-
1
-
-
33645450631
-
Statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes
-
Abdo Z, Schütte UME, Bent SJ, Williams CJ, Forney LJ, Joyce P. (2006). Statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes. Environ Microbiol 8: 929-938.
-
(2006)
Environ Microbiol
, vol.8
, pp. 929-938
-
-
Abdo, Z.1
Schütte, U.M.E.2
Bent, S.J.3
Williams, C.J.4
Forney, L.J.5
Joyce, P.6
-
2
-
-
0242384034
-
Review and re-analysis of domain-specific 16S primers
-
Baker GC, Smith JJ, Cowan DA. (2003). Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 55: 541-555.
-
(2003)
J Microbiol Methods
, vol.55
, pp. 541-555
-
-
Baker, G.C.1
Smith, J.J.2
Cowan, D.A.3
-
3
-
-
0005687347
-
Diversity of planktonic Foraminifera in deep sea sediments
-
Berger W, Parker FL. (1970). Diversity of planktonic Foraminifera in deep sea sediments. Science 168: 1345-1347.
-
(1970)
Science
, vol.168
, pp. 1345-1347
-
-
Berger, W.1
Parker, F.L.2
-
4
-
-
0037388225
-
Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity
-
passim
-
Crosby LD, Criddle CS. (2003). Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity. Biotechniques 34: 790-794, 796, 798 passim.
-
(2003)
Biotechniques
, vol.34
-
-
Crosby, L.D.1
Criddle, C.S.2
-
5
-
-
33751226288
-
What is the extent of prokaryotic diversity?
-
Curtis TP, Head IM, Lunn M, Woodcock S, Schloss PD, Sloan WT. (2006). What is the extent of prokaryotic diversity? Philos Trans R Soc Lond B Biol Sci 361: 2023-2037.
-
(2006)
Philos Trans R Soc Lond B Biol Sci
, vol.361
, pp. 2023-2037
-
-
Curtis, T.P.1
Head, I.M.2
Lunn, M.3
Woodcock, S.4
Schloss, P.D.5
Sloan, W.T.6
-
7
-
-
2942566096
-
Prokaryotic diversity and its limits: Microbial community structure in nature and implications for microbial ecology
-
Curtis TP, Sloan WT. (2004). Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology. Curr Opin Microbiol 7: 221-226.
-
(2004)
Curr Opin Microbiol
, vol.7
, pp. 221-226
-
-
Curtis, T.P.1
Sloan, W.T.2
-
8
-
-
0036624813
-
Molecular community analysis of microbial diversity
-
Dahllof I. (2002). Molecular community analysis of microbial diversity. Curr Opin Biotechnol 13: 213-217.
-
(2002)
Curr Opin Biotechnol
, vol.13
, pp. 213-217
-
-
Dahllof, I.1
-
9
-
-
0035527414
-
Environmental diversity of bacteria and archaea
-
DeLong EF, Pace NR. (2001). Environmental diversity of bacteria and archaea. Syst Biol 50: 470-478.
-
(2001)
Syst Biol
, vol.50
, pp. 470-478
-
-
DeLong, E.F.1
Pace, N.R.2
-
11
-
-
0032914126
-
Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning
-
Dunbar J, Takala S, Barns SM, Davis JA, Kuske CR. (1999). Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl Environ Microbiol 65: 1662-1669.
-
(1999)
Appl Environ Microbiol
, vol.65
, pp. 1662-1669
-
-
Dunbar, J.1
Takala, S.2
Barns, S.M.3
Davis, J.A.4
Kuske, C.R.5
-
12
-
-
0031981808
-
Santa Rosalia revisited: Why are there so many species of bacteria?
-
Dykhuizen DE. (1998). Santa Rosalia revisited: why are there so many species of bacteria? Antonie Van Leeuwenhoek 73: 25-33.
-
(1998)
Antonie Van Leeuwenhoek
, vol.73
, pp. 25-33
-
-
Dykhuizen, D.E.1
-
13
-
-
0029032318
-
Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species
-
Farrelly V, Rainey FA, Stackebrandt E. (1995). Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl Environ Microbiol 61: 2798-2801.
-
(1995)
Appl Environ Microbiol
, vol.61
, pp. 2798-2801
-
-
Farrelly, V.1
Rainey, F.A.2
Stackebrandt, E.3
-
14
-
-
0032710940
-
Quantification of bias related to the extraction of DNA directly from soils
-
Frostegard A, Courtois S, Ramisse V, Clerc S, Bernillon D, Le Gall F et al. (1999). Quantification of bias related to the extraction of DNA directly from soils. Appl Environ Microbiol 65: 5409-5420.
-
(1999)
Appl Environ Microbiol
, vol.65
, pp. 5409-5420
-
-
Frostegard, A.1
Courtois, S.2
Ramisse, V.3
Clerc, S.4
Bernillon, D.5
Le Gall, F.6
-
15
-
-
23944525404
-
Computational improvements reveal great bacterial diversity and high metal toxicity in soil
-
Gans J, Wolinsky M, Dunbar J. (2005). Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309: 1387-1390.
-
(2005)
Science
, vol.309
, pp. 1387-1390
-
-
Gans, J.1
Wolinsky, M.2
Dunbar, J.3
-
16
-
-
0031842162
-
Biased 16S rDNA PCR amplification caused by interference from DNA flanking the template region
-
Hansen MC, Tolker-Nielsen T, Givskov M, Molin S. (1998). Biased 16S rDNA PCR amplification caused by interference from DNA flanking the template region. FEMS Microbiol Ecol 26: 141-149.
-
(1998)
FEMS Microbiol Ecol
, vol.26
, pp. 141-149
-
-
Hansen, M.C.1
Tolker-Nielsen, T.2
Givskov, M.3
Molin, S.4
-
17
-
-
33845521652
-
Community structure analyses are more sensitive to differences in soil bacterial communities than anonymous diversity indices
-
Hartmann M, Widmer F. (2006). Community structure analyses are more sensitive to differences in soil bacterial communities than anonymous diversity indices. Appl Environ Microbiol 72: 7804-7812.
-
(2006)
Appl Environ Microbiol
, vol.72
, pp. 7804-7812
-
-
Hartmann, M.1
Widmer, F.2
-
18
-
-
2942556578
-
Richness and diversity of bacterioplankton species along an estuarine gradient in Moreton Bay, Australia
-
Hewson I, Fuhrman J. (2004). Richness and diversity of bacterioplankton species along an estuarine gradient in Moreton Bay, Australia. Appl Environ Microbiol 70: 3425-3433.
-
(2004)
Appl Environ Microbiol
, vol.70
, pp. 3425-3433
-
-
Hewson, I.1
Fuhrman, J.2
-
19
-
-
0000006498
-
Diversity and evenness: A unifying notation and its consequences
-
Hill MO. (1973). Diversity and evenness: a unifying notation and its consequences. Ecology 54: 427-432.
-
(1973)
Ecology
, vol.54
, pp. 427-432
-
-
Hill, M.O.1
-
22
-
-
0022849288
-
Theories and models of species abundance
-
Hughes RG. (1986). Theories and models of species abundance. Am Nat 128: 897-899.
-
(1986)
Am Nat
, vol.128
, pp. 897-899
-
-
Hughes, R.G.1
-
23
-
-
33646876613
-
Entropy and diversity
-
Jost L. (2006). Entropy and diversity. Oikos 113: 363-375.
-
(2006)
Oikos
, vol.113
, pp. 363-375
-
-
Jost, L.1
-
24
-
-
0343618412
-
When species accumulation curves intersect: Implications for ranking diversity using small samples
-
Lande R, DeVries PJ, Walla TR. (2000). When species accumulation curves intersect: implications for ranking diversity using small samples. Oikos 89: 601-605.
-
(2000)
Oikos
, vol.89
, pp. 601-605
-
-
Lande, R.1
DeVries, P.J.2
Walla, T.R.3
-
25
-
-
0030661563
-
Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA
-
Liu WT, Marsh TL, Cheng H, Forney LJ. (1997). Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63: 4516-4522.
-
(1997)
Appl Environ Microbiol
, vol.63
, pp. 4516-4522
-
-
Liu, W.T.1
Marsh, T.L.2
Cheng, H.3
Forney, L.J.4
-
26
-
-
33644838781
-
Denaturing gradient electrophoresis (DGE) and single-strand conformation polymorphism (SSCP) molecular fingerprintings revisited by simulation and used as a tool to measure microbial diversity
-
Loisel P, Harmand J, Zemb O, Latrille E, Lobry C, Delgenes J-P et al. (2006). Denaturing gradient electrophoresis (DGE) and single-strand conformation polymorphism (SSCP) molecular fingerprintings revisited by simulation and used as a tool to measure microbial diversity. Environ Microbiol 8: 720-731.
-
(2006)
Environ Microbiol
, vol.8
, pp. 720-731
-
-
Loisel, P.1
Harmand, J.2
Zemb, O.3
Latrille, E.4
Lobry, C.5
Delgenes, J.-P.6
-
27
-
-
18844436544
-
Native Thistles: Expendable or integral to ecosystem resistance to invasion?
-
Kareiva P and Levin SA eds, Princeton University Press: Princeton NJ. pp
-
Louda SM, Rand TA. (2002). Native Thistles: expendable or integral to ecosystem resistance to invasion?. In: Kareiva P and Levin SA (eds). The Importance of Species: Perspectives on Expendability and Triage. Princeton University Press: Princeton NJ. pp 5-15.
-
(2002)
The Importance of Species: Perspectives on Expendability and Triage
, pp. 5-15
-
-
Louda, S.M.1
Rand, T.A.2
-
28
-
-
0035018373
-
Extraction and purification of DNA in rhizosphere soil samples for PCR-DGGE analysis of bacterial consortia
-
Maarit Niemi R, Heiskanen I, Wallenius K, Lindstrom K. (2001). Extraction and purification of DNA in rhizosphere soil samples for PCR-DGGE analysis of bacterial consortia. J Microbiol Methods 45: 155-165.
-
(2001)
J Microbiol Methods
, vol.45
, pp. 155-165
-
-
Maarit Niemi, R.1
Heiskanen, I.2
Wallenius, K.3
Lindstrom, K.4
-
29
-
-
0003071920
-
On the relative abundance of species
-
MacArthur RH. (1960). On the relative abundance of species. Am Nat 94: 25-36.
-
(1960)
Am Nat
, vol.94
, pp. 25-36
-
-
MacArthur, R.H.1
-
30
-
-
0002970941
-
Patterns of species abundance and diversity
-
Diamond JM, Cody ML eds, Belknap Press: Cambridge, MA. pp
-
May RM. (1975). Patterns of species abundance and diversity. In: Diamond JM, Cody ML (eds). Ecology and Evolution of Communities. Belknap Press: Cambridge, MA. pp 81-120.
-
(1975)
Ecology and Evolution of Communities
, pp. 81-120
-
-
May, R.M.1
-
31
-
-
2342449125
-
Gram-positive bacteria are a major reservoir of Class 1 antibiotic resistance integrons in poultry litter
-
Nandi S, Maurer JJ, Hofacre C, Summers AO. (2004). Gram-positive bacteria are a major reservoir of Class 1 antibiotic resistance integrons in poultry litter. Proc Natl Acad Sci USA 101: 7118-7122.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 7118-7122
-
-
Nandi, S.1
Maurer, J.J.2
Hofacre, C.3
Summers, A.O.4
-
32
-
-
3042723492
-
Modeling bacterial species abundance from small community surveys
-
Narang R, Dunbar J. (2004). Modeling bacterial species abundance from small community surveys. Microb Ecol 47: 396-406.
-
(2004)
Microb Ecol
, vol.47
, pp. 396-406
-
-
Narang, R.1
Dunbar, J.2
-
34
-
-
33144466522
-
New threshold and confidence estimates for terminal restriction fragment length polymorphism analysis of complex bacterial communities
-
Osborne CA, Rees GN, Bernstein Y, Janssen PH. (2006). New threshold and confidence estimates for terminal restriction fragment length polymorphism analysis of complex bacterial communities. Appl Environ Microbiol 72: 1270-1278.
-
(2006)
Appl Environ Microbiol
, vol.72
, pp. 1270-1278
-
-
Osborne, C.A.1
Rees, G.N.2
Bernstein, Y.3
Janssen, P.H.4
-
35
-
-
0346816538
-
Characterization of microbial diversity in hypersaline environments by melting profiles and reassociation kinetics in combination with terminal restriction fragment length polymorphism (T-RFLP)
-
Ovreas L, Daae FL, Torsvik V, Rodriguez-Valera F. (2003). Characterization of microbial diversity in hypersaline environments by melting profiles and reassociation kinetics in combination with terminal restriction fragment length polymorphism (T-RFLP). Microb Ecol 46: 291-301.
-
(2003)
Microb Ecol
, vol.46
, pp. 291-301
-
-
Ovreas, L.1
Daae, F.L.2
Torsvik, V.3
Rodriguez-Valera, F.4
-
36
-
-
0034467819
-
Effects of agronomic treatments on structure and function of ammonia-oxidizing communities
-
Phillips CJ, Harris D, Dollhopf SL, Gross KL, Prosser JI, Paul EA. (2000). Effects of agronomic treatments on structure and function of ammonia-oxidizing communities. Appl Environ Microbiol 66: 5410-5418.
-
(2000)
Appl Environ Microbiol
, vol.66
, pp. 5410-5418
-
-
Phillips, C.J.1
Harris, D.2
Dollhopf, S.L.3
Gross, K.L.4
Prosser, J.I.5
Paul, E.A.6
-
37
-
-
0001572401
-
The commonness, and rarity, of species
-
Preston FW. (1948). The commonness, and rarity, of species. Ecology 29: 254-283.
-
(1948)
Ecology
, vol.29
, pp. 254-283
-
-
Preston, F.W.1
-
38
-
-
0035145056
-
Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning
-
Qiu X, Wu L, Huang H, McDonel PE, Palumbo AV, Tiedje JM et al. (2001). Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning. Appl Environ Microbiol 67: 880-887.
-
(2001)
Appl Environ Microbiol
, vol.67
, pp. 880-887
-
-
Qiu, X.1
Wu, L.2
Huang, H.3
McDonel, P.E.4
Palumbo, A.V.5
Tiedje, J.M.6
-
41
-
-
33344464667
-
Measurement of diversity
-
Simpson EH. (1949). Measurement of diversity. Nature 163: 688.
-
(1949)
Nature
, vol.163
, pp. 688
-
-
Simpson, E.H.1
-
42
-
-
0027842316
-
The use of species accumulation functions for the prediction of species richness
-
Soberon J, Llorente J. (1993). The use of species accumulation functions for the prediction of species richness. Conserv Biol 7: 480-488.
-
(1993)
Conserv Biol
, vol.7
, pp. 480-488
-
-
Soberon, J.1
Llorente, J.2
-
43
-
-
0035989633
-
Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology
-
Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kampfer P, Maiden MC et al. (2002). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52: 1043-1047.
-
(2002)
Int J Syst Evol Microbiol
, vol.52
, pp. 1043-1047
-
-
Stackebrandt, E.1
Frederiksen, W.2
Garrity, G.M.3
Grimont, P.A.4
Kampfer, P.5
Maiden, M.C.6
-
44
-
-
33751258603
-
The bacterial species dilemma and the genomic-phylogenetic species concept
-
Staley JT. (2006). The bacterial species dilemma and the genomic-phylogenetic species concept. Philos Trans R Soc Lond B Biol Sci 361: 1899-1909.
-
(2006)
Philos Trans R Soc Lond B Biol Sci
, vol.361
, pp. 1899-1909
-
-
Staley, J.T.1
-
45
-
-
0030067991
-
Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR
-
Suzuki MT, Giovannoni SJ. (1996). Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62: 625-630.
-
(1996)
Appl Environ Microbiol
, vol.62
, pp. 625-630
-
-
Suzuki, M.T.1
Giovannoni, S.J.2
-
47
-
-
77956844644
-
Species abundance patterns and community structure
-
Begon M, Fitter AH eds, Academic Press: London, UK. pp
-
Tokeshi M. (1993). Species abundance patterns and community structure. In: Begon M, Fitter AH (eds). Advances in Ecological Research. Academic Press: London, UK. pp 112-186.
-
(1993)
Advances in Ecological Research
, pp. 112-186
-
-
Tokeshi, M.1
-
48
-
-
0032219204
-
Novel techniques for analysing microbial diversity in natural and perturbed environments
-
Torsvik V, Daae FL, Sandaa RA, Ovreas L. (1998). Novel techniques for analysing microbial diversity in natural and perturbed environments. J Biotechnol 64: 53-62.
-
(1998)
J Biotechnol
, vol.64
, pp. 53-62
-
-
Torsvik, V.1
Daae, F.L.2
Sandaa, R.A.3
Ovreas, L.4
-
49
-
-
0036679334
-
How many species of prokaryotes are there?
-
Ward BB. (2002). How many species of prokaryotes are there? Proc Natl Acad Sci USA 99: 10234-10236.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 10234-10236
-
-
Ward, B.B.1
-
50
-
-
0038265142
-
Resolving functional diversity in relation to microbial community structure in soil: Exploiting genomics and stable isotope probing
-
Wellington EM, Berry A, Krsek M. (2003). Resolving functional diversity in relation to microbial community structure in soil: exploiting genomics and stable isotope probing. Curr Opin Microbiol 6: 295-301.
-
(2003)
Curr Opin Microbiol
, vol.6
, pp. 295-301
-
-
Wellington, E.M.1
Berry, A.2
Krsek, M.3
-
52
-
-
84986765232
-
Methods for fitting dominance/diversity curves
-
Wilson JB. (1991). Methods for fitting dominance/diversity curves. J Veg Sci 2: 35-46.
-
(1991)
J Veg Sci
, vol.2
, pp. 35-46
-
-
Wilson, J.B.1
-
53
-
-
0023184331
-
Bacterial evolution
-
Woese CR. (1987). Bacterial evolution. Microbiol Rev 51: 221-271.
-
(1987)
Microbiol Rev
, vol.51
, pp. 221-271
-
-
Woese, C.R.1
-
54
-
-
0033574013
-
Biodiversity and ecosystem productivity in a fluctuating environment: The insurance hypothesis
-
Yachi S, Loreau M. (1999). Biodiversity and ecosystem productivity in a fluctuating environment: the insurance hypothesis. Proc Natl Acad Sci USA 96: 1463-1468.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 1463-1468
-
-
Yachi, S.1
Loreau, M.2
-
55
-
-
0037772204
-
Microarrays for bacterial detection and microbial community analysis
-
Zhou J. (2003). Microarrays for bacterial detection and microbial community analysis. Curr Opin Microbiol 6: 288-294.
-
(2003)
Curr Opin Microbiol
, vol.6
, pp. 288-294
-
-
Zhou, J.1
-
56
-
-
34249945020
-
Differences in the composition of vaginal microbial communities found in healthy Caucasian and black women
-
Zhou X, Brown CJ, Abdo Z, Davis CC, Hansmann MA, Joyce P et al. (2007). Differences in the composition of vaginal microbial communities found in healthy Caucasian and black women. ISME J 1: 121-133.
-
(2007)
ISME J
, vol.1
, pp. 121-133
-
-
Zhou, X.1
Brown, C.J.2
Abdo, Z.3
Davis, C.C.4
Hansmann, M.A.5
Joyce, P.6
|