-
2
-
-
33644963915
-
2 modifies total and metabolically active bacterial communities in the rhizosphere of two perennial grasses grown under field conditions
-
2 modifies total and metabolically active bacterial communities in the rhizosphere of two perennial grasses grown under field conditions. Fems Microbiology Ecology 55: 339-350.
-
(2006)
Fems Microbiology Ecology
, vol.55
, pp. 339-350
-
-
Jossi, M.1
Fromin, N.2
Tarnawski, S.3
Kohler, F.4
Gillet, F.5
-
8
-
-
76649140502
-
Soil microbial community responses to multiple experimental climate change drivers
-
Castro HF, Classen AT, Austin EE, Norby RJ, Schadt CW (2010) Soil microbial community responses to multiple experimental climate change drivers. Applied and Environmental Microbiology 76: 999-1007.
-
(2010)
Applied and Environmental Microbiology
, vol.76
, pp. 999-1007
-
-
Castro, H.F.1
Classen, A.T.2
Austin, E.E.3
Norby, R.J.4
Schadt, C.W.5
-
9
-
-
52949113790
-
Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment
-
Prosser JI, Nicol GW (2008) Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. Environmental Microbiology 10: 2931-2941.
-
(2008)
Environmental Microbiology
, vol.10
, pp. 2931-2941
-
-
Prosser, J.I.1
Nicol, G.W.2
-
10
-
-
34248178641
-
New processes and players in the nitrogen cycle: The microbial ecology of anaerobic and archaeal ammonia oxidation
-
Francis CA, Beman JM, Kuypers MMM (2007) New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. ISME Journal 1: 19-27.
-
(2007)
ISME Journal
, vol.1
, pp. 19-27
-
-
Francis, C.A.1
Beman, J.M.2
Kuypers, M.M.M.3
-
11
-
-
23644433664
-
In situ stable isotope probing of methanogenic archaea in the rice rhizosphere
-
Lu YH, Conrad R (2005) In situ stable isotope probing of methanogenic archaea in the rice rhizosphere. Science 309: 1088-1090.
-
(2005)
Science
, vol.309
, pp. 1088-1090
-
-
Lu, Y.H.1
Conrad, R.2
-
12
-
-
28644435323
-
Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling
-
Treusch AH, Leininger S, Kletzin A, Schuster SC, Klenk HP, et al. (2005) Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environmental Microbiology 7: 1985-1995.
-
(2005)
Environmental Microbiology
, vol.7
, pp. 1985-1995
-
-
Treusch, A.H.1
Leininger, S.2
Kletzin, A.3
Schuster, S.C.4
Klenk, H.P.5
-
13
-
-
25644435673
-
Isolation of an autotrophic ammonia-oxidizing marine archaeon
-
Konneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, et al. (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437: 543-546.
-
(2005)
Nature
, vol.437
, pp. 543-546
-
-
Konneke, M.1
Bernhard, A.E.2
de la Torre, J.R.3
Walker, C.B.4
Waterbury, J.B.5
-
14
-
-
38549131184
-
Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol
-
de la Torre JR, Walker CB, Ingalls AE, Konneke M, Stahl DA (2008) Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environmental Microbiology 10: 810-818.
-
(2008)
Environmental Microbiology
, vol.10
, pp. 810-818
-
-
de la Torre, J.R.1
Walker, C.B.2
Ingalls, A.E.3
Konneke, M.4
Stahl, D.A.5
-
15
-
-
52949137846
-
The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria
-
Nicol GW, Leininger S, Schleper C, Prosser JI (2008) The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environmental Microbiology 10: 2966-2978.
-
(2008)
Environmental Microbiology
, vol.10
, pp. 2966-2978
-
-
Nicol, G.W.1
Leininger, S.2
Schleper, C.3
Prosser, J.I.4
-
16
-
-
33747479446
-
Archaea predominate among ammonia-oxidizing prokaryotes in soils
-
Leininger S, Urich T, Schloter M, Schwark L, Qi J, et al. (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442: 806-809.
-
(2006)
Nature
, vol.442
, pp. 806-809
-
-
Leininger, S.1
Urich, T.2
Schloter, M.3
Schwark, L.4
Qi, J.5
-
17
-
-
34547800097
-
Pyrosequencing enumerates and contrasts soil microbial diversity
-
Roesch LF, Fulthorpe RR, Riva A, Casella G, Hadwin AKM, et al. (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME Journal 1: 283-290.
-
(2007)
ISME Journal
, vol.1
, pp. 283-290
-
-
Roesch, L.F.1
Fulthorpe, R.R.2
Riva, A.3
Casella, G.4
Hadwin, A.K.M.5
-
19
-
-
66749133568
-
Rising atmospheric carbon dioxide concentration and the future of C4 crops for food and fuel
-
Leakey ADB (2009) Rising atmospheric carbon dioxide concentration and the future of C4 crops for food and fuel. Proceedings of the Royal Society BBiological Sciences 276: 2333-2343.
-
(2009)
Proceedings of the Royal Society BBiological Sciences
, vol.276
, pp. 2333-2343
-
-
Leakey, A.D.B.1
-
20
-
-
13144283719
-
2 enrichment (FACE)? A meta-analytic review of the responses of photosynthesis, canopy
-
2 enrichment (FACE)? A meta-analytic review of the responses of photosynthesis, canopy. New Phytologist 165: 351-371.
-
(2005)
New Phytologist
, vol.165
, pp. 351-371
-
-
Ainsworth, E.A.1
Long, S.P.2
-
21
-
-
14944385367
-
2] enrichment (FACE) stimulates photosynthesis while decreasing in vivo Rubisco capacity
-
2] enrichment (FACE) stimulates photosynthesis while decreasing in vivo Rubisco capacity. Planta 220: 434-446.
-
(2005)
Planta
, vol.220
, pp. 434-446
-
-
Bernacchi, C.J.1
Morgan, P.B.2
Ort, D.R.3
Long, S.P.4
-
25
-
-
70349785705
-
Will elevated carbon dioxide concentration amplify the benefits of nitrogen fixation in legumes?
-
Rogers A, Ainsworth EA, Leakey ADB (2009) Will elevated carbon dioxide concentration amplify the benefits of nitrogen fixation in legumes? Plant Physiology 151: 1009-1016.
-
(2009)
Plant Physiology
, vol.151
, pp. 1009-1016
-
-
Rogers, A.1
Ainsworth, E.A.2
Leakey, A.D.B.3
-
26
-
-
33748487811
-
Increased C availability at elevated carbon dioxide concentration improves N assimilation in a legume
-
Rogers A, Gibon Y, Stitt M, Morgan PB, Bernacchi CJ, et al. (2006) Increased C availability at elevated carbon dioxide concentration improves N assimilation in a legume. Plant Cell and Environment 29: 1651-1658.
-
(2006)
Plant Cell and Environment
, vol.29
, pp. 1651-1658
-
-
Rogers, A.1
Gibon, Y.2
Stitt, M.3
Morgan, P.B.4
Bernacchi, C.J.5
-
28
-
-
0034964968
-
The diversity of archaea and bacteria in association with the roots of Zea mays L
-
Chelius MK, Triplett EW (2001) The diversity of archaea and bacteria in association with the roots of Zea mays L. Microbial Ecology 41: 252-263.
-
(2001)
Microbial Ecology
, vol.41
, pp. 252-263
-
-
Chelius, M.K.1
Triplett, E.W.2
-
29
-
-
0028983870
-
Molecular phylogenetic analysis of a soil microbial community in a soybean field
-
Ueda T, Suga Y, Matsuguchi T (1995) Molecular phylogenetic analysis of a soil microbial community in a soybean field. European Journal of Soil Science 46: 415-421.
-
(1995)
European Journal of Soil Science
, vol.46
, pp. 415-421
-
-
Ueda, T.1
Suga, Y.2
Matsuguchi, T.3
-
34
-
-
2542508293
-
Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval
-
Grosskopf R, Janssen PH, Liesack W (1998) Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Applied and Environmental Microbiology 64: 960-969.
-
(1998)
Applied and Environmental Microbiology
, vol.64
, pp. 960-969
-
-
Grosskopf, R.1
Janssen, P.H.2
Liesack, W.3
-
35
-
-
3042802223
-
Decadalscale fates of 15N tracers added to oak and pine stands under ambient and elevated N inputs at the Harvard Forest (USA)
-
Nadelhoffer KJ, Colman BP, Currie WS, Magill A, Aber JD (2004) Decadalscale fates of 15N tracers added to oak and pine stands under ambient and elevated N inputs at the Harvard Forest (USA). Forest Ecology and Management 196: 89-107.
-
(2004)
Forest Ecology and Management
, vol.196
, pp. 89-107
-
-
Nadelhoffer, K.J.1
Colman, B.P.2
Currie, W.S.3
Magill, A.4
Aber, J.D.5
-
37
-
-
34249050929
-
Monitoring and source tracking of tetracycline resistance genes in lagoons and groundwater adjacent to swine production facilities over a 3-year period
-
Koike S, Krapac IG, Oliver HD, Yannarell AC, Chee-Sanford JC, et al. (2007) Monitoring and source tracking of tetracycline resistance genes in lagoons and groundwater adjacent to swine production facilities over a 3-year period. Applied and Environmental Microbiology 73: 4813-4823.
-
(2007)
Applied and Environmental Microbiology
, vol.73
, pp. 4813-4823
-
-
Koike, S.1
Krapac, I.G.2
Oliver, H.D.3
Yannarell, A.C.4
Chee-Sanford, J.C.5
-
38
-
-
26844541457
-
Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean
-
Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB (2005) Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proceedings of the National Academy of Sciences of the United States of America 102: 14683-14688.
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, pp. 14683-14688
-
-
Francis, C.A.1
Roberts, K.J.2
Beman, J.M.3
Santoro, A.E.4
Oakley, B.B.5
-
39
-
-
34547686149
-
Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammoniaoxidizing archaea of a Chinese upland red soil under long-term fertilization practices
-
He J, Shen J, Zhang L, Zhu Y, Zheng Y, et al. (2007) Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammoniaoxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environmental Microbiology 9: 2364-2374.
-
(2007)
Environmental Microbiology
, vol.9
, pp. 2364-2374
-
-
He, J.1
Shen, J.2
Zhang, L.3
Zhu, Y.4
Zheng, Y.5
-
40
-
-
34948842866
-
Accuracy and quality of massively parallel DNA pyrosequencing
-
Huse SM, Huber JA, Morrison HG, Sogin ML, Mark Welch D (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biology 8.
-
(2007)
Genome Biology
, pp. 8
-
-
Huse, S.M.1
Huber, J.A.2
Morrison, H.G.3
Sogin, M.L.4
Mark Welch, D.5
-
41
-
-
40149103278
-
Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex
-
Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R (2008) Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nature Methods 5: 235-237.
-
(2008)
Nature Methods
, vol.5
, pp. 235-237
-
-
Hamady, M.1
Walker, J.J.2
Harris, J.K.3
Gold, N.J.4
Knight, R.5
-
42
-
-
34548293679
-
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology 73: 5261-5267.
-
(2007)
Applied and Environmental Microbiology
, vol.73
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
Cole, J.R.4
-
43
-
-
34047240607
-
Query-dependent banding (QDB) for faster RNA similarity searches
-
Nawrocki EP, Eddy SR (2007) Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Computational Biology 3: 540-554.
-
(2007)
PLoS Computational Biology
, vol.3
, pp. 540-554
-
-
Nawrocki, E.P.1
Eddy, S.R.2
-
44
-
-
58149200948
-
The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis
-
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Research 37: D141-D145.
-
(2009)
Nucleic Acids Research
, vol.37
-
-
Cole, J.R.1
Wang, Q.2
Cardenas, E.3
Fish, J.4
Chai, B.5
-
45
-
-
33747827586
-
NAST: A multiple sequence alignment server for comparative analysis of 16S rRNA genes
-
DeSantis TZ, Hugenholtz P, Keller K, Brodie EL, Larsen N, et al. (2006) NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Research 34: W394-W399.
-
(2006)
Nucleic Acids Research
, vol.34
-
-
De Santis, T.Z.1
Hugenholtz, P.2
Keller, K.3
Brodie, E.L.4
Larsen, N.5
-
46
-
-
65449188232
-
Jalview Version 2-a multiple sequence alignment editor and analysis workbench
-
Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ (2009) Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics 25: 1189-1191.
-
(2009)
Bioinformatics
, vol.25
, pp. 1189-1191
-
-
Waterhouse, A.M.1
Procter, J.B.2
Martin, D.M.A.3
Clamp, M.4
Barton, G.J.5
-
47
-
-
33750403801
-
RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
Stamatakis A (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
-
(2006)
Bioinformatics
, vol.22
, pp. 2688-2690
-
-
Stamatakis, A.1
-
48
-
-
33845873289
-
Interactive Tree Of Life (iTOL): An online tool for phylogenetic tree display and annotation
-
Letunic I, Bork P (2007) Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23: 127-128.
-
(2007)
Bioinformatics
, vol.23
, pp. 127-128
-
-
Letunic, I.1
Bork, P.2
-
49
-
-
33748713890
-
UniFrac-An online tool for comparing microbial community diversity in a phylogenetic context
-
Lozupone C, Hamady M, Knight R (2006) UniFrac-An online tool for comparing microbial community diversity in a phylogenetic context. Bmc Bioinformatics 7.
-
(2006)
Bmc Bioinformatics
, pp. 7
-
-
Lozupone, C.1
Hamady, M.2
Knight, R.3
-
50
-
-
33644606606
-
FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries
-
Yu YN, Breitbart M, McNairnie P, Rohwer F (2006) FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries. Bmc Bioinformatics 7.
-
(2006)
Bmc Bioinformatics
, pp. 7
-
-
Yu, Y.N.1
Breitbart, M.2
McNairnie, P.3
Rohwer, F.4
-
51
-
-
0027968068
-
Clustal-W-improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson JD, Higgins DG, Gibson TJ (1994) Clustal-W-improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673-4680.
-
(1994)
Nucleic Acids Research
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
52
-
-
3242810318
-
MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment
-
Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings in Bioinformatics 5: 150-163.
-
(2004)
Briefings in Bioinformatics
, vol.5
, pp. 150-163
-
-
Kumar, S.1
Tamura, K.2
Nei, M.3
-
53
-
-
77949718257
-
FastTree 2-approximately maximumlikelihood trees for large alignments
-
Price MN, Dehal PS, Arkin AP (2010) FastTree 2-approximately maximumlikelihood trees for large alignments. PLoS ONE 5: e9490.
-
(2010)
PLoS ONE
, vol.5
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
54
-
-
0004244096
-
-
Schinner F, Ohlinger R, Kandeler E, Margesin R, eds, New York: Springer
-
Schinner F, Ohlinger R, Kandeler E, Margesin R, eds (1996) Methods in Soil Biology. New York: Springer.
-
(1996)
Methods in Soil Biology
-
-
-
56
-
-
34748886657
-
PAST: Paleontological Statistics Software Package for Education and Data Analysis
-
Hammer Ø, Harper DAT, Ryan PD (2001) PAST: Paleontological Statistics Software Package for Education and Data Analysis. Palaeontologia Electronica 4: 9.
-
(2001)
Palaeontologia Electronica
, vol.4
, pp. 9
-
-
Hammer, O.1
Harper, D.A.T.2
Ryan, P.D.3
-
59
-
-
43349108617
-
Hydrogen emission from nodulated soybeans [Glycine max (L.) Merr.] and consequences for the productivity of a subsequent maize (Zea mays L.) crop
-
Peoples MB, McLennan PD, Brockwell J (2008) Hydrogen emission from nodulated soybeans [Glycine max (L.) Merr.] and consequences for the productivity of a subsequent maize (Zea mays L.) crop. Plant and Soil 307: 67-82.
-
(2008)
Plant and Soil
, vol.307
, pp. 67-82
-
-
Peoples, M.B.1
McLennan, P.D.2
Brockwell, J.3
-
61
-
-
63849254954
-
Testing the functional significance of microbial community composition
-
Strickland MS, Lauber C, Fierer N, Bradford MA (2009) Testing the functional significance of microbial community composition. Ecology 90: 441-451.
-
(2009)
Ecology
, vol.90
, pp. 441-451
-
-
Strickland, M.S.1
Lauber, C.2
Fierer, N.3
Bradford, M.A.4
-
62
-
-
19944368795
-
Linking microbial community composition and soil processes in a California annual grassland and mixed-conifer forest
-
Balser TC, Firestone MK (2005) Linking microbial community composition and soil processes in a California annual grassland and mixed-conifer forest. Biogeochemistry 73: 395-415.
-
(2005)
Biogeochemistry
, vol.73
, pp. 395-415
-
-
Balser, T.C.1
Firestone, M.K.2
-
66
-
-
40549127742
-
Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile
-
Hansel CM, Fendorf S, Jardine PM, Francis CA (2008) Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile. Applied and Environmental Microbiology 74: 1620-1633.
-
(2008)
Applied and Environmental Microbiology
, vol.74
, pp. 1620-1633
-
-
Hansel, C.M.1
Fendorf, S.2
Jardine, P.M.3
Francis, C.A.4
-
67
-
-
49649087440
-
Simultaneous assessment of soil microbial community structure and function through analysis of the metatranscriptome
-
Urich T, Lanzen A, Qi J, Huson DH, Schleper C, et al. (2008) Simultaneous assessment of soil microbial community structure and function through analysis of the metatranscriptome. PLoS ONE 3: e2527.
-
(2008)
PLoS ONE
, vol.3
-
-
Urich, T.1
Lanzen, A.2
Qi, J.3
Huson, D.H.4
Schleper, C.5
-
68
-
-
1642267395
-
Comparison of crenarchaeal consortia inhabiting the rhizosphere of diverse terrestrial plants with those in bulk soil in native environments
-
Sliwinski MK, Goodman RM (2004) Comparison of crenarchaeal consortia inhabiting the rhizosphere of diverse terrestrial plants with those in bulk soil in native environments. Applied and Environmental Microbiology 70: 1821-1826.
-
(2004)
Applied and Environmental Microbiology
, vol.70
, pp. 1821-1826
-
-
Sliwinski, M.K.1
Goodman, R.M.2
-
69
-
-
23744458464
-
Cultivation of mesophilic soil crenarchaeotes in enrichment cultures from plant roots
-
Simon HM, Jahn CE, Bergerud LT, Sliwinski MK, Weimer PJ, et al. (2005) Cultivation of mesophilic soil crenarchaeotes in enrichment cultures from plant roots. Applied and Environmental Microbiology 71: 4751-4760.
-
(2005)
Applied and Environmental Microbiology
, vol.71
, pp. 4751-4760
-
-
Simon, H.M.1
Jahn, C.E.2
Bergerud, L.T.3
Sliwinski, M.K.4
Weimer, P.J.5
|