Biodiversity of freshwater microorganisms - achievements, problems, and perspectives

• Autorzy: Weisse Thomas
• Języki publikacji: EN

Abstrakty

EN

The extent and significance of the diversity of freshwater microbes is at present controversially debated. Until 1980 it was assumed that there are no freshwater-specific bacteria and that the total number of bacterial species is low. The advent of molecular tools over the last ten years revealed that there is a bacterial freshwater assemblage which is phylogenetically different from soil and marine bacteria; secondly, it became obvious that the total number of cultured bacterial species ([similar to] 5900) underestimates bacterial diversity by several orders of magnitude. The current debate centres on 1) how to define a bacterial species and 2) if there is a microbial biogeography. The latter relates to the issue of ubiquity and cosmopolitanism, which is controversially discussed primarily in relation to eukaryotic microorganisms, namely ciliates. Although solid evidence is scarce, many microbial ecologists assume, in accordance with Baas Becking's famous 70-year old dictum - "everything is everywhere, the environment selects" - that freshwater microorganisms are easily dispersed and, therefore, potentially cosmopolitan. This review focuses on the often neglected second part of Baas Becking's metaphor. Evidence is accumulating rapidly that the environment does not simply act as a filter sensu Gleason's individualistic concept for widely dispersed microbes. Rather, prokaryotic and eukaryotic microorganisms have adapted to their specific habitat and perform better in this environment than newly invading congeners. There is an enormous ecophysiological diversity among closely related freshwater microbes which is neither obvious at the morphospecies level nor at the level of evolutionarily conserved genes, such as the small ribosomal RNA gene. Although this large diversity has been demonstrated for various groups of bacteria and protists, there is currently no measure available to compare microbial biodiversity across prokaryotic and eukaryotic domains. The current challenge is to link genetic divergence to ecophysiological diversity in the major taxa.

Słowa kluczowe

EN

fresh water; future perspectives; microbial diversity; species problem

PL

ekologia; mikroorganizmy; słodka woda

• Wydawca: Museum and Institute of Zoology, Polish Academy of Sciences
• Czasopismo: Polish Journal of Ecology
• Rocznik: 2006
• Tom: Vol. 54, nr 4
• Strony: 633--652

Twórcy

autor

Weisse Thomas

• Institute for Limnology of the Austrian Academy of Sciences, Mondseestr. 9, A-5310 Mondsee, Austria

• Institute for Limnology of the Austrian Academy of Sciences, Mondseestr. 9, A-5310 Mondsee, Austria,

Bibliografia

• Acinas S.G., Klepac-Ceraj V., Hunt D.E., Pharino C., Ceraj I., Distel D.L., Polz M.F. 2004 – Fine-scale phylogenetic architecture of a complex bacterial community – Nature, 430: 551–554.
• Agatha S. 2004 – A cladistic approach for the classification of oligotrichid ciliates (Ciliophora: Spirotricha) – Acta Protozool. 43: 201–217.
• Atwood K.C., Schneider L.K., Tyan F.J. 1951 – Periodic selection in Escherichia coli – Proc. Natl. Acad. Sci. USA, 37: 146–155.
• Azam F., Fenchel T., Field J.G., Gray J.S., Meyer-Reil L.A., Thingstad F. 1983 – The ecological role of water-column microbes in the sea – Mar. Ecol. Prog. Ser. 10: 257–263.
• Bachmann K. 1998 – Species as units of diversity: an outdated concept – Theory Biosci. 117: 213–230.
• Barth D., Krenek S., Fokin S.I., Berendonk T.U. 2006 – Intraspecific genetic variation in Paramecium, revealed by mitochondrial COI sequences – J. Eukaryot. Microbiol. 53: 20–25.
• Becker S., Fahrbach M., Böger P., Ernst A. 2002 – Quantitative tracing, by Taq nuclease assays, of a Synechococcus ecotype in a highly diversified natural population – Appl. Environ. Microbiol. 68: 4486–4494.
• Becks L., Hilker F.M., Malchow H., Jürgens K., Arndt H. 2005 – Experimental demonstration of chaos in a microbial food web – Nature, 435: 1226–1229.
• Bell G. 2001 – Neutral macroecology – Science, 293: 2413–2418.
• Beszteri B., Ács É., Medlin L.K. 2005 – Ribosomal DNA sequence variation among sympatric strains of the Cyclotella meneghiana complex (Bacillariophyceae) reveals cryptic diversity – Protist, 156: 317–333.
• Boenigk J., Pfandl K., Stadler P., Chatzinotas A. 2005 – High diversity of the “Spumella-like” flagellates: an investigation based on the SSU rRNA gene sequences of isolates from habitats located in six different geographic regions – Environ. Microbiol. 7: 685–697.
• Boenigk J., Stadler P., Wiedlroither A., Hahn M.W. 2004 – Strain-specific differences in the grazing sensitivities of closely related ultramicrobacteria affiliated with the Polynucleobacter cluster – Appl. Environ. Microbiol. 70: 5787–5793.
• Claridge M.F., Dawah H.A., Wilson M.R. 1997 – Practical approaches to species concepts for living organisms (In: Species – The units of biodiversity, Eds: M.F. Claridge, H.A. Dawah, M.R. Wilson) – Chapman and Hall, London, pp. 1–15.
• Cohan F.M. 2001 – Bacterial species and speciation – Syst. Biol. 50: 513–524.
• Cohan F.M. 2002 – What are bacterial species? – Annu. Rev. Microbiol. 56: 457–487.
• Coleman A.W. 2002 – Microbial eukaryote species – Science, 297: 337.
• Collins S., Bell G. 2004 – Phenotypic consequences of 1000 generations of selection at elevated CO2 in a green alga – Nature, 431: 566–569.
• Cooper V.S., Bennett A.F., Lenski R.E. 2001 – Evolution of thermal dependence of growth rate of Escherichia coli populations during 20 000 generations in a constant environment – Evolution, 55: 889–896.
• Cracraft J. 1983 – Species concepts and speciation analysis – Current Ornithology, 1: 159–187.
• Cronberg G. 1986 – Chrysophycean cysts and scales in lake sediments: a review (In: Chrysophytes: aspects and problems, Eds: J. Kristiansen, R.A. Andersen) – Cambridge Univ. Press, Cambridge, pp. 281–337.
• Cronberg G., Sandgren C.D. 1986 – A proposal for the development of standardized nomenclature and terminology for chrysophycean statospores (In: Chrysophytes: aspects and problems, Eds: J. Kristiansen, R.A. Andersen) – Cambridge Univ. Press, Cambridge, pp. 317–328.
• Crosbie N.D., Pöckl M., Weisse T. 2003a – Dispersal and phylogenetic diversity of nonmarine picocyanobacteria, inferred from 16S rRNA gene and cpcBA-intergenic spacer sequence analyses – Appl. Environ. Microbiol. 69: 5716–5721.
• Crosbie N.D., Pöckl M., Weisse T. 2003b – Rapid establishment of clonal isolates of freshwater autotrophic picoplankton by single-cell and single-colony sorting – J. Microbiol. Meth. 55: 361–370.
• Crump B.C., Hobbie J.E. 2005 – Synchrony and seasonality in bacterioplankton communities of two temperate rivers – Limnol. Oceanogr. 50: 1718–1729.
• Curtis T.P., Sloan W.T. 2004 – Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology – Curr. Opin. Microbiol. 7: 221–226.
• Darling K.F., Wade C., Stewart I.A., Kroon D., Dingle R., Leigh Brown A.J. 2000 – Molecular evidence for genetic mixing of Arctic and Antarctic subpolar populations of planktonic foraminifers – Nature, 405: 43–47.
• Darwin C. 1859 – On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life – John Murray, London, 502 pp. http://www.britishlibrary.net/charles.darwin/texts/origin1859/).
• Dieckmann U., Doebeli M. 1999 – On the origin of species by sympatric speciation – Nature, 400: 354–357.
• Dini F., Nyberg D. 1993 – Sex in ciliates (In: Advances in microbial ecology, Vol 13, Ed. J.G. Jones) – Plenum Press, New York, pp.129–144.
• Dini F., Nyberg D. 1999 – Growth rates of marine ciliates on diverse organisms reveal ecological specializations within morphospecies – Microb. Ecol. 37: 13–22.
• Dorigo U., Volatier L., Humbert J.-F. 2005 – Molecular approaches to the assessment of biodiversity in aquatic microbial communities – Wat. Res. 39: 2207–2218.
• Dykhuizen D.E. 1998 – Santa Rosalia revisited: Why are there so many species in bacteria? – Antonie van Leeuwenhoek, 73: 25–33.
• Ernst A., Becker S., Wollenzien U.I.A., Postius C. 2003 – Ecosystem-dependent adaptive radiations of picocyanobacteria inferred from 16S rRNA and ITS-1 sequence analysis – Microbiology, 149: 217–228.
• Fenchel T. 1987 – Ecology of protozoa. The biology of free-living phagotrophic protists – Science Tech. – Springer, 197 pp.
• Fernando P., Vidya T.N.C., Payne J., Stuewe M., Davison G., Alfred R.J., Andau P., Bosi E., Kilbourn A., Don J., Melnick D.J. 2003 – DNA analysis indicates that Asian elephants are native to Borneo and are therefore a high priority for conservation. PLOS Biology, 1: p. 6. (http://biology.plosjournals.org ).
• Finlay B.J. 2002 – Global dispersal of free-living microbial eukaryote species – Science, 296: 1061–1063.
• Finlay B.J. 2004 – Protist taxonomy: an ecological perspective – Phil. Trans. Roy. Soc. Lond. B, 359: 599–610.
• Finlay B.J., Corliss J.O., Esteban G.F., Fenchel T. 1996 – Biodiversity at the microbial level: the number of free-living ciliates in the biosphere – Quart. Rev. Biol. 71: 221–237.
• Finlay B.J., Esteban G.F., Fenchel T. 1998 – Protozoan diversity: converging estimates of the global number of free-living ciliate species – Protist, 149: 29–37.
• Finlay B.J., Esteban G.F., Fenchel T. 2004 – Protist diversity is different? – Protist, 155: 15–22.
• Finlay B.J., Fenchel T. 1999 – Divergent perspectives on protist species richness – Protist, 150: 229–233.
• Finlay B.J., Fenchel T. 2004 – Cosmopolitan metapopulations of free-living microbial eukaryotes – Protist, 155: 237–244.
• Foissner W. 1999 – Protist diversity: estimates of the near-imponderable – Protist, 150: 363–368.
• Foissner W., Agatha S., Berger H. 2002 – Soil ciliates (Protozoa, Ciliophora) from Namibia (Southwest Africa), with emphasis on two contrasting environments, the Etosha region and the Namib Desert – Denisia, 5: 1–1459.
• Foissner W., Stoeck T., Schmidt H., Berger H. 2001 – Biogeographical differences in a common soil ciliate, Gonostomum affine (Stein), as revealed by morphological and RAPD-fingerprint analysis – Acta Protozool. 40: 83–97.
• Foissner W., Strüder-Kypke M., van der Staay G.W.M., Moon-van der Staay S.-Y., Hackstein J.H.P. 2003 – Endemic ciliates (Protozoa, Ciliophora) from tank bromeliads (Bromeliaceae): a combined morphological, molecular, and ecological study – Europ. J. Protistol. 39: 365–372.
• Gavrilets S. 2003 – Perspective: Models of speciation: what have we learned in 40 years? – Evolution, 57, 2197–2215.
• Giovannoni S. 2004 – Oceans of bacteria – Nature, 430: 515–516.
• Gleason H.A. 1926 – The individualistic concept of the plant association – Bull. Torrey Bot. Club, 53: 7–26.
• Glöckner F.O., Zaichikov E., Belkova N., Denissova L., Pernthale J., Pernthaler A., Amann R. 2000 – Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of Actinobacteria – Appl. Environ. Microbiol. 66: 5053–5065.
• Gogarten J.P., Townsend J.P. 2005 – Horizontal gene transfer, genome innovation and evolution – Nat. Rev. Microbiol. 3: 679–687.
• Gosling E. 1999 – The periwinkle, a perfect model for biodiversity studies. In: The Irish scientist year book, (http://www.irishscientist.ie/GITEG115.htm)
• Green J.L., Holmes A.J., Westoby M., Oliver I., Briscoe D., Dangerfield M., Gillings M., Beattie A.J. 2004 – Spatial scaling of microbial eukaryote diversity – Nature, 432: 747–750.
• Güde H. 1989 – The role of grazing on bacteria in plankton succession (In: Plankton ecology: succession in plankton communities, Ed. U. Sommer) – Brock/Springer series in contemporary bioscience. Springer, Berlin, pp. 337–364.
• Hahn M.W. 2003 – Isolation of strains belonging to the cosmopolitan Polynucleobacter necessarius cluster from freshwater habitats located in three climatic zones – Appl. Environ. Microbiol. 69: 5248–5254.
• Hahn M.W., Lünsdorf H., Wu Q.L., Schauer M., Höf le M.G., Boenigk J., Stadler P. 2003 – Isolation of novel ultramicrobacteria classified as Actinobacteria from five freshwater habitats in Europe and Asia – Appl. Environ. Microbiol. 69: 1442–1451.
• Hahn M.W., Pöckl M. 2005 – Ecotypes of planktonic Actinobacteria with identical 16S rRNA genes adapted to thermal niches in temperate, subtropical, and tropical freshwater habitats – Appl. Environ. Microbiol. 71: 766–773.
• Hahn M.W., Pöckl M., Wu Q.L. 2005 – Low intraspecific diversity in a Polynucleobacter subcluster population numerically dominating bacterioplankton of a freshwater pond – Appl. Environ. Microbiol. 71: 4539–4547.
• Hey J. 2001 – Genes, categories and species – Oxford University Press, Oxford, 217 pp.
• Hillebrand H., Blencker T. 2002 – Regional and local impact on species diversity – from pattern to processes – Oecologia, 132: 479–491.
• Hillebrand H., Watermann F., Karez R., Berninger U.-G. 2001 – Differences in species richness patterns between unicellular and multicellular organisms – Oecologia, 126: 114–124.
• Hiorns W.D., Methé E.A., Nierzwicki-Bauer S.A., Zehr J.P. 1997 – Bacterial diversity in Adirondack mountain lakes as revealed by 16S rRNA gene sequences – Appl. Environ. Microbiol. 63: 2957–2960.
• Horner-Devine M.C., Lage M., Hughes J.B., Bohannan B.J.M. 2004 – A taxa-area relationship for bacteria – Nature, 432: 750–753.
• Hubbel S.P. 2001 – The unified neutral theory of biodiversity and biogeography. Princeton Univ. Press, Princeton, NJ, 375 pp.
• Huey R.B., Berrigan D. 1996 – Testing evolutionary hypotheses of acclimation (In: Animals and temperature: phenotypic and evolutionary adaptation, Eds: I.A . Johnston, A.F. Bennett) – Cambridge University Press, Society for Experimental Biology Seminar Series 59, Cambridge, pp. 205–237.
• Hughes Martiny J.B., Bohannan B.J.M., Brown J.H, Colwell R.K., Fuhrman J.A., Green J.L., Horner-Devine M.C., Kane M., Krumins J.A., Kuske C.R., Morin P.J., Naeem S., Řvreĺs L., Reysenbach A.-L., Smith V.H., Staley J.T. 2006 – Microbial biogeography: putting microorganisms on the map – Nat. Rev. Microbiol. 4: 102–112.
• Hull D.L. 1997 – The ideal species concept – and why we can’t get it (In: Species – The units of biodiversity, Eds: M.F. Claridge, H.A. Dawah, M.R. Wilson) – Chapman and Hall, London, pp. 357–380.
• Hutchinson G.E. 1965 – The niche: an abstractly inhabited hypervolume (In: The ecological
• theatre and the evolutionary play, Ed. G.E. Hutchinson) – Yale University Press, New Haven, pp. 26–78.
• Jablonka E., Lachmann M., Lamb M.J. 1992 – Evidence, mechanisms and models of the inheritance of acquired characters – J. Theor. Biol. 158: 245–268.
• Jablonka E., Lamb M.J. 1995 – Epigenetic inheritance and evolution – the Lamarckian dimension – Oxford University Press, Oxford, 360 pp.
• Jackson R.B., Linder C.R., Lynch M., Purrugganan M., Somerville S., Thayer S.S. 2002 – Linking molecular insight and ecological research – Trends Ecol. Evol. 17: 409–414.
• Jaspers E., Overmann J. 2004 – Ecological significance of microdiversity: identical 16S rRNA gene sequences can be found in bacteria with highly divergent genomes and ecophysiologies – Appl. Environ. Microbiol. 70: 4831–4839.
• Jerome C.A., Simon E.M., Lynn D.H. 1996 – Description of Tetrahymena empidokyrea n. sp., a new species in the Tetrahymena pyriformis sibling species complex (Ciliophora, Oligohymenophorea), and an assessment of its phylogeneitc position using small-subunit rRNA sequences – Can. J. Zool. (Rev. Can. Zool.), 74: 1898–1906.
• Jürgens K., Pernthaler J., Schalla S., Amann R. 1999 – Morphological and compositional changes in a planktonic bacterial community in response to enhanced protozoan grazing – Appl. Environ. Microbiol. 65: 1241–1250.
• Kamenik C., Schmidt R., Koinig K.A., Panareda A.A., Thompson R., Psenner R. 2001 – The chrysophyte stomatocyst composition in a high alpine lake (Gossenköllesee, Tyrol, Austria) in relation to seasonality, temperature and land-use – Nova Hedwigia, Beihefte, 122: 1–22.
• Katz L.A., McManus G.B., Snoeyenbos-West O.L.O., Griffin A., Pirog K., Costas B., Foissner W. 2005 – Reframing the “Everything is everywhere” debate: evidence for high gene flow and diversity in ciliate morphospecies – Aquat. Microb. Ecol. 41: 55–65.
• Kim E., Wilcox L., Graham L. 2004 – Genetically distinct populations of the Dinoflagellate Peridinium limbatum in neighboring northern Wisconsin Lakes – Microb. Ecol. 48: 521–527.
• King M. 1993 – Species evolution: the role of chromosome change – Cambridge University Press, Cambridge, UK, 336 pp.
• Kurmayer R., Christiansen G., Fastner J., Börner T. 2004 – Abundance of active and inactive microcystin genotypes in populations of the toxic cyanobacterium Planktothrix spp. – Environ. Microbiol. 6: 831–841.
• Kusch J. 1995 – Adaptation of inducible defense in Euplotes daidaleos (Ciliophora) to predation risks by various predators – Microb. Ecol. 30: 79–88.
• Kusch J. 1998 – Local and temporal distribution of different genotypes of pond-dwelling Stentor coeruleus – Protist, 149: 147–154.
• Kusch J., Welter H., Stremmel M., Schmidt H.J. 2000 – Genetic diversity in populations of a freshwater ciliate – Hydrobiologia, 431: 185–192.
• Lachance M.-A. 2004 – Here and there or everywhere – BioScience, 54: 884.
• Langenheder S., Lindström E.S., Tranvik L.J. 2006 – Structure and function of bacterial communities emerging from different sources under identical conditions – Appl. Environ. Microbiol. 72: 212–220.
• Leander B.S., Keeling P.J. 2003 – Morphostasis in alveolate evolution – Trends Ecol. Evol. 18: 395–402.
• Lenormand T. 2002 – Gene flow and the limits to natural selection – Trends Ecol. Evol. 17: 183–189.
• Lenski R.E. 2004 – Microbial evolution in action – Microbiology Today, 31: 158.
• Lindström E.S. 2000 – Bacterioplankton community composition in five lakes differing in trophic status and humic content – Microb. Ecol. 40: 104–113.
• Lindstöm E.S., Kamst-Van Agterveld M.P., Zwart G. 2005 – Distribution of typical freshwater bacterial groups is associated with pH, temperature and lake water retention time – Appl. Environ. Microbiol. 71: 8201–8206.
• Lowe C.D., Day A., Kemp S.J., Montagnes D.J.S. 2005 – There are high levels of functional and genetic diversity in Oxyrrhis marina – J. Eukaryot. Microbiol. 52: 250–257.
• Lucas M.C., Baras E. 2001 – Migration of freshwater fishes – Blackwell Science, London, 420 pp.
• Lynn D.H. 2003 – Morphology or molecules: How do we identify the major lineages of ciliates (Phylum Ciliophora)? – Europ. J. Protistol. 39: 356–364.
• Mayden R.L. 1997 – A hierarchy of species concepts: the denouement in the saga of the species problem (In: Species – The units of biodiversity, Eds: M.F. Claridge, H.A. Dawah, M.R. Wilson) – Chapman and Hall, London, pp. 381–424.
• Mayr E. 1942 – Systematics and the origin of species – Columbia Univ. Press, New York, 330 pp.
• Mayr E. 1963 – Animal species and evolution – Harvard Univ. Press, Cambridge, 797 pp.
• Mayr E. 2004 – 80 years of watching the evolutionary scenery – Science, 365: 46–47.
• Methé B.A., Hiorns W.D., Zehr J.P. 1998 – Contrasts between marine and freshwater bacterial community composition: Analyses of communities in Lake George and six other Adirondack lakes – Limnol. Oceanogr. 43: 368–374.
• Mitchell E.A.D., Meisterfeld R. 2005 – Taxonomic confusion blurs the debate on cosmopolitanism versus local endemism of free-living protists – Protist, 156: 263–267.
• Mongold J.A., Bennett A.F., Lenski R.E. 1996 – Experimental investigations of evolutionary adaptation to temperature (In: Animals and temperature: phenotypic and evolutionary adaptation, Eds: I.A. Johnston, A.F. Bennett) – Cambridge University Press, Cambridge, pp. 239–264.
• Montagnes D.J.S., Weisse T. 2000 – Fluctuating temperatures affect growth and production rates of planktonic ciliates – Aquat. Microb. Ecol. 21: 97–102.
• Moore L.R., Rocap G., Chisholm S.W. 1998 – Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes – Nature, 393: 464–467.
• Müller H. 2000 – Evidence of dormancy in planktonic oligotrich ciliates – Verh. Internat. Verein. Limnol. 27: 3206–3209.
• Müller H., Stadler P., Weisse T. 2002 – Seasonal dynamics of cyst formation of strombidiid ciliates in alpine Lake Mondsee, Austria – Aquat. Microb. Ecol. 29: 181–188.
• Müller H., Wünsch C. 1999 – Seasonal dynamics of cyst formation of pelagic strombidiid ciliates in a deep prealpine lake – Aquat. Microb. Ecol. 17: 37–47.
• Nanney D.L. 1999 – When is a Rose?: The kinds of Tetrahymena (In: Species: New interdisciplinary essays, Ed. R.A. Wilson) – MIT Press, Cambridge, Mass. pp. 93–118.
• Nanney D.L. 2004 – No trivial pursuit – Bio-Science, 54: 720–721.
• Nanney D.L. 2005 – The systematics and biogeography of ciliated protozoa – SILnews, 44: 6–7.
• Ogunseitan O. 2005 – Microbial diversity – Form and function in Prokaryotes – Blackwell, Malden, MA, USA, 312 pp.
• Padisák J. 2003 – Phytoplankton (In: The lakes handbook, Vol. 1, Eds: P. O’Sullivan, C.S. Reynolds) – Blackwell Science Ltd, Oxford, pp. 251–308.
• Palys T., Berger E., Mitrica I., Nakamura L.K., Cohan F.M. 2000 – Protein-coding genes as molecular markers for ecologically distinct populations: the case of two Bacillus species – Int. J. Syst. Evol. Microbiol. 50: 1021–1028.
• Palys T., Cohan F.M., Nakamura L.K. 1997 – Discovery and classification of ecological diversity in the bacterial world: the role DNA sequence data – Int. J. Syst. Evol. Microbiol. 47: 1145–1156.
• Papke R.T., Ramsing N.B., Bateson M.M., Ward D.M. 2003 – Geographical isolation in hot spring cyanobacteria – Environ. Microbiol. 5: 650–659.
• Papke R.T., Ward D.M. 2004 –The importance of physical isolation to microbial diversification – FEMS Microbiol. Ecol. 48: 293–303.
• Pedrós-Alió C. 1989 – Toward an autecology of bacterioplankton (In: Plankton ecology: succession in plankton communities, Ed. U. Sommer) – Brock/Springer series in contemporary bioscience, Berlin, pp. 297–336.
• Pomeroy L.R. 1974 – The ocean´s food web: a changing paradigm – BioScience, 24: 499-504.
• Porter K.G., Pearl H., Hodson R., Pace M., Priscu J., Riemann B., Scavia D., Stockner J. 1988 – Microbial interactions in lake foodwebs (In: Complex interactions in lake communities, Ed. S.R. Carpenter) – Springer, Berlin, pp. 234–255.
• Quispel A. 1998 – Lourens G.M. Baas Becking (1895–1963), inspirator for many
• (micro)biologists – Internatl. Microbiol. 69–72.
• Rainey P. 2004 – Bacterial populations adaptgenetically, by natural selection – even in the lab! – Microbiol. Today, 31: 160–162.
• Rheinheimer G. 1992 – Aquatic Microbiology, 4th edition – Wiley, New York, 363 pp.
• Richards T.A., Vepritskiy A.A., Gouliamova D.E., Nierzwicki-Bauer S.A. 2005 – The molecular diversity of freshwater picoeukaryotes from an oligotrophic lake reveals diverse, distinctive and globally dispersed lineages – Environ. Microbiol. 1413–1425.
• Rigler F.H., Peters R.H. 1995 – Science and limnology – Excellence in Ecology, Book Ecology Institute, Oldendorf/Luhe, 239 pp.
• Rosselló-Mora R., Amann R. 2001 – The species concept for prokaryotes – FEMS Microbiol. Rev. 25: 39–67.
• Ryder O.A. 1986 – Species conservation and systematics: the dilemma of subspecies Trends Ecol. Evol. 1: 9–10.
• Salonen K., Rosenberg M. 2000 – Advantages from diel vertical migration can explain explain the dominance of Goniostomum semen (Raphidophycea) in a small, steeply-stratified humic lake – J. Plankton Res. 22: 1841–1853.
• Schauer M., Hahn M.W. 2005 – Diversity and phylogenetic affiliations of morphologically conspicuous large filamentous bacteria occurring in the pelagic zones of a broad spectrum of freshwater habitats – Appl. Environ. Microbiol. 71: 1931–1940.
• Schauer M., Jing J., Hahn M.W. 2006 – Recurrent seasonal development in abundance and composition of filamentous SOL bacteria (Saprospiraceae, Bacteroidetes) in oligo-mesotrophic Lake Mondsee (Austria) – Appl. Environ. Microbiol. 72: 4704–4712.
• Schlegel M., Meisterfeld R. 2003 – The species problem in protozoa revisited – Europ. J. Protistol. 39: 349–355.
• Šimek K., Kojecká P., Nedoma J., Hartman P., Vrba J., Dolan J.R. 1999 – Shifts in bacterial community composition associated with different microzooplankton size fractions in a eutrophic reservoir – Limnol. Oceanogr. 44: 1634–1644.
• Šimek K., Nedoma J., Pernthaler J., Posch T., Dolan J.R. 2002 – Altering the balance between bacterial production and protistan bacterivory triggers shifts in freshwater bacterial community composition – Antonie van Leeuwenhoek, 81: 453–463.
• Simpson G.G. 1961 – Principles of animal taxonomy – Columbia Univ. Press, New York.
• Snoeyenbos-West O.L.O., Salcedo T., McManus G.B., Katz L.A. 2002 – Insights into the diversity of choreotrich and oligotrich ciliates (Class: Spirotrichea) based on genealogical analyses of multiple loci – Int. J. Syst. Evol. Microbiol. 52: 1901–1913.
• Sommer U. 1988 – Some size relationships in phytoplankton motility – Hydrobiologia, 161: 125–131.
• Sommer U. 1989 – Plankton ecology : succession in plankton communities – Brock/Springer series in contemporary bioscience, Berlin, 369 pp.
• Sommer U., Gliwicz Z.M. 1986 – Long range vertical migration of Volvox in tropical Lake Cahora Bassa (Mozambique) – Limnol. Oceanogr. 31: 650–653.
• Sommer U., Gliwicz Z.M., Lampert W., Duncan A. 1986 – The PEG-model of seasonal succession of planktonic events in fresh waters – Arch. Hydrobiol. 106: 433–471.
• Sonneborn T.M. 1937 – Sex, sex inheritance and sex determination in Paramecium aurelia – Proc. Natl. Acad. Sci. USA, 23: 378–385.
• Sonneborn T.M. 1957 – Breeding systems, reproductive methods, and species problems in protozoa (In: The species problem, Ed. E. Mayr) – American Association for the Advancement of Science, Washington, pp. 155–324.
• Stackebrandt E., Frederiksen W., Garrity G.M., Grimont P.A.D., Kampfer P., Maiden M.C.J., Nesme X., Rossello-Mora R., Swings J., Trüper H.G., Vauterin L., Ward A.C., Whitman W.B. 2002 – Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology – Int. J. Syst. Evol. Microbiol. 52: 1043–1047.
• Stackebrandt E., Goebel B.M. 1994 – Taxonomic note: a place for DNA-DNA reassociations and 16S rRNA sequence analysis in the present species definition in Bacteriology – Int. J. Syst. Bacteriol. 44: 846–849.
• Templeton A.T. 1989 – The meaning of species and speciation: a genetic perspective (In: Speciation and its consequences, Eds: D. Otte, J.A. Endler) – Sunderland, MA, Sinauaer Associates, pp. 3–27.
• Thompson J.R., Pacocha S., Pharino C., Klepac-Ceraj V., Hunt D.E., Benoit J., Sarma-Rupavtarm R., Distel D.L., Polz M.F. 2005 – Genotypic diversity within a coastal bacterioplankton population – Science, 307: 1311–1313.
• Torsvik V., Øvreås L., Thingstad T.F. 2002 – Prokaryotic diversity – magnitude, dynamics, and controlling factors – Science, 296: 1064–1066.
• Turesson G. 1922 – The genotypic response of the plant species to the habitat – Hereditas, 3: 211–350.
• Van der Gucht K., Sabbe K., De Meester L., Vloemans N., Zwart G., Gillis M., Vyverman W. 2001 – Contrasting bacterioplankton community composition and seasonal dynamics in two neighbouring hypertrophic freshwater lakes – Environ. Microbiol. 3: 680–690.
• Van der Gucht K., Vandekerckhove T., Vloemans N., Cousin S., Muylaert K., Sabbe K., Gillis M., Declerck S., De Meester L., Vyverman W. 2005 – Characterization of bacterial communities in four freshwater lakes differing in nutrient load and food web structure – FEMS Microbiol. Ecol. 53: 205–220.
• Vandermere J.H. 1972 – Niche theory – Annu. Rev. Ecol. Syst. 3: 107–132.
• Van Valen L. 1976 – Ecological species, multispecies, and oaks – Taxon, 25: 233–239.
• Walochnik J., Michel R., Aspöck H. 2002 – Discrepancy between morphological and molecular biological characters in a strain of Hartmannella vermiformis Page 1967 (Lobosea, Gymnamoebia) – Protistology, 2: 185–188.
• Waples R.S. 1991 – Pacific salmon, Oncorhynchus spp., and the definition of “species” under the Endangered Species Act – Mar. Fish. Rev. 53: 11–22.
• Wayne L.G., Brenner D.J., Colwell R.R., Grimont P.A.D., Kandler P., Krichevsky M.I., Moore L.H., Murray R.G.E., Stackebrandt E., Starr M.P., Trüper H.G. 1987 – Report of the ad hoc committee on reconciliation of approaches to bacterial systematics – Int. J. Syst. Bacteriol. 37: 463–464.
• Weisse T. 2003 – Pelagic microbes – Protozoa and the microbial food web (In: The lakes handbook, Vol. 1, Eds: P. O’Sullivan, C.S. Reynolds) – Blackwell Science Ltd, Oxford, pp. 417–460.
• Weisse T., Karstens N., Meyer V.C.M., Janke L., Lettner S., Teichgräber K. 2001 – Niche separation in common prostome freshwater ciliates: the effect of food and temperature – Aquat. Microb. Ecol. 26: 167–179.
• Weisse T., Lettner S. 2002 – The ecological significance of intraspecific variation among freshwater ciliates – Verh. Internat. Verein. Limnol. 28: 1880–1884.
• Weisse T., Montagnes D.J.S. 1998 – Effect of temperature on inter-and intraspecific isolates of Urotricha (Prostomatida, Ciliophora) – Aquat. Microb. Ecol. 15: 285–291.
• Weisse T., Rammer S. 2006 – Pronounced ecophysiological clonal differences of two common freshwater ciliates, Coleps spetai (Prostomatida) and Rimostrombidium lacustris (Oligotrichida), challenge the morphospecies concept – J. Plankton Res. 27: 55–63. (http://www. doi:10.1093/plankt/fbi100).
• Weisse T., Stadler P., Lindström E.S., Kimmance S.A., Montagnes D.J.S. 2002 – Interactive effect of temperature and food concentration on growth rate: A test case using the small freshwater ciliate Urotricha farcta – Limnol. Oceanogr. 47: 1447–1455.
• Whitfield J. 2005 – Biogeography: Is everything everywhere? – Science, 310: 960–961.
• Whitaker R.J., Grogan D.W., Taylor J.W. 2003 – Geographic barriers isolate endemic populations of hyperthermophilic Archaea – Science, 5635: 925–926.
• Whittaker R.H. 1970 – Communities and ecosystems – Macmillan, New York, 162 pp.
• Williams P.J. le B. 1981 – Incorporation of microheterotrophic processes into the classical paradigm of the planktonic food web – Kieler Meeresforsch. Sonderh. 1: 1–28.
• Wilson O.E. 1992 – The Diversity of Life – Harvard Univ. Press, Cambridge, MA, 432 pp.
• Wu Q.L., Boenigk J., Hahn M.W. 2004 – Successful predation of filamentous bacteria by a nanoflagellate challenges current models of flagellate bacterivory – Appl. Environ. Microbiol. 70: 332–339.
• Wu Q.L., Hahn M.W. 2006 – Differences in structure and dynamics of Polynucleopbacter communities in a temperate and a subtropical lake, revealed at three phylogenetic levels – FEMS Microbiol. Ecol. 57: 67–79.
• Yannarell A.C., Triplett E.W. 2004 – Within- and between-lake variability in the composition of bacterioplankton communities: Investigations using multiple spatial scales – Appl. Environ. Microbiol. 70: 214–223.
• Zwart G., Crump B.C., Kamst-van-Agterveld M.P., Hagen F., Han S.-K. 2002 – Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers – Aquat. Microb. Ecol. 28: 141–155.
• Zwisler W., Selje N., Simon M. 2003 – Seasonal patterns of the bacterioplankton community composition in a large mesotrophic lake – Aquat. Microb. Ecol. 31: 211–225.