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
Barroin G (2003) Gestion des risques. Sante ´ et environnement : le cas
des nitrates, Phosphore, azote et prolife ´ration des ve ´ge ´taux
aquatiques. Courr Environ 48:13–26
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
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
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
Bensaadi-Merchermek N, Salvado JC, Cagnon C, Karama S, Mouche `s
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
Bergersen FJ, Hipsley EH (1970) The presence of N2-fixing bacteria in
the intestines of man and animals. J Gen Microbiol 60:61–65
Bernal-Martinez A, Carre `re H, Patureau D, Delgene `s JP (2007) Ozone
pre-treatment as improver of PAH removal during anaerobic digestion of urban sludge. Chemosphere 68:1013–1019
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
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
Bittner L et al (2013) Diversity patterns of uncultured Haptophytes
unravelled by pyrosequencing in Naples Bay. Mol Ecol 22:87–101
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
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
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
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
Bouvier T, del Giorgio PA (2007) Key role of selective viral-induced
mortality in determining marine bacterial community composition.
Environ Microbiol 9:287–297
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
Braun J, Wei B (2007) Body traffic: ecology, genetics, and immunity in
inflammatory bowel disease. Annu Rev Pathol 2:401–429
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
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
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
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
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
Cavigelli MA, Robertson GP (2000) The functional significance
of denitrifier community composition in a terrestrial ecosystem.
Ecology 81:1402–1414
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
Coburn SP, Mahuren JD, Wostmann BS, Snyder DL, Townsend DW
(1989) Role of intestinal microflora in the metabolism of vitamin
B-6 and 4
0 -deoxypyridoxine examined using germfree guinea pigs
and rats. J Nutr 119:181–188
Colwell RK, Mao CX, Chang J (2004) Interpolating, extrapolating, and
comparing incidence-based species accumulation curves. Ecology
85:2717–2727
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
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
Delwiche CF, Palmer JD (1996) Rampant horizontal transfer and
duplication of rubisco genes in eubacteria and plastids. Mol Biol
Evol 13:873–882
Edwards KJ, Bach W, Rogers DR (2003) Geomicrobiology of the
ocean crust: a role for chemoautotrophic Fe-bacteria. Biol Bull
204:180–185
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
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
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
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
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
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
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
Floyd R, Eyualem A, Papert A, Blaxter ML (2002) Molecular barcodes
for soil nematode identification. Mol Ecol 11:839–850
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
8 Biodiversity and Microbial Ecosystems Functioning
287
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
Barroin G (2003) Gestion des risques. Sante ´ et environnement : le cas
des nitrates, Phosphore, azote et prolife ´ration des ve ´ge ´taux
aquatiques. Courr Environ 48:13–26
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
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
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
Bensaadi-Merchermek N, Salvado JC, Cagnon C, Karama S, Mouche `s
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
Bergersen FJ, Hipsley EH (1970) The presence of N2-fixing bacteria in
the intestines of man and animals. J Gen Microbiol 60:61–65
Bernal-Martinez A, Carre `re H, Patureau D, Delgene `s JP (2007) Ozone
pre-treatment as improver of PAH removal during anaerobic digestion of urban sludge. Chemosphere 68:1013–1019
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
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
Bittner L et al (2013) Diversity patterns of uncultured Haptophytes
unravelled by pyrosequencing in Naples Bay. Mol Ecol 22:87–101
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
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
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
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
Bouvier T, del Giorgio PA (2007) Key role of selective viral-induced
mortality in determining marine bacterial community composition.
Environ Microbiol 9:287–297
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
Braun J, Wei B (2007) Body traffic: ecology, genetics, and immunity in
inflammatory bowel disease. Annu Rev Pathol 2:401–429
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
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
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
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
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
Cavigelli MA, Robertson GP (2000) The functional significance
of denitrifier community composition in a terrestrial ecosystem.
Ecology 81:1402–1414
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
Coburn SP, Mahuren JD, Wostmann BS, Snyder DL, Townsend DW
(1989) Role of intestinal microflora in the metabolism of vitamin
B-6 and 4
0 -deoxypyridoxine examined using germfree guinea pigs
and rats. J Nutr 119:181–188
Colwell RK, Mao CX, Chang J (2004) Interpolating, extrapolating, and
comparing incidence-based species accumulation curves. Ecology
85:2717–2727
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
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
Delwiche CF, Palmer JD (1996) Rampant horizontal transfer and
duplication of rubisco genes in eubacteria and plastids. Mol Biol
Evol 13:873–882
Edwards KJ, Bach W, Rogers DR (2003) Geomicrobiology of the
ocean crust: a role for chemoautotrophic Fe-bacteria. Biol Bull
204:180–185
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
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
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
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
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
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
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
Floyd R, Eyualem A, Papert A, Blaxter ML (2002) Molecular barcodes
for soil nematode identification. Mol Ecol 11:839–850
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
8 Biodiversity and Microbial Ecosystems Functioning
287