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
Fourcans A, Sole ´ 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
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
Frostegard A, Tunlid A, Baath E (2011) Use and misuse of PLFA
measurements in soils. Soil Biol Biochem 43:1621–1625
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
Gans J, Wolinsky M, Dunbar J (2005) Computational improvements
reveal great bacterial diversity and high metal toxicity in soil.
Science 309:1387–1390
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
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
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
Grice EA et al (2008) A diversity profile of the human skin microbiota.
Genome Res 18:1043–1050
Griffiths BS et al (2001) An examination of the biodiversity-ecosystem
function relationship in arable soil microbial communities. Soil Biol
Biochem 33:1713–1722
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
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
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
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
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
Herrera A, He ´ry M, Stach JEM, Jaffre ´ 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
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
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
Hoffmann KH, Rodriguez-Brito B, Breitbart M, Bangor D, Angly F,
Felts B, Nulton J, Rohwer F, Salamon P (2007) Power law rankabundance models for marine phage communities. FEMS Microbiol
Lett 273:224–228
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
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
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
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
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
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
Juan-Garcı ´a 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
Kazanov MD, Vitreschak AG, Gelfand MS (2007) Abundance and
functional diversity of riboswitches in microbial communities.
BMC Genomics 8:347
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
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
Kinkel LL, Andrews JH, Berbee FM, Nordheim EV (1987a) Leaves as
islands for microbes. Oecologia 71:405–408
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
Kinkel LL, Andrews JH, Nordheim EV (1989) Fungal immigration
dynamics and community development on apple leaves. Microb
Ecol 18:45–58
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
Kruskal JB, Wish M (1978) Multidimensional scaling. Sage University
Series, Beverly Hills
Kyselkova M, Kopecky ´ J, Frapolli M, De ´fago G, Sa ´gova ´-Mareckova ´
M, Grundmann GL, Moe ¨nne-Loccoz Y (2009) Comparison of
rhizobacterial community composition in soil suppressive or conducive to tobacco black root rot disease. ISME J 3:1127–1138
Lavire C, Normand P, Alekhina I, Bulat S, Prieur D, Birrien J-L,
Fournier P, Ha ¨nni 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
Lawrence D, Schoenike R, Quispel A, Bond G (1967) The role of
Dryas drummondii in vegetation development following ice
288
P. Normand et al.
in a hypersaline microbial mat community (Salins-de-Giraud,
Camargue, France). FEMS Microbiol Ecol 51:55–70
Fourcans A, Sole ´ 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
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
Frostegard A, Tunlid A, Baath E (2011) Use and misuse of PLFA
measurements in soils. Soil Biol Biochem 43:1621–1625
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
Gans J, Wolinsky M, Dunbar J (2005) Computational improvements
reveal great bacterial diversity and high metal toxicity in soil.
Science 309:1387–1390
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
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
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
Grice EA et al (2008) A diversity profile of the human skin microbiota.
Genome Res 18:1043–1050
Griffiths BS et al (2001) An examination of the biodiversity-ecosystem
function relationship in arable soil microbial communities. Soil Biol
Biochem 33:1713–1722
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
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
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
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
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
Herrera A, He ´ry M, Stach JEM, Jaffre ´ 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
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
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
Hoffmann KH, Rodriguez-Brito B, Breitbart M, Bangor D, Angly F,
Felts B, Nulton J, Rohwer F, Salamon P (2007) Power law rankabundance models for marine phage communities. FEMS Microbiol
Lett 273:224–228
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
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
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
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
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
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
Juan-Garcı ´a 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
Kazanov MD, Vitreschak AG, Gelfand MS (2007) Abundance and
functional diversity of riboswitches in microbial communities.
BMC Genomics 8:347
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
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
Kinkel LL, Andrews JH, Berbee FM, Nordheim EV (1987a) Leaves as
islands for microbes. Oecologia 71:405–408
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
Kinkel LL, Andrews JH, Nordheim EV (1989) Fungal immigration
dynamics and community development on apple leaves. Microb
Ecol 18:45–58
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
Kruskal JB, Wish M (1978) Multidimensional scaling. Sage University
Series, Beverly Hills
Kyselkova M, Kopecky ´ J, Frapolli M, De ´fago G, Sa ´gova ´-Mareckova ´
M, Grundmann GL, Moe ¨nne-Loccoz Y (2009) Comparison of
rhizobacterial community composition in soil suppressive or conducive to tobacco black root rot disease. ISME J 3:1127–1138
Lavire C, Normand P, Alekhina I, Bulat S, Prieur D, Birrien J-L,
Fournier P, Ha ¨nni 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
Lawrence D, Schoenike R, Quispel A, Bond G (1967) The role of
Dryas drummondii in vegetation development following ice
288
P. Normand et al.