Marine microbial diversity: can it be determined?

Estimates of the order of magnitude for the total number of microbial species on Earth range from 10(3) to 10(9). Despite global dispersal of microorganisms, this number is probably rather large. The total biodiversity of an ecosystem is composed of two elements: first, a set of abundant taxa that carry out most ecosystem functions, grow actively and suffer intense losses through predation and viral lysis. These taxa are retrievable with molecular techniques but are difficult to grow in culture. Second, there is a seed bank of many rare taxa that are not growing or grow extremely slowly, do not experience viral lysis and predation is reduced. Such taxa are seldom retrieved by molecular techniques but many can be grown in culture, which explains the dictum 'everything is everywhere'.

[1]  R. Wachter,et al.  Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity , 2001, Nature.

[2]  Robert M. May,et al.  How Many Species Are There on Earth? , 1988, Science.

[3]  T. Thingstad Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems , 2000 .

[4]  C. Pedrós-Alió Diversity of Microbial Communities: The Case of Solar Salterns , 2005 .

[5]  Tamra C. Mendelson,et al.  Sexual behaviour: Rapid speciation in an arthropod , 2005, Nature.

[6]  E. Casamayor,et al.  Identification of and Spatio-Temporal Differences between Microbial Assemblages from Two Neighboring Sulfurous Lakes: Comparison by Microscopy and Denaturing Gradient Gel Electrophoresis , 2000, Applied and Environmental Microbiology.

[7]  A. Bull Microbial Diversity and Bioprospecting , 2003 .

[8]  S. Via,et al.  Sympatric speciation in animals: the ugly duckling grows up. , 2001, Trends in ecology & evolution.

[9]  A. Uitterlinden,et al.  Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA , 1993, Applied and environmental microbiology.

[10]  Stuart Bearhop,et al.  Assortative Mating as a Mechanism for Rapid Evolution of a Migratory Divide , 2005, Science.

[11]  P. Kemp,et al.  Bacterial diversity in aquatic and other environments: what 16S rDNA libraries can tell us. , 2004, FEMS microbiology ecology.

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

[13]  J. Couzin Small RNAs Make Big Splash , 2002, Science.

[14]  D. Moreira,et al.  Global dispersal and ancient cryptic species in the smallest marine eukaryotes. , 2006, Molecular biology and evolution.

[15]  J. Pernthaler Predation on prokaryotes in the water column and its ecological implications , 2005, Nature Reviews Microbiology.

[16]  S. Acinas,et al.  Fine-scale phylogenetic architecture of a complex bacterial community , 2004, Nature.

[17]  David M. Karl,et al.  Microbiological oceanography: Hidden in a sea of microbes , 2002, Nature.

[18]  Molecular genetic analyses of species boundaries in the sea , 2000 .

[19]  R. Rosenzweig,et al.  Microbial evolution in a simple unstructured environment: genetic differentiation in Escherichia coli. , 1994, Genetics.

[20]  A. W. Coleman,et al.  The significance of a coincidence between evolutionary landmarks found in mating affinity and a DNA sequence. , 2000, Protist.

[21]  T. Fenchel Marine Bugs and Carbon Flow , 2001, Science.

[22]  J. Fuhrman,et al.  Marine ecology: Microbial microdiversity , 1998, Nature.

[23]  E. Delong Archaea in coastal marine environments. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[24]  J. Whitfield Is Everything Everywhere? , 2005, Science.

[25]  E. Delong,et al.  Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing , 1991, Journal of bacteriology.

[26]  Erko Stackebrandt,et al.  Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in Bacteriology , 1994 .

[27]  Ramon Massana,et al.  Study of Genetic Diversity of Eukaryotic Picoplankton in Different Oceanic Regions by Small-Subunit rRNA Gene Cloning and Sequencing , 2001, Applied and Environmental Microbiology.

[28]  N. Knowlton Molecular genetic analyses of species boundaries in the sea , 2000, Hydrobiologia.

[29]  F. Rohwer,et al.  Use of 16S Ribosomal DNA for Delineation of Marine Bacterioplankton Species , 2002, Applied and Environmental Microbiology.

[30]  E. Casamayor,et al.  Dynamics of whole community bacterial production and grazing losses in seawater incubations as related to the changes in the proportions of bacteria with different DNA content , 2001 .

[31]  D. Potter,et al.  Convergent evolution masks extensive biodiversity among marine coccoid picoplankton , 2004, Biodiversity & Conservation.

[32]  G. Procaccini,et al.  Multiple rDNA ITS-types within the diatom Pseudo-nitzschia delicatissima (Bacillariophyceae) and their relative abundances across a spring bloom in the Gulf of Naples , 2004 .

[33]  O. White,et al.  Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.

[34]  C. Pedrós-Alió Diversity of bacterioplankton. , 1993, Trends in ecology & evolution.

[35]  N. E. Stork,et al.  How many species are there? , 1993, Biodiversity & Conservation.

[36]  J. Kolasa,et al.  Diversity concept in ecology , 1984 .

[37]  B. Finlay Global Dispersal of Free-Living Microbial Eukaryote Species , 2002, Science.

[38]  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.

[39]  S. Baldauf,et al.  The Deep Roots of Eukaryotes , 2003, Science.

[40]  Kristen Yarincik,et al.  The Census of Marine Life: goals, scope and strategy , 2005 .

[41]  E. Pennisi,et al.  Evolution in Action , 2005, Science.

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

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

[44]  Terry L. Erwin,et al.  How Many Species Are There?: Revisited , 1991 .

[45]  S. Giovannoni,et al.  Genetic diversity in Sargasso Sea bacterioplankton , 1990, Nature.

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

[47]  B. Finlay,et al.  Ubiquitous Dispersal of Free-Living Microorganisms , 2004 .

[48]  T. Fenchel Cosmopolitan microbes and their cryptic species , 2005 .

[49]  J. Copley,et al.  All at sea , 2002, Nature.

[50]  A. Quispel Lourens G. M. Baas Becking (1895-1963). Inspirator for many (micro)biologists. , 1998, International microbiology : the official journal of the Spanish Society for Microbiology.

[51]  R. Amann,et al.  Microheterogeneity in 16S Ribosomal DNA-Defined Bacterial Populations from a Stratified Planktonic Environment Is Related to Temporal Changes and to Ecological Adaptations , 2002, Applied and Environmental Microbiology.

[52]  J. Pinhassi,et al.  Biogeographic analysis of ribosomal RNA clusters from marine bacterioplankton , 2005 .

[53]  C. Pedrós-Alió,et al.  Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton , 2001, Nature.

[54]  B. Ward,et al.  Worldwide Distribution of Nitrosococcus oceani, a Marine Ammonia-Oxidizing γ-Proteobacterium, Detected by PCR and Sequencing of 16S rRNA and amoA Genes , 2002, Applied and Environmental Microbiology.

[55]  J. Whitfield Biogeography. Is everything everywhere? , 2005, Science.

[56]  T. Fenchel Where are all the species , 2005 .

[57]  W. Moore,et al.  Taxonomic Note : A Place for DNA-DNA Reassociation and 16 s rRNA Sequence Analysis in the Present Species Definition in , 2022 .

[58]  R. Margalef Diversity and biodiversity - their possible meaning in relation with the wish for sustainable development , 1994 .

[59]  A. Davis Novel major archaebacterial group from marine plankton , 1992, Nature.

[60]  B. Ward,et al.  How many species of prokaryotes are there? , 2002, Proceedings of the National Academy of Sciences of the United States of America.

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

[62]  G. Muyzer Profiling ofComplexMicrobial Populations byDenaturing Gradient GelElectrophoresis Analysis ofPolymerase Chain Reaction-Amplified GenesCodingfor16SrRNA , 1993 .

[63]  A. Magurran,et al.  Explaining the excess of rare species in natural species abundance distributions , 2003, Nature.

[64]  Frede Thingstad,et al.  Prokaryotic genetic diversity throughout the salinity gradient of a coastal solar saltern. , 2002, Environmental microbiology.