Skip to main content
SpringerLink
Log in

Biodiversity and Microbial Ecosystems Functioning

  • Chapter
  • First Online:
Environmental Microbiology: Fundamentals and Applications

Abstract

All ecosystems are composed of multiple species performing numerous functions. This plurality identified as biodiversity has become a research topic of general importance for understanding how ecosystems function. The word “biodiversity” has subsequently received different interpretations we aim to describe. Microbial systems can be used to illustrate these definitions and to clarify paradigms that have emerged in general ecology. Microbial biodiversity can be characterized by the kind of biodiversity (taxa or functional groups present), the representativeness of samples, and the culturability of samples or taxa, in terms of genetic, functional, or physiological characteristics. Biodiversity is a major driver of ecosystem functioning, and this relation is described in the case of several biotopes. Several mathematical approaches have been used to quantify microbial diversity, and the various indices are described and discussed.

Chapter Coordinator

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 119.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 159.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 159.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Achenbach LA, Carey J, Madigan MT (2001) Photosynthetic and phylogenetic primers for detection of anoxygenic phototrophs in natural environments. Appl Environ Microbiol 67:2922–2926

    CAS  PubMed Central  PubMed  Google Scholar 

  • Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169

    CAS  PubMed Central  PubMed  Google Scholar 

  • Andrews JH, Kinkel LL, Berbee FM, Nordheim EV (1987) Fungi, leaves, and the theory of island biogeography. Microb Ecol 14:277–290

    CAS  PubMed  Google Scholar 

  • Attard E, Poly F, Commeaux C, Laurent F, Terada A, Smets BF, Recous S, Le Roux XL (2010) Shifts between Nitrospira- and Nitrobacter-like nitrite oxidizers underlie the response of soil potential nitrite oxidation to changes in tillage practices. Environ Microbiol 12:315–326

    CAS  PubMed  Google Scholar 

  • Attard E, Recous S, Chabbi A, De Berranger C, Guillaumaud DN, Labreuche J, Philippot L, Schmid B, Le Roux X (2011) Soil environmental conditions rather than denitrifier abundance and diversity drive potential denitrification after changes in land-uses. Global Change Biol 17:1975–1989

    Google Scholar 

  • Barroin G (2003) Gestion des risques. Santé et environnement : le cas des nitrates, Phosphore, azote et prolifération des végétaux aquatiques. Courr Environ 48:13–26

    Google Scholar 

  • Basso O, Lascourreges J-F, Jarry M, Magot M (2005) The effect of cleaning and disinfecting the sampling well on the microbial communities of deep subsurface water samples. Environ Microbiol 7:13–21

    PubMed  Google Scholar 

  • Bauer K, Diez B, Lugomela C, Seppala S, Borg AJ, Bergman B (2008) Variability in benthic diazotrophy and cyanobacterial diversity in a tropical intertidal lagoon. FEMS Microbiol Ecol 63:205–221

    CAS  PubMed  Google Scholar 

  • Bell T, Newman JA, Silverman BW, Turner SL, Lilley AK (2005) The contribution of species richness and composition to bacterial services. Nature 436:1157–1160

    CAS  PubMed  Google Scholar 

  • Bensaadi-Merchermek N, Salvado JC, Cagnon C, Karama S, Mouchès C (1995) Characterization of the unlinked 16s rDNA and 23S-5s rRNA operon of Wolbachia pipientis, a prokaryotic parasite of insect gonads. Gene 165:81–86

    CAS  PubMed  Google Scholar 

  • Bergersen FJ, Hipsley EH (1970) The presence of N2-fixing bacteria in the intestines of man and animals. J Gen Microbiol 60:61–65

    CAS  PubMed  Google Scholar 

  • Bernal-Martinez A, Carrère H, Patureau D, Delgenès JP (2007) Ozone pre-treatment as improver of PAH removal during anaerobic digestion of urban sludge. Chemosphere 68:1013–1019

    CAS  PubMed  Google Scholar 

  • Bertin PN et al (2011) Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta- and proteo-genomics. ISME J 5:1735–1747

    CAS  PubMed Central  PubMed  Google Scholar 

  • Bik EM, Eckburg PB, Gill SR, Nelson KE, Purdom EA, Francois F, Perez-Perez G, Blaser MJ, Relman DA (2006) Molecular analysis of the bacterial microbiota in the human stomach. Proc Natl Acad Sci U S A 103:732–737

    CAS  PubMed Central  PubMed  Google Scholar 

  • Bittner L et al (2013) Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay. Mol Ecol 22:87–101

    CAS  PubMed  Google Scholar 

  • Blanchot J, Rodier M (1996) Picophytoplankton abundance and biomass in the western tropical Pacific Ocean during the 1992 El Nino year: Results from flow cytometry. Deep Sea Res Part I: Oceanogr Res Pap 43:877–895

    Google Scholar 

  • Bordenave S, Goni-Urriza MS, Caumette P, Duran R (2007) Effects of heavy fuel oil on the bacterial community structure of a pristine microbial mat. Appl Environ Microbiol 73:6089–6097

    CAS  PubMed Central  PubMed  Google Scholar 

  • Bossio DA, Scow KM (1998) Impacts of carbon and flooding on soil microbial communities: phospholipid fatty acid profiles and substrate utilization patterns. Microb Ecol 35:265–278

    CAS  PubMed  Google Scholar 

  • Boubakri H, Beuf M, Simonet P, Vogel TM (2006) Development of metagenomic DNA shuffling for the construction of a xenobiotic gene. Gene 375:87–94

    CAS  PubMed  Google Scholar 

  • Bouvier T, del Giorgio PA (2007) Key role of selective viral-induced mortality in determining marine bacterial community composition. Environ Microbiol 9:287–297

    CAS  PubMed  Google Scholar 

  • Boyle SA, Rich JJ, Bottomley PJ, Cromack K, Myrold DD (2006) Reciprocal transfer effects on denitrifying community composition and activity at forest and meadow sites in the Cascade Mountains of Oregon. Soil Biol Biochem 38:870–878

    CAS  Google Scholar 

  • Braun J, Wei B (2007) Body traffic: ecology, genetics, and immunity in inflammatory bowel disease. Annu Rev Pathol 2:401–429

    CAS  PubMed  Google Scholar 

  • Briand E, Escoffier N, Straub C, Sabart M, Quiblier C, Humbert JF (2008) Spatiotemporal changes in the genetic diversity of a bloom-forming Microcystis aeruginosa (cyanobacteria) population. ISME J 3:419–429

    PubMed  Google Scholar 

  • Brown R, Price RJ, King MG, Husband AJ (1988) Autochthonous intestinal bacteria and coprophagy: a possible contribution to the ontogeny and rhythmicity of slow wave sleep in mammals. Med Hypotheses 26:171–175

    CAS  PubMed  Google Scholar 

  • Bruneel O, Duran R, Casiot C, Elbaz-Poulichet F, Personne JC (2006) Diversity of microorganisms in Fe-As-rich acid mine drainage waters of Carnoules, France. Appl Environ Microbiol 72:551–556

    CAS  PubMed Central  PubMed  Google Scholar 

  • Buckley DH, Huangyutitham V, Hsu SF, Nelson TA (2007) Stable isotope probing with 15N2 reveals novel noncultivated diazotrophs in soil. Appl Environ Microbiol 73:3196–3204

    CAS  PubMed Central  PubMed  Google Scholar 

  • Buee M, Reich M, Murat C, Morin E, Nilsson RH, Uroz S, Martin F (2009) 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol 184:449–456

    CAS  PubMed  Google Scholar 

  • Cavigelli MA, Robertson GP (2000) The functional significance of denitrifier community composition in a terrestrial ecosystem. Ecology 81:1402–1414

    Google Scholar 

  • Cebron A, Bodrossy L, Stralis-Pavese N, Singer AC, Thompson IP, Prosser JI, Murrell JC (2007) Nutrient amendments in soil DNA stable isotope probing experiments reduce the observed methanotroph diversity. Appl Environ Microbiol 73:798–807

    CAS  PubMed Central  PubMed  Google Scholar 

  • Coburn SP, Mahuren JD, Wostmann BS, Snyder DL, Townsend DW (1989) Role of intestinal microflora in the metabolism of vitamin B-6 and 4′-deoxypyridoxine examined using germfree guinea pigs and rats. J Nutr 119:181–188

    CAS  PubMed  Google Scholar 

  • Colwell RK, Mao CX, Chang J (2004) Interpolating, extrapolating, and comparing incidence-based species accumulation curves. Ecology 85:2717–2727

    Google Scholar 

  • Coyne MS, Arunakumari A, Averill BA, Tiedje JM (1989) Immunological identification and distribution of dissimilatory heme cd1 and nonheme copper nitrite reductases in denitrifying bacteria. Appl Environ Microbiol 55:2924–2931

    CAS  PubMed Central  PubMed  Google Scholar 

  • Daly K, Sharp RJ, McCarthy AJ (2000) Development of oligonucleotide probes and PCR primers for detecting phylogenetic subgroups of sulfate-reducing bacteria. Microbiology 146:1693–1705

    CAS  PubMed  Google Scholar 

  • Delwiche CF, Palmer JD (1996) Rampant horizontal transfer and duplication of rubisco genes in eubacteria and plastids. Mol Biol Evol 13:873–882

    CAS  PubMed  Google Scholar 

  • Edwards KJ, Bach W, Rogers DR (2003) Geomicrobiology of the ocean crust: a role for chemoautotrophic Fe-bacteria. Biol Bull 204:180–185

    CAS  PubMed  Google Scholar 

  • Eiland F, Klamer M, Lind AM, Leth M, Baath E (2001) Influence of initial c/n ratio on chemical and microbial composition during long term composting of straw. Microb Ecol 41:272–280

    CAS  PubMed  Google Scholar 

  • Enwall K, Philippot L, Hallin S (2005) Activity and composition of the denitrifying bacterial community respond differently to long-term fertilization. Appl Environ Microbiol 71:8335–8343

    CAS  PubMed Central  PubMed  Google Scholar 

  • Fang J, Chan O, Kato C, Sato T, Peeples T, Niggemeyer K (2003) Phospholipid FA of piezophilic bacteria from the deep sea. Lipids 38:885–887

    CAS  PubMed  Google Scholar 

  • Febria CM, Beddoes P, Fulthorpe RR, Williams DD (2012) Bacterial community dynamics in the hyporheic zone of an intermittent stream. ISME J 6:1078–1088

    CAS  PubMed Central  PubMed  Google Scholar 

  • Fernandez A, Huang S, Seston S, Xing J, Hickey R, Criddle C, Tiedje J (1999) How stable is stable? Function versus community composition. Appl Environ Microbiol 65:3697–3704

    CAS  PubMed Central  PubMed  Google Scholar 

  • Fierer N, Hamady M, Lauber CL, Knight R (2008) The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci U S A 105:17994–17999

    CAS  PubMed Central  PubMed  Google Scholar 

  • Fisher MM, Triplett EW (1999) Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 65:4630–4636

    CAS  PubMed Central  PubMed  Google Scholar 

  • Floyd R, Eyualem A, Papert A, Blaxter ML (2002) Molecular barcodes for soil nematode identification. Mol Ecol 11:839–850

    CAS  PubMed  Google Scholar 

  • Forbes GM, Glaser ME, Cullen DJ, Warren JR, Christiansen KJ, Marshall BJ, Collins BJ (1994) Duodenal ulcer treated with Helicobacter pylori eradication: seven-year follow-up. Lancet 343:258–260

    CAS  PubMed  Google Scholar 

  • Fourcans A et al (2004) Characterization of functional bacterial groups in a hypersaline microbial mat community (Salins-de-Giraud, Camargue, France). FEMS Microbiol Ecol 51:55–70

    CAS  PubMed  Google Scholar 

  • Fourcans A, Solé A, Diestra E, Ranchou-Peyruse A, Esteve I, Caumette P, Duran R (2006) Vertical migration of phototrophic bacterial populations in a hypersaline microbial mat from Salins-de-Giraud (Camargue, France). FEMS Microbiol Ecol 57:367–377

    CAS  PubMed  Google Scholar 

  • Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR (2007) Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A 104:13780–13785

    CAS  PubMed Central  PubMed  Google Scholar 

  • Frostegard A, Tunlid A, Baath E (2011) Use and misuse of PLFA measurements in soils. Soil Biol Biochem 43:1621–1625

    CAS  Google Scholar 

  • Gamo M, Shoji T (1999) A method of profiling microbial communities based on a most-probable-number assay that uses BIOLOG plates and multiple sole carbon sources. Appl Environ Microbiol 65:4419–4424

    CAS  PubMed Central  PubMed  Google Scholar 

  • Gans J, Wolinsky M, Dunbar J (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309:1387–1390

    CAS  PubMed  Google Scholar 

  • Gao Z, Tseng CH, Pei Z, Blaser MJ (2007) Molecular analysis of human forearm superficial skin bacterial biota. Proc Natl Acad Sci U S A 104:2927–2932

    CAS  PubMed Central  PubMed  Google Scholar 

  • Garland JL, Mills AL (1991) Classification and characterization of heterotrophic microbial communities on the basis of patterns of community level sole-carbon-source utilization. Appl Environ Microbiol 57:2351–2359

    CAS  PubMed Central  PubMed  Google Scholar 

  • Gast WRJ, Scott DW, Schmitt C et al (1991) Blue Mountains forest health report—new perspectives in forest health. U. S. Department of Agriculture, Forest Service, Pacific Northwest Region, Portland, p 182

    Google Scholar 

  • Grice EA et al (2008) A diversity profile of the human skin microbiota. Genome Res 18:1043–1050

    CAS  PubMed Central  PubMed  Google Scholar 

  • Griffiths BS et al (2001) An examination of the biodiversity-ecosystem function relationship in arable soil microbial communities. Soil Biol Biochem 33:1713–1722

    CAS  Google Scholar 

  • Guermazi S et al (2008) Discovery and characterization of a new bacterial candidate division by an anaerobic sludge digester metagenomic approach. Environ Microbiol 10:2111–2123

    CAS  PubMed Central  PubMed  Google Scholar 

  • Haack SK, Garchow H, Klug MJ, Forney LJ (1995) Analysis of factors affecting the accuracy, reproducibility, and interpretation of microbial community carbon source utilization patterns. Appl Environ Microbiol 61:1458–1468

    CAS  PubMed Central  PubMed  Google Scholar 

  • Haegeman B, Vanpeteghem D, Godon J-J, Hamelin J (2008) DNA reassociation kinetics and diversity indices: richness is not rich enough. Oikos 117:177–181

    Google Scholar 

  • Hayashi H, Sakamoto M, Benno Y (2002) Fecal microbial diversity in a strict vegetarian as determined by molecular analysis and cultivation. Microbiol Immunol 46:819–831

    CAS  PubMed  Google Scholar 

  • Hayashi H, Sakamoto M, Kitahara M, Benno Y (2003) Molecular analysis of fecal microbiota in elderly individuals using 16S rDNA library and T-RFLP. Microbiol Immunol 47:557–570

    CAS  PubMed  Google Scholar 

  • Herrera A, Héry M, Stach JEM, Jaffré T, Normand P, Navarro E (2007) Species richness and phylogenetic diversity comparisons of soil microbial communities affected by nickel-mining and revegetation efforts in New Caledonia. Eur J Soil Biol 43:130–139

    CAS  Google Scholar 

  • Hery M, Herrera A, Vogel TM, Normand P, Navarro E (2005) Effect of carbon and nitrogen input on the bacterial community structure of Neocaledonian nickel mine spoils. FEMS Microbiol Ecol 51:333–340

    CAS  PubMed  Google Scholar 

  • Hewson I, Jacobson Meyers ME, Fuhrman JA (2007) Diversity and biogeography of bacterial assemblages in surface sediments across the San Pedro Basin, Southern California Borderlands. Environ Microbiol 9:923–933

    CAS  PubMed  Google Scholar 

  • Hoffmann KH, Rodriguez-Brito B, Breitbart M, Bangor D, Angly F, Felts B, Nulton J, Rohwer F, Salamon P (2007) Power law rank-abundance models for marine phage communities. FEMS Microbiol Lett 273:224–228

    CAS  PubMed  Google Scholar 

  • Honerlage W, Hahn D, Zepp K, Zeyer J, Normand P (1994) A hypervariable region provides a discriminative target for specific characterization of uncultured and cultured Frankia. Syst Appl Microbiol 17:433–443

    Google Scholar 

  • Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO (2002) A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417:63–67

    CAS  PubMed  Google Scholar 

  • Jardillier L, Boucher D, Personnic S, Jacquet S, Thenot A, Sargos D, Amblard C, Debroas D (2005) Relative importance of nutrients and mortality factors on prokaryotic community composition in two lakes of different trophic status: microcosm experiments. FEMS Microbiol Ecol 53:429–443

    CAS  PubMed  Google Scholar 

  • Jenkins GJ, Burlinson B, Parry JM (2000) The polymerase inhibition assay: a methodology for the identification of DNA-damaging agents. Mol Carcinog 27:289–297

    CAS  PubMed  Google Scholar 

  • Jessup CM, Kassen R, Forde SE, Kerr B, Buckling A, Rainey PB, Bohannan BJ (2004) Big questions, small worlds: microbial model systems in ecology. Trends Ecol Evol 19:189–197

    PubMed  Google Scholar 

  • Jimenez E, Delgado S, Fernandez L, Garcia N, Albujar M, Gomez A, Rodriguez JM (2008) Assessment of the bacterial diversity of human colostrum and screening of staphylococcal and enterococcal populations for potential virulence factors. Res Microbiol 159:595–601

    PubMed  Google Scholar 

  • Juan-García A, Manyes L, Ruiz MJ, Font G (2013) Applications of flow cytometry to toxicological mycotoxin effects in cultured mammalian cells: a review. Food Chem Toxicol 56:40–59

    PubMed  Google Scholar 

  • Kazanov MD, Vitreschak AG, Gelfand MS (2007) Abundance and functional diversity of riboswitches in microbial communities. BMC Genomics 8:347

    PubMed Central  PubMed  Google Scholar 

  • Khelifi E, Bouallagui H, Touhami Y, Godon JJ, Hamdi M (2009) Bacterial monitoring by molecular tools of a continuous stirred tank reactor treating textile wastewater. Bioresour Technol 100:629–633

    CAS  PubMed  Google Scholar 

  • Kimura H, Sugihara M, Yamamoto H, Patel BK, Kato K, Hanada S (2005) Microbial community in a geothermal aquifer associated with the subsurface of the Great Artesian Basin, Australia. Extremophiles 9:407–414

    CAS  PubMed  Google Scholar 

  • Kinkel LL, Andrews JH, Berbee FM, Nordheim EV (1987a) Leaves as islands for microbes. Oecologia 71:405–408

    Google Scholar 

  • Kinkel LL, Andrews JH, Nordheim EV (1987b) Microbial introduction to apple leaves: influences of altered immigration on fungal community dynamics. Microb Ecol 18:161–173

    Google Scholar 

  • Kinkel LL, Andrews JH, Nordheim EV (1989) Fungal immigration dynamics and community development on apple leaves. Microb Ecol 18:45–58

    CAS  PubMed  Google Scholar 

  • Kowalchuk GA, Stephen JR, De Boer W, Prosser JI, Embley TM, Woldendorp JW (1997) Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments. Appl Environ Microbiol 63:1489–1497

    CAS  PubMed Central  PubMed  Google Scholar 

  • Kruskal JB, Wish M (1978) Multidimensional scaling. Sage University Series, Beverly Hills

    Google Scholar 

  • Kyselkova M, Kopecký J, Frapolli M, Défago G, Ságová-Marecková M, Grundmann GL, Moënne-Loccoz Y (2009) Comparison of rhizobacterial community composition in soil suppressive or conducive to tobacco black root rot disease. ISME J 3:1127–1138

    PubMed  Google Scholar 

  • Lavire C, Normand P, Alekhina I, Bulat S, Prieur D, Birrien J-L, Fournier P, Hänni C, Petit J-R (2006) Presence of Hydrogenophilus thermoluteolus DNA in accretion ice in the subglacial Lake Vostok, Antarctica, assessed using rrs, cbb and hox. Environ Microbiol 8:2106–2114

    CAS  PubMed  Google Scholar 

  • Lawrence D, Schoenike R, Quispel A, Bond G (1967) The role of Dryas drummondii in vegetation development following ice recession at Glacier Bay, Alaska, with special reference to its nitrogen fixation by root nodules. J Ecol 55:793–813

    Google Scholar 

  • Le Roux X, Philippot L, Degrange V, Poly F, Wertz S (2006) Relations entre biodiversité et fonctionnement chez les communautés microbiennes. Biofutur 268:50–53

    Google Scholar 

  • Le Roux X et al (2013) Soil environmental conditions and microbial build-up mediate the effect of plant diversity on soil nitrifying and denitrifying enzyme activities in temperate grasslands. PLoS One 8:e61069. doi:10.1371/journal.pone.0061069

    PubMed Central  PubMed  Google Scholar 

  • Leclerc M, Delgenes JP, Godon JJ (2004) Diversity of the archaeal community in 44 anaerobic digesters as determined by single strand conformation polymorphism analysis and 16S rDNA sequencing. Environ Microbiol 6:809–819

    CAS  PubMed  Google Scholar 

  • Lee HR, Pimentel M (2006) Bacteria and irritable bowel syndrome: the evidence for small intestinal bacterial overgrowth. Curr Gastroenterol Rep 8:305–311

    PubMed  Google Scholar 

  • Lemarchand K, Lebaron P (2003) Occurrence of Salmonella spp and Cryptosporidium spp in a French coastal watershed: relationship with fecal indicators. FEMS Microbiol Lett 218:203–209

    CAS  PubMed  Google Scholar 

  • Lichter J (1998) Primary succession and forest development on coastal Lake Michigan dunes. Ecol Monogr 68:487–510

    Google Scholar 

  • Loreau M et al (2001) Biodiversity and ecosystem functioning: current knowledge and future challenges. Science 294:804–808

    CAS  PubMed  Google Scholar 

  • Lundberg DS et al (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488:86–90

    CAS  PubMed Central  PubMed  Google Scholar 

  • MacArthur RH, Wilson EO (1963) An equilibrium theory of insular zoogeography. Evolution 17:373–387

    Google Scholar 

  • Mahaffee WF, Kloepper JW (1997) Bacterial communities of the rhizosphere and endorhiza associated with fieldgrown cucumber plants inoculated with a plant growth-promoting rhizobacterium or its genetically modified derivative. Can J Microbiol 43:344–353

    CAS  PubMed  Google Scholar 

  • Martin R, Heilig HG, Zoetendal EG, Jimenez E, Fernandez L, Smidt H, Rodriguez JM (2007) Cultivation-independent assessment of the bacterial diversity of breast milk among healthy women. Res Microbiol 158:31–37

    PubMed  Google Scholar 

  • Matsui K, Jun MS, Ueki M, Kawabata Z (2001) Functional succession of bacterioplankton on the basis of carbon source utilization ability by BIOLOG plates. Ecol Res 16:905–912

    CAS  Google Scholar 

  • Mazzella N, Molinet J, Syakti AD, Barriol A, Dodi A, Bertrand J-C, Doumenq P (2005) Effects of pure n-alkanes and crude oil on bacterial phospholipid classes and molecular species determined by electrospray ionization mass spectrometry. J Chromatogr B 822:40–53

    CAS  Google Scholar 

  • McCann KS (2000) The diversity-stability debate. Nature 405:228–233

    CAS  PubMed  Google Scholar 

  • Meyer B, Kuever J (2007) Molecular analysis of the diversity of sulfate-reducing and sulfur-oxidizing prokaryotes in the environment, using aprA as functional marker gene. Appl Environ Microbiol 73:7664–7679

    CAS  PubMed Central  PubMed  Google Scholar 

  • Mitchell CE, Tillman D, Groth JV (2002) Effects of grassland species diversity, abundance and composition on foliar fungal disease. Ecology 83:1713–1726

    Google Scholar 

  • Monier A, Claverie JM, Ogata H (2008) Taxonomic distribution of large DNA viruses in the sea. Genome Biol 9:R106

    PubMed Central  PubMed  Google Scholar 

  • Moreira D, Lopez-Garcia P (2002) The molecular ecology of microbial eukaryotes unveils a hidden world. Trends Microbiol 10:31–38

    CAS  PubMed  Google Scholar 

  • Morris CE et al (2002) Microbial biodiversity: approaches to experimental design and hypothesis testing in primary scientific literature from 1975 to 1999. Microbiol Mol Biol Rev 66:592–616

    PubMed Central  PubMed  Google Scholar 

  • Mosoni P, Chaucheyras-Durand F, Bera-Maillet C, Forano E (2007) Quantification by real-time PCR of cellulolytic bacteria in the rumen of sheep after supplementation of a forage diet with readily fermentable carbohydrates: effect of a yeast additive. J Appl Microbiol 103:2676–2685

    CAS  PubMed  Google Scholar 

  • Muller AK, Westergaard K, Christensen S, Sorensen SJ (2002) The diversity and function of soil microbial communities exposed to different disturbances. Microb Ecol 44:49–58

    CAS  PubMed  Google Scholar 

  • Muyzer G, Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek 73:127–141

    CAS  PubMed  Google Scholar 

  • Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700

    CAS  PubMed Central  PubMed  Google Scholar 

  • Naeem S (2002) Ecosystem consequences of biodiversity loss : the evolution of a paradigm. Ecology 83:1537–1552

    Google Scholar 

  • Nanba K, King GM, Dunfield K (2004) Analysis of facultative lithotroph distribution and diversity on volcanic deposits by use of the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase. Appl Environ Microbiol 70:2245–2253

    CAS  PubMed Central  PubMed  Google Scholar 

  • Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci U S A 70:3321–3323

    CAS  PubMed Central  PubMed  Google Scholar 

  • Nishiyama M, Horinouchi S, Kobayashi M, Nagasawa T, Yamada H, Beppu T (1991) Cloning and characterization of genes responsible for metabolism of nitrile compounds from Pseudomonas chlororaphis B23. J Bacteriol 173:2465–2472

    CAS  PubMed Central  PubMed  Google Scholar 

  • Nocker A, Sossa-Fernandez P, Burr MD, Camper AK (2007) Use of propidium monoazide for live/dead distinction in microbial ecology. Appl Environ Microbiol 73:5111–5117

    CAS  PubMed Central  PubMed  Google Scholar 

  • Nomura T et al (2005) Mucosa-associated bacteria in ulcerative colitis before and after antibiotic combination therapy. Aliment Pharmacol Ther 21:1017–1027

    CAS  PubMed  Google Scholar 

  • Normand P, Bousquet J (1989) Phylogeny of nitrogenase sequences in Frankia and other nitrogen-fixing microorganisms. J Mol Evol 29:436–447

    CAS  PubMed  Google Scholar 

  • Normand P, Ponsonnet C, Nesme X, Neyra M, Simonet P (1996) ITS analysis of prokaryotes. In: Akkermans ADL, van Elsas JD, De Bruijn FJ (eds) Molecular microbial ecology manual. Kluwer Academic Publishers, Dordrecht, pp 1–12

    Google Scholar 

  • Nubel U, Garcia-Pichel F, Kuhl M, Muyzer G (1999) Quantifying microbial diversity: morphotypes, 16S rRNA genes, and carotenoids of oxygenic phototrophs in microbial mats. Appl Environ Microbiol 65:422–430

    CAS  PubMed Central  PubMed  Google Scholar 

  • O’Keefe SJ, Chung D, Mahmoud N, Sepulveda AR, Manafe M, Arch J, Adada H, van der Merwe T (2007) Why do African Americans get more colon cancer than Native Africans? J Nutr 137:175S–182S

    PubMed  Google Scholar 

  • Parkes RJ et al (2005) Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 436:390–394

    CAS  PubMed  Google Scholar 

  • Patra AK et al (2006) Effects of management regime and plant species on the enzyme activity and genetic structure of N-fixing, denitrifying and nitrifying bacterial communities in grassland soils. Environ Microbiol 8:1005–1016

    CAS  PubMed  Google Scholar 

  • Patra AK, Le Roux X, Abbadie L, Clays-Josserand A, Poly F, Loiseau P, Louault F (2007) Effect of microbial activity and nitrogen mineralization on free-living nitrogen fixation in permanent grassland soils. J Agron Crop Sci 193:153–156

    CAS  Google Scholar 

  • Paul JH, Cazares L, Thurmond J (1990) Amplification of the rbcL gene from dissolved and particulate DNA from aquatic environments. Appl Environ Microbiol 56:1963–1966

    CAS  PubMed Central  PubMed  Google Scholar 

  • Pelissier R, Couteron P, Dray S, Sabatier D (2003) Consistency between ordination techniques and diversity measurements: two strategies for species occurrence data. Ecology 84:242–251

    Google Scholar 

  • Philippot L (2002) Denitrifying genes in bacterial and archaeal genomes. Biochim Biophys Acta 1577:355–376

    CAS  PubMed  Google Scholar 

  • Philippot L, Hallin S, Schloter M (2007) Ecology of denitrifying prokaryotes in agricultural soil. Adv Agron 96:249–305

    CAS  Google Scholar 

  • Picard C, Ponsonnet C, Paget E, Nesme X, Simonet P (1992) Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Appl Environ Microbiol 58:2717–2722

    CAS  PubMed Central  PubMed  Google Scholar 

  • Pointing SB, Warren-Rhodes KA, Lacap DC, Rhodes KL, McKay CP (2007) Hypolithic community shifts occur as a result of liquid water availability along environmental gradients in China’s hot and cold hyperarid deserts. Environ Microbiol 9:414–424

    CAS  PubMed  Google Scholar 

  • Poly F, Ranjard L, Nazaret S, Gourbiere F, Monrozier LJ (2001) Comparison of nifH gene pools in soils and soil microenvironments with contrasting properties. Appl Environ Microbiol 67:2255–2262

    CAS  PubMed Central  PubMed  Google Scholar 

  • Potrikus CJ, Breznak JA (1977) Nitrogen-fixing Enterobacter agglomerans isolated from guts of wood-eating termites. Appl Environ Microbiol 33:392–399

    CAS  PubMed Central  PubMed  Google Scholar 

  • Precigou S, Goulas P, Duran R (2001) Rapid and specific identification of nitrile hydratase (NHase) encoding genes in soil samples by polymerase chain reaction. FEMS Microbiol Lett 204:155–161

    CAS  PubMed  Google Scholar 

  • Radajewski S, Ineson P, Parekh NR, Murrell JC (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403:646–649

    CAS  PubMed  Google Scholar 

  • Ramette A, Tiedje JM (2007) Biogeography: an emerging cornerstone for understanding prokaryotic diversity, ecology, and evolution. Microb Ecol 53:197–207

    PubMed  Google Scholar 

  • Ranjard L, Brothier E, Nazaret S (2000) Sequencing bands of ribosomal intergenic spacer analysis fingerprints for characterization and microscale distribution of soil bacterium populations responding to mercury spiking. Appl Environ Microbiol 66:5334–5339

    CAS  PubMed Central  PubMed  Google Scholar 

  • Ratcliff AW, Busse MD, Shestak CJ (2006) Changes in microbial community structure following herbicide (glyphosate) additions to forest soils. Appl Soil Ecol 34:114–124

    Google Scholar 

  • Rényi A (1961) On measures of entropy and information. In: Neyman GE (ed) Proceedings of the fourth Berkeley symposium on mathematical statistics and probability. University of California Press, Berkeley, pp 547–561

    Google Scholar 

  • Ritchie NJ, Schutter ME, Dick RP, Myrold DD (2000) Use of length heterogeneity PCR and fatty acid methyl ester profiles to characterize microbial communities in soil. Appl Environ Microbiol 66:1668–1675

    CAS  PubMed Central  PubMed  Google Scholar 

  • Roller C, Ludwig W, Schleifer KH (1992) Gram-positive bacteria with a high DNA G + C content are characterized by a common insertion within their 23S rRNA genes. J Gen Microbiol 138:1167–1175

    CAS  PubMed  Google Scholar 

  • Roscher C, Schumacher J, Weisser WW, Schmid B, Schulze ED (2007) Detecting the role of individual species for overyielding in experimental grassland communities composed of potentially dominant species. Oecologia 154:535–549

    PubMed  Google Scholar 

  • Saikaly PE, Stroot PG, Oerther DB (2005) Use of 16S rRNA gene terminal restriction fragment analysis to assess the impact of solids retention time on the bacterial diversity of activated sludge. Appl Environ Microbiol 71:5814–5822

    CAS  PubMed Central  PubMed  Google Scholar 

  • Salles JF, Poly F, Schmid B, Le Roux X (2009) Community niche predicts the functioning of denitrifying bacterial assemblages. Ecology 90:3324–3332

    PubMed  Google Scholar 

  • Salles JF, Le Roux X, Poly F (2012) Relating phylogenetic and functional diversity among denitrifiers and quantifying their capacity to predict community functioning. Front Microbiol 3:0209

    CAS  Google Scholar 

  • Sapp M, Wichels A, Gerdts G (2007) Impacts of cultivation of marine diatoms on the associated bacterial community. Appl Environ Microbiol 73:3117–3120

    CAS  PubMed Central  PubMed  Google Scholar 

  • Schrenk MO, Kelley DS, Delaney JR, Baross JA (2003) Incidence and diversity of microorganisms within the walls of an active deep-sea sulfide chimney. Appl Environ Microbiol 69:3580–3592

    CAS  PubMed Central  PubMed  Google Scholar 

  • Selesi D, Schmid M, Hartmann A (2005) Diversity of green-like and red-like ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes (cbbL) in differently managed agricultural soils. Appl Environ Microbiol 71:175–184

    CAS  PubMed Central  PubMed  Google Scholar 

  • Shannon CE (1948) A mathematical theory of communication. Bell Syst Tech J 27:379–423

    Google Scholar 

  • Sheffield VC, Cox DR, Lerman LS, Myers RM (1989) Attachment of a 40-base-pair G + C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes. Proc Natl Acad Sci U S A 86:232–236

    CAS  PubMed Central  PubMed  Google Scholar 

  • Singleton DR, Furlong MA, Rathbun SL, Whitman WB (2001) Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl Environ Microbiol 67:4374–4376

    CAS  PubMed Central  PubMed  Google Scholar 

  • Sneath PHA (2005) Numerical taxonomy. In: Garrity GM (ed) Systematic bacteriology. Springer, East Lansing, pp 39–42

    Google Scholar 

  • Spear GT, Sikaroodi M, Zariffard MR, Landay AL, French AL, Gillevet PM (2008) Comparison of the diversity of the vaginal microbiota in HIV-infected and HIV-uninfected women with or without bacterial vaginosis. J Infect Dis 198:1131–1140

    PubMed Central  PubMed  Google Scholar 

  • Stach JE, Maldonado LA, Ward AC, Goodfellow M, Bull AT (2003) New primers for the class Actinobacteria: application to marine and terrestrial environments. Environ Microbiol 5:828–841

    CAS  PubMed  Google Scholar 

  • Takacs D (1996) The idea of biodiversity: philosophies of paradise. The Johns Hopkins University Press, Baltimore, 393 p

    Google Scholar 

  • Tang JC, Shibata A, Zhou Q, Katayama A (2007) Effect of temperature on reaction rate and microbial community in composting of cattle manure with rice straw. J Biosci Bioeng 104:321–328

    CAS  PubMed  Google Scholar 

  • Tasse L et al (2010) Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res 20:1605–1612

    CAS  PubMed Central  PubMed  Google Scholar 

  • Taylor D, Daulby A, Grimshaw S, James G, Mercer J, Vaziri S (2003) Characterization of the microflora of the human axilla. Int J Cosmet Sci 25:137–145

    CAS  PubMed  Google Scholar 

  • Torrallardona D, Harris CI, Fuller MF (1996) Microbial amino acid synthesis and utilization in rats: the role of coprophagy. Br J Nutr 76:701–709

    CAS  PubMed  Google Scholar 

  • Torsvik V, Salte K, Sorheim R, Goksoyr J (1990) Comparison of phenotypic diversity and DNA heterogeneity in a population of soil bacteria. Appl Environ Microbiol 56:776–781

    CAS  PubMed Central  PubMed  Google Scholar 

  • Torsvik V, Ovreas L, Thingstad TF (2002) Prokaryotic diversity-magnitude, dynamics, and controlling factors. Science 296:1064–1066

    CAS  PubMed  Google Scholar 

  • van der Heijden MGA, Klinomoros JN, Ursic M, Moutoglis P, Streitwolf-Engel R, Boller T, Wiemken A, Sanders IR (1998) Mycorrhizal fungal diversity determines plant biodiversity, ecosystem variability and productivity. Nature 396:69–71

    Google Scholar 

  • Vaulot D, Eikrem W, Viprey M, Moreau H (2008) The diversity of small eukaryotic phytoplankton (<or =3 microm) in marine ecosystems. FEMS Microbiol Rev 32:795–820

    CAS  PubMed  Google Scholar 

  • Venter JC et al (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74

    CAS  PubMed  Google Scholar 

  • Villanueva L, Navarrete A, Urmeneta J, White DC, Guerrero R (2007) Analysis of diurnal and vertical microbial diversity of a hypersaline microbial mat. Arch Microbiol 188:137–146

    CAS  PubMed  Google Scholar 

  • Villenave C, Saj S, Attard E, Klumpp K, Le Roux X (2011) Grassland management history affects the response of the nematode community to changes in above-ground grazing regime. Nematology 13:995–1008

    Google Scholar 

  • Vincent WF, Mueller DR, Bonilla S (2004) Ecosystems on ice: the microbial ecology of Markham Ice Shelf in the high Arctic. Cryobiology 48:103–112

    PubMed  Google Scholar 

  • Vitousek P, Walker L, Whiteaker L, Mueller-Dombois D, Matson P (1987) Biological invasion by Myrica faya alters ecosystem development in Hawaii. Science 238:802–804

    CAS  PubMed  Google Scholar 

  • Vogel TM et al (2009) TerraGenome: a consortium for the sequencing of a soil metagenome. Nat Rev Microbiol 7:252. doi:10.1038/nrmicro2119

    CAS  Google Scholar 

  • Wagner M, Roger A, Flax JL, Brusseau GA, Stahl DA (1998) Phylogeny of dissimilatory reductase supports an early origin of sulphate respiration. J Bacteriol 180:2975–2982

    CAS  PubMed Central  PubMed  Google Scholar 

  • Watson R, Blackwell B (2000) Purification and characterization of a common soil component which inhibits the polymerase chain reaction. Can J Microbiol 46:633–642

    CAS  PubMed  Google Scholar 

  • Watson GM, Tabita FR (1997) Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: a molecule for phylogenetic and enzymological investigation. FEMS Microbiol Lett 146:13–22

    CAS  PubMed  Google Scholar 

  • Webster G, Embley TM, Freitag TE, Smith Z, Prosser JI (2005) Links between ammonia oxidizer species composition, functional diversity and nitrification kinetics in grassland soils. Environ Microbiol 7:676–684

    CAS  PubMed  Google Scholar 

  • Wertz S, Degrange V, Prosser JI, Poly F, Commeaux C, Guillaumaud N, Le Roux X (2007) Decline of soil microbial diversity does not influence the resistance and resilience of key soil microbial functional groups following a model disturbance. Environ Microbiol 9:2211–2219

    PubMed  Google Scholar 

  • Wertz S, Poly F, Le Roux X, Degrange V (2008) Development and application of a PCR-denaturing gradient gel electrophoresis tool to study the diversity of Nitrobacter-like nxrA sequences in soil. FEMS Microbiol Ecol 63:261–271

    CAS  PubMed  Google Scholar 

  • Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A 95:6578–6583

    CAS  PubMed Central  PubMed  Google Scholar 

  • Whittaker RH (1972) Evolution and measurement of species diversity. Taxon 21:213–251

    Google Scholar 

  • Widmer F, Rasche F, Hartmann M, Fliessbach A (2006) Community structures and substrate utilization of bacteria in soils from organic and conventional farming systems of the DOK long-term field experiment. Appl Soil Ecol 33:294–307

    Google Scholar 

  • Wilcox BA (1984) In situ conservation of genetic resources: determinants of minimum area requirements. In: McNeely JA, Miller KR (eds) National parks, conservation and development: the role of protected areas in sustaining society. Smithsonian Institution Press, Washington, DC, pp 639–647

    Google Scholar 

  • Willerslev E, Hansen AJ, Rønn R, Brand TB, Wiuf C, Barnes I, Gilichinsky DA, Mitchell D, Cooper A (2004) Long-term persistence of bacterial DNA. Curr Biol 14:R9–R10

    CAS  PubMed  Google Scholar 

  • Williamson SJ et al (2008) The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples. PLoS One 3:e1456

    PubMed Central  PubMed  Google Scholar 

  • Wilson EO (1988) Biodiversity. National Academy Press, Washington, DC

    Google Scholar 

  • Wirth T, Wang X, Linz B, Novick RP, Lum JK, Blaser M, Morelli G, Falush D, Achtman M (2004) Distinguishing human ethnic groups by means of sequences from Helicobacter pylori: lessons from Ladakh. Proc Natl Acad Sci U S A 101:4746–4751

    CAS  PubMed Central  PubMed  Google Scholar 

  • Yelenik S, Perakis S, Hibbs D (2013) Regional constraints to biological nitrogen fixation in post-fire forest communities. Ecology 94:739–750

    PubMed  Google Scholar 

  • Yepremian C, Gugger MF, Briand E, Catherine A, Berger C, Quiblier C, Bernard C (2007) Microcystin ecotypes in a perennial Planktothrix agardhii bloom. Water Res 41:4446–4456

    CAS  PubMed  Google Scholar 

  • Zani S, Mellon MT, Collier JL, Zehr JP (2000) Expression of nifH genes in natural microbial assemblages in Lake George, New York, detected by reverse transcriptase PCR. Appl Environ Microbiol 66:3119–3124

    CAS  PubMed Central  PubMed  Google Scholar 

  • Zehr JP, McReynolds LA (1989) Use of degenerate oligonucleotides for amplification of the nifH gene from the marine cyanobacterium Trichodesmium thiebautii. Appl Environ Microbiol 55:2522–2526

    CAS  PubMed Central  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Microbial Ecology Center, UMR CNRS 5557 / USC INRA 1364, Université Lyon 1, 69622, Villeurbanne, France

    Philippe Normand & Xavier Le Roux

  2. Institut des Sciences Analytiques et de Physico-chimie pour l’Environnement et les Matériaux (IPREM), UMR CNRS 5254, Université de Pau et des Pays de l’Adour, B.P. 1155, 64013, Pau Cedex, France

    Robert Duran

  3. Unité de Recherches de Pathologie Végétale, INRA, Domaine St-Maurice, BP 94, 84143, Montfavet Cedex, France

    Cindy Morris

  4. Institut Méditerranéen d’Océanologie (MIO), UM 110, CNRS 7294 IRD 235, Université de Toulon, Aix-Marseille Université, Campus de Luminy, 13288, Marseille Cedex 9, France

    Jean-Christophe Poggiale

Authors
  1. Philippe Normand
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Robert Duran
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xavier Le Roux
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Cindy Morris
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jean-Christophe Poggiale
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Philippe Normand .

Editor information

Editors and Affiliations

  1. Université de Toulon, Aix-Marseille Université, Institut Méditerranéen d’Océanologie (MIO), UM 110, CNRS 7294 IRD 235, Cedex 9, Marseille, France

    Jean-Claude Bertrand

  2. Université de Pau et des Pays de l’Adour, Institut des Sciences Analytiques et de Physico-chimie pour l’Environnement et les Matériaux (IPREM), UM 110, CNRS 5254, Pau Cedex, France

    Pierre Caumette

  3. Observatoire Océanologique de Banyuls, Laboratoire de Biodiversité et Biotechnologie Microbiennes (LBBM), Sorbonne Universités, UPMC Univ, Paris 06, USR CNRS 3579, Banyuls-sur-Mer, France

    Philippe Lebaron

  4. Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE), UMR-CNRS-IRD 7263, Aix-Marseille Université, Cedex 20, Marseille, France

    Robert Matheron

  5. Microbial Ecology Center, UMR CNRS 5557/USC INRA 1364, Villeubanne, France

    Philippe Normand

  6. Laboratoire Microorganismes: Génome et Environnement (LMGE), UMR CNRS 6023, Université Blaise Pascal, Clermont Université, Aubère Cedex, France

    Télesphore Sime-Ngando

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Normand, P., Duran, R., Le Roux, X., Morris, C., Poggiale, JC. (2015). Biodiversity and Microbial Ecosystems Functioning. In: Bertrand, JC., Caumette, P., Lebaron, P., Matheron, R., Normand, P., Sime-Ngando, T. (eds) Environmental Microbiology: Fundamentals and Applications. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9118-2_8

Download citation

Publish with us

Policies and ethics

Search

Navigation