Abstract
Microbes play key roles in the functioning of the biosphere. Still, our knowledge about their total diversity is very limited. In particular, we lack a clear understanding of the evolutionary dynamics occurring within their populations (i.e. among members of the same biological species). Unlike animals and plants, microbes normally have huge population sizes, high reproductive rates and the potential for unrestricted dispersal. As a consequence, the knowledge of population genetics acquired from studying animals and plants cannot be applied without extensive testing to microbes. Next generation molecular tools, like High Throughput Sequencing (e.g. 454 and Illumina) coupled to Single Cell Genomics, now allow investigating microbial populations at a very fine scale. Such techniques have the potential to shed light on several ecological and evolutionary processes occurring within microbial populations that so far have remained hidden. Furthermore, they may facilitate the identification of microbial species. Eventually, we may find an answer to the question of whether microbes and multicellular organisms follow the same or different rules in their population diversification patterns.
Similar content being viewed by others
References
Green J. L., Bohannan B.J.M., Spatial scaling of microbial biodiversity, Trends Ecol Evol, 2006, 21, 501–507
Falkowski P.G., Fenchel T., Delong E.F., The microbial engines that drive Earth’s biogeochemical cycles, Science, 2008, 320, 1034–1039
Pedros-Alio C., Marine microbial diversity: can it be determined?, Trends Microbiol, 2006, 14, 257–263
Futuyma D.J., Evolutionary Biology, Sinauer Associates, Inc., Sunderland, Massachusetts, 1998
Coyne J.A., Orr H.A., Speciation, Sinauer Associates, Inc., Sunderland, Massachusetts, 2004
Dolan J.R., An introduction to the biogeography of aquatic microbes, Aquat Microb Ecol, 2005, 41, 39–48
Snoke M.S., Berendonk T.U., Barth D., Lynch M., Large global effective population sizes in Paramecium, Mol Biol Evol, 2006, 23, 2474–2479
Newton R.J., Jones S.E., Helmus M.R., McMahon K.D., Phylogenetic ecology of the freshwater Actinobacteria acI Lineage, Appl Environ Microb, 2007, 73, 7169–7176
Finlay B.J., Global dispersal of free-living microbial eukaryote species, Science, 2002, 296, 1061–1063
Pace N.R., A molecular view of microbial diversity and the biosphere, Science, 1997, 276, 734–740
Hughes Martiny J.B., Bohannan B.J.M., Brown J.H., Colwell R.K., Fuhrman J.A., Green J.L., et al., Microbial biogeography: putting microorganisms on the map, Nat Rev Microbiol, 2006, 4, 102–112
Logares R., Does the global microbiota consist of a few cosmopolitan species?, Ecol Austral, 2006, 16, 85–90
Lopez-Garcia P., Moreira D., Tracking microbial biodiversity through molecular and genomic ecology, Res Microbiol, 2008, 159, 67–73
Medlin L.K., Lange M., Nothig E.M., Genetic diversity in the marine phytoplankton: a review and a consideration of Antarctic phytoplankton, Antarct Sci, 2000, 12, 325–333
Rynearson T.A., Armbrust E.V., DNA fingerprinting reveals extensive genetic diversity in a field population of the centric diatom Ditylum brightwellii, Limnol Oceanogr, 2000, 45, 1329–1340
Shankle A.M., Mayali X., Franks P.J.S., Temporal patterns in population genetic diversity of Prorocentrum micans (Dinophyceae), J Phycol, 2004, 40, 239–247
Evans K.M., Kuhn S.F., Hayes P.K., High levels of genetic diversity and low levels of genetic differentiation in North Sea Pseudo-nitzschia pungens (Bacillariophyceae) populations, J Phycol, 2005, 41, 506–514
Iglesias-Rodriguez M.D., Schofield O.M., Batley J., Medlin L.K., Hayes P.K., Intraspecific genetic diversity in the marine coccolithophore Emiliania huxleyi (Prymnesiophyceae): The use of microsatellite analysis in marine phytoplankton population studies, J Phycol, 2006, 42, 526–536
Nagai S., Lian C., Yamaguchi S., Hamaguchi M., Matsuyama Y., Itakura S., et al., Microsatellite markers reveal population genetic structure of the toxic dinoflagellate Alexandrium tamarense (Dinophyceae) in Japanese coastal waters, J Phycol, 2007, 43, 43–54
Logares R., Boltovskoy A., Bensch S., Laybourn-Parry J., Rengefors K., Genetic Diversity Patterns in Five Protist Species Occurring in Lakes, Protist, 2009, 160, 301–317
Mes T.H.M., Microbial diversity — insights from population genetics, Environ Microbiol, 2008, 10, 251–264
Rynearson T.A., Armbrust E.V., Genetic differentiation among populations of the planktonic marine diatom Ditylum brightwellii (Bacillariophyceae), J Phycol, 2004, 40, 34–43
Lilly E.L., Halanych K.M., Anderson D.M., Phylogeny, biogeography, and species boundaries within the Alexandrium minutum group, Harmful Algae, 2005, 4, 1004–1020
Harnstrom K., Ellegaard M., Andersen T.J., Godhe A., Hundred years of genetic structure in a sediment revived diatom population, Proc Natl Acad Sci USA, 2011, 108, 4252–4257
Wilson A.E., Sarnelle O., Neilan B.A., Salmon T.P., Gehringer M.M., Hay M.E., Genetic variation of the bloom-forming cyanobacterium Microcystis aeruginosa within and among lakes: Implications for harmful algal blooms, Appl Environ Microb, 2005, 71, 6126–6133
Hunt D.E., David L.A., Gevers D., Preheim S.P., Alm E.J., Polz M.F., Resource partitioning and sympatric differentiation among closely related bacterioplankton, Science, 2008, 320, 1081–1085
Logares R., Rengefors K., Kremp A., Shalchian-Tabrizi K., Boltovskoy A., Tengs T., et al., Phenotypically different microalgal morphospecies with identical ribosomal DNA: A case of rapid adaptive evolution?, Microb Ecol, 2007, 53, 549–561
Logares R., Daugbjerg N., Boltovskoy A., Kremp A., Laybourn-Parry J., Rengefors K., Recent evolutionary diversification of a protist lineage, Environ Microbiol, 2008, 10, 1231–1243
Avise J.C., Phylogeography: the history and formation of species, Harvard University Press, Cambridge, Massachusetts, 2000
Massana R., Terrado R., Forn I., Lovejoy C., Pedros-Alio C., Distribution and abundance of uncultured heterotrophic flagellates in the world oceans, Environ Microbiol, 2006, 8, 1515–1522
Salcher M. M., Pernthaler J., Posch T., Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria ‘that rule the waves’ (LD12), ISME J, 2011, 5, 1242–1252
Logares R., Brate J., Heinrich F., Shalchian-Tabrizi K., Bertilsson S., Infrequent transitions between saline and fresh waters in one of the most abundant microbial lineages (SAR11), Mol Biol Evol, 2010, 27, 347–357
Binga E.K., Lasken R.S., Neufeld J.D., Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology, ISME J, 2008, 2, 233–241
Marcy Y., Ishoey T., Lasken R.S., Stockwell T.B., Walenz B.P., Halpern A.L., et al., Nanoliter reactors improve multiple displacement amplification of genomes from single cells, PLOS GENET, 2007, 3, e155
Stepanauskas R., Sieracki M.E., Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time, Proc Natl Acad Sci USA, 2007, 104, 9052–9057
Pinard R., de Winter A., Sarkis G.J., Gerstein M.B., Tartaro K.R., Plant R.N., et al., Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing, Bmc Genomics, 2006, 7, 216
Spits C., Le Caignec C., De Rycke M., Van Haute L., Van Steirteghem A., Liebaers I., et al., Optimization and evaluation of single-cell wholegenome multiple displacement amplification, Hum Mutat, 2006, 27, 496–503
Taylor J.W., Jacobson D.J., Kroken S., Kasuga T., Geiser D.M., Hibbett D.S., et al., Phylogenetic species recognition and species concepts in fungi, Fungal Genet Biol, 2000, 31, 21–32
Coleman A.W., Is there a molecular key to the level of “biological species” in eukaryotes? A DNA guide, Mol Phylogenet Evol, 2009, 50, 197–203
Mayr E., Systematics and the Origin of Species, Columbia University Press, New York, 1942
Ronaghi M., Uhlen M., Nyren P., A sequencing method based on real-time pyrophosphate, Science, 1998, 281, 363–365
Trombetti G.A., Bonnal R.J.P., Rizzi E., De Bellis G., Milanesi L., Data handling strategies for high throughput pyrosequencers, Bmc Bioinformatics, 2007, 8, S1–22
Glenn T.C., Field guide to next-generation DNA sequencers, Mol Ecol Resour, 2011, 11, 759–769
Yoon H.S., Price D.C., Stepanauskas R., Rajah V.D., Sieraki M.E., Wilson W.H., et al., Single-Cell genomics reveals organismal interactions in uncultivated marine protists, Science, 2011, 332, 714–717
Dupont C.L., Chappell D., Logares R., Vila-Costa M., A hitchhiker’s guide to the new molecular toolbox for ecologists, In: P. Kemp (Ed.), Eco-DAS VIII Symposium Proceedings (11–16 October 2008, Hawaii, USA), ASLO, 2010, 17–29
Author information
Authors and Affiliations
Corresponding author
About this article
Cite this article
Logares, R. Population genetics: the next stop for microbial ecologists?. cent.eur.j.biol. 6, 887–892 (2011). https://doi.org/10.2478/s11535-011-0086-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.2478/s11535-011-0086-9