recession at Glacier Bay, Alaska, with special reference to its
nitrogen fixation by root nodules. J Ecol 55:793–813
Le Roux X, Philippot L, Degrange V, Poly F, Wertz S (2006) Relations
entre biodiversite ´ et fonctionnement chez les communaute ´s
microbiennes. Biofutur 268:50–53
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
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
Lee HR, Pimentel M (2006) Bacteria and irritable bowel syndrome:
the evidence for small intestinal bacterial overgrowth. Curr
Gastroenterol Rep 8:305–311
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
Lichter J (1998) Primary succession and forest development on coastal
Lake Michigan dunes. Ecol Monogr 68:487–510
Loreau M et al (2001) Biodiversity and ecosystem functioning: current
knowledge and future challenges. Science 294:804–808
Lundberg DS et al (2012) Defining the core Arabidopsis thaliana root
microbiome. Nature 488:86–90
MacArthur RH, Wilson EO (1963) An equilibrium theory of insular
zoogeography. Evolution 17:373–387
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
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
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
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
McCann KS (2000) The diversity-stability debate. Nature
405:228–233
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
Mitchell CE, Tillman D, Groth JV (2002) Effects of grassland species
diversity, abundance and composition on foliar fungal disease.
Ecology 83:1713–1726
Monier A, Claverie JM, Ogata H (2008) Taxonomic distribution of
large DNA viruses in the sea. Genome Biol 9:R106
Moreira D, Lopez-Garcia P (2002) The molecular ecology of
microbial eukaryotes unveils a hidden world. Trends Microbiol
10:31–38
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
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
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
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
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
Naeem S (2002) Ecosystem consequences of biodiversity loss : the
evolution of a paradigm. Ecology 83:1537–1552
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
Nei M (1973) Analysis of gene diversity in subdivided populations.
Proc Natl Acad Sci U S A 70:3321–3323
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
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
Nomura T et al (2005) Mucosa-associated bacteria in ulcerative colitis
before and after antibiotic combination therapy. Aliment Pharmacol
Ther 21:1017–1027
Normand P, Bousquet J (1989) Phylogeny of nitrogenase sequences in
Frankia and other nitrogen-fixing microorganisms. J Mol Evol
29:436–447
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
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
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
Parkes RJ et al (2005) Deep sub-seafloor prokaryotes stimulated at
interfaces over geological time. Nature 436:390–394
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
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
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
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
Philippot L (2002) Denitrifying genes in bacterial and archaeal
genomes. Biochim Biophys Acta 1577:355–376
Philippot L, Hallin S, Schloter M (2007) Ecology of denitrifying
prokaryotes in agricultural soil. Adv Agron 96:249–305
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
8 Biodiversity and Microbial Ecosystems Functioning
289
nitrogen fixation by root nodules. J Ecol 55:793–813
Le Roux X, Philippot L, Degrange V, Poly F, Wertz S (2006) Relations
entre biodiversite ´ et fonctionnement chez les communaute ´s
microbiennes. Biofutur 268:50–53
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
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
Lee HR, Pimentel M (2006) Bacteria and irritable bowel syndrome:
the evidence for small intestinal bacterial overgrowth. Curr
Gastroenterol Rep 8:305–311
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
Lichter J (1998) Primary succession and forest development on coastal
Lake Michigan dunes. Ecol Monogr 68:487–510
Loreau M et al (2001) Biodiversity and ecosystem functioning: current
knowledge and future challenges. Science 294:804–808
Lundberg DS et al (2012) Defining the core Arabidopsis thaliana root
microbiome. Nature 488:86–90
MacArthur RH, Wilson EO (1963) An equilibrium theory of insular
zoogeography. Evolution 17:373–387
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
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
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
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
McCann KS (2000) The diversity-stability debate. Nature
405:228–233
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
Mitchell CE, Tillman D, Groth JV (2002) Effects of grassland species
diversity, abundance and composition on foliar fungal disease.
Ecology 83:1713–1726
Monier A, Claverie JM, Ogata H (2008) Taxonomic distribution of
large DNA viruses in the sea. Genome Biol 9:R106
Moreira D, Lopez-Garcia P (2002) The molecular ecology of
microbial eukaryotes unveils a hidden world. Trends Microbiol
10:31–38
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
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
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
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
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
Naeem S (2002) Ecosystem consequences of biodiversity loss : the
evolution of a paradigm. Ecology 83:1537–1552
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
Nei M (1973) Analysis of gene diversity in subdivided populations.
Proc Natl Acad Sci U S A 70:3321–3323
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
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
Nomura T et al (2005) Mucosa-associated bacteria in ulcerative colitis
before and after antibiotic combination therapy. Aliment Pharmacol
Ther 21:1017–1027
Normand P, Bousquet J (1989) Phylogeny of nitrogenase sequences in
Frankia and other nitrogen-fixing microorganisms. J Mol Evol
29:436–447
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
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
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
Parkes RJ et al (2005) Deep sub-seafloor prokaryotes stimulated at
interfaces over geological time. Nature 436:390–394
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
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
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
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
Philippot L (2002) Denitrifying genes in bacterial and archaeal
genomes. Biochim Biophys Acta 1577:355–376
Philippot L, Hallin S, Schloter M (2007) Ecology of denitrifying
prokaryotes in agricultural soil. Adv Agron 96:249–305
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
8 Biodiversity and Microbial Ecosystems Functioning
289