitraryand broadly
based approach that uses multiple
criteriais clearlynecessary
that differences have arisen by mutation
of single bases. Such a model seems
most reasonable when sequences are
clearly similar, such aswhen viruses in a
genus are compared. When other sorts
of sequence variation have happened,
such as recombination, these simple
comparison techniques are likely to
lead to erroneous conclusions. This is
vrvrdly illustrated by the genomes of
viruses that are classifi.edin the family
Luteoviidae. There is no dispute that
viruses in this famrly are related both
in sequence details and in their biology
(all are transmitted by aphids in a
circulative fashion that involves virions
crossing several barriers inside aphid
bodies). The RNA genomes of luteovirids consi.stlargely of two geneblocks,
one of structural genes and the other
of replication-related (pol) genes (Fig.
been formed by recombination
( oining of parts of separategenomes
to produce a new genome) anilor
reassortment (making new combinations among separate pafts
of the genomes of viruses with
genomes, such as
influenza viruses), resulting in
chimeric viruses with polyphyletic
(i.e. hybrid) genomes whose origins cannot be represented in a
monophyletic scheme.
2. Genomes of some viruses seem to
contain genes acquired from their
3 . Viruses are unlikely to be descended
from one original'protovirus'; they
probably arose more than once,
but when and how many times is
4 . Genomes of some viruses (..g.
retroviruses) integrate into the
genomes of the hosts, where they
are subject to selection pressures
Biological taxonomy is well suited to
classifying organisms that are related
to one another via simple branched
and diverging descent, with reiatively
long evolutionary distances between
successive branch points. However,
virus evolution differs from this simple
paradigm in several ways.
1. Genomes of some viruses, such as
luteovirids (see above; Fig. l), have
1). The phylogenetic trees obtained by
comparing luteovirid structural genes
confirm the family cluster and show a
separation of species into the constituent genera. But when pol genes are
compared with those of other viruses,
the genera Luteovirus and Polerovirus
differ greatly and each seems more
closely related to one or the other nonluteovirid genus. It seems that recom-
t e n e r ai n t h e f a m i l y
o r i g i n so f t h e g e n o m e so f v i r u s e si n d i f f e r e n g
V F i g .1 . D i a g r a mo f p o s s i b l e
The upper boxescontainhypotheticalgenomesand assumethatthe ancestorsof
t o m b u s v i r u s easn d s o b e m o v i r u s ehsa dg e n o m e sl i k et h o s eo f t h e i r c u r r e n t - d acyo u n t e r p a r t s .
Redboxesrepresentblocksofstructuralproteingenes.pol signifiesreplication-related
? signifiesa gene block of unknowntype. Furtherdetailscan be found in the 8th ICTVReport.
fami ly Luteovi
microbiologytoday n*v il6
different from those applying to independently replicating
5. Some viruses infect more than one type of host (one often
serving as vector for transmission between other hosts)
and therefore will have evolved in response to complex
selection pressures.
Any or all of these factors greatly complicate, if not vitiate,
attempts to deduce phylogeny from studies of current genome
sequences and thus, whatever the taxonomic arrangement,
some viruses and/or taxa will always seem to be misfits.
Notwithstanding the complications, some sort of classifi.cation
is fundamentai to most virological research, whether it be
deducing the nature of a new disease agent by working out
which of the known taxa it most resembles or developing a
better understanding of the nature of a virus by predicting
properties based on its assumed classification.
To develop and maintain such a classification, ICTV communicates with virologists in several ways. Via its website,
ICTV provides marry of the details of its organizatron as well
as current issues in virus taxonomy ICTV also publishes
regular formal repofts (such as the recent 8th ICTV Report)
and occasional notes in the Virolog;r Division News section
of.Archives of Virolog,. AIso, workshops, such as the recent
meeting on virus evolution and taxonomy which has been
summarized by U. Desselberger,^re held and, as work progresses,ICTV expects to org nuzefurther such workshops.
New viruses are being discovered all the time. Some can
be fitted into existing taxonomic structures (e.g. Severe
acute respiratory syndrome coronavirus; SARS-CoV), making
it possible to predict their properties, and others are unlike
anything seen previously (e.g. Acanthamoeba polyphaga
mimivirus). Thus, virus taxonomy must have both an
internal logical justification and a capability of expansion to
accommodate novelty Whatever the virological endeavour,
virus taxonomy should provide a provocative framework to
whlch all virologrsts can contribute. Current ICTV practice
aims to achieve this.
Monod,CNRSand Universities
- Tour43,75251Paris
andVll, 2 Place
Cedex05, France
(e [email protected]
Mike Mayo
ScottishCrop Research
D undeeD D 2 5D A ,U l <
(e [email protected])
Fauquet,C.M.,Mayo,M.A., Malinoff,J.,Desselberger,
& Ball, L.A. (editors) (2005). Virustaxonomy,VlllthReport
U. (2005). Reporton an lCTV-sponsored
q'rnposiumon virus evolution.ArchVirol L50,629-635.
must have
bothan internal
o f expansion
logicalj ustification anda capability
to accommodate
providea provocative
frameworkto whichall
microbiologytoday nsv fi6
morethan 300
Facedwith classifying
from insectguts,
hashadto consider
ne, two, three ... 300? At a time when
systematists are interested in biodiversity,
it is important to be abie to enumerate
numbers of organisms. For example
mycologists believe that many fungi
remain to be discovered to reach the
totai estimated 1.5 million species.Numbers of speciesare
dependent to some extent on a choice of a speciesconcept, a
topic that has been the subject of heated discussions among
systematists of all organisms. My colleagues and I study
yeasts that inhabit the gut of insects feeding on fungi. After
6 years of periodic collecting in Panama and the southern
USA, a limited geographical range, we believe we have
approximately 300 novel ascomycete yeast species in a
group (Saccharomycetales) currently estimated to contain
about 800 species.Yeastsare essenlial to decomposition in
many environments and some are imporlant economically We hope to discover that our yeastsare both ecologicaily
and economically significant, but for the moment we are
preoccupied with determining and describing unique species
from the poorly investigated beetle gut habitat.
A dramatic shift in my research occurred when I put
aside the study of life cycles and phylogenies of insectdispersed fungi with complex life histories, some involving
m i c r o b i o l o g yt o d a y n * r i * S
[wo unrelated hosts and as many as
three distinct morphological states in
the same life cycle. I was diverted from
such remarkable fungi by Dr Sung-Oui
Suh, a postdoctoral researcher in the
laboratory to the study of yeasts from
the gut of mushroom-feeding beetles.
Our researchemphasis changed, therefore, not only to fungi with an extremely
simple morphology, but also to resolving different questionsset at lower taxonomic leveis.Becauseof the presenceof
relatively few morphological characters
in yeasts,physiological traits have been
used as phenotypic characters,but such
traits often are too plastic to serve as
stable markers for species.
What is a species?
Our need for a speciesconcept became
urgent when, in our first year of studying insect gut yeasts, we discovered
almost 100 potentially undescribed
taxa. Then there were 200, and today,
aimost 300 undescribed yeasts. We
spoke glibly about numbers of
without considering exactly how we
defined them. There is no shortage
of species concepts from which to
choose, and, perhaps much of the confusion surrounding the topic rests with
m i crobi o logy today il i,:riJ'
separating theory from practice. An
excellent discussionof speciesconcepts
applied specifically to fungi byJohn W
Taylor and colleagues, distinguishes
theoreticalandoperationalaspectsof the
question. In their evaluation of species
concepls, outlined by R.L. Mayden,
they acceptedthe Evolutionary Species
Concept (ESC) of G.G. Simpson as a
primary theoretical species concept.
Briefly, the ESC defines a species as
a group of organisms with a history
of common descent that
its identig from other such lineages...'
Mayden considered other concepts:
Morphological SpeciesConcept (MSC),
Biological Species Concept (BSC) and
Phylogenetic SpeciesConcept (PSC) to
be secondary to, but compatible with,
the ESC.
Taylor and colleagues discussed
speciesconceptsin terms of recognition
criteria and pointed out that these are
not specifiedby the ESC, although they
are inherent in secondary operational
concepts such as the MSC, BSC
and PSC. Moreover, theoretical and
operational concepts can be separated
4 F a rl e f t :W
. o o d - b o r i n gp a s s a l ibde e t l e sa t t e m p ta n e s c a p ei n t o t h e i r t u n n e l s T
. h eb e e t l e s
i n h a b i tw o o d p r e v i o u s liyn f e c t e db y w h i t e r o t b a s i d i o m y c e t e
t hsa t h a v er e m o v e dc e l l u l o s e
a n d l i g n i n ,m a k i n gt h e w o o d s u i t a b l ef o r b e e t l ei n v a s i o nT. h e s eb e e t l e sh a r b o u rv e r yd i f f e r e n t
y e a s t sw h e n c o m p a r e dt o t h o s eo f f u n g u s - f e e d i nbge e t l e sa, n d t h e i r h i n d g u t m i c r o b i o t a
{ Farright.Where are all the yeasts?Novelgut yeastsare known from the beetleEllipticus
shown feedingon sporulatingpatchesof Tinctoporellus
a )h.eb a s i d i o m y c e ti se o n e o f t h e s p e c i e tsh a t i s w i d e s p r e a d
i n L o u i s i a naas
w e l l a s o t h e r p a r t so f t h e C a r i b b e a nb,u t t h u s f a r a s s o c i a t eidn s e c t sa n d y e a s t sh a v em u c h
more restricteddistributions.
)osephV. McHugh
V L e f t .Y e a s t - h a r b o u r ienngd o m y c h i db e e t l e sa r ef o u n d f e e d i n go n a v a r i e t yo f f u n g i ,i n c l u d i n g
the dark patchesseenhere.JosephV.McHugh
V Right.The largererotylidbeetle(Megischysus
sp.)and three scaphidiine(Staphylinidae)
f e e d i n go n a r e s u p i n a tpeo l y p o r eT. h ep r e s e n c o
e f d i f f e r e n tb e e t l e so n t h e s a m ef r u i t i n gb o d y
h a sb e e np o s t u l a t e a
d s p r o v i d i n go p p o r t u n i t yf o r h o s ts w i t c h i n gb y t h e i r g u t y e a s t sJ. o s e p hV .
concept' and
on the basis of
recognition'. The criteria for
recognition of species are inherent in
the name of the concepts: basically
morphology, (2) reproductive
competence and (3) position in a
phylogenetic tree. For most fungi
morphology is very simple - in fact
that is why yeasts (and bacteria) were
distinguished by physiological trails
early in the history of their systematics.
Physiological traits, while no longer
considered to be the best charactersfor
recognizing species, do provide clues
to ecological function and help in the
recognition of yeast guilds that share
similar nutritional resources. Tests
of the BSC relying on reproductive
compatibility do not work well for
most fungi, because many are asexuaL
and many more are self-compatible
and do not outcross. 20 o/o of alL
fungi are estimated to be asexual; for
ascomycete yeasts the proportion is
even greater with 215 asexual to 265
ascospore-producersrecorded in I 998.
That many of the ascospore-formers
are non-outcrossing yeasts increases
the count even more.
The use of two of the criteria,
morphology and sexual compatibility,
to distinguish specieshas been played
down on the grounds that these
recognition criteria cannot be applied
with an expectation of precise success.
The criteria, however, should not
be completely disregarded, because
they have been the basis of so many
currently recognized fungi. Recent
comparisons of fungal speciesbased on
morphological or reproductive compatibiiity criteria, however, indicate
that species numbers usually, although
not always,are underestimatedby comparison with species recognized on
the basis of DNA analysis, because
changes in morphology and reproductive capacfiy often Iug behind
genetic change. Phylogenetic species
recognition is also favoured because
it can be applied readily to all fungi.
Fungi share characters from DNA
sequences that, regardless of morphology or reproductive capability, can
be collected and analysed to produce
gene genealogiesof potential species.
Linesof demarcation
At this point an operational problem
arises:where to draw the speciesline?
Is it appropriate simply to draw a line
based on a clusterinq of terminal taxa
in a tree?Taylor and colleaguesappiied
a non-arbitrary method, genealogical
concordance, that relies on agreemenl
of several different gene genealogies to
indicate placement of the line of species
limits. Varyrng degrees of discordance
among genealogies indicates that
lineage sorting and fixation of genes
is not compiete and isolation of
the population has not happened.
Phylogenetic Species Recognition by
genealogical concordance has been
applied successfully to a wide variety
of basidiomycetes and ascomycetesas
well asnon-fungal organisms, including
Delimiting300 new species?
How do we delimit and describe 300
new yeasts within the 6-year period of
granl funding? This is a huge problem
becauseof the constraintsof community
expectations and nomenclature code
resfrictions. We characterrze the yeasts
using DNA sequences, a feat rapidly
accomplished by a team of hardworking undergraduates. By I99B
Cletus Kurtzman and colleagues had
sequenced the Dl/D2 region of the
large subunit nuclear ribosomal RNA
gene (LSU rDNA) of all available yeast
m i c r o b i o l o g yt o d a yn e l v# * ;
Our fieedfor a spefies
me ursenr
, in ourf rsf year o!
f&snf&erewsrr ;00, iSO...
A Trip.Many insectshaveintimateassociations
with yeasts,but so do
o t h e ra n i m a l sT. h en e s to f a p a n a m a n i abni r d c o n t a i n s p e c k l e de g g s
a n d i s c o m p o s e di n l a r g ep a r to f r h i z o m o r p h st h, e d a r k , n a r r o w _
d i a m e t e fri l a m e n t st h a t a r e m a d eu p o f r o p e so f m i c r o s c o p itch r e a o l i k es o m a t i cs t r u c t u r eos f f u n g i . N h uH . N g u y e n
A S o t t n m ,C a r m e nR o d r i g u e(zU n i v e r s i toyf C e o r g i aa) n d N h u N g u y e n
( L o u i s i a nSat a t eU n i v e r s i t y p
) ,a r t i c i p a n ti sn t h e N a t i o n aS
l cience
F o u n d a t i oR
n e s e a r cE
h x p e r i e n c ef os r U n d e r g r a d u a t e
p sr o g r a m ,
c o l l e c tb e e t l e sa t t h e s m i t h s o n i a T
n r o p i c aR
l e s e a r cIhn s t i t u t eB
, arro
C o l o r a d ol s l a n ds i t e ,P a n a m aS. t u d e n t sa c q u i r em a n ys k i l l sf r o m
c o l l e c t i n gi s, o l a t i n g
a n d p u r i f y i n gy e a s t si n c u l t u r et o p e r f o r m i n ga
n u m b e ro f m o l e c u l atre c h n i q u e sJ.o s e p hV .M c H u g h
{ L e f t .B u d sm a k et h e y e a s tT
. h i sp h o t o m i c r o g r a pohf t h e t y p e o f a
n e w s p e c i e cs o l l e c t e da t t h e s m i t h s o n i a T
n r o p i c aR
l e s e a r cIhn s t i t u t e ,
B a r r oC o l o r a d ol s l a n d ,P a n a m ai ,l l u s t r a t eyse a s tb u d s .T h en a m eo f
t h e s p e c i e si s, o l a t e df r o m g u t o f a f u n g u s - e a t i nbge e t l e ,C a n d i d a
sinolaborantium, commemorates
the Chi neselabourerswhose
l i v e sw e r el o s tt o b u i l dt h e t r a n s i s t h m i arna i l r o a dt h a t p r e c e d e d
of the PanamaCanal.CennetErbil
{ Righf.Polyporus
a delicatewood-decayingbasidiomycete
i sa f a v o u r i t e
f o o d o f m a n yb e e t l e st h a t h a r b o u ry e a s t si n t h e i rg u t .
Nhu H. Nguyen
m i c r o b i o l o g y t o d a y n { : i ' i[r} { " {
species. Their original database, to which we and others
have added hundreds of additional sequences, makes it
possible to find close relatives of new yeasts using not
only nusr searchesbut also phylogenetic anarysesfor clade
recognition and to provide a basis for delimiting species.It
is common for gut yeasts to vary by as many as 30_20 bp
in the DI/DZ region. Other yeasrs may vary by only a few
base pairs from a known srrain, and these are more difficult,
becausethe question of where to draw the speciesline arises.
Kurtzman suggestedthat a substitution rare greater than I %
in about 600 bp in rhe DI/DZ region be used ro separare
species- approximately 4 or more base pairs difference for
ascomyceteyeasts.The difference correlates well with oata
from mating tesrs in a study of biological species in yeasts
that could be crossed. The I o/osolution, however, failed to
distinguish s accharomycescerevisiae and S. bayanus, and other
close relatives, and almost certainly provides a conservarive
estimate of speciesnumbers as suggestedfor other fungi.
In practice, in our rush to characterize yeasts, we do not
obtain sequencesof several independent DNA regions for
the novel yeasts.We do, however, use additional markers,
e.g. microsatellites and the plastic physiological trairs
that are useful at low taxonomic level. These markers are
more variable than sequences, and we almost certainly
underestimate speciesnumbers in order to handre the large
numbers of novel isolates.
Needsfnr yeastsysterTtatics
We are fortunate to have a dense LSU rDNA database,and
many literature resourcesare widely available for the study
of yeasts. In addition to the required classic, The yeasts,a
TaxonomicStudy (Kurtzman & Fell), wirh a fifrh edition rn
preparation, an essential online resource, the BioloMICS
database of the centraalbureau voor schimmelcultures
(CBS) (wwwcbs.knaw.nV) based on the book, has characrers
of all species,an online identification system and up-to-date
references.Theseresourcesavailableforyeastsare exceptional
among fungi, and yeast systematists are fi.nding many new
species that can be identified to near species level rapidly
using DNA sequences- or can be recognizedasundescribed.
In fact rapid deposition of DNA sequencesto GenBank has
promoted collaboration among yeast workers with similar
sequencesin distant localities, including, in our experience,
P artama,Br az7l,Portu gal and Belgium.
Although rDNA is well sampled for many species and
about 20 complete genome sequences are avarlable, more
sequences,especially for protein-coding genes, are needed
for basal yeasts to provide a well-supported predictive
phylogenetic framework for or ganizing yeast taxa. Genomes
will help to access additional appropriate DNA regions
for use in sys[ematics. Continued collecting from natural
habitats will lead to the discovery of many more predicted
novel yeasts. Additional sampling will also help to establish
biogeographical limits of many speciescurrentlyknown from
only few localities.
What more could we wish for to help characterize 300
yeastspecies?Our most immediate need is for rapid methods
to determine yeasl physiological profiles. We culture 1-3
isolates of every yeast we describe in about 100 different
ways to determine physioiogical and morphological traits.
This tedious characterrzatron procedure is a part of the
description recognized by the community of
yeast systematists, one that aiso gives value added data on
potentiaily valuable biological organisms - especially aL a
time when discussions of petroleum alternatives are intense.
The elimination of the Latin diagnosis required for
valid publication by the International Code of Botanical
Nomenclature, would dramatically hasten the publication
of our 200 novel yeast backlog. Time spent on lranslating
a diagnosis to Latin or discussing wheflrer a description
shouid be in the nominative or the ablative case, could be
used for more rapid publication of essential organisms in our
How manyfungi?
Search for and discovery of novel fungi were common
themes of papers and entire symposia at the Bth International
Mycological Congress held in Cairns, Australia, in late
August. In our owrl presentation we suggested that known
ascomycele yeast numbers had increased by almost 30o/o,
and we predicted that sampling of previously collected insecl
gut habitats in just Panama and the southern USA could
easily yield another 100 species, something Dr Suh and I
are close to achieving. Yeastshave been, and will continue to
be, useful models in population studies that will lead to an
understanding of mechanisms of speciation. Some degree of
host and geographical specialization of nearly 300 insect gut
yeastsand the vast regions left to sample for insect gut yeasts,
indicates that these organisms will contribute signifi.cantly to
increasing the numbers of ascomycete yeasts and indeed the
total number of all funei.
Meredith Blackwell
Departmentof Biological
70803,USA(e [email protected])
Blackwell,M. (1994).Minutemycologicalmystenes:the
influenceof arthropodson the livesof h:ng;. trtlycologa86,
Boekhout,T. (2005).Gut feelingfor yeasts.Nature434,
Hawksworth, D.L. (2001). The magnitudeof fungaldiversity:
the 1.5 million speciesestimaterevisited.MycolResL05,
Moncalvo,J.-M. (2005).Molecularsystematics:
phylogenicgroupsand fungaispeciesconcepts.lnEvolutronary
oJFung1,pp. 1-33. EditedbyJ.n Xu. Norwich:
Honzon ScientificPress.
Rokas,A., Williams,8.L., King, N. & Carroll,S.B.(2003).
approachesto resolvingincongruencein molecular
. Nature425, 798-804.
Suh,S.-O.,McHugh,J.V,Pollock,D. & Blackwell,M. (2005).
The beetlegut: a hyperdiversesourceof novelyeasts.Iv$colRes
Suh,S.-O.,Nguyen,N.H. & Blackwell,M. (2005).Nine
new CandidaspeciesnearCandidamembranifaciens
insects.MycolRes109, 1045-1056.
DJ., Kroken,S.,Kasuga,T., Geiser,
D.M., Hibbett,D.S.& Fisher,M.C. (2000).Phylogenetic
speciesrecognitionand conceptsin fungi. FungalGenetBiol31,
White, TJ., Bruns,T., Lee,S. & Taylor,J.(1990).Amplification
and direct sequencingof fungalribosomalRNA genesfor
- a Guideto Methodsand
phylogenetics.ln PCRProtocols
Editedby M.A. Innis,D.H. Gelfand,
JJ. Sninsky& TJ. White. SanDiego,CA:AcademicPress.
microbiology today nustil1fi
e most abundant predators
on earlh are not animals
like lions or ants, but the
protozoa. When I was a
ptolozoa were
treated as one phylum in the animal
kingdom, with just four classes:
amoebae, flagellates, ciliates and the
purely parasitic Sporozoa. Now they
are recognrzed as a separatekingdom
comprising l l phy1a. Ciliates remain
as one phylum, Ciliophora, which
also includes the highly specialized
Suctoria that lack cilia in their
sedentary adult stages,having evolved
eiaborate tentacles with explosive
organelles for trapping prey. But
amoebaeand flagellatesare abandoned
as formal taxa, while Sporozoa have
been drastically refined, by removal of
microsporidia to Fungi and Myxozoa
to Animalia, in a radical overhaul of
protozoan systematics that lasted for
three decadesbut is now settling down,
after extensive lively controversies,
into a period of broad consensus.
As a student in the 1960s I realizecthat electron microscopy showed protozoan cells as architecturally far more
diverse than animal or plant celis.
Classically, the boundary between
protozoa and algae was fuzzy, with
several goups claimed both by zoologists and botanists, in pailicular dinoflagellates, euglenoids, cryptomonads
and chrysomonads, some of which
are photosynthetic algae while others
are predatory heterotrophs; a few,
notably some dinoflagellates,that feed
both ways were an especial probiem
for eafly classifications based just
on nutrition and motility The first
major break from the simple 19th
cen[ury fourfoid division occurred
25 years ago when I established the
kingdom Chromista for a mixture of
algae and former proLozoa and treated
the remaining Protozoa as a separate
kingdom, in which flagellates were
split into several phyla (Fig. 1). By then
it was widely accepted that chloroplasts
originated by the enslavement of a
cyanobacterium and that all eukaryote
algae evolved ultimately from heterotrophic ancestors. We now know that
the primary diversification of eukaryote
cells took place among zooflagellates:
non-photosynthetic predatory cells having one or more flagella for swimming,
and often also generatingwater currents
for pulling in prey
Evolutionof earlyeukaryotes
Cilia of ciliates and oviducs, and flagella of flagellates and sperm, are
homologous structures that grow from
centrioles with a beautiful g-triplet
microtubule structure; i here adopt the
increasing tendency to refer to both as
cilia. The traditional distinction that
cilia are short and many, whereas flagella
are long and few, is trivial and often fails,
asdoesthe idea of a distinctbeat pattem.
Cilia share no evolutionary relationship with the rotary extracellular flagella of bacteria, but are specializations
of the eukaryote cytoskeleton that
probably evolved at the same time as
the nucleus and the enslavement of
an alphaproteobacterium as the first
the nnost
microbiologytoday ru*.rrr
an immensediversity
of singlecelledpredators
and numerous
causingd iseases
As Thomas
werethe firsteul<aryote
givingriseto all higherkingdoms,
in theirhigh-level
mitochondrion. Thus the first eukaryore cell was a fIagelIate,
very likely one wirh amoeboid tendencies, no[ a rigid pellicle - and probably oniy one cilium. Amoeboid prorozoa
arose several times from flagellate ancestors by evolving
highly varied pseudopodia for creeping and ciawling;
some, notably the secondarlly anaerobic mastigamoebae
and Multicilia (both Amoebozoa) retained a cilium or cilia,
but others lost them altogether or kept them only for wider
dispersal,suppressing them during crawling/feeding.
than sequencetrees.Genesequencetreesexcelin estabrishing
close clusters of strongly related organisms, but sequence
evolution is more complex and variabie than sometlmes
thought, so is sometimes extremely misleading, yielding
partially wrong topologies. The resr of a good phylogeny and
classification is that different independent lines of er,rdence
yreld congruenr conclusions. We arc approaching this happy
state of affairs for protozoan large-scalesystematics,though
problems and controversiesremain.
The roleof nnolecular
cationand diversity
Some thoughtful lgth century proLozoologists suspected
that flagellatespreceded amoebae,asjust asserted.But until
DNA sequencing and molecuiar systematics burgeoned in
the 1980sand 1990s the often more popular idea of Haeckel
that amoebae came first and flagellateswere more advanced
could not be disproved. Sequences enabled calculation
of phylogenetic trees based on differing degrees of gene
sequence divergence. Equally importantly, they reveal much
rarer and more substantial discrete molecular changes, e.g.
gene fusions, splitting of genes,insertion and loss of introns,
gene duplications and indels (insertions or deletions).
Such characters, treatable by the cladistic reasoning that
morphologlsts used for centudes,aresometimesmore decisive
The emerging picture (Fig. I) shows rhe primary diversification of eukaryotesas involving changesin the development
microbiologytoday vl*rv{.rfl-
A T r a n s m i s s i oenl e c t r o nm i c r o g r a p hosf c h o a n o f f a g e l l apt er o t o z o a .
c h o a n o f l a g e l l a tfeese d o n b a c t e r i ab y t r a p p i n gt h e m w i t h a c o l l a ro f
m i c r o v i la
l i r o u n dt h e b a s eo f t h e c i l i u m ,m u c ha sd o t h e r e m a r k a b l y
s i m i l a irn t e r n afle e d i n gc e l l so f s p o n g e st h, e m o s tp r i m i t i v ea n i m a l s .
I t i s p r o b a b l et h a t a n i m a l se v o l v e df r o m a c h o a n o z o apnr o t o z o a n
similarto a choanoffagellate.
rop Cosmoeca
sp.;lower leftAcanthoeca
right Parvicorbicula
sp.Dr per R. Flood/ Natural
{ D a r kf i e l dl i g h t m i c r o g r a p h
o f a l i v es p e c i m e no f t h e p r e d a t o r y
Dr perR. Flood/ Natural
l yi c i l i a t e )
b i k o n t s( a n c e s t r a l b
, Excavataiii
chromal veol ates
K i ngdomC hromi sta
Cryptista Heterokonta
rioles I l
l a k o b e ai
P l a s t i di n s i d eR E R ) { t u b u l a rc i l i a r vh a i r s \
E F 1 - ai n s e r t i o n
nonaoea latea{lJ
P o s t e r i ocr i l i u m; f i l o p o d i a ;
ffat mitochondrialcristae
Rhiz ar ia
A moebozoa
Broad c o m o t o r yp s e u d o p o d s ;
a n t e r i or
760 My
i n t e r n adl u p l i c a t i o n
P o l y u b i q u i t i inn s e r t i o n
r roots\
m i c r o t u b u l abr a n d sa s c i l i a n
Thr r e em y o s i nd o m a i nf u s i o n s+ o n e
ins e r t i o n( g l y c i n ei n m y o s i nl l h e a d )
iu bular mitochondrial cristae;
heterotrophicuniciliateand unicentriolar
as nets (reticulopodia) in Foraminifera
(predominantly benthic Retaria, the
most abundant seafloor predators)
and Radiozoa (major micropredators
of oligotrophic oceans: acantharia
and polycystine radiolaria). Cercozoa
include flagellates, the peculiar chlorarachnean algae formed by the enslavement of a green alga (G in Fig. 1),
amoebae with filopodia (many with
shells that evolved independently of
sheilsof someAmoebozoa)and amoeboflagellates; they are the most abundant
in soils, ye[ were only recogpredators
Rhizaria, Excavata), and
phylum in 1998, they also
closest relatives are unclear. Ancestraily . include parasites of commercia\
important shellfish (e.g. oysters) and
bikonts had two diverging cilia: the
crops (e.g. sugarbeetand cabbages).
anterior undulates for swimming or
Parasitism developed more strongly
prey attaction; the posterior serves
in phylum Myzozoa, named after their
for gliding on surfaces in many groups
widespread feeding by myzocytosis
(likely its ancestral condition), but
(sucking out the interior of cells
secondarily adapted for swimming
than engulfing them whole by
in others
phagocytosis). Sporozoa sensu stncto,
make secondary uniciliates, not to be
e.g. malaria parasites, are aII parasites
confused with genuine unikonts, which
and are grouped with some freeJiving
confusingiy are sometimes secondarily
sucking predatory zooflagellatesas subbiciliate). A11major eukaryote groups
phylum Apicomplexa, within Myzozoa
except Ciliophora include severely
modified organisms that lost cilia; some
became highly amoeboid.
Among bikonts emphasis on pseudopodia is greatest in Rhizaria, comprising two phyla (Cercozoa, Retaria)
in which pseudopods are typicaliy very
feet') and often
thin (filopodia:
branch or fusetogether in elaboratefeeding networks: especially well developed
of cilia and structure of microtubular
roots that attach them to the rest of the
cell. Unikonts comprise animals, fungi
and the protozoan phyla closestto them:
Choanozoa (e.g. choanoflagellates) and
Amoebozoa (typical amoebae with
broad pseudopods, slime moulds like
Dictyostelium and mastigamoebae),
which all share the same myosin II
as our muscles, which is absent from
all bikonts. Bikonts comprise the
plant and chromist kingdoms, three
protozoan infrakingdoms (Alveolata,
together with Dinozoa (dinoflagellates
and relatives), also often parasites.
Myzozoa and Ciliophora comprise Alveolata, typically with well-developed
cortical alveoli: smooth vesicles with
skeletal and calcium segregating functions. Alveolates are sisters of kingdom
Chromista, being jointly called chromalveolates.The ancestralchromalveolate
flagellate had phagotrophic nutrition
and chloroplasts surrounded by extra
membranes arising from their origin by
intracellular enslavement of a red alga
(Rhodophyta; Fig. 1). Chromaiveolates
comprise chromophyte aIgae, whose
chloroplasts bear chlorophyll
and many derived lineages that lost
photosynthesis and sometimes plastids
altogether,e.g. ciliates,oomycetechromists. Chromists differ from alveolates in
that the phagocytic vacuole membrane
around the enslaved red alga fused with
the nuclear envelope, placing their
plastids inside the rough endoplasmic
reticulum. This contrasts markedly wrth
kingdom Plantae, where chloroplasts
lie in the cytosol and were never lost,
even in chlorophyll-free plants.
Thefesfofa goodphylogeny
tion ls that different
independentlinesof evidence
congruent conclusions,
m i c r o b i o l o g y t o d a y r l E : l li l t t i
{ F i g .1 , T h ee u k a r y o t e v o l u t i o n a rtyr e e .T a x ai n b l a c kc o m p r i s et h e b a s a kl i n g d o mP r o t o z o a .
T h et h u m b n a isl k e t c h e s h o wt h e c o n t r a s t i n m
g i c r o t u b u l es k e l e t o nos f u n i k o n t sa n d b i k o n t s
i n r e d .T h ed a t e sh i g h l i g h t e di n y e l l o w a r ef o r t h e m o s ta n c i e n tf o s s i l sk n o w nf o r e a c hm a j o r
g r o u pM
. a j o r i n n o v a t i o ntsh a t h e l pg r o u p h i g h e rt a x aa r e s h o w nb y b a r s .F o u rm a j o rc e l l
e n s l a v e m e nttos f o r m c e l l u l a cr h i m a e r aasr es h o w nb y h e a v ya r r o w s( e n s l a v ebda c t e r i ao) r
dashedarrows(enslavedeukaryotealgae).Fourfeaturesof the tree need more research.(1)
A r e c e n t r o h e l i dH e l i o z o a( n o n - p h o t o s y n t h e tai cn d n o n - f l a g e l l a p
t er e d a t o rtsh a t c a t c hp r e y b y
s l e n d er a d i a t i n g
a x o p o d i as u p p o r t e db y m i c r o t u b u l e sr )e a l l ys i s t e r so f H a p t o p h y t ad;o t h e y
e v e nb e l o n gi n C h r o m i s t a(?2 ) A r eA p u s o z o ap e r h a p ss i s t e r so f a l l o t h e r b i k o n t sa n d n o t r e a l l y
(3) Was a greenalga(C) reallyenslavedby the ancestralcabozoan
(4) Are Rhizariaand Excavata
by Cercozoaand euglenoids(asterisks)?
reallvsisters?T. Cavalier-Smith
Within excavates, the strictly non-amoeboid Loukozoa
('groovy animals') have a well developed ventral feeding
groove with a scooped out,
look that gives
the infrakingdom its name; their mitochondrial genome
retains more bacterial genes than in other eukaryoles.
Percolozoa are predominantly amoeboflagellates (Heterolobosea, e.g. the human pathogen Naeglena fowlen),
sometimes pure amoebae (having lost cilia and groove),
rarcly pure flagellates. Other excavates are largely nonamoeboid flagellates.Mehmonada are secondary anaerobes,
having converted mitochondria into hydrogenosomes or
mitosomes, with a marked tendency to multipiy clha and/
or nuclei, e.g. Giardia, h"chomonas.Euglenozoa include the
sedouslypathogenic trypanosomatids (e.g. sleeping sickness
agents),the ubiquitous bodonid zooflagellates(the weeds of
eukaryotic microbiology), and the euglenoids (with Qomplex
pellicular strips: phototrophs like Euglena,phagotrophs like
Peranemaor saprotrophs like Rhabdomonas).
Bikonts share a compiex pattern of ciliary development
with the anterior cilium being younger and transforming in
the next cell cycle into a posterior cilium, often structuraily
and behaviourally different. This anterior-to-posterior ciliary
transformation is unique to bikonts; it probably evolved
in their common ancestor as an adaptation to gliding on
surfaces,using the posterior cilium as a skid. Bikonts have
two distinct posterior bands of microtubules as ciliary roots
and ancestrally a structuraily different anterior band. This
cytoskeletal aqtmmetry was similarly adaptive, becoming
secondarily more syrnmetrical in many algal lineages after
they became planktonic and abandoned eating prey Thus
past nutritional history is reflected in cell structure of
protozoa and their modern descendants. But the picture
was confusing, because of repeated evolutionary losses of
organelles,until molecular evidence helped sort it out.
In marked contrast to bikonts, unikonts ancestrally had
only one centriole and no microtubular bands, instead
a simple cone of microtubules anchored the centriole to
today ruarv
the nucleus and the rest of the cell. I consider this simpler
slructure the ancestral state for eukaryotes that evolved
together with the cell nucleus. In only slightly modified
form this ancestralunikont patlern is still seen in zoospores
of lower fungi, choanoflagellates,the best model for animal
ancestors,and our own sperm - such is the force of stasis
in cellular evolution, much of which we can reconstruct
by studyrng those most fascinating of all organisms, the
protozoa, our relativesand ances[ors.
Thomas Cavalier-SmithFRS
President, British Societyfor Protist Biology
Department of Zoology, Universityof Oxford, South
ParksRoad, Oxford OX1 3P5, Ul( (e [email protected])
Bass,D. & Cavalier-Smith,T. (2004). Phylum-specific
environmentalDNA analysisrevealsremarkablyhigh global
biodiversityof Cercozoa(Protozoa).lntJ SystEvolMicrobiol54,
Cavalier-Smith,T. (2003). Protisrphylogenyand the high-level
classificationof Protozoa.EurJ Protistol39,338-348.
Cavalier-Smith,T. (2004). Chromalveolate
cell megaevolution:
interplayof membranes,genomesand
. In Organelles,
68.,pp. 75-108.Edited
by R.PHirt & D.S.Horner.London:CRCPress.
Cavalier-Smith,T. (2006). Cell evolutionand earthhistory:
stasisand revolution.PhiITransR SocLondB 361, 969-1006.
Cavalier-Smith,T. (2006). The tiny enslavedgenomeof a
rhizaian alga.ProcNatlAcadSciU 5 A 103,9739-9780.
Richards,T. & Cavalier-Smith,T. (2005). Myosindomain
evolutionand the primary divergenceof eukaryotes.Nature436,
he exponential growth in publicly available
molecular sequencedata has created a gold mine
of encoded information covering billions of years
of evolution. One of the most immediate ways to
make senseof these data is by the comparison of
the sequencesin phylogenetic analyses.Getting a
simple tree is relatively easyand potentially very informative
(if not exactly publishable). A deeper understanding of the
methods can help you grow trees thal are more reiiable and
reveal complex evolutionary histories.
Il it is relationshipsamong organismsthat you are inierested in, it is becoming clear that a tree of organisms based on
a single gene or its corresponding protein sequence may
not necessarily represent lhe true history of the organisms
in the tree. Rather, it tells the story of the evolutionary
history of that particular gene while another gene a few
bases away in Lhe genome may have experienced quite a
different evolutionary history This is partlcularly true ln
'illegitimate' trading of genes ts
bacterial genomes, where
rampanl (seebelow). Used with care, and perhaps a heaithy
dose of scepticism, phylogenetics offers powerful tools for
tracing the often entangled evolutionary trails of genes. For
bacteria, it is especiallyuseful for revealing phenomena such
as lateral gene transfer (LGT), and in all domarns of life, gene
duplications and, sometimes, true organismal relationships.
This article is intended as a brief tutorial on how to
interpret phylogenelic lree diagrams and an introduction
to the methods of preparing raw data and building a LTee.
g the
SandraL. Baldaufprcvide
Throughout, we wish to emphasize that phylogenetics, like
any other branch of science, requires informed judgement
in the selection and application of methods to maximize the
accuracy of the results.
a guideto interpreting
GemmaC. Atkinsonand
l v
of phylogenetic
Leaves,branches and nodes. Phylogenetictrees,or phylogenies, display deduced evolutionary reiationships in the
form of multiple branching lineages (Fig. l). The sources
'operalionai taxonomic units' (OTUs),
of the sequences,or
are the tips or leaves of the tree. Nodes (junctions where
two or more branches join), represent a divergence event
(gene duplication or speciation) and also the hypothetical
last common ancestor of all the branches arising from them.
The further a node is from the tips, the further back in time
the divergencehappened, with the root of the tree being the
mosl ancientnode.
m i c ro b i o lo gy todaY ti i.ri',ri-i:i
Root .',,.-
) F i g .1 . E q u i v a l e npth y l o g e n e t itcr e e s .
All thesehypotheticaltreeshaveexactly
t h e s a m et o p o l o g ya n d d i f f e ro n l y
in presentationstyle.(a, b) Rooted
c l a d o g r a m sw, h i c h s h o w b r a n c h i n go r d e r
b u t n o i n f o r m a t i o no n t h e a m o u n to f
e v o l u t i o no n e a c hb r a n c h ;( c , d ) r o o t e d
p h y l o g r a m sw, h i c h s h o w b r a n c hl e n g t h s
p r o p o r t i o n atlo e v o l u t i o n a rdyi s t a n c ea; n d
(e) unrootedand (0 rooted radialtrees.
N o t e :t h e n o d e h e i g h ti n t r e e s( a ) ,( c ) a n d
( d ) i s p u r e l ya d e v i c ef o r e v e ns p a c i n go f
b r a n c h e s6. . C .A t k in s o n
{ E n t w i n e dt r a i l so f c a ra n d r o a d l i g h t s ,
r e p r e s e n t i ntgh e t a n g l e dt r a i l so f e v o l u t i o n .
BrandX Pictures,/ Punchstock
trollsof evolutlorl
Orthologues and paralogues. All
sequencesthat sharea common ancestor
are homologues. Homologues come
in several different flavours (Fig. 2).
Orthologues are the direct descendents
from a single ancestral sequence and
are duplicated along with the rest of the
genome in each generation. Paralogues
arise by gene duplication, thus giving
rise to multigene families.
Xenologues. Phylogenetic trees are
one of the best means of detecting
LGT, which is rampant in bacteria and
archaea, and also occurs at a lower, if
largely unknown, frequency in eukaryotes. Xenologues are homologues that
m i c r o b i o l o gtyo d a yi " l * v# 6
have undergone LGT and can be identified in phylogenetic trees by their
tendency [o nest with sequences fuom
the donoqs lineage (Fig. 2b).
Crowingyour own tree
Digging in the databases.A huge,
exponentially growing amount of
nucleotide and protein sequences is
stored in public sequence databases
(Table I), the main ones of which are
updated againsteach other daily These
are usually the first port of call when
assembling or augmenting a dataset.As
annotations are unreliable, the best way
to find homologous sequences is by
doing BIASror FASrA
sequence similarity
searches.These look for matches to a
user-provided query sequence in one
or many sequencedatabases(Table 1).
The alignment: the foundation
from which a tree grows. Once
you have found your sequences, the
next step is to align them (Table 1).
A phylogenetic tree is only as good as
the alignmenr ir is buik on. Muhiple
sequence alignment programs have
continuously improved over the years,
but they still tend to perform badly in
regions of poor sequenceconseruation.
Here, the human eye is often better
at recognizing homologous patterns.
Therefore, all alignments should be
inspected by eye before building trees
(Fig. 3). Only homologous positions
should be used to build trees; gaps and
ambiguously aligned regions should, as
a general rule, be excluded.
Minimizing distances and hiking
through tree landscapes. There
are two main classes of methods for
building trees:distance and discr ete data
methods. Distance methods (UPGMA,
With the increasing
ral andfu rctionalinformation
it is becoming
now available,
in proteinfrrction
to mapchanges
summarize all
neighbour joining)
the information between pairs of
sequencesinto a single statistic. This is
the distance, essentiaily the percentage
difference, between two sequences.
OTUs are clustered into groups in the
multiple methods. Greater confidence
in results can be gained if different
methods produce congruent trees.
tree based on these pair-wise distances.
Parsimony, maximum likelihood (ML)
and Bayesian inference methods are
discrete data methods as they treat each
column in the aiignment as a discrete
data point. These methods search'treespace', a probabilistic landscape of hills
and valleys made up of all possible trees
and their'fitness', in a quest to find the
tree or set of trees that best fit the data.
All tree building methods have their
strengths and limitations. Therefore, it
is a good idea to repeat analyses with
Mod e | | i ng evo Iuti o n . All phylogenetic
programs assume some evolutionary
model to explain amino acid or
nucleotide substitution patterns. These
are used by the various phylogeny
programs to attach weights to different
classes of substitutions, rather than
assuming all mutations are equally
likely This is important for accurate
trees. For example, a mutation that
results in an amino acid substituting
for another with similar chemica^
properties tends to have a minimal
effect on the function of the protein.
Such substitutions are frequent and
indicate less evolutionary time than
changes at slowly evolving sites; this is
taken into account by the gamma rate
Where is the root? Almost all phylogenetic programs produce unrooted
trees from molecuiar data. However,
a root is essential for establishing the
order of divergences in a tree. Often,
the first diverging sequence in a dataset
is unknown. In this case, an outgroup
of one or more OTUs can be included
O r t h o l o g u eI s
T ;I
ffi-*Tl tEffiifl
m i c r o b i o l o g yt o d a y r u * v# S
T a b l e1 . P h y l o g e n e t irce s o u r c e s
Major databanks
U\J LL-,,
EukaryoteCenomePortal www-users.york.ac.uk/-ct505/Ph
D_Projed5/ Eukaryote_H
http :/ / n cbi.ni h.govlBLAST/
/ index.htmI
ft.p:/ /ftp.ebi.ac.uk/
www. d rive5.com/ muscle
www. ch.embnet.o rglsoftware/T Coffee.htmI
http :/ / paup.csit.fsu.edu/
http://evolutio n.genetics.wash
http:/ / atgc.lirmm .fr/ phyml/
www. bio.utexas.
edu/grad/ zwi ckl/ web/garli.htmI
www. megasoftware.
http:/ /taxonomy.zoology.gla.ac.uk/rodltreevi
www. ics.forth.grl-stamatak/i
http://evolutio n.genetics.wash
i ngton.edu/phylip/software.
{ Fig.2. Orthologues,
x e n o l o g u e sH
. o m o l o g o u sg e n e s c a n
a r i s eb y v e r t i c a ld e s c e n to r s p e c i a t i o n
( o r t h o l o g u e s )d, u p l i c a t i o n ( p a r a l o g u e s )a, n d
LCT (xenologues).The latter two can result
i n n o n - c a n n o n i c apl h y l o g e n e t i ct r e e s . ( a )
C e n e sX a n d Y a r e a n c i e n t h o m o l o g u e s ,
w i t h X b e i n g t h e e u k a r y o t i cv e r s i o n a n d
Y t h e b a c t e r i a ol n e . A h y p o t h e t i c a lg e n e
d u p l i c a t i o ne v e n t p r i o r t o t h e o r i g i n o f
p l a n t s ,a n i m a l sa n d f u n g i l e a d st o t h e X '
p a r a l o g u ew
, h i c h i s i n h e r i t e db y d e s c e n d e n t
s p e c i e s .I n o n e l i n e a g e ,X ' i s r e p l a c e d b y Y ' ,
a x e n o l o g o u sv e r s i o no f t h e g e n e b r o u g h t
about by LCTofgene Y. (b) The resulting
phylogeny.Since the fungal X' gene is lost
i n t h i s e x a m p l e ,t h i s g e n e w o u l d n o t a p p e a r
in the phylogeny (dotted line). 6.C. Atkinson
F i g .3 . E d i t i n ga n a l i g n m e n t b y e y e . ( a ) A
section of a cLusrnlx (Table 1) alignment of
bacterialprotein sequencesbefore editing.
F i v ec o l u m n sc o n t a i n i n s e r t i o n s( s h a d e d
c o l u m n s ) .( b ) T h e r e f i n e d a l i g n m e n t .
O n l y t w o c o l u m n sc o n t a i n i n s e r t i o n s ,a
m o r e p a r s i m o n i o u sa r r a n g e m e n ta s f e w e r
i n s e r t i o no r d e l e t i o n e v e n t s a r e a s s u m e d .
today i|{-i( i.liri
in the dataset.This is essentially an external point of reference
to identify the oldest node in the tree, which is the outgroup's
closest relative. For example, for a tree of mammalian genes,
one could use the orthologus gene from a marsupial as the
- how strongisthat branch?
testsfor supporL
a tree is,
There are various ways to determine how
that is, how much better it is than other possible trees. The
most commonly used method is bootslrapping. This involves
phylogenetic analysesof multiple random subsamples of your
dataset. The bootstrap support for each branch corresponds
to the percentage of analyseswhere that branch appears.
Bayesian inference is becoming increasingly popular in
moiecular phylogeny Instead of bootstrapping, this discrete
data method uses all the trees it encounters in the tree space
to calculate the posterior probability for each branch in a
consensus tree of all encountered trees. This is fundamentally
very different from bootstrapping and posterior probability
and bootstrap support values are nol directly comparable.
o/ocan be
Generally, a bootstrap percentage greater than 70
taken as good support, but only probabilities greater than
95 o/oare reasonable support for Bayesianinference trees.
Fatal attraction: the curse of long branches. The rate
of molecular evolution is not uniform across a tree; some
OTUs may have acquired more mutations than others over
time and therefore grow longer branches in the tree of their
evolutionary history Tree-building programs have problems
with such branches, and tend to group long-branched
OTUs together due to spurious sequence similarities. This
is the notorious'long-branch attraction' or LBA. Likelihood
methods are on the whole less likely to be duped by
variations in evolution ry rate, and the use of more accurate
evolutionary models can give any algorithm a helping hand.
However, likelihood methods are not beyond failure and
there is no perfect model of evolution. Therefore, the easiest
remedy for LBA is often to include intermediate sequencesto
break up long branches. Alternatively, if the long branches
are not essential for the questions you are asking of the tree,
it is often best just to leave them out.
Phylogenetics allows us to piece together clues left by chance
to retrace evolutionary history but the clues are patchy
as most taxa and many genes are extinct. Because of this,
phylogenetic methods rely on the experience and judgement
of the researcher for the quality of the results they deliver,
and knowledge of how to interpret trees is essential for
making sense of the patterns within them. The rewards are
great, however, as retracing the evolution of a gene with
phylogenetic analysis can reveal complex and often surprising
stories of molecular history With the increasing amount of
structural and functional information now available, it is
becoming possible to map changes in protein function and
structure onto evolutionary trees. This will allow us to begin
to ask not just how organisms work, but why they do the
sometimes seemingly very strange things that they do.
GemmaC. Atkinsonand SandraL. Baldauf
of York,
of Biology,
YorkYO105YW,Ul( (t 01904328635;
uk, [email protected]
e [email protected]
m i c r o b i o l o g yt o d a y * * v $ 6
S c h o o lM
s e m b e r s h i cpo s t so n l yf . 1 0a y e a r .B e n e f i tisn c l u d e
Today,advancecopiesof new teachingresources
a n dd i s c o u n t efde e so n S C M I N S E Tc o u r s e sT.oj o i n s e e
r gk o t o
w w w . s g m . a c . uEk n
. q u i r i e se:d u c a t i o n @ s g m . a co. u
for full detailsof resources
and activities.
ltcecnt edLreiltinnill
hrsilltnilnd dismils#
Eleanor (aged 10) thought the books
were attractive and full of useful
information, but felt that the style was
a bit too childish for her age grouP
and suggested that they would be
most suitable for children in years 3
and 4.Isobel (age 6Vz)was not able to
read the books for herself, but enjoyed
listening to me read and looking at
and discussing the illustrations. I
think the books would make a useful
addition to any primary school library
and would suppoft the science and
PSHE teaching at KSI and KS2. Both
books cover information relevant to
the micro-organisms unit in the KS2
Specifications, but the style might be
off-putting to a more advanced reader.
I Jane Westwell
I sCnnExternal
Forthe younger
Why Must I Wash MY Hands?
W h y M u s t I B r u s hM Y ? e e t h ?
comprehensively answered in two
books published by the CommunitY
Practitioners and Health Visitors'
Association. The books are Packed
fuli of information and cover far more
material than the titles would suggest,
including the structure of teeth,
healthy eating, history of soaP and
toothpaste, food safety and personal
hygiene. The text is simPle and the
illustrations include lots of photos
of children which help engage the
younger reader. Each spread has a
main theme and ends with points to
remember. They also include some
fascinating facts related to the theme.
I had a slight problem navigating
the pages until I became used to the
styie and use of font to distinguish
the narrative from the factoids. As
a microbiologist, I was keen to see
how microbes were represented and
on the whole was impressed with the
books, apart from the description of
bacteria as'types of germ' tnWlry must
Ibrushmy teeth?,although the author
did point out that many bacteria are
harmless or useful to humans.
Since the books are in a style aimed
at primary school children, I asked
my daughters for their point of view
in AAsdernScience
The Discovery
Thescopeof thissmallbookis
much wider than indicated by its
title, perhaps chosen for consistency
with others in the series. It is
attractively presented, clearly written
by an experienced science writer,
not overburdened with text, and
generously illustrated with attractive
photographs and diagrams and
information boxes. This provides
an inviting balance for the intended
readership, KS3 upwards.
There is a brief introduction to
DNA and genetics, followed by five
other chapters dealing with a history
of genetics, the discovery of DNA and
its structure, protein slmthesis and
mutations, applications to genetics,
and future prospects. There is also a
m i c r o b i o l o g yt o d a yn * v S S
timeline, glossary sourcesof further
information (websites and books) and
an index.
and'Facts' to break up the text. I
was particularly impressed by the
picture research,which has produced
some unusual and highly relevant
illustrations alongside the diagrams. I
suspect that this may be a factor in the
cost of the books. Good quality science
photographs do not come cheap!
The book is appropriate for a school
library but where resources are scarce
it is an expensive purchase when a
similar coverage and more pages can
be obtained elsewhere for little more
than half the price.
In my former life as a school librarian,
I would have snapped up these books;
they meet all the selection criteria.
Their content is excellent, presentsa
balanced view and does not shy away
from the controversy, uncertainty and
personality clashes that make up real
i John Grainger
i Chairman, MISAC
f'fta*est*nes im {tfz***rn %*E*nr,* *
T ? t *f f i t s r * ' s * r*yf # * n t * t f t l u n
Somewhatsurprisingly these titles
are written by Guy de la Bedoyere,
who is more commonly associated
with archaeologicaldigs on TY but
neverthelessare very well researched
and highly readable.Each book
coversfar more than its title suggests,
ranging over different aspects of the
history of medical microbiology whilst
bringing the subject bang up-to-date.
Eachintroduction summarizes the
book in two pagesand probably gives
enough facts for the averagestudent
to understand the topic and even do
their homework. However, another
34 pagespacked with interesting
information follows, complimented by
a timeline, giossaryand index.
The further reading includes some
recent, quite challenging books, as
well as useful websites.
The chapters in the polio volume
are headed: early experiments with
vaccines,the polio virus, Salks
investigations,the vaccine works field tests and mass trials, new
vaccines,polio today Chapters in
penicillin book are: bacteria and
disease,the path to peniciilin, making
penicillin work, penicillin for all, and
penicillin today.
I really liked the layout, which is
easily navrgated and bucks the current
trend in educational books for a lurid
scattergun design, whilst still using
colour-codedboxes about'Key People'
Tke ffiaxe#\derv#f mflllA
Camillade Ia B6doydre,
EvansBrothersLtd (2005)
t 1 4 . 0 0 ,p p . 4 8 , I S B N0 - 2 3 7 5 2 - 7 4 0 - 5
Th* FsrstW*€io
Cuy de la B6doydre,
EvansBrothersLtd (2005)
fI4.OO,pp.48, ISBN0-23752-738-3
*{ WsnErilE|n
Cuy de la B6doydre,
EvansBrothersLtd (2005)
f 1 4 . O Op, p .4 8 , I S B N0 - 2 3 7 5 2 - 7 3 9 - 1
f.11.99,pp.32, lSBN1 -84234-190-1
today **v {"}{i
JanetH urst
SCM ExternalRelations
ffi w a\tkamrj * i seax*
Here is a book with a strange concept.
It is one of a series,ShahespearesWorld.
The book covers a rarrgeof topics and
on each page there is a quotation from
the great bard with an explanation
of what this teachesus about life in
Tudor times. Of course there is no
microbiology, becauseno-one knew
that unseen life forms were the cause
of infections, but the doctors of rhe
day were beginning to understand the
scientific reasonsfor illness. The book
explains this quite clearly.
Two-pagespreadscover health and
hygiene, theories about health,
common complaints, surviving birth
and childhood, plague, doctors,
healers,cures and remedies,herbs and
herbals, madness,hospitals, wounds
and operations. I was quite surprised
to seehow often Shakesoearerefers
to doctors and medicine in his olavs.
The book is attractively laid out and
beautifullyillustrated.It is cleariy
written and appearsto have been well
researched.I really enloyed reading it.
However, I am not sure who it is for,
or how it would be used in school as it
crossesover history Englishliterature
and science.
JanetH urst
SCM ExternalRelations
n e m b e risn t h e e a r l y
C r a d l i naei m st o i n f o r ma n de n t e r t a im
lf you haveanynews
of theircareerin microbiology.
to seeanytopicsfeatured,
or wouldlil<e
or stories,
JaneWestwell([email protected]
The biotech industry has been slow to mature, but is finally coming of age. The
number of biopharmaceuticalsbeing approved for human therapy is increasing
year on year andmany traditional pharmaceutical companies are turning their
attention to this area.
Biopharmaceuticalsare typically complex molecules that are expensive
to manufacture. Their increaseduse in human therapy is placing alarge
fi.nancial burden on healthcare providers. A high profile example is Herceptin
(trastuzumab; Genentech./Roche),
a monoclonal antibody indicated for the
treatment of breast cancer,which has beEn the subject of a public campaign to
make the drug widely available on the NHS and a debate over its affordability
It will be up to bioprocessscienlists to develop low-cost manufacturing
technologiesto ensure biopharmaceuticalscan be made widely available
whilst maintaining the highest quality standards.
Sustaining the biologics growth, particularly as product pipelines malure,
will require expansion of bioprocessing capabilities.A recent reporl to
government by the Bioscience and Inovation Growth Team (BIGT) on
mainlaining rhe UK's competitive position in bioscience identified the need
to build a strong bioprocessingsub-sector as one of six major
recommendations (www.bioindustry. orglbigtreport/).
David Glover, UCB Celltech
A D a v i dC l o v e r
A therapeuticagentnroduced
Dyorgarusmsuslng recombinant
DNA technoiogr Theseinclude
and genetherapyproducts.
area subset
of biologics.
using living orgpnisms,rissuesand
cells.Biologrcsinclude prophylaCtiC
vaccines,blood products,Loxkrsand
stemcell therapiesin addition to
H'fi"#::*Ti-ffi :"rac'lunng
and deliveryThesetechniques
include molecularbiology,microbial
and analysis.Personalized
medicines. such as certain stem cell .
therapies, also require bioprocessing.
m i c r o b i o l o g y t o d a y i l { , } t i{ " l t i
N a m eD a v i dC l o v e r
Age 39
P r e s e not c c u p a t i o nD i r e c t o r ,
B i o P r o c e sRs& D , U C BC e l l t e c h
P r e v i o uesm p l o y m e n t
UCBCelltech;2OO305, ClaxoSmith
Celltech;1991-95, Universityof
; 199V91, BioExcellence;
1988-89,HoechstAnimal Health
E d u c a t i oU
n niversito
y f Birmingham,
PhD Biochemistry
S u n d e r l a nP
d olytechniB
c ,S cA p p l i e d
influencedyour decisionto
a PhD?
The early part of my careerwas very
much influenced by the Spinks reporr
and the euphoria of the 1980s that
surrounded the predicted impact
biotechnologywould have on our
lives.I was fascinatedby the concept
of making a new generation of
The applied and multi-disciplinary
nature of biotechnology appealed,bur
I particulariy wanted to contribute to
further understanding of this emerging
science.Thus it seemedobvious
I shouid study for a PhD, out of
fundamentalinterest and to equip me
for a careerin the biotech industry
did you chooseyour
I alwaysintended doing a PhD, but
worked in industry for ayear before
returning to academia.I selecteda
project that was multi-disciplinary
in nature, being run jointly between
the Schoolsof Biochemistry and
Biochemical Engineering at the
University of Birmingham. I was
using fermentation and physiological
profiling tools to study the regulation
of geneexpressionby environmental
factorsin a yeast system. The interest
to the field of biochemistry was
further understanding of control of
geneexpressionperse,whereas the
biochemicalengineerswere looking
today n*,.rl..r{::r
for real systemsto study the impact
of poor mixing on cell physiology in
large fermenters.
easywas the transitionto
Slresearch in the commerctalsector
after your PhD?
Tiansition to the commercial sector
was not as difficult as might be
expected.Explaining what my PhD
was about to lay persons (my parents,
for instancel) and why it was relevant
to the real world was always difficult.
Suddenly I was able to relate what
I did to something tangible and of
benefit to mankind - I could refer to
familiar diseasesand how the drugs I
worked on could make a difference.
Of course, the need to deliver to strict
timelines and remain focused on the
goals was a bit of a culture shock. In
industry it's not always possible to
further explore that interesting result,
particularly if this means departing
from the main project. However, the
buzz from working on something that
may ultimately help parienrsis great.
is rewardingaboutyour
The UK has long been associatedwith
innovative researchin bioscienceand
medicine."However, it is bioprocessing
that takes ideas for medicines from
the lab to patients via commercially
viable expression and manufacturing
technoiogies.Being responsible for
making sure a new drug gets to all the
patients, at the right time, and to the
highest quality standardsto ensure
their safety is highly rewarding.
you describea typical
The work varies considerably from
day to day One day I might be
reviewing a technology initiative for
a novel drug design or a new protein
expressionsystem, the next I could
be involved with a regulatory filing to
gain approval for our most advanced
drug. in between these activities, I
could be involved in the selection of
antibody-based drugs; development
of fermentation and purification
processesfor their production;
analysisfor quality attributes; scale-up
and manufacture for clinical trials
and interaction with the regulatory
agenciesto ensure patient safety and
approval of plans.
(-\Do you have any adviceto anyone
V-planning a researchcareerin the
biop harmaceuti cal industry?
Implementation of rhe BIGT
recommendations will see increased
opportunities for rraining in the
biosciences.For example, the research
councils and industryhave formed
the BioprocessingResearchIndustry
Club (BRIC) to steer and fund
industrially relevant academic research
in bioprocessing (www.bbsrc.ac.uk/
science/initiatives/bric).I would advise
those interested in a careerin the
biopharmaceurical industry to embark
on training of a muhi-disciplinary
nature, such as that provided under
the BRIC programme. Whilsr expefiise
in a particular areais required, we like
our scientiststo have an appreciation
of where and how their expertise
interfaceswith other areasneeded to
discover and develop new drugs.
do you seeyour
We face the challenge of developing
the infrastructure to attract and train
new bioprocessscientiststo support
the growth of both my own company
and the wider UK bioscience sector. I
seemy future plapng a role in both.
- rheDTIwww.bioprocessuk.org
dedicatedto the advancement
of the
1 .
bioprocessingsector in the UK. The
website contains information on training,
careersand jobs in the UK.
www. b ioi nd ustry.org - The Biolndustry
Association is the trade association for
the UK's bioscience sector, representing
the industry to stakeholders - from
patient groups and politicians to rhe
media and financial sector.
t r R e c i p i e n t so f S C M V a c a t i o n
S t u d e n t s h i p si n 2 O O 5 . L e f t t o
r i g h t : A l i s o n T h o r n t o n ,C a l u m
D a v i s ,H a n n a h T r e w b y , H e l e n
E w l e s ,J a n e t S m i t h , J o s h u a
W i l l o u g h b y ,L e e W i e r s m a .
n award allows a studenl lo conduct a
research project in some aspect of microbiology during the summer vacation prior
to their final year of study.Around 50 awards
are made annually At the end of the project,
the student submits a brief report of the
research. A selection of the 2005 reports are summarized
below. They illustrate the diverse nature of the projects and
alsohow the studentsviewed theirbrief encounterwilhmicrobiological research.Seep. 146 for details of the 2007 scheme.
Alis#n Thornton worked with Dr Evelpr Doyle, Department
of Industrial Microbiology, University College Dublin. Her
project was concerned with the bioremediation of sheep
dips containing slmthetic pyrethroids. These compounds
are highly toxic to aquatic creatures and potentially serious
contaminants of water courses.Alison examined the capacity
of a naturally occurring soil Pseudomonasto degrade the
s)'ntheticpyrethroid most commoniy used in sheepdip, cypermethrin. The level of cypermethrin degradation observedby
the bacterium in this study is the highest reported to-date for
properly, although high concentrations are usually toxic.
However, some plants tolerate and even actively accumulate
high concentrations of hear,y metals. The metal-hyperaccumulating plant Thlaspi caetulescenswas grown on
a ralrge of Zn concentrations and then inoculated with
the plant pathogen Pseudomonassynngae pv. maculicola.
Bacterial growth was inhibited in plants treated with higher
Zn concen[rations. The resuits suggest that the increased
diseaseresistanceof metal hyper-accumulating plants could
be due to a direct toxic effect of metals on pathogens and
explain the benefit of the energy-costly process of metal
studentshtpproved an invaluableexpenence,not only in
allowing me to carry out researchover the summer,but also
in glvingme a tasteof what researchis like. I now'hnowthat I
w ould lihe to continue in biologicaI research.'
worked with Dr Eirwen Morgan, Institute for
Animal H eaI th on the id enti fi cati on of Salm oneIIa c olonizatron
factors in chi.cks. Salmonellaentenca serovar Tlphimurium
produces enteritis in a wide range of animals, including
a pure culture of a bacterium.
man. The introduction of Salmonellarnto the food chain via
project allowed me to worh. with some highly skilled infected chicken carcassesand eggsis a major causeof human
food poisoning. The mechanisms Salmonellduses to colonize
scientistswLtoguided and advised me throughout. The worlt
oJthefeldl choose poultry are thereforeof key public health importance and also
impact on poultry welfare and the economics of the industry.
in the future.'
Hannah used signature-taggedmutagenesis(STM) to screen
{aiurn AaztiEworked with Dr Gail Preston, Department a bank of random Salmonella Typhimurium transposon
insertion mutants for thelr abiiity to infect 1-day-old chicks.
of Plant Sciences, University of Oxford, on the effects of
Her results confirmed previous findings that genes in the
metal hyper-accumulation on plant disease resistance.All
SalmonelloPathogenicity Islands SPI-l and SPI-2 are needed
plants require healy metals, such as Zn and Ni, lo function
Wootlon work
#ffif,*r SueAssinderreviewssfirne
*f 5fiAA
mfth* r#p#rtswrlttmr:hy thc r#{:ipi*nts
ips!n 2#*5.
m i c r o b i o l o g y t o d a y i r i " , "{, " i { i
for r,rrulence. She identified ma:ny
mutants that cannot cause disease in
l-day-oid chicks but which are known
to colonize calves and l4-day-oId
chicks. These mutants must therefore
have transposon insertions in genes
which could influence host soecificitv
a yet student it was particularly
interestingto seewhat goes0n to achieve
the sciencethat vets tend to accept
without question. Also interestingwas
the mental U-turn neededto go from
thinhingintermsoJthe wholeanimal to
considenngdiseasefrom the microbial
Helen Frrulesworked wirh Dr Adam
Roberts,EastmanDental Institute, UCL.
to charactertze a novel tetracycline
resistancegene, tet(32), isolated from
human mouth bacteria. Antibiotic resistanceis an ever-increasingproblem.
Oral microflora harbouring novel
tetracyclineresistancegenescould play
an impoftant role in spreading resistance to pathogens. A fully characterized gene would provide information
on resistancemobility, and the method
oftetracyclineresistance.Helen'sinvestigationsshowedthat tet(32)is not mobile
and that it is inducible by rerracycline.
She also amplified parr of the tet(32)
gene,generatingnew sequence data.
Further studies of tet(32) may aid the
developmentof new drugs and possible
methodsto overcomeresistance.
'I thoroughly
enjoyed my slrmmer
It helpedme enormously
with prepanngfor my third jear
asweIIasconfirmingnry desire
a careerin research.'
ianet Smith worked with Dr Brian
Gibson in the Brewing Yeast Research
I-ab at Oxford Brookes University on
today il,ri,i-l{;;
the role of glutaredoxins in protecting
brewing yeast against peroxide stress.
Oxygen is essentialto maintain a viable
yeast culture during fermentation, but
the accumulation of harmful oxygen
derivatives, known as reactive oxygen
species,can damage yeast cells. Glutaredoxins are small proteins found in
Saccharomycescerevisiae, which are
known to protect cells from these
damaging effects.They are encoded by
genes GRXL and GRX2. Janet showed
that mutant S. cerevisiaestrarrlslacking
one or other of these genes were less
tolerant to exposure to hydrogen peroxide than the wild-t1pe srrain and rhat
GRX2accountsfor the majority of gluraredoxin activity in yeast. The relative
sensitivitiesto peroxide stressof a wildt;,pe strain and four brewing strains
were also investigated. Of the brewing
strains, one ale strain was particularly
sensitiveto hydrogen peroxide, whereas
the sensitilrty of the lager strains was
comparable to the wild-type strain.
Thesereslrltswerepresentedat a malting
and brewing seminar in Belgium and
have recently been published (Gibson,
B.R. & others, 2006; Cerevisia- BeIgJ
BrewBiotechnol3L. 25).
this projectgave me the chance
to spend more time in the lab tLtan
would normally be possible in an
undergraduatedegree.BecauseI enjoyed
it so much, I'd lihe to worh in clinical
scienceor researchin the future.'
Joshua Wiil*ughby worked with
Professor Geoff Turner, University of
Sheffield, on whether actin cables or
microtubules direct the movement of
peroxisomes in a filamentous fungus.
Peroxisomes oxidize specific organic
substrates in a reaction that produces
hydrogen peroxide. They are important,
organellesfor fatty acid metabolism and
some of the steps of antibiotic sfithesis
in fungi. In humans, peroxisomes
make lipids which insulate nerve cells,
so peroxisomal defecb can result rn
severe neurological diseases.A related
organelleis essentialfor pathogenesisin
the economically significant rice blasr
pathogen Magnaporthe gnsea. Joshua
used a strain of the fungal model organ,
rsm Asperglllusnidulansin which green
fluorescent proiein was fused to the
peroxisomally located enzqeisocitrate
lyase. Peroxisomeswere easily seen in
live hlphae using W lighr microscopy
The drugs benomyl and cytochalasin
were used to disrupt microtubules and
actin, respectively Both affected fungal
growth, but neither dru g alone appeared
to prevent migration of peroxisomes
into hyphae.
studentshiphad a strongpositive
1 inJluencein the decisionto do a P\"LD.'
Ls* Wiersma worked with Professor
Stuart Siddell, University of Bristol.
Her project was on feline infectious
peritonitis (FIP), a condition caused
by FIP! a coronavirus. Up to 40o/o
of UK cats are thought ro be infected
with it and 5-10 % of rhem develon
FIB which is invariably fata|. Lee
aimed to express rhe nucleocapsid (N)
prorein of FIP! which is one of the
structural proteins. She cloned the N
gene into a bacterial plasmid designed
for expressionin bacteria. The bacteria
with the expressedprotein were lysed
and the protein was purified by affinity
chromatography The resultant N
protein was of sufficient purity and
quantity to be used in the production
of monoclonal antibodies (mAb). These
mAbs will be useful rools for further
study of the molecular cellular biology
of the virus wrth the aim of developing
an effectivevaccine against FIP
a lookat somerecent
writerMeriel Jonestal<es
p a p e r isn S C Mj o u r n a l sw h i c hh i g h l i g hnt e w a n de x c i t i n g
in microbiological
to TB controlusinggranulysin
New appraach
L i u ,8 . , L i u ,S . ,Q u , X . & L i u ,J .
of a eukaryotic
systemfor granulysin
its orotectiveeffectin mice infected
with Mycobacterium tubercuIosis.
J Med Microbiol55,1389-1393.
Tuberculosis,causedby the bacterium
trrlycobactenumtuberculosis,kills around
3 million people eachyear.Even more
worryingly, resistanceto existing anti-TB
drugs is increasing,so new therapies
at the School
are needed.Researchers
of Medicine in Wuhan University in
China have been exploring whether a
peptide antibiotic made by somehuman
cells can be developed as an effective
treatment. Granulysin is produced
by human cytotoxic T l;.nnphocytes
and natural killer cells, and acts in
combination with a second pore-forming
protein called perforin and proteinases
called granzqes to destroy cancerous
and virus-infected cells within the body
However, in laboratory lests, granulysin
can kill or inhibit many bacteria,
fungi and
including M. tuberculo.sis,
parasiteson its own.
The researchershave demonstratedthat
human granulysin provides protection
to mice infected with M. tuberculosis
when it is made by their own cells.
To do this the researchersisolated the
sequencefor the granulysin geneand
insertedit into an expressionplasmid,
a circular piece of DNA containing all
the instructions to allow any animal
cell to sprthesize granulysin. They
checked that this worked using a cell
culture, and then injected mice with
the granulysin expressionplasmid.
Some of the mice were then infected
After a month
with M. tuberculosis.
the mice had the sort of inflammation
and lesionsthat occur in tuberculosis.
However, theses1'rnptomswere much
milder in the mice immunizedwith the
granulysin expressionplasmid. There
were significantly fewer bacteria in
thesemice as well, with many bacteria
showrng signs of damage.This is the first
evidencethat a granulysin expression
vector can protect againstM. tuberculosis
infection and suggestsa new approach
to TB control.
to fossilfuelsare a
) Left.Alternatives
c h a l l e n g feo r t h e 2 ' 1s t c e n t u r ya s d e m a n d
but reservesbecome
depleted.JeremyWalker/ Science
) Right.Hibiscusflower from Rarotonga,
with nitidulid beetles(Aethinasp.).Andre
{ C o l o u r e dX - r a yo f a p a t i e n t ' sc h e s ts h o w i n g
u b e r c u l o s i(sT B )i n t h e l u n g s
d i s s e m i n a t et d
T h el u n g sc o n t a i nl e s i o n s( t u b e r c l e sp,i n k )
. u Cane
c o n s i s t i nogf i n f e c t e dd e a dt i s s u e D
Medical lmagingLtd / SciencePhoto Library
SARSin horseshoebats
of two
Ren,W., Li, W., Yu,M. & others(2005).Full-length
J GenVirol
in horseshoe
batsand geneticvariationanalysis.
87. 3355-3359.
Severeacute respiratory syndrome (SARS)took the medical world by surprise when
it was first reported as a new diseasein Asia in February 2003. There was concern
becauseof its rapid worldwide spreadand high mortality rate,with an estimatedTT4
deathsamong the 8,098 peoplewho contractedSARSin the 2003 outbreak.Rapid
work identified the causalagent as a coronavirus.Although no new caseshave been
recorded since late 2004 among the public, researchersstill want to know more
about where the virus came from.
Researchersfrom China have already detectedvirus from the SARScluster
coronavirusesin at least five horseshoebat speciesfrom the genus Rhinolophus,
suggestingthat bats might be the natural home of the virus. The sequenceof all of
the genesof some of thesegroup 2b coronaviruses(G2b-CoV) is now known, and is
similar to that of viruses isolated from humans and civets in 2003. The researchers
have now characterrzedtwo additional G2b-CoV genome sequencesfrom bats and
have compared all of the genome sequencesto seewhether this gives clues about why
the virus was so virulent or how it was transmitted between different animal hosts.
The bat Gb2-CoV isolateshave an identical genome organization and share an overall
identity of 88-92 o/oamongthemselves,and between them and isolatesfrom civets
or humans. However, there is considerablediversity in their detailed DNA sequences,
even though researchersthink that they all evolved from a common ancestorof the
SARSvirus. The researcherscame up with different relationships among the strains
depending on which genesequencesthey used. This often indicates that there has
been recombination between viruses in the past, although more sequenceswould
be neededto prove this. One isolatefrom bats,Rfl, had a unique featurethat
might make it an evolutionary intermediate between the virus that infects bats and
srrainsfound in people. Further testssuggestedthat the viruses in bats had evolved
independently for a long time, whereasthe ones from humans and civets had recently
undergone strong positive selection,reinforcing the idea that something has recently
allowed the virus to crossbetween species.
m i c r o b i o l o g yt o d a yn * v S 6
in insects
L a c h a n c eM, . - A . ,B o w l e sJ, . M . ,
W i e n s ,F . ,D o b s o n J, . & E w i n g ,C . p .
(2006).Metschnikowia orientalis
sp.nov.,an Australasian
nitidulidbeetles.lnt.l SystEvol
M icrobio| 56, 2489-2493.
Microdieselfrom E. coli- an afternativeto fossilfuels?
R.,Stolting,T. & Steinbrichel,
A. (2006).Microdiesel'.
I engineered
for fuel production.Microbiology
Practicalahernativesto fossilfuels are a challengefor the 2lsr cenrury.Not only
arethe number of exploltableoi1reservesaround the world decreasingas demand
but using this non-renewableresourcealso contributesto global warming.
Amongthe solutionsis biodiesel,an alternativeto petroleum-baseddieselmade
fromplant oi1s.Its major drawbackis that the acreageof orl crops hke oilseedrape,
and oil palm neededto meet the world's current demandswould leave
littlespacefor food crops.However,most of the carbonrn plants is within structural
materialslike celluloseand starchrather than the seedoils. Biodieselwould be much
morepracticalif it could be made from thesechemicals.A secondproblem is that
biodieselis currently produced by convertingthe plant oils to fatry acid methyl
esters(FAMEs)using methanol,which is both toxic and derived from non-renewable
producedbiologically,have similar fuel propertiesto FAMEs,but are more expensive
to makeby chemicalsyrrthesis.
at the wesrfalischewilhelms-University in Germanyhave [aken a
lateralapproachto theseproblemsto seewhether bacteriacan help. Their solution
hasdemonstratedthat bacteriacanbe designedto make'Microdiesel',resembling
The researchers
brought togethergenesfrom three differentbacteria.They
hadbeenworking with the speciesAcinetobacter
baylyithat makesfats to storewirhin
its cells.The key enzyme(WS/DGAT) in this biosyrrthesisturns our ro work well
with a remarkablybroad rangeof substrates,including many never encounteredin
nature.Thrsenzymethereforemight make Microdiesellf it was supplied with suitable
Unfortunately,A. baylyi cannot syethesizesuitableamountsof ethanol.The
solutionwas to add two genesfrom anotherbacterium,Zymomonas
mobilis,to the
workhorse Escherichia
coli,giving it the capacityto synthesizeenough
ethanol.Addlng the genefor WS/DGAT from A. baylyi aswell createdgenerically
modifiedbacteriathat could churn out up to 26 o/oof their dry weight as FAEEs,
oncesuppliedwith sugarsand fatty acids.
Higherefficiencyand yields would be neededin a practicalindustrial process,as
we1lasthe ability to use crude plant materialsas substrates.However,the versatility
withinbacterialmetabohsmmeansthat this may well be possibleusing the righr
of genesand bacteria.The Germanresearchers
have shown that the
conceptworks and have openedup the way for further developments.
m i c r o b i o l o gt o\ d a y,
Nitidulid beetles
live on fruir.flowers,
leavesand otherdiscarded
plants,and can be a pestin dried fruit.
However,three of thesesmall beetles
have posedan interestingquestionabout
distribution,not of beetles,but
of yeasts.The beetleswere collected
from roadsidesseparated
by 11,000
km of land and oceanin cool regionsof
Rarotongain the Cook Islandsand the
CameronHighlandsin Malaysia.A novel
speciesof yeast,Metschnilzowia
wasdiscoveredin rheir droppings.
Remarkably,M. orientalishas not been
detectedbeforein extensivecollections
from habitatsin Australia,New
Caledoniaand Fiji. Researchers
Canadahave been surveying the insectborne yeastflora of theseareas.The
only tenuousclue linking M. oientalis to
thesetwo locationsis the low maximum
temperatureat which the yeastwill
grow.This must not exceed30-31 'C,
which could limit the number of suitable
habitatsin thesetropical regions.
The researcherssuspectedthat
they had a novel specieswhen they
recoveredseveralstrains of a yeast
that would apparenriyonly reproduce
asexuallyfrom two nitidulid beerles
in Rarotonga
in \999.In 2005 they
found a single isolate from an insect on
roadsideflowers in Malaysiathat had
similar growth and DNA charac[erisrrcs
to the Rarotongayeasrs.The only way
to distinguish this novei speciesfrom
other yeastsis to either examine DNA
sequencesor test for the production of
sexualsporesonce possibleisolatesare
mixed with authentic strains of each
- " -: -r ^t i' n
. bo
The question of why the strainswere
found so far apart,and where others
Iilay Lurn up, ts snlr open.
' a ^ r 7
t r r v h
i ^
^ * : l l
" ^
irr Sehools
SueAssinder(SCM Education
Officer)gaveoral evidenceon
behalfof the Biosciences
(BSF)to the recentHouseof Lords
SelectCommitteeenquiryon Science
T e a c h i n ign S c h o o l sa, l o n g s i d e
from the RoyalSociety,
the Instituteof Physicsand the Royal
Societyof Chemistry.
concernedwith the decline
i n t h e n u m b e ro f A - l e v e le n t r i e si n t h e
sciencesand focusedon the role that
teachersand teachingmethodscan
play in reversingthat decline.
S u et o l d t h e e n q u i r yt h a t t h e B S F
was keento seean improvement
at Ain the take-upof all sciences
level.Insightsfrom chemistryand
physicsare increasingly
bioscienceresearchand the declinein
their popularitythreatenedto hinder
d e v e l o p m e n tisn t h e b i o s c i e n c e lsf .t h e
recent Covernmenttargetsto increase
t h e n u m b e ro f p u p i l st a k i n gs c i e n c eA levelswere to be met, it was important
to focuson pupils'engagementwith
t h e s c i e n c e sn,o t j u s t t h e i r l e v e l s
Pupilswould be
of achievement.
persuadedto continueto A-levelonly
if they were excitedabout science
to them.
and appreciatedits relevance
Membersof learnedsocietieslike the
SCM potentiallyhad an important part
>- Lo C
b.0 m ho
I n a w i d e - r a n g i n dg i s c u s s i o no,t h e r
issuesraisedincludedthe perception
that CCSEand A-levelsin the sciences
are more difficultthan in other
subjects,the problemof gender
imbalancein the physicalsciences,
the poor qualityof careersadvice
offeredby some schoolsand the
currentshortageof specialistphysics
and chemistryteachers.The issueof
Healthand Safetyin practicalswas also
d i s c u s s e dg,i v i n gS u et h e o p p o r t u n i t y
to highlightthe importantrole that the
SCM playsin givingadviceand training
to teachersabout safemicrobiology
It is alwaysdifficultto judge the
impactof these sorts of activities.
However,the Lordshad clearlydone
t h e i r h o m e w o r k ,i n c l u d i n gv i s i t st o
schools,and appearedinterestedin
the evidenceoresentedto them. The
Committeeis expectedto publishits
report by the end ofthe year.
SueAssinder(e [email protected]
feature Measlesand Clostridiumdiffcile, adding to MRSA,
Malariaand TB. Plansare also in hand for future eventsat
W e s t m i n s t ear n d i n l r e l a n d .
9; E
t o p l a yi n e n t h u s i n gs c h o o lc h i l d r e n
about scienceand many of them
alreadydid so. However,a major
problemwas that schooloutreachwork
carriedout by universityacademics
was often not highlyvaluedby their
The Society'scampaignto raisethe profileof microbiology
t o C o v e r n m e nat n d o t h e r o p i n i o nf o r m e r sc o n t i n u e sI.n
Novemberwe will once againhavea standat the Royal
Societyof Chemistry'sScottishParliamentDay,where we
will be trying to persuadeMSPsand their advisersof the
importanceof hand hygiene.We will also be distributing
literaturesuchas the popularone-pagebriefingson
issues.The latesttwo briefings
[email protected]
l{[email protected]*e6!i4E,[email protected]
[email protected]
&fu;[email protected]
@[email protected]@F4#
[email protected]
[email protected]
[E:[email protected]
[email protected]'.tuh,DlIft
d. A*EN
d (. d/&'.
microbiology today ri*v rJ6
Ferl\ /-'\nrnnr
e re tcld
sfond up
for selenc#l
I t c a no f t e n s e e mt h a t t h e p u b l i c ' s
p e r c e p t i oo
n f s c i e n c ei s o f m e n i n w h i t e
coatsworking awaybehindcloseddoors
d e t e r m i n e tdo a l t e rl i v e si n u n w e l c o m e
ways.Thisdetachmentof scientistshas
ledto recentdebatesover scientific
i s s u ebs e i n ga l a r m i n g l m
y isinformed.
a b o u tS c i e n c ew, h i c h w o r k sw i t h
to promoteevidenceand good
s c i e n c ien p u b l i cd i s c u s s i oonf t o p i c a l
runningVoiceof YoungScience(VoYS)
mediaworkshopssince2004. These
to voiceconcernsabout talkingto the
mediaand providean opportunityto
form viewson how scienceis portrayed
a n dc o m m u n i c a t e da,n d t o q u e s t i o n
peopleon the 'frontline'directly.
Whatwasapparentin the workshops
wasthe enthusiasmof early-career
to get involvedin promoting
goodscience,but uncertaintyas to
how to go about it. With that in mind,
our VoYSwriting team, made up of
r e s o l vteh i s p r o b l e m ,h a sc o m p i l e da
short-guideto the media;Standingup
Thiscolourfulguide contains
for Science.
with scientists
and journalists
to givean insightinto how the media
repoftsscienceand givespracticaltips
on how they can get more involvedin
p u b l i cd e b a t e sa b o u ts c i e n c e .
L-, \-/ I \--, \-, I
5CM is one of our partners.Janet
Hurst,Deputy ExecutiveSecretary,
highlightswhy they wantedto be
involved:'With so many scientifc issues
in the headlinesaffectingnot only our
own well-beingbut that of the planet,
it has neverbeenmore importantfor
scientiststo interactpro-activelywith
the media ... SCM is thereforedelighted
to support this guide, which seeksto
encourage early-career scienti sts to
communicateenthusiasticallyand clearly
to the mediaabout their work.'
and the
internetreachinto the home and the
workplacethroughoutthe country.lt
is a fact of 21st centurylife that the
m e d i ai s i n e s c a p a b al en d , l i k e i t o r n o t ,
most scientists
will find that they are
approachedby journalistsat some
p o i n t i n t h e i r c a r e e tr o t a l ka b o u t
t h e i r o w n o r s o m e o n ee l s e ' sr e s e a r c h .
Whilstthis may be a dauntingprospect,
i t n e e d n ' tb e a n e g a t i v e x p e r i e n c e ;
t o t h e m e d i aa l l o w st h e m t o
s h a r et h e i r e n t h u s i a s m
f o r t h e i rs u b j e c t ,
and givesthe opportunityto influence
p u b l i co p i n i o na n d p u b l i cp o l i c y .
The concernsdealtwith in the guide
go from why not all sciencejournalists
to the fear
o f m i s r e p r e s e n t a t iionnt h e m e d i aa n d
the fearthat when simplifyingthe
languagefor the interestedlay person
y o u w i l l e n d u p s a y i n gs o m e t h i n gt h a t
s o u n d si n a c c u r a t es ,t u p i do r b o t h .
Everyoneinterviewedagreedthat these
problemswere easilyavoidableand all
the interviewees,
jou rnalists
and pressofficersalike,expressed
their optimismat the part which
can playin the
c o m m u n i c a t i oonf s c i e n c ef,o r m i n gt h e
perfectbridgebetweenthe publicand
the professor.
Standingup for Sclenceis the
o f m o n t h so f h a r dw o r k
f u e l l e db y a b e l i e ft h a t w i t h a h e l p i n g
hand, early-career
standup and makea difference.lt is
by no meansa definitiveguideto all
d e a l i n gw
s i t h t h e m e d i a ,b u t i t g i v e s
i n d i v i d u a ltsh e k n o w l e d g et,o o l sa n d
inspirationto go out and standup for
s c i e n c et h e m s e l v e s .
A copy of Standingup for Science
is enclosedwith everySCM
of MicrobiologyToday.lt is availableon
ou r website,www.senseaboutscience.
orglVoYS,where hard copiescan also
be freelyordered.Hereyou can find
other waysto get involvedin the VoYS
network. ContactFrancesDowney
at [email protected]
or O2O7478 4380 for further
SarahAnderson and FrancesDowney
l f y o u w o u l d l i l < ey o u r n a m et o b e a d d e dt o o u r d a t a b a soef
pleasecompletethe book reviewerinterests
. c l a s s i f i ecdo m p e n d i u mo f r e v i e w s
f o r m o n t h e S C M w e b s i t eA
f r o m 1 9 9 6 t o t h e p r e s e n its a l s oa v a i l a b loen t h e w e b s i t e .
M a n u a lo f M o l e c u l a r
and ClinicalLaboratory
l m m u n o l o g yT,t h e d n
, .c.Hamilton
E d i t e db y B . D e t r i c kR
& J . D .F o l d s
S o c i e t fyo r
P u b l i s h ebdy A m e r i c a n
U S $ 1 7 9 . 9 5p p 1 3 7 4
lsBN 1-55581-364-X
Most clinical immunology laboratories
will have at leastone previousedition
of the Manual of ClinicalLaboratory
Immunologtfrom ASM Presssomewhere
on their shelves(we have three -
Given the changein title and new
direction this textbook seriesis taking,
the temptationmay havebeento
veer too far awayfrom non-molecular
However,the authors
and editors seemto incorporatethe
expandingapplication of molecular
techniqueswithout ignoring traditionai
non-moleculartechniquesthat remain
standardin many laboratoriesand wilcontinue to be used for some time.
Aside from the new molecular emphasis,
additional chaptershave been included
concerningtopics that have come to
prominencesince the publication of the
lastedition in 2002. examplesbeing
chapters on Bacillusanthracisfrom its
potential use as an agentof bioterrorism
and coronaviruses,the causativeagent
of SARS.
a2nd, a 3rd and a 6th). As with
similar tomes from the ASM, such as
t}reManual of ClinicalMicrobiology,
book aims to be a definitive reference
text for its targetlaboratories.Certainly,
a descriptionof every immunological
As with many collaborativeworks
test we perform can be found within
there is wide variety in the language
its pagestogetherwith a number of
and proseused in differeni chapters,
some are definitely more reader-friendly
For textbooks of this kind to remain
than others.This is to some extent due
relevantand fulfil their remit,it is
to the subjectmatter of eachsection
essentialthat they evolvewith current
and chapterand an expert eye would
trends in laboratory practice.To achieve
probably appreciatethe specificsof
this, the manual has been updated to a
their chosenfield.
new edrtion approximatelyevery 5 years
as it
The indexing is as comprehensive
since the first edition was pubiished
needsto be, making navigationthrough
in 1976.Furthermore.the quantity
the 1,340 pagesstraightforwardand
and complexity of molecular biology
allowing quick accessto specifictopics.
containedwithin this 7th edition is
featurecannot be overlooked
considerablein comparisonto
given the competition from online- and
editions, a fact that the editors obviously
wishedto emphasizeby the inclusion
'Molecular'in the titie. Rather
wheresearchlacilitiesareol sreal
than appendinga few chapters
concernedwith molecular techniques,
As one would expectwith welleachsectionand chapterhas been
establishedreferencematerial of
expanded,rewritten and reorganrzedto
this type,the scientificaccuracy
include the relevantmateriai.
cannotbe disputedaseachchapter
is extensivelyreferencedto include
up-to-date original researchand review
articles.Each topic is introduced and
discussedin depth and then followed by
detaileddescriptionsof the techniques,
of specificapplications
and guidelineson test selectionfor
individual clinical situationsand
interpretation of findings.
Only the keenes[of studentsand other
individualswill considerpurchasing
a personalcopy.In any casethe most
benefit from referencevolumes of
this type is probably obtained when
used in the actual laboratory setting,
whether clinical or academic,so that the
informationcanbe put direcLlyin the
context of patient care or research.The
brief final sectionconcernslaboratory
management,indicating that the book
is targetedat institutions and laboratory
reiying on a previous edition as a
primary referencemanuai would
definitely benefit from purchasingthis
extensivelyrevisededition, which will
more than satisfytheir current needs.
Furthermore,the increasedemphasison
molecular biology in this edition should
guaranteeits relevancefor severalyears
to come, at leastuntil advancementof
the field necessitates
an 8th edition.
Martin Stearn,RoyalBromptonHospital
Editedby Y.Motaryemi
& M, Adams
P u b l i s h ebdy W o o d h e a d
f I 5 0 . o o / U s $ 2 7 0 . 0 0p p .6 3 4
lsBN 1-85573-963-1
Despitemajor advancesin food safety
and public health microbiology,foodborne diseaseremainsa leading cause
of illnessworldwide and, becauseof
multifactorial influences,new foodborne pathogenswill continue to
emergeand old ones re-emerge.This
well-writtenbook bringstogether
currentknowledgeand concepts
providing a good introduction and
overviewol emergingfood-borne
pathogens,covering evolution of
microbiologytoday *r":':r
microbiology and risk assessment.
The secondpart of the book, with a
more conventionallayout, consists
of chapterson individual emerging
pathogensand is comprehensivein its
Overall,I found the book
highly informative,up-to-dateand easy
to read,providing essentialinformation
for all food microbiologistsas well as
food scientistswith an interestin food
safety All scientistsworking with food
pathogensor involved with food safety
would benefit from having accessto a
Kathie Grant,HealthProtectionAgency
2 n de d n
ByJ.M. Janda& S.L.Abbott
by AmericanSocietyfor
U S $ 1 1 9 . 9 5p p . 4 2 6
The Enterobactenaceae
are a hugeiy
significant and increasingly diverse
family of pathogenicbacteria.The
book is an outstandinglyauthoritative
and detailedreferencesourceon
the phenotypic, and to some extent
genotypic, characterizationand
identificationof theseorganisms.As
such it is excellent value for the clinical
laboratoryor medical microbiologist.
Yet,it neglectstotally the paradigmshifting insights that arc now flowing
fast and freely from whole-genome
sequencingof organismswithin the
family,for which there are now about
40 completeor near-completegenome
These dataaretotally
changingour concept of the species,
amongboth the Enterobactenaceae
bacteriain general.In a nutshell, the
book is a fantasticresourcefor the
sciencethat representsthe culmination
of the era of classicalmicrobiology,
but contributeslittle to the increasing
needsfor post-genomicre-evaluationof
enterobacterialdiversity and phylogeny,
wherethe inteliectual challengesfor
the future lie.
CharlesPenn,Universityof Birmingham
m i c r o b i o l o gtyo d a y n * v * 1 6
O I E/FAOInternational
Scientific Conferenceon
Avian Influenza
E d i t e db y A . S c h u d e&l M . L o m b a r d
by S. l(argerAC (2006)
U S $ 2 3 6 . 5 op p . 2 7 B
Avian influenza has had an enormous
economicand socialimpact on affected
countries,and the risk of this animal
diseaseevolving into a human pandemic
is of globalconcern.
In order to effectivelycombat the
disease,veterinaryand human
health organizationsneed to work
rogerher.This book highlighrs and
discussesimportant areasof research
and collaboration,for example,the
implementation of more surveillance
and epidemiologicalstudiesin
migratory birds to understand
disseminationof highly pathogenic
avian influenza (HPAI), aswell as
increasingawarenessof pathogenesis,
symptoms and diseasesignsof HPAI.
There are comprehensivediscussions
of ecology,epidemiology,pathogenesis,
human health implications, diagnostics
and the control of avian influenza,
including vaccination.
This book has extensivebackground
informatioh about all areasof avian
influenza and would be ideal for anyone
looking for a summary and overview of
the current situation for avian influenza,
and how organizationssuch as OIE/
FAO and WHO are implemenring ways
to control and combat outbreaksand
spreadofthe disease.
Ruth Harvey, Universityof Oxford
on the web
Reviewsof the following books are
availableon the websiteat wwwsgm.
ac.uVpubs/micro_to daylreviews.cfm
ImmunoIogical and Mo lecuIar Aspects
2nd edn
of 6eneManipulationand
Tth edn
of lmmunity:
Theldentificationof Fungi
of BeanDiseases
of Turfgrass
3rd edn
6ene Cloning& DNAAnalysis
An lntroduction
A Solutionto the AntibioticsCrisisT
Biodiversityand Ecophysiology
of Yeasts
ClinicalApplicationsof PCR,2nd edn
ExperimentalDesignfor the Life Sciences,
2nd edn
2nd edn
BacterialWilt Disease
and the Ralstonia
m Species CompIex
Fungiin Biogeochemical
rial Cel|-to-CelI Communication
Rolein Virulenceand PathogenesB
DiseaseEcologyCommunity Structure
and PathogenDynamics
lntroductionto Glycobiology,
2nd edn
Immunology and Immunotechnology
New and Emergi
ng ProteomicTechniques
Evolutionof MicrobialPathogens
al Bioinformatics
lnhibitorsin HIV/
AIDS Therapy
Emerginglssueson HPV lnfectionsfrom
Scienceto Practice
3rd edn
in the Era
of ClobalTrade
BacterialFlorain DigestiveDiseaseFocus
on Rifaximin
TheBiologyof Vibrios
BrewingYeastand Fermentation
in Real-world
MolecuIar Diagnostics:Current
noIogy and Appl ications
2nd edn,
Sidney [?euben Elsder-r
fll 3 il/i ffiWru
who hasdiedat the ageof 91, wasHeadof the
from 1949
of Sheffield
at the University
to 1965and Directorof the Agricultural
Institutefrom 1965to 1977.Inadditionto hisexperimental
he wasresponsible
to biochemical
of boththese
and earlydevelopment
leadingthe establishment
Elsdenwasan originalmemberandthen an Honorary
g n C o u n c iflr o m 1 9 6 3t o 1 9 6 7a n da s
M e m b e ro f t h e S C M ,s e r v i n o
from 1969to 1972.In 1967 he wasawardedthe Marjory
Sidney Elsden spent his early years in Cambridge and, after
attending the Cambridge & County High School for Boys,
entered Fitzwilliam House, where he held a Goldsmiths'
Company Exhibition, and graduated in 1936 with a double
first in the Natural Sciences Tiipos. Following a year of
research in the Cambridge Biochemistry Department under
Dr Maqory Stephenson, who kindled his lifelong interest in
micro-organisms, he was appointed to a lectureship in the
Physiology Department of Edinburgh University In I94I he
gained his PhD from Cambridge University for biochemical
work on bacteria and on muscle d55ns.'His long association
with the Agricultural ResearchCouncil (ARC) began in1942
when he joined their Unit of Animal Physiology in Cambridge.
Here he devised an innovative method for the separation of
short-chain fatty acids on silica gel columns and used it to
investigate their microbial production in ruminants.
In 1948 Elsden was appointed Senior Lecturer in the
University of Sheffield, heading a biochemistry-based subdepartment within the Bacteriology Department, and a l-year
postgraduatecoursein microbiology was introduced in 1950.
At that time, the commercial production of biochemical app^ratus was in its infancy, but Elsden'sforesight.and the skills of
the Medical Faculty's workshop placed the department in a
strong position to exploit new techniques, such as the Hughes
press and other methods for the production of bacterial cellfree extracts, radioactive tracers, continuous culture methods
and gasJiquid chromatography
Elsdens research was many-faceted. He was adept at
connecting a fistula to a sheep's rumen and he could thus
easily obtain rumen conlenls with their plethora of microorganisms. Many of these are fastidious anaerobes and,
having been exposedto the methods of C.B. van Niel, Elsden
was well equipped to isolate and manipulate such bacteria.
One of his isolates was an hitherto unknown, Iarge, Gramnegative, non-sporing, anaerobic coccus which produced
C1-C6 fatty acids. This organism was eventually adopted as
the tlpe species of a new genus and appropriately named
In 1952, Sheffield University created a separate Department of Microbiology with Elsden as its head and the ARC
then appointed him Honorary Director of a Unit for Microbiology which they established within the new Department.
The research programme expanded steadily and embraced
photosynthedc bacteria, growth pelds in relation to AfP
generation, bacteriophage and bacteriocins as well as numerous aspects of anaerobes. In 1959, the West Riding of
Yorkshire endowed a Chair of Microbiologr with Elsden as
the first incumbent. The Departmenl's increasing reputation
attracted a steady flow of postgraduate studenb and visiting
workers, many of them from overseas countries, including
Australia, Norway, Sri Lanka and the USA.
In 1965, Elsden startedthe second phaseof his professional
career by accepting the Directorship of the new ARC Food
Research Institute to be built in Norwich. His careful planning and excellent rapport with the architects resulted
in a spacious and elegant building with a good balance of
standardized laboratories and specialized areas for services
and large equipment. The layout subsequently proved easyto
adapt-[o meet changes in the research programme and safety
regulations. The new institute was intended to bring together
several of the ARC's staff from research groups in Sheffield,
Cambridge, Aberdeen and Ditton in Kent. To facilitate the
integration of these diverse groups, a nucleus of staff from
each was built up at a temporary laboratory in Norwich in
o y t o d a yn o r ' # * ,
the years immediately before the new
building was occupied in 1968. The
Institute was sited close to the newly
founded University of East Anglia
(UEA) which had a strong biological
ethosand a closeassociationdeveloped
betweenthe two.
Following the Rothschild Report of
I97I-72, the researchprogramme was
increasinglysubjected to more centralized control, with a Iarge part of the
Institute's budget coming from work
contractedby MAFF InI97 5 a Director's
Advisory Board was set up to improve
contact with the food processingindustry Major changes followed, including
the introduction of work on nutrition
and the [ransferof work onpoultrymeat
to the Meat ResearchInstitute at Bristol.
Thesechangeswere well under wayby
the time Elsden retired in 1977.
society4fiD/or opplied
[email protected]
Inevitably,Elsdenbecameincreasingly involved in a wide ra:nge of committee and advisory work relating to
food researchand biology, both locally
and nationally Despite these pressures
he occasionallymanagedto spend time
working with his assistanton properties of clostridia relating to their classifi.cation. After retirement, he continued
wrth his scientific interests for a few
years at UEA before reverting to his
Iong-standing hobbies of gardening,
fishing and cooking. tn 1985, rhe
University of Sheffield recognized his
distinction as a microbiologist and as
Director of the Food ResearchInstitute
by awarding him the degree of Doctor
of Science,honoriscausa.
Sidney Elsdenhadalasting interestin
new techniquesand was keen to ensure
that his staff were well equipped in that
ffiw societyry
respect. His attitude to his colleagues
was forthright, but encouraging and
q,rynpathetic, particularly with regard
to personal problems. Early in his
career his own domestic life had been
clouded by the sudden death of his
first wife, Frances. His second wife,
Erica, whom he married in 1948,
survives him, together with their twin
sons. Despite increasing frailty in his
final years Sidney retained a iively
and good-humoured outlook until his
death shortly after his glst birthday. He
leaves behind a wealth of happy and
grateful memories among those who
were prir,rleged to work \Mith him.
JohnL. Peel
BernardA. Fry
11-12 January
University of York
g s e s s i o snp o n s o r e bd y t h e C e n e t i c S
s ociety
Emailjpjcl @york.ac.uk
f or a registration
m i c r o b i o l o gtyo d a yn * : v
New and excitingwaysof
i n a t i n gi n f o r m a t i o n
di s s e m
t o t h e p u b l i ca n ds t u d e n t s
t h e i n c r e a s i npgo p ul a r i t y
o f d e v i c es u c ha sm p 3
t h a t p o d c a s t i nagn do t h e r
W e b 2 . 0t e c hn o l o g i eos f fe r
a greatopporlunityto
icrobiologybyteswordpressoonn promote microbiology.
Podcastingis the distribution of
multimedia files over the internet. The
fi.lescan be downloaded and viewed or
listened to on a computer or a mobile
device such as an mp3 player or mobiie
this group wrth current and engaging
info rm ation about m icrobiology.
After experimentingwrth podcasts
for Universityof Leicesterstudents
for the pasLyear,1 beganproducinga
to havean
phone. lt is not necessary
iPod to listento podcasts- any
computer or mp3 player wiildo.
Unlike other file downioads, a key
leaiureof podcastingis the ability to
subscribethrough RSS(ReallySimple
regular public microbi,ology podcast
in Apnl 2006 - microbiologybytes.
wordpress.com.More than 3,500
Syrrdication) feeds.There is a wide
range of software avaiiable to manage
and listento podcasts,most of which
is lree.Once the softwareis installed,
listeners subscribe to the podcast feed
which te1lsthem when new podcasts
are availableand automatically
it is possible
to manually download the fi.lesto a
computer by clicking on the episode
links on the podcasthomepage.
Podcastinghas grown enormously
in the last few years,but is set to move
into the mainstreamas a malor source
of information dunng the next year
by the
with the currenl investmenL
BBC and other broadcaslersand the
featuresincluded in Microsofi Windows
Vista, due to be releasedinJanuary
2007 (e.g. RSSsuppon in InLernel
Explorer).Podcastingcurrentlyhas a
young demographic,predominantly
used by the age IB-24 age group. Many
students and potential students now
turn lo the internet as their first source
of information. Podcastsare optimally
placed as the medium of choice to reach
r,, iPod nano. Ausfu / SciencePhoto Library
New technologysuch as Web2.0 - the
read-write internet - aliows us to
c h i r e t h i q , h v h l n o o i.n' , ob :* n
nodcnst ino
rs to
The aim of MicrobLolog'rBytes
bnng people the latest news from the
forefront of biomedical researchin a
form thll everv,rne
- ' - ' - / - . 'can
. undcrstand.
Obviously, the hope is rhat this wrll
people from over 50 countnes
d ownloaded a MicrobtologtBytes podcast
in September.and the number of
Lstenersis doubling eachmonth.
After being featuredrecentlyin
'NetWatch'column, the
the Science
Apple iTunesStore'New and Notable
also attract more studentsto undertake
microbiology degrees,but it rs not
and Wordpress.comb'Blog
the Day'.this excitingnew projecthas
just received sponsorship from the SGM
should have wrth the public.
in the form of a Public Understanding
of Sciencegrant.
Unlike other universily podcasts,
ts not simply recyciing
of lecture contenl in audio format.
Its content is tailor-made to engagethe
largestpossibleaudienceby presenting
current topics in microbiologt in a
form that everyonecan understand.
Over a period of time, the contentof
the podcastscovers the whole field of
microbiologz Recenttopics include:
ls there a roleJor SV40in human
Quorumsensingin bactena
Escherichiacoli in spinach
How HIV causesAIDS
from the 14th to the 21stcentury
and still goingsLrong
Thereis a tremendoussLorehouse
knowied.gelocked up in universities.
reasonablelo expect Lhatsomeone
in. say.
who listcnsto Microbiol,;g',Bytcs
l\,4r-vir-nurill rrrrn
r* rHn n n
r)rrr dnorcten
wantingto stud; for a degree.ILsall
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r Wikipedia: Podcast.en.wikipedia.or{
, wiki/podcast (last accessed:3.10.06).
C a n n . A . ) . R e a l l yS i m p l cS ; n d r c a t i o n .
Teaching Bi oscience Enhan cingLear ning
Serjes- \ffective LIseof TechnoLogtin
, the Teachmg o.fBloscience- UK Higher
EdttcatronAcadenty Centre.for Bioscience.
, www.bioscience.heacademy.ac.uk/
, publications (last accessed:3.10.06).
Podcastinggains an important foothold
www. nielsen-netratings. com/prlpr_
060712.pdf (last accessed:3.10.06).
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Pleasenofe that view< exaressed in Comment do not
n e c e s s a r i l yr e f e t L o l f c i a l p o l t c y o f t h e S C M C o u n t t l .
m i c r o b i o l o gtyo d a y