-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
2
-
-
34547152047
-
Serial analysis of rRNA genes and the unexpected dominance of rare members of microbial communities
-
Ashby, M. N., J. Rine, E. Mongodin, K. E. Nelson, and D. Dimster-Denk. 2007. Serial analysis of rRNA genes and the unexpected dominance of rare members of microbial communities. Appl. Environ. Microbiol. 73:4532-4542.
-
(2007)
Appl. Environ. Microbiol
, vol.73
, pp. 4532-4542
-
-
Ashby, M.N.1
Rine, J.2
Mongodin, E.3
Nelson, K.E.4
Dimster-Denk, D.5
-
3
-
-
33748799671
-
New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras
-
Ashelford, K. E., N. A. Chuzhanova, J. C. Fry, A. J. Jones, and A. J. Weightman. 2006. New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl. Environ. Microbiol. 72:5734-5741.
-
(2006)
Appl. Environ. Microbiol
, vol.72
, pp. 5734-5741
-
-
Ashelford, K.E.1
Chuzhanova, N.A.2
Fry, J.C.3
Jones, A.J.4
Weightman, A.J.5
-
4
-
-
33748805463
-
Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation
-
Brodie, E. L., T. Z. DeSantis, D. C. Joyner, S. M. Baek, J. T. Larsen, G. L. Andersen, T. C. Hazen, P. M. Richardson, D. J. Herman, T. K. Tokunaga, J. M. Wan, and M. K. Firestone. 2006. Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl. Environ. Microbiol. 72:6288-6298.
-
(2006)
Appl. Environ. Microbiol
, vol.72
, pp. 6288-6298
-
-
Brodie, E.L.1
DeSantis, T.Z.2
Joyner, D.C.3
Baek, S.M.4
Larsen, J.T.5
Andersen, G.L.6
Hazen, T.C.7
Richardson, P.M.8
Herman, D.J.9
Tokunaga, T.K.10
Wan, J.M.11
Firestone, M.K.12
-
5
-
-
50949133397
-
-
Colwell, R. K. 2006. EstimateS: statistical estimation of species richness and shared species from samples, version 8
-
Colwell, R. K. 2006. EstimateS: statistical estimation of species richness and shared species from samples, version 8. http://viceroy.eeb.uconn. edu/estimateS.
-
-
-
-
6
-
-
34248159346
-
High-density universal 16S rRNA microarray analysis reveals broader diversity that typical clone libraries when sampling the environment
-
DeSantis, T. Z., E. L. Brodie, J. P. Moberg, I. X. Zobieta, Y. M. Piceno, and G. L. Anderson. 2007. High-density universal 16S rRNA microarray analysis reveals broader diversity that typical clone libraries when sampling the environment. Microb. Ecol. 53:371-383.
-
(2007)
Microb. Ecol
, vol.53
, pp. 371-383
-
-
DeSantis, T.Z.1
Brodie, E.L.2
Moberg, J.P.3
Zobieta, I.X.4
Piceno, Y.M.5
Anderson, G.L.6
-
7
-
-
33747827586
-
NAST: A multiple sequence alignment server for comparative analysis of 16S rRNA genes
-
DeSantis, T. Z., P. Hugenholtz, K. Keller, E. L. Brodie, N. Larsen, Y. M. Piceno, R. Phan, and G. L. Andersen. 2006. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acid Res. 34:D394-D399.
-
(2006)
Nucleic Acid Res
, vol.34
-
-
DeSantis, T.Z.1
Hugenholtz, P.2
Keller, K.3
Brodie, E.L.4
Larsen, N.5
Piceno, Y.M.6
Phan, R.7
Andersen, G.L.8
-
8
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
DeSantis, T. Z., P. Hugenholtz, N. Larsen, M. Rojas, E. L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu, and G. L. Anderson. 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72:5069-5072.
-
(2006)
Appl. Environ. Microbiol
, vol.72
, pp. 5069-5072
-
-
DeSantis, T.Z.1
Hugenholtz, P.2
Larsen, N.3
Rojas, M.4
Brodie, E.L.5
Keller, K.6
Huber, T.7
Dalevi, D.8
Hu, P.9
Anderson, G.L.10
-
9
-
-
0036269049
-
Empirical and theoretical bacterial diversity in four Arizona soils
-
Dunbar, J., S. M. Barns, L. O. Ticknor, and C. R. Kuske. 2002. Empirical and theoretical bacterial diversity in four Arizona soils. Appl. Environ. Microbiol. 6:3035-3045.
-
(2002)
Appl. Environ. Microbiol
, vol.6
, pp. 3035-3045
-
-
Dunbar, J.1
Barns, S.M.2
Ticknor, L.O.3
Kuske, C.R.4
-
10
-
-
33947236971
-
Toward an ecological classification of soil bacteria
-
Fierer, N., M. A. Bradford, and R. B. Jackson. 2007. Toward an ecological classification of soil bacteria. Ecology 88:1354-1364.
-
(2007)
Ecology
, vol.88
, pp. 1354-1364
-
-
Fierer, N.1
Bradford, M.A.2
Jackson, R.B.3
-
11
-
-
22144470189
-
Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays
-
Fierer, N., J. A. Jackson, R. Vilgalys, and R. B. Jackson. 2005. Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Appl. Environ. Microbiol. 71:4117-4120.
-
(2005)
Appl. Environ. Microbiol
, vol.71
, pp. 4117-4120
-
-
Fierer, N.1
Jackson, J.A.2
Vilgalys, R.3
Jackson, R.B.4
-
12
-
-
0037316454
-
Influence of depth and sampling time on bacterial community structure in an upland grassland soil
-
Griffiths, R. I., A. S. Whiteley, A. G. O'Donnell, and M. J. Bailey. 2003. Influence of depth and sampling time on bacterial community structure in an upland grassland soil. FEMS Microbiol. Ecol. 43:35-43.
-
(2003)
FEMS Microbiol. Ecol
, vol.43
, pp. 35-43
-
-
Griffiths, R.I.1
Whiteley, A.S.2
O'Donnell, A.G.3
Bailey, M.J.4
-
13
-
-
30444458666
-
Predicting microbial species richness
-
Hong, S.-H., J. Bunge, S.-O. Jeon, and S. S. Epstein. 2006. Predicting microbial species richness. Proc. Natl. Acad. Sci. USA 103:117-122.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 117-122
-
-
Hong, S.-H.1
Bunge, J.2
Jeon, S.-O.3
Epstein, S.S.4
-
14
-
-
35148888609
-
Microbial population structures in the deep marine biosphere
-
Huber, J. A., D. B. M. Welch, H. G. Morrison, S. M. Huse, P. R. Neal, D. A. Butterfield, and M. L. Sogin. 2007. Microbial population structures in the deep marine biosphere. Science 318:97-100.
-
(2007)
Science
, vol.318
, pp. 97-100
-
-
Huber, J.A.1
Welch, D.B.M.2
Morrison, H.G.3
Huse, S.M.4
Neal, P.R.5
Butterfield, D.A.6
Sogin, M.L.7
-
15
-
-
0031662188
-
Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity
-
Hugenholtz, P., B. M. Goebel, and N. R. Pace. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180:4765-4774.
-
(1998)
J. Bacteriol
, vol.180
, pp. 4765-4774
-
-
Hugenholtz, P.1
Goebel, B.M.2
Pace, N.R.3
-
16
-
-
33644952722
-
Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes
-
Janssen, P. H. 2006. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microbiol. 72:1719-1728.
-
(2006)
Appl. Environ. Microbiol
, vol.72
, pp. 1719-1728
-
-
Janssen, P.H.1
-
17
-
-
0001857117
-
16S/23S rRNA sequencing
-
E. Stackebrandt and M. Goodfellow ed, John Wiley & Sons, Chichester, United Kingdom
-
Lane, D. J. 1991. 16S/23S rRNA sequencing, p. 115-174. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons, Chichester, United Kingdom.
-
(1991)
Nucleic acid techniques in bacterial systematics
, pp. 115-174
-
-
Lane, D.J.1
-
18
-
-
2442709377
-
Seasonal changes in an alpine soil bacterial community in the Colorado Rocky Mountains
-
Lipson, D. A., and S. K. Schmidt. 2004. Seasonal changes in an alpine soil bacterial community in the Colorado Rocky Mountains. Appl. Environ. Microbiol. 70:2867-2879.
-
(2004)
Appl. Environ. Microbiol
, vol.70
, pp. 2867-2879
-
-
Lipson, D.A.1
Schmidt, S.K.2
-
19
-
-
35549007148
-
Short pyrosequencing reads suffice for accurate microbial community analysis
-
Liu, Z., C. Lozupone, M. Hamady, F. D. Bushman, and R. Knight. 2007. Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res. 35:120-130.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 120-130
-
-
Liu, Z.1
Lozupone, C.2
Hamady, M.3
Bushman, F.D.4
Knight, R.5
-
20
-
-
34547433545
-
Global patterns in bacterial diversity
-
Lozupone, C. A., and R. Knight. 2007. Global patterns in bacterial diversity. Proc. Natl. Acad. Sci. USA 104:11436-11440.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 11436-11440
-
-
Lozupone, C.A.1
Knight, R.2
-
21
-
-
2542523843
-
ARB: A software environment for sequence data
-
Ludwig, W., O. Strunk, R. Westram, L. Richter, H. Meier, Y. kumar, A. Buchner, T. Lai, S. Steppi, G. Jobb, W. Förster, I. Brettske, S. Gerber, A. W. Ginhart, O. Gross, S. Grumann, S. Hermann, R. Jost, A. König, T. Liss, R. Lüßmann, M. May, B. Nonhoff, B. Reichel, R. Strehlow, A. Stamatakis, N. Stuckmann, A. Vilbig, M. Lenke, T. Ludwig, A. Bode, and K.-H. Schleifer. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32:1363-1371.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1363-1371
-
-
Ludwig, W.1
Strunk, O.2
Westram, R.3
Richter, L.4
Meier, H.5
kumar, Y.6
Buchner, A.7
Lai, T.8
Steppi, S.9
Jobb, G.10
Förster, W.11
Brettske, I.12
Gerber, S.13
Ginhart, A.W.14
Gross, O.15
Grumann, S.16
Hermann, S.17
Jost, R.18
König, A.19
Liss, T.20
Lüßmann, R.21
May, M.22
Nonhoff, B.23
Reichel, B.24
Strehlow, R.25
Stamatakis, A.26
Stuckmann, N.27
Vilbig, A.28
Lenke, M.29
Ludwig, T.30
Bode, A.31
Schleifer, K.-H.32
more..
-
22
-
-
0035846111
-
Acclimatization of soil respiration to warming in a tall grass prairie
-
Luo, Y., S. Wan, D. Hui, and L. L. Wallace. 2001. Acclimatization of soil respiration to warming in a tall grass prairie. Nature 413:622-625.
-
(2001)
Nature
, vol.413
, pp. 622-625
-
-
Luo, Y.1
Wan, S.2
Hui, D.3
Wallace, L.L.4
-
23
-
-
34547540925
-
Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth
-
Marcy, Y., C. Ouverney, E. M. Bik, T. Losekann, N. Ivanova, H. G. Martin, E. Szeto, D. Platt, P. Hugenholtz, and S. R. Quake. 2007. Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc. Natl. Acad. Sci. USA 140:11889-11894.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.140
, pp. 11889-11894
-
-
Marcy, Y.1
Ouverney, C.2
Bik, E.M.3
Losekann, T.4
Ivanova, N.5
Martin, H.G.6
Szeto, E.7
Platt, D.8
Hugenholtz, P.9
Quake, S.R.10
-
24
-
-
33744745905
-
Marine microbial diversity: Can it be determined
-
Pedros-Alio, C. 2006. Marine microbial diversity: can it be determined. Trends Microbiol. 14:257-263.
-
(2006)
Trends Microbiol
, vol.14
, pp. 257-263
-
-
Pedros-Alio, C.1
-
25
-
-
34249701816
-
Targeted access to the genomes of low abundance organisms in complex microbial communities
-
Podar, M., C. B. Abulencia, M. Walcher, D. Hutchison, K. Zengler, J. A. Garcia, T. Holland, D. Cotton, L. Hauser, and M. Keller. 2007. Targeted access to the genomes of low abundance organisms in complex microbial communities. Appl. Environ. Microbiol. 73:3205-3214.
-
(2007)
Appl. Environ. Microbiol
, vol.73
, pp. 3205-3214
-
-
Podar, M.1
Abulencia, C.B.2
Walcher, M.3
Hutchison, D.4
Zengler, K.5
Garcia, J.A.6
Holland, T.7
Cotton, D.8
Hauser, L.9
Keller, M.10
-
26
-
-
20444383583
-
Extensive diversity of ionizing-radiation-resistant bacteria recovered from Sonoran Desert soil and description of nine new species of the genus Deinococcus obtained from a single soil sample
-
Rainey, F. A., K. Ray, M. Ferreira, B. Z. Gatz, M. F. Nobre, D. Bagaley, B. A. Rash, M.-J. Park, A. M. Earl, N. C. Shank, A. M. Small, M. C. Henk, J. R. Battista, P. Kämpfer, and M. S. da Costa. 2005. Extensive diversity of ionizing-radiation-resistant bacteria recovered from Sonoran Desert soil and description of nine new species of the genus Deinococcus obtained from a single soil sample. Appl. Environ. Microbiol. 71:5225-5235.
-
(2005)
Appl. Environ. Microbiol
, vol.71
, pp. 5225-5235
-
-
Rainey, F.A.1
Ray, K.2
Ferreira, M.3
Gatz, B.Z.4
Nobre, M.F.5
Bagaley, D.6
Rash, B.A.7
Park, M.-J.8
Earl, A.M.9
Shank, N.C.10
Small, A.M.11
Henk, M.C.12
Battista, J.R.13
Kämpfer, P.14
da Costa, M.S.15
-
27
-
-
34547800097
-
-
Roesch, L. F. W., R. R. Fulthorps, A. Riva, G. Casella, A. K. M. Hadwin, A. D. Kent, S. M. Daroub, F. A. O. Camargo, W. G. Farmerie, and E. W. Triplett. 2007. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 1:283-290.
-
Roesch, L. F. W., R. R. Fulthorps, A. Riva, G. Casella, A. K. M. Hadwin, A. D. Kent, S. M. Daroub, F. A. O. Camargo, W. G. Farmerie, and E. W. Triplett. 2007. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 1:283-290.
-
-
-
-
28
-
-
15444362001
-
Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness
-
Schloss, P. D., and J. Handelsman. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71:1501-1506.
-
(2005)
Appl. Environ. Microbiol
, vol.71
, pp. 1501-1506
-
-
Schloss, P.D.1
Handelsman, J.2
-
29
-
-
33746639717
-
Toward a census of bacteria in soil
-
Schloss, P. D., and J. Handelsman. 2006. Toward a census of bacteria in soil. PLoS Comput. Biol. 2:786-793.
-
(2006)
PLoS Comput. Biol
, vol.2
, pp. 786-793
-
-
Schloss, P.D.1
Handelsman, J.2
-
30
-
-
0035487320
-
Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: Plant-dependent enrichment and seasonal shifts revealed
-
Smalla, K., G. Wieland, A. Buchner, A. Zock, J. Parzy, S. Kaiser, N. Roskot, H. Heuer, and G. Berg. 2001. Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl. Environ. Microbiol. 67:4742-4751.
-
(2001)
Appl. Environ. Microbiol
, vol.67
, pp. 4742-4751
-
-
Smalla, K.1
Wieland, G.2
Buchner, A.3
Zock, A.4
Parzy, J.5
Kaiser, S.6
Roskot, N.7
Heuer, H.8
Berg, G.9
-
31
-
-
0035344248
-
Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods
-
Smit, E., P. Leeflang, S. Gommans, J. V. d. Broek, S. van Mil, and K. Wernars. 2001. Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Appl. Environ. Microbiol. 67:2284-2291.
-
(2001)
Appl. Environ. Microbiol
, vol.67
, pp. 2284-2291
-
-
Smit, E.1
Leeflang, P.2
Gommans, S.3
Broek, J.V.D.4
van Mil, S.5
Wernars, K.6
-
32
-
-
33747073504
-
Microbial diversity in the deep sea and the underexplored rare biosphere
-
USA
-
Sogin, M. L., H. G. Morrison, J. A. Huber, D. M. Welch, S. M. Huse, P. R. Neal, J. A. Arrieta, and G. H. Herndl. 2006. Microbial diversity in the deep sea and the underexplored "rare biosphere." Proc. Natl. Acad. Sci. USA 103:12115-12120.
-
(2006)
Proc. Natl. Acad. Sci
, vol.103
, pp. 12115-12120
-
-
Sogin, M.L.1
Morrison, H.G.2
Huber, J.A.3
Welch, D.M.4
Huse, S.M.5
Neal, P.R.6
Arrieta, J.A.7
Herndl, G.H.8
-
33
-
-
0036657601
-
Fungal diversity in ectomycorrhizal communities: Sampling effort and species detection
-
Taylor, A. F. S. 2002. Fungal diversity in ectomycorrhizal communities: sampling effort and species detection. Plant Soil 244:19-28.
-
(2002)
Plant Soil
, vol.244
, pp. 19-28
-
-
Taylor, A.F.S.1
-
34
-
-
2142829555
-
Copy number of ribosomal operons in prokaryotes and its effect on phylogenetic analyses
-
Tourova, T. P. 2003. Copy number of ribosomal operons in prokaryotes and its effect on phylogenetic analyses. Microbiology 72:437-452.
-
(2003)
Microbiology
, vol.72
, pp. 437-452
-
-
Tourova, T.P.1
-
35
-
-
20244376755
-
Comparative metagenomics of microbial communities
-
Tringe, S. G., C. von Mering, A. Kobayashi, A. A. Salamov, K. Chen, H. M. Chang, M. Podar, J. M. Short, E. J. Mathur, J. C. Detter, P. Bork, P. Hugenholtz, and E. M. Rubin. 2005. Comparative metagenomics of microbial communities. Science 308:554-557.
-
(2005)
Science
, vol.308
, pp. 554-557
-
-
Tringe, S.G.1
von Mering, C.2
Kobayashi, A.3
Salamov, A.A.4
Chen, K.5
Chang, H.M.6
Podar, M.7
Short, J.M.8
Mathur, E.J.9
Detter, J.C.10
Bork, P.11
Hugenholtz, P.12
Rubin, E.M.13
-
36
-
-
34548293679
-
Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
Wang, Q., G. M. Garrity, J. M. Tiedje, and J. R. Cole. 2007. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73:5261-5267.
-
(2007)
Appl. Environ. Microbiol
, vol.73
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
Cole, J.R.4
-
37
-
-
34247371936
-
2 efflux under experimental warming and clipping in a grassland ecosystem
-
2 efflux under experimental warming and clipping in a grassland ecosystem. Global Change Biol. 13:761-775.
-
(2007)
Global Change Biol
, vol.13
, pp. 761-775
-
-
Zhou, X.1
Luo, Y.2
|