An ecological perspective on bacterial biodiversity

Bacteria may be one of the most abundant and species–rich groups of organisms, and they mediate many critical ecosystem processes. Despite the ecological importance of bacteria, past practical and theoretical constraints have limited our ability to document patterns of bacterial diversity and to understand the processes that determine these patterns. However, recent advances in molecular techniques that allow more thorough detection of bacteria in nature have made it possible to examine such patterns and processes. Here, we review recent studies of the distribution of free–living bacterial diversity and compare our current understanding with what is known about patterns in plant and animal diversity. From these recent studies a preliminary picture is emerging: bacterial diversity may exhibit regular patterns, and in some cases these patterns may be qualitatively similar to those observed for plants and animals.

[1]  J. Saunders,et al.  Microbial Evolution, Diversity, and Ecology: A Decade of Ribosomal RNA Analysis of Uncultivated Microorganisms , 1998, Microbial Ecology.

[2]  J. T. Staley,et al.  Biodiversity: are microbial species threatened? , 1997, Current opinion in biotechnology.

[3]  P. Abrams Monotonic or unimodal diversity-productivity gradients : what does competition theory predict? , 1995 .

[4]  G. Zwart,et al.  Patterns and governing forces in aquatic microbial communities , 1998, Aquatic Ecology.

[5]  D. Dykhuizen Santa Rosalia revisited: Why are there so many species of bacteria? , 2004, Antonie van Leeuwenhoek.

[6]  J. Coyne ERNST MAYR AND THE ORIGIN OF SPECIES , 1994, Evolution; international journal of organic evolution.

[7]  A. Osborn,et al.  Genetic diversity within mer genes directly amplified from communities of noncultivated soil and sediment bacteria , 1995, Molecular ecology.

[8]  Jill McGrady-Steed,et al.  Biodiversity regulates ecosystem predictability , 1997, Nature.

[9]  W. Whitman,et al.  Prokaryotes: the unseen majority. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[10]  W. Liesack,et al.  The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations , 1997, Applied and environmental microbiology.

[11]  J. Lawton Are there general laws in ecology , 1999 .

[12]  L. Øvreås,et al.  Prokaryotic Diversity--Magnitude, Dynamics, and Controlling Factors , 2002, Science.

[13]  M. Madigan,et al.  Brock Biology of Microorganisms , 1996 .

[14]  J. Tiedje,et al.  High Levels of Endemicity of 3-Chlorobenzoate-Degrading Soil Bacteria , 1998, Applied and Environmental Microbiology.

[15]  B. Kerr,et al.  Big questions, small worlds: microbial model systems in ecology. , 2004, Trends in ecology & evolution.

[16]  E. Stackebrandt,et al.  Microbial community dynamics in Mediterranean nutrient-enriched seawater mesocosms: changes in the genetic diversity of bacterial populations. , 2001, FEMS microbiology ecology.

[17]  K. J. Clarke,et al.  Ubiquitous dispersal of microbial species , 1999, Nature.

[18]  J. Borneman,et al.  Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation , 1997, Applied and environmental microbiology.

[19]  Jillian F Banfield,et al.  Microbial communities in acid mine drainage. , 2003, FEMS microbiology ecology.

[20]  D. Crowley,et al.  Microbial diversity along a transect of agronomic zones. , 2002, FEMS microbiology ecology.

[21]  Grundmann,et al.  Geostatistical analysis of the distribution of NH(4)(+) and NO(2)(-)-oxidizing bacteria and serotypes at the millimeter scale along a soil transect. , 2000, FEMS microbiology ecology.

[22]  S. Sørensen,et al.  Ecosystem response of pasture soil communities to fumigation-induced microbial diversity reductions: an examination of the biodiversity-ecosystem function relationship , 2000 .

[23]  Anthony V. Palumbo,et al.  Spatial and Resource Factors Influencing High Microbial Diversity in Soil , 2002, Applied and Environmental Microbiology.

[24]  J. Thioulouse,et al.  Relationship between Spatial and Genetic Distance in Agrobacterium spp. in 1 Cubic Centimeter of Soil , 2003, Applied and Environmental Microbiology.

[25]  H. Vlamakis,et al.  Evidence for Extensive Resistance Gene Transfer amongBacteroides spp. and among Bacteroides and Other Genera in the Human Colon , 2001, Applied and Environmental Microbiology.

[26]  J. Tiedje,et al.  A Two-Species Test of the Hypothesis That Spatial Isolation Influences Microbial Diversity in Soil , 2002, Microbial Ecology.

[27]  R. Lenski,et al.  Hierarchical analysis of linkage disequilibrium in Rhizobium populations: evidence for sex? , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[28]  J. Newbold,et al.  TURBULENT TRANSPORT OF SUSPENDED PARTICLES AND DISPERSING BENTHIC ORGANISMS : HOW LONG TO HIT BOTTOM? , 1997 .

[29]  K. Schleifer,et al.  Phylogenetic identification and in situ detection of individual microbial cells without cultivation. , 1995, Microbiological reviews.

[30]  J. Tiedje,et al.  Response of microbial communities to changing environmental conditions: chemical and physiological approaches , 1993 .

[31]  R. Amann,et al.  The species concept for prokaryotes. , 2013, FEMS microbiology reviews.

[32]  Graham Bell,et al.  Disturbance and diversity in experimental microcosms , 2000, Nature.

[33]  J. V. van Elsas,et al.  Structural diversity of microorganisms in chemically perturbed soil assessed by molecular and cytochemical approaches. , 2001, Journal of microbiological methods.

[34]  H. Freeze,et al.  Thermus aquaticus gen. n. and sp. n., a Nonsporulating Extreme Thermophile , 1969, Journal of bacteriology.

[35]  T. Schmidt,et al.  The structure of microbial communities in soil and the lasting impact of cultivation , 2001, Microbial Ecology.

[36]  Mark E. Miller,et al.  Comparison of Soil Bacterial Communities in Rhizospheres of Three Plant Species and the Interspaces in an Arid Grassland , 2002, Applied and Environmental Microbiology.

[37]  P M Field,et al.  Repair of adult rat corticospinal tract by transplants of olfactory ensheathing cells. , 1997, Science.

[38]  V. Torsvik,et al.  Pesticide effects on bacterial diversity in agricultural soils – a review , 2001, Biology and Fertility of Soils.

[39]  T. Martin Embley,et al.  Grassland Management Regimens Reduce Small-Scale Heterogeneity and Species Diversity of β-Proteobacterial Ammonia Oxidizer Populations , 2002, Applied and Environmental Microbiology.

[40]  J. Hughes,et al.  Counting the Uncountable: Statistical Approaches to Estimating Microbial Diversity , 2001, Applied and Environmental Microbiology.

[41]  R. Lenski,et al.  Evidence for multiple adaptive peaks from populations of bacteria evolving in a structured habitat. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[42]  S. Sørensen,et al.  The effect of long-term mercury pollution on the soil microbial community. , 2001, FEMS microbiology ecology.

[43]  G. Bell,et al.  Diversity peaks at intermediate productivity in a laboratory microcosm , 2000, Nature.

[44]  P. White,et al.  The Ecology of Natural Disturbance and Patch Dynamics , 1986 .

[45]  David M. Ward,et al.  A Natural View of Microbial Biodiversity within Hot Spring Cyanobacterial Mat Communities , 1998, Microbiology and Molecular Biology Reviews.

[46]  H. Spencer,et al.  Why we need a new genetic species concept , 1989 .

[47]  J. Connell Diversity in tropical rain forests and coral reefs. , 1978, Science.

[48]  J. Tiedje,et al.  Soil Bacterial Community Shift Correlated with Change from Forest to Pasture Vegetation in a Tropical Soil , 1999, Applied and Environmental Microbiology.

[49]  J. T. Staley,et al.  Microbial Endemism and Biogeography , 2004 .

[50]  P. White,et al.  The Ecology of Natural Disturbance and Patch Dynamics , 1986 .

[51]  C. R. Lovell,et al.  Spatial and Temporal Assessment of Diazotroph Assemblage Composition in Vegetated Salt Marsh Sediments Using Denaturing Gradient Gel Electrophoresis Analysis , 1999, Microbial Ecology.

[52]  H. Dawah,et al.  Species :the units of biodiversity , 1997 .

[53]  G. Muyzer,et al.  Matching molecular diversity and ecophysiology of benthic cyanobacteria and diatoms in communities along a salinity gradient. , 2000, Environmental microbiology.

[54]  D. M. Ward,et al.  16S rRNA sequences reveal numerous uncultured microorganisms in a natural community , 1990, Nature.

[55]  John W. Taylor,et al.  Geographic Barriers Isolate Endemic Populations of Hyperthermophilic Archaea , 2003, Science.

[56]  A. Balmford,et al.  Using higher-taxon richness as a surrogate for species richness: I. Regional tests , 1996, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[57]  J. Hughes,et al.  New approaches to analyzing microbial biodiversity data. , 2003, Current opinion in microbiology.

[58]  Eric E. Roden,et al.  SUCCESSIONAL CHANGES IN BACTERIAL ASSEMBLAGE STRUCTURE DURING EPILITHIC BIOFILM DEVELOPMENT , 2001 .

[59]  G. Robertson,et al.  THE FUNCTIONAL SIGNIFICANCE OF DENITRIFIER COMMUNITY COMPOSITION IN A TERRESTRIAL ECOSYSTEM , 2000 .

[60]  R M May,et al.  Extinction rates can be estimated from molecular phylogenies. , 1994, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[61]  K. Duncan,et al.  GENETIC EXCHANGE BETWEEN BACILLUS SUBTILIS AND BACILLUS LICHENIFORMIS: VARIABLE HYBRID STABILITY AND THE NATURE OF BACTERIAL SPECIES , 1989, Evolution; international journal of organic evolution.

[62]  S. Gage,et al.  Ecological scaling of aerobiological dispersal processes , 1999 .

[63]  P. Normand,et al.  Microscale Diversity of the GenusNitrobacter in Soil on the Basis of Analysis of Genes Encoding rRNA , 2000, Applied and Environmental Microbiology.

[64]  M. Feldman,et al.  Local dispersal promotes biodiversity in a real-life game of rock–paper–scissors , 2002, Nature.

[65]  V. Torsvik,et al.  High diversity in DNA of soil bacteria , 1990, Applied and environmental microbiology.

[66]  J. Ahlquist,et al.  DNA hybridization evidence of hominoid phylogeny: A reanalysis of the data , 1990, Journal of Molecular Evolution.

[67]  O. Kandler,et al.  Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[68]  Shahid Naeem,et al.  Biodiversity enhances ecosystem reliability , 1997, Nature.

[69]  M. Goodfellow,et al.  Handbook of new bacterial systematics , 1993 .

[70]  Gerard Muyzer,et al.  Quantifying Microbial Diversity: Morphotypes, 16S rRNA Genes, and Carotenoids of Oxygenic Phototrophs in Microbial Mats , 1999, Applied and Environmental Microbiology.

[71]  U. Sommer,et al.  Diversity in planktonic communities: An experimental test of the intermediate disturbance hypothesis , 1999 .

[72]  B. Lighthart The ecology of bacteria in the alfresco atmosphere , 1997 .

[73]  R. Lenski,et al.  The Relative Importance of Competition and Predation Varies with Productivity in a Model Community , 2000, The American Naturalist.

[74]  D. Crowley,et al.  Soil and plant specific effects on bacterial community composition in the rhizosphere , 2001 .

[75]  P. Price A habitat for psychrophiles in deep Antarctic ice. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[76]  J. Andrews Comparative Ecology of Microorganisms and Macroorganisms , 2017, Brock/Springer Series in Contemporary Bioscience.

[77]  Michael Travisano,et al.  Adaptive radiation in a heterogeneous environment , 1998, Nature.

[78]  F. Cohan,et al.  Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. , 1997, International journal of systematic bacteriology.

[79]  F. Rodríguez-Valera,et al.  Bacterial diversity in two coastal lagoons deduced from 16S rDNA PCR amplification and partial sequencing , 1995 .

[80]  C. Woese,et al.  Bacterial evolution , 1987, Microbiological reviews.

[81]  D. Kelly,et al.  The prokaryotes: an evolving electronic resource for the microbiological community - , 2002 .

[82]  T. Phelps,et al.  What's up down there? , 1998, Current opinion in microbiology.

[83]  A. Buckling,et al.  Mechanisms linking diversity, productivity and invasibility in experimental bacterial communities , 2002, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[84]  M. Roberts,et al.  RECOMBINATION AND MIGRATION RATES IN NATURAL POPULATIONS OF BACILLUS SUBTILIS AND BACILLUS MOJAVENSIS , 1995, Evolution; international journal of organic evolution.

[85]  J. Tiedje,et al.  Biogeography and Degree of Endemicity of Fluorescent Pseudomonas Strains in Soil , 2000, Applied and Environmental Microbiology.

[86]  T. D. Brock Thermophilic Microorganisms and Life at High Temperatures , 1978, Springer Series in Microbiology.

[87]  B. Bohannan,et al.  Bacterial diversity patterns along a gradient of primary productivity , 2003 .

[88]  A. Kent,et al.  Microbial communities and their interactions in soil and rhizosphere ecosystems. , 2002, Annual review of microbiology.

[89]  Thomas P. Curtis,et al.  Estimating prokaryotic diversity and its limits , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[90]  R. Sandaa,et al.  Novel techniques for analysing microbial diversity in natural and perturbed environments. , 1998, Journal of biotechnology.

[91]  A. Felske,et al.  Spatial Homogeneity of Abundant Bacterial 16S rRNA Molecules in Grassland Soils , 1998, Microbial Ecology.

[92]  M. Coyne Soil microbiology : an exploratory approach , 1999 .

[93]  W. Sousa Disturbance in Marine Intertidal Boulder Fields: The Nonequilibrium Maintenance of Species Diversity , 1979 .

[94]  F. Cohan What are bacterial species? , 2002, Annual review of microbiology.

[95]  J. Crawford,et al.  In Situ Spatial Patterns of Soil Bacterial Populations, Mapped at Multiple Scales, in an Arable Soil , 2002, Microbial Ecology.

[96]  K. Jürgens,et al.  Predation as a shaping force for the phenotypic and genotypic composition of planktonic bacteria , 2002, Antonie van Leeuwenhoek.

[97]  A. Buckling,et al.  The emergence and maintenance of diversity: insights from experimental bacterial populations. , 2000, Trends in ecology & evolution.

[98]  Chung-I Wu The genic view of the process of speciation , 2001 .

[99]  N. Brown,et al.  Horizontal spread of mer operons among gram-positive bacteria in natural environments. , 1998, Microbiology.

[100]  J. Prosser,et al.  Molecular Analysis of Bacterial Community Structure and Diversity in Unimproved and Improved Upland Grass Pastures , 1999, Applied and Environmental Microbiology.

[101]  K. Gross,et al.  Patterns of diversity in plant and soil microbial communities along a productivity gradient in a Michigan old-field , 2000, Oecologia.

[102]  M. S. Lee Species concepts and species reality: salvaging a Linnaean rank , 2003, Journal of evolutionary biology.

[103]  D. M. Ward,et al.  Geographical isolation in hot spring cyanobacteria. , 2003, Environmental microbiology.

[104]  L. Shimkets,et al.  Persistence and Dissemination of Introduced Bacteria in Freshwater Microcosms , 1998, Microbial Ecology.

[105]  Paul R. Ehrlich,et al.  Has the Biological Species Concept Outlived Its Usefulness , 1961 .

[106]  T. Atkinson,et al.  Isolation and characterisation of the glycerol dehydrogenase from Bacillus stearothermophilus. , 1989, Biochimica et biophysica acta.

[107]  E. Mosley‐Thompson,et al.  Isolation of bacteria and 16S rDNAs from Lake Vostok accretion ice. , 2001, Environmental microbiology.

[108]  Mark V. Lomolino,et al.  Species Diversity in Space and Time. , 1996 .

[109]  A. Tunlid Molecular biology : a linkage between microbial ecology, general ecology and organismal biology , 1999 .

[110]  R. Kolter,et al.  Evolution of microbial diversity during prolonged starvation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[111]  N. Fierer,et al.  Influence of Drying–Rewetting Frequency on Soil Bacterial Community Structure , 2002, Microbial Ecology.

[112]  R M May,et al.  The reconstructed evolutionary process. , 1994, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[113]  T. Dobzhansky A Critique of the Species Concept in Biology , 1935, Philosophy of Science.

[114]  P. Tyler,et al.  Global distribution of free‐living microbial species , 1999 .

[115]  Katherine L. Gross,et al.  WHAT IS THE OBSERVED RELATIONSHIP BETWEEN SPECIES RICHNESS AND PRODUCTIVITY , 2001 .

[116]  T. D. Brock The study of microorganisms in situ progress and problems , 1987 .

[117]  R. Amann,et al.  Extremely Halophilic Bacteria in Crystallizer Ponds from Solar Salterns , 2000, Applied and Environmental Microbiology.

[118]  B. Haubold,et al.  Genetic and ecotypic structure of a fluorescent Pseudomonas population , 1996 .

[119]  U. Göbel,et al.  Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. , 1997, FEMS microbiology reviews.