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WHAT ARE BACTERIAL SPECIES?

WHAT ARE BACTERIAL SPECIES?

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Published by conlib
Annual Review of Microbiology
Vol. 56: 457-487 (Volume publication date October 2002)
(doi:10.1146/annurev.micro.56.012302.160634)
First published online as a Review in Advance on May 10, 2002
WHAT ARE BACTERIAL SPECIES?
Frederick M. Cohan
Department of Biology, Wesleyan University, Middletown, Connecticut 06459-0170; e-mail: fcohan@wesleyan.edu

▪ Abstract Bacterial systematics has not yet reached a consensus for defining the fundamental unit of biological diversity, the species. The past half-century of bacterial systematics has been characterized by improvements in methods for demarcating species as phenotypic and genetic clusters, but species demarcation has not been guided by a theory-based concept of species. Eukaryote systematists have developed a universal concept of species: A species is a group of organisms whose divergence is capped by a force of cohesion; divergence between different species is irreversible; and different species are ecologically distinct. In the case of bacteria, these universal properties are held not by the named species of systematics but by ecotypes. These are populations of organisms occupying the same ecological niche, whose divergence is purged recurrently by natural selection. These ecotypes can be discovered by several universal sequence-based approaches. These molecular methods suggest that a typical named species contains many ecotypes, each with the universal attributes of species. A named bacterial species is thus more like a genus than a species.
Annual Review of Microbiology
Vol. 56: 457-487 (Volume publication date October 2002)
(doi:10.1146/annurev.micro.56.012302.160634)
First published online as a Review in Advance on May 10, 2002
WHAT ARE BACTERIAL SPECIES?
Frederick M. Cohan
Department of Biology, Wesleyan University, Middletown, Connecticut 06459-0170; e-mail: fcohan@wesleyan.edu

▪ Abstract Bacterial systematics has not yet reached a consensus for defining the fundamental unit of biological diversity, the species. The past half-century of bacterial systematics has been characterized by improvements in methods for demarcating species as phenotypic and genetic clusters, but species demarcation has not been guided by a theory-based concept of species. Eukaryote systematists have developed a universal concept of species: A species is a group of organisms whose divergence is capped by a force of cohesion; divergence between different species is irreversible; and different species are ecologically distinct. In the case of bacteria, these universal properties are held not by the named species of systematics but by ecotypes. These are populations of organisms occupying the same ecological niche, whose divergence is purged recurrently by natural selection. These ecotypes can be discovered by several universal sequence-based approaches. These molecular methods suggest that a typical named species contains many ecotypes, each with the universal attributes of species. A named bacterial species is thus more like a genus than a species.

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Annu. Rev. Genet. 2004. 38:525–52doi: 10.1146/annurev.genet.38.072902.091216Copyrightc
2004 by Annual Reviews. All rights reservedFirst published online as a Review in Advance on July 14, 2004
M
ETAGENOMICS
:
Genomic Analysisof Microbial Communities
Christian S. Riesenfeld,
1,2
Patrick D. Schloss,
1
and Jo Handelsman
1,2
 Department of Plant Pathology,
1
 Microbiology Doctoral Training Program,
2
University of Wisconsin-Madison, Madison, Wisconsin 53706; email: joh@plantpath.wisc.edu
Key Words
microbial ecology, environmental genomics, community genomics,culture-independent, and unculturable bacteria
Abstract
Uncultured microorganisms comprise the majority of the planet’s bio-logicaldiversity.Microorganismsrepresenttwoofthethreedomainsoflifeandcontainvast diversity that is the product of an estimated 3.8 billion years of evolution. In manyenvironments, as many as 99% of the microorganisms cannot be cultured by standardtechniques, and the uncultured fraction includes diverse organisms that are only dis-tantlyrelatedtotheculturedones.Therefore,culture-independentmethodsareessentialtounderstandthegeneticdiversity,populationstructure,andecologicalrolesofthema- jorityofmicroorganisms.Metagenomics,ortheculture-independentgenomicanalysisof an assemblage of microorganisms, has potential to answer fundamental questions inmicrobial ecology. This review describes progress toward understanding the biologyof uncultured Bacteria, Archaea, and viruses through metagenomic analyses.
CONTENTS
INTRODUCTION
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
526METAGENOMICS DEFINED
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
527LINKING PHYLOGENY AND FUNCTION WITHIN SPECIES
. . . . . . . . . . . . . . .
529Phylogenetic Anchors
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
529Function Then Phylogeny
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
529Phylogeny Then Function
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
533Acidobacterium Phylogeny and Function
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
533Archaeal Phylogeny and Function
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
534Proteorhodopsin Function and Phylogeny
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
535LINKING PHYLOGENY AND FUNCTION IN MICROBIALCOMMUNITIES: METAGENOME RECONSTRUCTION
. . . . . . . . . . . . . . . . . . .
536Metagenomic Analysis of Bacteriophage
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
536Metagenome of the Microbial Community in Acid Mine Drainage
. . . . . . . . . . . . .
537Metagenome of the Microbial Community in the Sargasso Sea
. . . . . . . . . . . . . . . .
538CHALLENGES WITH METAGENOMIC ANALYSIS
. . . . . . . . . . . . . . . . . . . . . . . .
539Phylogenetic Anchors
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5390066-4197/04/1215-0525$14.00
525
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526
RIESENFELD
SCHLOSS
HANDELSMANSize of Metagenomes
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
540Size of Inserts
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
541Identifying Sequences of Interest in Large Metagenomic Libraries
. . . . . . . . . . . . .
542INTEGRATING METAGENOMICS AND COMMUNITY ECOLOGY
. . . . . . . . . .
543Microscopy
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
543Stable Isotopes
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
543CONCLUDING REMARKS
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
545
INTRODUCTION
Obtainingbacteriainpurecultureistypicallythefirststepininvestigatingbacterialprocesses. However, standard culturing techniques account for 1% or less of thebacterial diversity in most environmental samples (2). Although some significantbreakthroughshaveresultedfromrecentattemptstoculturetheas-yet-unculturablebacteria (56, 89, 99, 127), a suite of culture-independent techniques are needed tocomplement efforts to culture the thousands or millions of unknown species in theenvironment.A new era of microbial ecology was initiated when sequencing of ribosomalRNAsandthegenesencodingthemwasintroducedtodescribeunculturedbacteriain the environment. The first approach was to sequence clones from a 5S rRNAcDNA library derived from the symbiotic community within the tubeworm
Riftia pachyptila
(109). Variations of this method generated a set of culture-independenttechniques to (
a
) reconstruct phylogenies, (
b
) compare microbial distributionsamong samples using either nucleotide sequence or restriction fragment lengthpolymorphisms (RFLPs), and (
c
) quantify the relative abundance of each taxo-nomicgroupusingmembranehybridizationorfluorescentinsituhybridization(2,47, 57, 78–80).The most startling result of the many microbial diversity studies that haveemployed16SrRNAculture-independentmethodsistherichnessoftheunculturedmicrobialworld.AsofApril1,2004,GenBankcontained21,46616SrRNAgenesfrom cultured prokaryotes and 54,655 from uncultured prokaryotes, according tothe search terms described by Rapp´e & Giovannoni (90), and many of those fromunculturedorganismsaffiliatewithphylathatcontainnoculturedmembers.WhenWoese(121)originallyproposeda16SrRNA-basedphylogeny,12bacterialphylawere recognized, each with cultured representatives. Since then, 14 additionalphyla with cultured representatives have been identified. In addition, 16S rRNAgene sequence analysis suggests 26 candidate phyla that have no known culturedrepresentatives(90).Therefore,halfoftheknownmicrobialphylahavenoculturedrepresentatives.Among the phyla that contain cultured members, a few contain many isolatesand the rest contain too few to represent the full spectrum of diversity in thephylum. For example, Hugenholtz (53) found that 97% of prokaryotes depositedin the Australian Culture of Microorganisms in 2001 were members of just fourphyla: the Proteobacteria (54%), Actinobacteria (23%), Firmicutes (14%), and
   A  n  n  u .   R  e  v .   G  e  n  e   t .   2   0   0   4 .   3   8  :   5   2   5  -   5   5   2 .   D  o  w  n   l  o  a   d  e   d   f  r  o  m  a  r   j  o  u  r  n  a   l  s .  a  n  n  u  a   l  r  e  v   i  e  w  s .  o  r  g   b  y   S   t  a  n   f  o  r   d   U  n   i  v  e  r  s   i   t  y  -   M  a   i  n   C  a  m  p  u  s  -   R  o   b  e  r   t   C  r  o  w  n   L  a  w   L   i   b  r  a  r  y  o  n   0   7   /   0   7   /   0   9 .   F  o  r  p  e  r  s  o  n  a   l  u  s  e  o  n   l  y .
 
METAGENOMICS
527
Bacteroidetes (6%). Within GenBank, 76% of the 16S rRNA gene sequences of cultured prokaryotes are from these four groups. But other phyla may be morediverse, prevalent, and ecologically consequential in the environment. 16S rRNAgene sequences from the Acidobacterium phylum are among the most abundantin clone libraries obtained from soil and have been found in all soils examined,suggesting that the Acidobacteria play important roles in soil ecosystems. How-ever, of the 684 Acidobacterium 16S rRNA gene sequences in GenBank, only 19(2.8%) are from cultured isolates, providing an inadequate collection to describethe physiological diversity of the phylum. Other than 16S rRNA gene sequences,littleisknownaboutthebacteriawithinthe22poorlyculturedphylaand26candi-date phyla. Many terms, such as unculturable, uncultivated, as yet uncultured, andnot yet cultured, are used to refer to microorganisms that we know of only throughculture-independent means. In this review, we refer to them as uncultured.Describingthephylogeneticdiversityofunculturedmicroorganismsisonlythefirst step. A greater challenge is to assign ecological roles to them. The unculturedmicrobiota must play pivotal roles in natural environmental processes and are alargeuntappedresourceforbiotechnologyapplications.Exploitingtherichmicro-bial biodiversity for enzyme and natural product discovery is an active researcharea that has been reviewed elsewhere (39, 45, 46, 65, 66, 77, 97, 104). This re-viewdiscussestheapplicationofculture-independentgenomics-basedapproachesto understand the genetic diversity, population structure, and ecology of complexmicrobial assemblages (26, 93, 94).
METAGENOMICS DEFINED
“Metagenomics” describes the functional and sequence-based analysis of the col-lective microbial genomes contained in an environmental sample (Figure 1) (45).Other terms have been used to describe the same method, including environ-mental DNA libraries (110), zoolibraries (55), soil DNA libraries (68), eDNAlibraries (13), recombinant environmental libraries (22), whole genome treasures(77), community genome (114), whole genome shotgun sequencing (115), andprobably others. In this review, we use metagenomics to describe work that hasbeen presented with all of these names because it is the most commonly used term(15,27,35,59–61,65,66,82,105,107,117,118),wasusedforthetitleoftherstinternational conference on the topic (“Metagenomics 2003” held in Darmstadt,Germany), and is the focus of an upcoming issue of the journal
Environmental Mi-crobiology
. The definition applied here excludes studies that use PCR to amplifygene cassettes (52) or random PCR primers to access genes of interest (17, 32),sincethesemethodsdonotprovidegenomicinformationbeyondthegenesthatareamplified. Many environments have been the focus of metagenomics, includingsoil,theoralcavity,feces,andaquatichabitats,aswellasthehospitalmetagenome,a term intended to encompass the genetic potential of organisms in hospitals thatconribute to public health concerns such as antibiotic resistance and nosocomialinfections (20).
   A  n  n  u .   R  e  v .   G  e  n  e   t .   2   0   0   4 .   3   8  :   5   2   5  -   5   5   2 .   D  o  w  n   l  o  a   d  e   d   f  r  o  m  a  r   j  o  u  r  n  a   l  s .  a  n  n  u  a   l  r  e  v   i  e  w  s .  o  r  g   b  y   S   t  a  n   f  o  r   d   U  n   i  v  e  r  s   i   t  y  -   M  a   i  n   C  a  m  p  u  s  -   R  o   b  e  r   t   C  r  o  w  n   L  a  w   L   i   b  r  a  r  y  o  n   0   7   /   0   7   /   0   9 .   F  o  r  p  e  r  s  o  n  a   l  u  s  e  o  n   l  y .

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