Bacterial Systematics

265 Pages·1994·10.92 MB·English

by  Niall A. Logan(auth.)

Bacterial Systematics
Bacterial Systematics Niall A. Logan
© 1994 Blackwell Scientific Publications. ISBN: 978-0-632-03775-9
Bacterial Systematics
NIALL A. LOGAN BSc PhD
DepartmentofBiologicalSciences
GlasgowCaledonian University
OXFORD
Blackwell Scientific Publications
LONDON EDINBURGH BOSTON
MELBOURNE PARIS BERLIN VIENNA
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CataloginginPublicationData
Firstpublished1994 Logan, NiallA.
Bacterialsystematics/NiallA.Logan.
SetbyD& N Publishing,Ramsbury,Wilts p. cm.
PrintedandboundinGreatBritain Includesbibliographicalreferencesand
atTheAldenPress,Oxford index.
ISBN0-632-03775-X
1. Bacteriology-Classification.L Title
QR81.L64 1994
.589.9'0012-dc20
Contents
Preface, vi
1 Introduction, 1
2 Phenotypic characters, 13
3 Genotypic characters, 35
4 Similarityandarrangement, 47
5 Identification, 62
6 Evolution and the archaea, 79
7 The spirochaetes, 97
8 Helical andcurvedbacteria, 105
9 Gram-negative aerobic bacteria, 115
10 Gram-negative, facultatively and
strictly anaerobic bacteria, 143
11 The Gram-positive rods, 165
12 The Gram-positive cocci, 183
13 The mollicutes, 198
14 The actinomycetes, 211
Furtherreading, 232
Organismindex, 243
Subjectindex, 257
v
Preface
I havelongfelt theneedfor anintroductorytextcoveringthetheory
andpractice ofbacterialclassificationandidentification, and this is
myattempt atsuchabook.Itwaswrittenat atimeofrapidprogress
inthesubject, andwhiletheuseofmolecularsequencingtechniques
inevolutionary studies has tendedto dominate the literature, ithas
also revivedinterestinalltheotheraspects ofbacterialsystematics.
I thank the authors and publishers who kindly allowed me to
adapt theirfigures for this book, andammostgratefulto thefollow
ing people who generously provided material for illustrations:
Dr G.K. Adak, PHLS Comillunicable Disease Surveillance Centre
(Fig. 8.2); MrJ.Bagshaw,bioMerieuxUK(FigsS.3a &.5.5);DrR.C.W.
Berkeley, University of Bristol (Fig. 2.8); Dr P. Berry, Mercia Diag
nostics IFig. 5.3cl; MrN. Claxton, BectonDickinson} UK (Fig. 5.3b);
Dr P. De Vos, Universiteit Gent (Figs 2.4, 2.5 &. 3.6); Dr M. Gillis,
UniversiteitGent(Fig.6.3); Prof. M. Goodfellow, UniversityofNew
castle uponTyne (Fig. 14.2); DrA.C. Hill, Medical Research Coun
cil Toxicology Unit (Fig. 13.1); and Dr C.W. Moss, Centers For
Disease Control, Atlanta (Figs 2.2 &. 9.8); I also thank Mr J.
McWilliams, Glasgow Caledonian University, for the photography.
I am indebted to Prof. P.H.A. Sneath, University of Leicester, for
explaining to me the taxon-radius model for identification, to Prof.
M. Goodfellow for reading the Inanuscript and offering much help
ful comment, andto mywife and childrenfor theirforbearance.
NIALL A. LOGAN
vi
1 Introduction
Not Chaos-like, togethercrush'dand bruis'd,
But as the World, harmoniouslyconfus'd:
Where Orderin Variety we see,
Andwhere, tho' allthings differ, allagree.
AlexanderPope, 1713, Windsor Forest
The developmentofbacterial classification
Michel Adanson's proposal in 1764for natural classifications basedupon
manycharactersandhis contemptfor 'systems'basedupon aselectedfew
broughthimintoconflictwithCarlvonLinne(LinnaeusJ,whohaddevised
suchsystemsforplants, animalsandminerals.Linnaeusdoubtedthevalue
of microscopy and was therefore unable to classify the animalcules
describedbyAntonievan Leeuwenhoekand othersforwant ofcharacters;
heplacedthemallinaclassofinvertebrateswhichhecalled'Chaos'- the
shape ofmatterbeforeit was reduced to order.
Most microscopists of the 17th and 18th centuries did not try to clas
sify the infusion animalcules that they observed and often described so
meticulously. Withworkspublishedin 1773and1774theDanishnatural
ist Otto Muller was the first to attempt a systematic arrangement of the
animalcules,buthedidnotmakeacleardistinctionbetweenwhatwenow
callprotozoaandbacteria. Forhislastworkhowever,whichwaspublished
posthumously in 1786, he did create two form genera, Monas and Vibrio,
which contained bacteria and accommodated the punctiform and elon
gatedtypes.
In 1838 Christian Ehrenberg considerably extended Muller's nomen
clature and added the helical bacteria. He was handicapped by the micro
scopesofhisday, andmanyofthegroupsthathe describedcannotnowbe
recognized. Nonetheless, heestablishedgenusandspeciesnames, suchas
Spirochaeta plicatilis and Spirillum volutans, that are still in use. Subse
quent workers devisedsimplerclassifications, but all theseearlybacterial
systematistsbasedtheirarrangements uponmicroscopic morphology, and
assumedconstancyofformatatimewhenthetheoriesofspontaneousgen
erationandpleomorphism(i.e. noconstancyofform)werestillwidelyheld
and thegerm theory ofdisease hadyet to be proven.
In the 1870s Ferdinand Cohn, having satisfied himself that bacterial
forms were constantirrespective ofenvironmental conditions, recognized
the existenceofawide diversityofbacteriabutconsideredthem toform a
distinct group that was unrelated to fungi, yct had close affinities with
blue-green algae. He arranged bacteria in six form genera, which he
believedtobethenaturalones, andmanyprovisional species,butappreci
ated that the physiologies, products andpathogenicities of similar-shaped
organismsmightdiffer, andsousedsuchpropertiesinsubdividinghisgen-
era. In Bacillus he placed B. subtilis, having recognized its spores as 1
Bacterial Systematics Niall A. Logan
© 1994 Blackwell Scientific Publications. ISBN: 978-0-632-03775-9
Chapter 1 persistentforms, andanothersporeformer, B. anthracis, whoselifehistory
Introduction RobertKochdemonstratedtohimin1876- therebyprovingthegermthe
oryofdisease.FrOlnhisstudiesofinfectiousdiseases, Kochlaterconcluded
thatthe differentforms ofpathogenicbacteriamustberegardedas distinct
andconstant species.
Cohn found it necessary to defend his beliefs, based as they were on
careful observation, against those who still tried to prove, using defective
methods, that bacteria were merely stages in the development of fungi
(after the foundation of medical mycology in the 1840s several diseases,
includingcholeraandmeasles, hadbeenattributedtofungibysomework
ers), and that changes in environmental conditions alteredbacterial mor
phology. In 1882EdouardBuchnerclaimedtohave convertedB. subtilisto
B. anthracisby shakingit inmedia at different temperatures!
Purecultures
Theconceptofbacterialspecies ledto the idea that pure cultures mightbe
obtainable.By 1872Cohn'sco-workerJosephSchroeterhadcultivatedpure
colonies of chromogenic bacteria, including the violet-pigmented organ
ismsnowinformallyreferred to as chromobacteria, on avariety of starchy
foods, eggsandmeat, andin1878JosephListerobtainedapurecultureofa
milk-souringorganismbydilution. Kochhadturnedfromusinganimalpas
sagefor purifyinghis pathogenic strains to developingplates ofcultivation
media solidifiedby gelatin, which was subsequently replaced by agar, and
hedemonstratedandpublishedhisInethodsintheearly1880s.Sobeganthe
'golden age of microbiology'- bacteria could now be isolated routinely by
streak dilution culture and, as Perkins observedin 1928, this 'discovery of
theprinciplesofpure-culturestudyresultedinsuchasuddenburstofinves
tigation that it was a lost month in which a new organism was not
described, catalogued, and laid away, very frequently in the wrong grave',
andledtothedevelopmentofthemanydiversecharacterizationtests, such
astheVoges-Proskauer(1898)testforacetylmethylcarbinol, themethyl-red
test (1915) for production of copious acid from glucose, and the tests for
cytochrome oxidase (1928) and urea hydrolysis (1946), that were described
over thenext80years.
The various later workers who developed classifications drawn up by
Cohncontinuedtoregardsphericalorganisms(cocci)asprilnitiveformsand
theyemphasizedmorphologicalcharacters,especiallyshapeandsizeofcells,
arrangement orabsenceofflagella, andproductionofspores, intheirhigher
divisions of bacteria. This Linnaean approach caused confusion; B. subtilis
and B. anthracis, for example, wereputtogetheras sporefonners, orsimply
as rodsbysome, andplacedinseparategenerabyothersbecausetheformer
is motile andthe latterisnot. Itwas onlyintheseconddecadeofthetwen
tiethcentury, followingtheworkofOrIa-Jensen, andwiththereportsofthe
Society ofAmericanBacteriologists' Committee onBacterialClassification
and Nomenclature in 1917 and 1920, that physiological characters such as
2 aerobic or anaerobic growth became widelyused in descriptions of genera.
Chapter 1
Bergey'sManual
Introduction
Bergey's Manual ofDeterminative Bacteriology, publishedin 1923, was
written to provide amodernidentification keyfor bacteriabutlittle ofit
was based on direct experience of the organisms and this first and five
subsequent editions, which were very difficult to use in the laboratory
unless organisms were alreadyidentifiedto genus level, came to be used
more as the authoritative reference works on bacterial classification. In
successive editions of Bergey's Manual, and in the absence of a usable
fossil record, a quasi-evolutionary approach to arrangement, as used for
plants and animals, was adopted; in the seventh edition, published in
1957,thephotoautotrophswereregardedasthemostprimitiveforms and
the rickettsias, to which the viruses were tentativelyattached, the most
advanced. Intheeighthedition,whichwaspublishedin 1974,itwascon
sidered that such an approach was no longer justifiable and the genera,
sometimesgroupedinfamilieswherethoughtuseful, werearrangedin19
parts. Each ofthese was basedupon afew readily determinedcharacters
andboreavernacularnamesuchas 'Gram-positivecocci'; hence, noevo
lutionaryrelationships were implied. Instead, a tentative subdivision of
the Kingdom Procaryotae was given- proposals for the recognition of
such a kingdom of anucleate organisms had been made since the late
1930s and were subsequently supported by microscopy, including elec
tron microscopy, and molecular studies.
Numerical taxonomy
As thevarietyofmethodsfor characterizingbacteriaincreased, sobacter
ial systematists suffered more and more from the lack of quantitative
approaches to classification. In 1957Peter Sneathrevolutionizedthe sub
ject with his two papers 'Some Thoughts on Bacterial Classification' and
'The Application of Computers to Taxonomy' (taxonomy being the sci
ence of classification; it is often used as a synonym for classification) in
which he described numerical methods of grouping bacteria using the
chromobacteria together with some other Gram-negative rods as his
example.
Insubsequentpublications,includingtwobooks(1963, 1973)writtenin
collaboration with Robert Sokal, Sneath summarized the fundamental
position of numerical taxonomy (the grouping by numerical methods of
taxonomicunitsbasedupontheircharacterstates),inprinciplesreferredto
as neo-Adansonian and which included the need for many and equally
weightedcharacters.Therapiddevelopmentandavailabilityofcomputers
enabled the integration of many different pieces and types of data into
the classification process, which consequently benefited from greater
information content and the more objective recognition ofgroups ortaxa;
thus, therealizationofAdanson'sideasafter200yearsdepended, toagreat
extent, ontheadventofelectronic computing.
3
Chapter 1
Modern methods
Introduction
Theperiodthat sawthedevelopment ofnumericaltaxonomyalso sawthe
rise of chemotaxonomy- the application of modernbiochemical analyti
cal techniques, principally chromatographic and electrophoretic separa
tion methods, to the study of distributions of specific chemicals such as
aluino acids, proteins, sugars and lipids in bacteria. Of particular interest
are studies of nucleic acids, the ultimate objective being rapid and direct
sequencing.DatafromDNA-rRNAreassociationexperinlentsandprotein
sequencing, and from methods of inferring and comparing sequences of
rRNA molecules, which have evolved very slowly so that the base
sequencesofmanycistronsarehighlyconserved,havebeenusedlikeabac
terialfossilrecord(butwithouttimeunits) tofacilitate the constructionof
prokaryote 'phylogenies' (genealogical trees) that are quite different to
those impliedin the seventh edition ofBergey's Manual.
The first of four volumes of Bergey's Manual of Systematic Bacteriol
ogy, publishedin 1984,wasarrangedinsectionsmuchliketheparts ofthe
eightheditionofBergey'sManualofDeterminativeBacteriology, andpro
posedarevision ofthehighertaxaofprokaryotesconsistentwiththe phy
logenetic information then available. It is becoming clear that most
existingbacterialclassifications,whicharebaseduponphenotypiccharac
ters(observableexpressionsofthegenotype)withaviewtoprovidingiden
tification schemes, correlate poorly with the evolutionary relationships
that appear to exist between thehighertaxa. Theproblem nowfacing tax
onomists is the construction of a single and practical scheme capable of
incorporating genotypic and phenotypic information. Consequently,
polyphasic taxonomic studies, which userangesofbothgenomic andphe
notypic approaches, arenowwidelyfavoured.
Why classify bacteria?
Classification, thegroupingofthingstogether, isacomlnonandimportant
humanactivitythathasbeenpractisedsinceearliesttimes.Indealingwith
largenumbers ofobjectsorpiecesofinfonnationsomeconvenientsystem
oforderlyarrangern.ent is needed for the purposes ofstorage and retrieval,
and in any scientific work up-to-date classifications are essential. Books}
for example, may be grouped by author, subject, title or a combination of
these; without suchasystemalibrarywouldbevirtuallyunusableandthe
retrieval ofinformationfroln ithopelesslyinefficient.
Inbacteriology,classificationisameansofsummarizingourknowledge
of prokaryotes and cataloguing that knowledge. As this information is
constantlyandrapidlyexpanding, so classifications evolveandincreasein
importance, withcontemporaryschemesreflectingourstateofknowledge
about the organisms concerned. Such schemes may thenlselves be classi
fied intonatural andartificial(orspecialpurpose) types.
4
Chapter 1
Natural classifications
Introduction
What constitutes a natural orlogical classificationis hard to define for any
group oforganisms; as the late Sam Cowan commentedin 1978: 'thebiolo
gist ...isattunedtothevagariesoflivingthingsanddoesnotexpectanexper
imenttobeexactlyrepeatable...issurprisedbytheexpected,andastounded
bythefulfilment ofaforecast orprediction.Thus, ifwesaythata classifica
tion is logical we know that it is not a classification of biological units,
whereasifwesaythatitisexpedientwewillbereadytolayoddsonitsbeing
the workofabiologist dealingwithunits ofhis (orher) own creation'- the
bacteriologistmustneverforgetthatgeneraandspeciesareartificialconcepts
andthatthebacteriashownointerestin theirclassification.
In thepre-DarwineraAristotles theories were applied, the idea beingto
classifyaccordingtoanitem's 'essentialnature'byrepeatedsubdivision,but
afterthepublicationofDarwin'stheoriesanevolutionaryapproach,usingfos
silrecords, was generallyadopted. However, theapplication ofthis phyletic
methodtobacteriawasimpractical,notonlybecauseoftheabsenceofusable
fossilevidence,lackofinformationabouttheextentofconvergentevolution,
andthesimplicityofbacterialmorphology,butalsobecauseofthebreadthof
biologicalvariationthatoccursinsuchrapidlyreproducingorganismsowing
to mutation, adaptabilityandlateralgene transfer. Untilrecently, therefore,
most 'natural' classifications ofbacteriawere phenetic (fromphenotypeand
genetic);theywerebaseduponstudiesoflargenumbersofpropertiesanalysed
by numerical methods, and did not attempt to imply evolutionaryrelation
ships. The groups recognized by these methods are described as polythetic;
theyareformedbytheirmembershavinglargenumbersofcharactersincom
mon, and they tolerate limited numbers of the exceptional characters that
mightbeexpectedasaresult ofbiologicalvariation.
Artificial classifications
Theterm'artificial' wasformerly appliedto those classificationsthat were
madeforsingle,clearlydefinedpurposessuchasdistinguishingbetweenthe
pathogenic member ofa genus and the rest andthey couldbemonothetic,
thatistosaybaseduponasingledefiningcharacter. Nowthatphyleticclas
sificationsofbacteriaarebeingattempted, asaresultofthemolecularstud
iesreferredtoearlier,andbecauseofadvancesinidentificationmethodsand
increasingawarenessofthedangersofdrawingrigidboundariesbetween,for
example, pathogensand non-pathogens, the definitions andapplications of
the different types ofmicrobial classifications are changing.
We see, therefore, that even classifications of classifications have to
evolve. Natural orphylogenetic classifications of bacteria are now based
upongenotypicinformation, andphenetictaxonomies mightberegarded
as artificial and general-purpose when polythetic but special-purpose
when monothetic. Until a workable and useful unified classification is
constructed, we must consider the aims of phylogenetic and phenetic
schemes separately. 5