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
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
Potrikus CJ, Breznak JA (1977) Nitrogen-fixing Enterobacter
agglomerans isolated from guts of wood-eating termites. Appl
Environ Microbiol 33:392–399
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
Radajewski S, Ineson P, Parekh NR, Murrell JC (2000) Stable-isotope
probing as a tool in microbial ecology. Nature 403:646–649
Ramette A, Tiedje JM (2007) Biogeography: an emerging cornerstone
for understanding prokaryotic diversity, ecology, and evolution.
Microb Ecol 53:197–207
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
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
Re ´nyi 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
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
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
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
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
Salles JF, Poly F, Schmid B, Le Roux X (2009) Community niche
predicts the functioning of denitrifying bacterial assemblages.
Ecology 90:3324–3332
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
Sapp M, Wichels A, Gerdts G (2007) Impacts of cultivation of marine
diatoms on the associated bacterial community. Appl Environ
Microbiol 73:3117–3120
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
Selesi D, Schmid M, Hartmann A (2005) Diversity of green-like and
red-like ribulose-1,5-bisphosphate carboxylase/oxygenase largesubunit genes (cbbL) in differently managed agricultural soils.
Appl Environ Microbiol 71:175–184
Shannon CE (1948) A mathematical theory of communication. Bell
Syst Tech J 27:379–423
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
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
Sneath PHA (2005) Numerical taxonomy. In: Garrity GM (ed)
Systematic bacteriology. Springer, East Lansing, pp 39–42
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
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
Takacs D (1996) The idea of biodiversity: philosophies of paradise.
The Johns Hopkins University Press, Baltimore, 393 p
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
Tasse L et al (2010) Functional metagenomics to mine the human gut
microbiome for dietary fiber catabolic enzymes. Genome Res
20:1605–1612
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
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
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
Torsvik V, Ovreas L, Thingstad TF (2002) Prokaryotic diversitymagnitude, dynamics, and controlling factors. Science
296:1064–1066
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
Vaulot D, Eikrem W, Viprey M, Moreau H (2008) The diversity of
small eukaryotic phytoplankton (
Venter JC et al (2004) Environmental genome shotgun sequencing of
the Sargasso Sea. Science 304:66–74
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
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
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
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
Vogel TM et al (2009) TerraGenome: a consortium for the sequencing
of a soil metagenome. Nat Rev Microbiol 7:252. doi:10.1038/
nrmicro2119
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
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
290
P. Normand et al.
(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
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
Potrikus CJ, Breznak JA (1977) Nitrogen-fixing Enterobacter
agglomerans isolated from guts of wood-eating termites. Appl
Environ Microbiol 33:392–399
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
Radajewski S, Ineson P, Parekh NR, Murrell JC (2000) Stable-isotope
probing as a tool in microbial ecology. Nature 403:646–649
Ramette A, Tiedje JM (2007) Biogeography: an emerging cornerstone
for understanding prokaryotic diversity, ecology, and evolution.
Microb Ecol 53:197–207
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
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
Re ´nyi 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
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
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
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
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
Salles JF, Poly F, Schmid B, Le Roux X (2009) Community niche
predicts the functioning of denitrifying bacterial assemblages.
Ecology 90:3324–3332
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
Sapp M, Wichels A, Gerdts G (2007) Impacts of cultivation of marine
diatoms on the associated bacterial community. Appl Environ
Microbiol 73:3117–3120
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
Selesi D, Schmid M, Hartmann A (2005) Diversity of green-like and
red-like ribulose-1,5-bisphosphate carboxylase/oxygenase largesubunit genes (cbbL) in differently managed agricultural soils.
Appl Environ Microbiol 71:175–184
Shannon CE (1948) A mathematical theory of communication. Bell
Syst Tech J 27:379–423
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
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
Sneath PHA (2005) Numerical taxonomy. In: Garrity GM (ed)
Systematic bacteriology. Springer, East Lansing, pp 39–42
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
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
Takacs D (1996) The idea of biodiversity: philosophies of paradise.
The Johns Hopkins University Press, Baltimore, 393 p
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
Tasse L et al (2010) Functional metagenomics to mine the human gut
microbiome for dietary fiber catabolic enzymes. Genome Res
20:1605–1612
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
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
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
Torsvik V, Ovreas L, Thingstad TF (2002) Prokaryotic diversitymagnitude, dynamics, and controlling factors. Science
296:1064–1066
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
Vaulot D, Eikrem W, Viprey M, Moreau H (2008) The diversity of
small eukaryotic phytoplankton (
Venter JC et al (2004) Environmental genome shotgun sequencing of
the Sargasso Sea. Science 304:66–74
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
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
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
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
Vogel TM et al (2009) TerraGenome: a consortium for the sequencing
of a soil metagenome. Nat Rev Microbiol 7:252. doi:10.1038/
nrmicro2119
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
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
290
P. Normand et al.