-
1
-
-
53449086190
-
Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use
-
Acosta-Martínez V, Dowd S, Sun Y & Allen V (2008) Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biol Biochem 40: 2762-2770.
-
(2008)
Soil Biol Biochem
, vol.40
, pp. 2762-2770
-
-
Acosta-Martínez, V.1
Dowd, S.2
Sun, Y.3
Allen, V.4
-
2
-
-
33745942317
-
The role of root exudates in rhizosphere interactions with plants and other organisms
-
Bais HP, Weir TL, Perry LG, Gilroy S & Vivanco JM (2006) The role of root exudates in rhizosphere interactions with plants and other organisms. Annu Rev Plant Biol 57: 233-266.
-
(2006)
Annu Rev Plant Biol
, vol.57
, pp. 233-266
-
-
Bais, H.P.1
Weir, T.L.2
Perry, L.G.3
Gilroy, S.4
Vivanco, J.M.5
-
3
-
-
36549064652
-
Soil biota, ecosystem services and land productivity
-
Barrios E (2007) Soil biota, ecosystem services and land productivity. Ecol Econ 64: 269-285.
-
(2007)
Ecol Econ
, vol.64
, pp. 269-285
-
-
Barrios, E.1
-
4
-
-
79958265126
-
Generation of multi-million 16S rRNA gene libraries from complex microbial communities by assembling paired-end Illumina reads
-
Bartram AK, Lynch MDJ, Stearns JC, Moreno-Hagelsieb G & Neufeld JD (2011) Generation of multi-million 16S rRNA gene libraries from complex microbial communities by assembling paired-end Illumina reads. Appl Environ Microbiol 77: 3846-3852.
-
(2011)
Appl Environ Microbiol
, vol.77
, pp. 3846-3852
-
-
Bartram, A.K.1
Lynch, M.D.J.2
Stearns, J.C.3
Moreno-Hagelsieb, G.4
Neufeld, J.D.5
-
5
-
-
79955057814
-
Examining the global distribution of dominant archaeal populations in soil
-
Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R & Fierer N (2011) Examining the global distribution of dominant archaeal populations in soil. ISME J 5: 908-917.
-
(2011)
ISME J
, vol.5
, pp. 908-917
-
-
Bates, S.T.1
Berg-Lyons, D.2
Caporaso, J.G.3
Walters, W.A.4
Knight, R.5
Fierer, N.6
-
6
-
-
84866156946
-
Archaeal abundance across a pH gradient in an arable soil and its relationship with bacterial and fungal growth rates
-
Bengtson P, Sterngren AE & Rousk J (2012) Archaeal abundance across a pH gradient in an arable soil and its relationship with bacterial and fungal growth rates. Appl Environ Microbiol 78: 5906-5911.
-
(2012)
Appl Environ Microbiol
, vol.78
, pp. 5906-5911
-
-
Bengtson, P.1
Sterngren, A.E.2
Rousk, J.3
-
7
-
-
83155178360
-
Barcoded primers used in multiplex amplicon pyrosequencing bias amplification
-
Berry D, Mahfoudh KB, Wagner M & Loy A (2011) Barcoded primers used in multiplex amplicon pyrosequencing bias amplification. Appl Environ Microbiol 77: 7846-7849.
-
(2011)
Appl Environ Microbiol
, vol.77
, pp. 7846-7849
-
-
Berry, D.1
Mahfoudh, K.B.2
Wagner, M.3
Loy, A.4
-
8
-
-
54549102367
-
Forward selection of explanatory variables
-
Blanchet FG, Legendre P & Borcard D (2008) Forward selection of explanatory variables. Ecology 89: 2623-2632.
-
(2008)
Ecology
, vol.89
, pp. 2623-2632
-
-
Blanchet, F.G.1
Legendre, P.2
Borcard, D.3
-
9
-
-
0034700482
-
Disturbance and diversity in experimental microcosms
-
Buckling A, Kassen R, Bell G & Rainey PB (2000) Disturbance and diversity in experimental microcosms. Nature 408: 961-964.
-
(2000)
Nature
, vol.408
, pp. 961-964
-
-
Buckling, A.1
Kassen, R.2
Bell, G.3
Rainey, P.B.4
-
11
-
-
78650295170
-
Archaea, a timeline of the third domain
-
Cavicchioli R (2011) Archaea, a timeline of the third domain. Nat Rev Microbiol 9: 51-61.
-
(2011)
Nat Rev Microbiol
, vol.9
, pp. 51-61
-
-
Cavicchioli, R.1
-
12
-
-
0035154463
-
Oxidizible organic carbon fractions and soil quality changes in an oxic paleustalf under different pasture leys
-
Chan KY, Bowman A & Oates A (2001) Oxidizible organic carbon fractions and soil quality changes in an oxic paleustalf under different pasture leys. Soil Sci 166: 61-67.
-
(2001)
Soil Sci
, vol.166
, pp. 61-67
-
-
Chan, K.Y.1
Bowman, A.2
Oates, A.3
-
13
-
-
0344898137
-
Nonparametric estimation of Shannon's index of diversity when there are unseen species in sample
-
Chao A & Shen TJ (2003) Nonparametric estimation of Shannon's index of diversity when there are unseen species in sample. Environ Ecol Stat 10: 429-443.
-
(2003)
Environ Ecol Stat
, vol.10
, pp. 429-443
-
-
Chao, A.1
Shen, T.J.2
-
15
-
-
69249109724
-
Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine
-
Claesson MJ, O'Sullivan O, Wang Q et al. (2009) Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS ONE 4: e6669.
-
(2009)
PLoS ONE
, vol.4
-
-
Claesson, M.J.1
O'Sullivan, O.2
Wang, Q.3
-
16
-
-
0017806329
-
Diversity in tropical rain forests and coral reefs
-
Connell JH (1978) Diversity in tropical rain forests and coral reefs. Science 199: 1302-1310.
-
(1978)
Science
, vol.199
, pp. 1302-1310
-
-
Connell, J.H.1
-
17
-
-
0041851187
-
Isolation, characterization and comparison of bacteria from swine faeces and manure storage pits
-
Cotta MA, Whitehead TR & Zeltwanger RL (2003) Isolation, characterization and comparison of bacteria from swine faeces and manure storage pits. Environ Microbiol 5: 737-745.
-
(2003)
Environ Microbiol
, vol.5
, pp. 737-745
-
-
Cotta, M.A.1
Whitehead, T.R.2
Zeltwanger, R.L.3
-
18
-
-
0032976388
-
Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia River, its estuary, and the adjacent coastal ocean
-
Crump BC, Armbrust EV & Baross JA (1999) Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia River, its estuary, and the adjacent coastal ocean. Appl Environ Microbiol 65: 3192-3204.
-
(1999)
Appl Environ Microbiol
, vol.65
, pp. 3192-3204
-
-
Crump, B.C.1
Armbrust, E.V.2
Baross, J.A.3
-
19
-
-
85104323037
-
Particle fractionation and particle-size analysis
-
Black CA, ed) ASA, Madison.
-
Day PR (1965) Particle fractionation and particle-size analysis. Methods of Soil Analysis (Black CA, ed), pp. 545-567. ASA, Madison.
-
(1965)
Methods of Soil Analysis
, pp. 545-567
-
-
Day, P.R.1
-
20
-
-
79955783694
-
Characterization of trapped lignin-degrading microbes in tropical forest soil
-
Deangelis KM, Allgaier M, Chavarria Y et al. (2011) Characterization of trapped lignin-degrading microbes in tropical forest soil. PLoS ONE 6: e19306.
-
(2011)
PLoS ONE
, vol.6
-
-
Deangelis, K.M.1
Allgaier, M.2
Chavarria, Y.3
-
21
-
-
79953232393
-
Accessing the soil metagenome for studies of microbial diversity
-
Delmont TO, Robe P, Cecillon S et al. (2011) Accessing the soil metagenome for studies of microbial diversity. Appl Environ Microbiol 77: 1315-1324.
-
(2011)
Appl Environ Microbiol
, vol.77
, pp. 1315-1324
-
-
Delmont, T.O.1
Robe, P.2
Cecillon, S.3
-
22
-
-
84865344067
-
Structure, fluctuation and magnitude of a natural grassland soil metagenome
-
Delmont TO, Prestat E, Keegan KP et al. (2012) Structure, fluctuation and magnitude of a natural grassland soil metagenome. ISME J 6: 1677-1687.
-
(2012)
ISME J
, vol.6
, pp. 1677-1687
-
-
Delmont, T.O.1
Prestat, E.2
Keegan, K.P.3
-
23
-
-
33747827586
-
NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes
-
DeSantis TZ, Hugenholtz P, Keller K et al. (2006) NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34: W394-W399.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
DeSantis, T.Z.1
Hugenholtz, P.2
Keller, K.3
-
24
-
-
1142306112
-
VEGAN, a package of R functions for community ecology
-
Dixon P (2003) VEGAN, a package of R functions for community ecology. J Veg Sci 14: 927-930.
-
(2003)
J Veg Sci
, vol.14
, pp. 927-930
-
-
Dixon, P.1
-
25
-
-
79961181125
-
UCHIME improves sensitivity and speed of chimera detection
-
Edgar RC, Haas BJ, Clemente JC, Quince C & Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200.
-
(2011)
Bioinformatics
, vol.27
, pp. 2194-2200
-
-
Edgar, R.C.1
Haas, B.J.2
Clemente, J.C.3
Quince, C.4
Knight, R.5
-
26
-
-
38249032636
-
Glucosidases and galactosidases in soils
-
Eivazi F & Tabatabai A (1988) Glucosidases and galactosidases in soils. Soil Biol Biochem 20: 601-606.
-
(1988)
Soil Biol Biochem
, vol.20
, pp. 601-606
-
-
Eivazi, F.1
Tabatabai, A.2
-
27
-
-
61849108201
-
C-13-Isotopomer-based metabolomics of microbial groups isolated from two forest soils
-
Fan TWM, Bird JA, Brodie EL & Lane AN (2009) C-13-Isotopomer-based metabolomics of microbial groups isolated from two forest soils. Metabolomics 5: 108-122.
-
(2009)
Metabolomics
, vol.5
, pp. 108-122
-
-
Fan, T.W.M.1
Bird, J.A.2
Brodie, E.L.3
Lane, A.N.4
-
28
-
-
0024783287
-
Nitrate reductase-activity in soils - effects of trace-elements
-
Fu MH & Tabatabai MA (1989) Nitrate reductase-activity in soils - effects of trace-elements. Soil Biol Biochem 21: 943-946.
-
(1989)
Soil Biol Biochem
, vol.21
, pp. 943-946
-
-
Fu, M.H.1
Tabatabai, M.A.2
-
29
-
-
79956136196
-
Beyond the bacterium: Planctomycetes challenge our concepts of microbial structure and function
-
Fuerst JA & Sagulenko E (2011) Beyond the bacterium: Planctomycetes challenge our concepts of microbial structure and function. Nat Rev Microbiol 9: 403-413.
-
(2011)
Nat Rev Microbiol
, vol.9
, pp. 403-413
-
-
Fuerst, J.A.1
Sagulenko, E.2
-
30
-
-
4744340843
-
Microbial diversity in soil: selection of microbial populations by plant and soil type and implications for disease suppressiveness
-
Garbeva P, van Veen JA & van Elsas JD (2004) Microbial diversity in soil: selection of microbial populations by plant and soil type and implications for disease suppressiveness. Annu Rev Phytopathol 42: 243-270.
-
(2004)
Annu Rev Phytopathol
, vol.42
, pp. 243-270
-
-
Garbeva, P.1
van Veen, J.A.2
van Elsas, J.D.3
-
31
-
-
84856563821
-
Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes
-
Gihring TM, Green SJ & Schadt CW (2011) Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes. Environ Microbiol 14: 285-290.
-
(2011)
Environ Microbiol
, vol.14
, pp. 285-290
-
-
Gihring, T.M.1
Green, S.J.2
Schadt, C.W.3
-
32
-
-
78149429458
-
Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products
-
Gloor GB, Hummelen R, Macklaim JM, Dickson RJ, Fernandes AD, MacPhee R & Reid G (2010) Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products. PLoS ONE 5: e15406.
-
(2010)
PLoS ONE
, vol.5
-
-
Gloor, G.B.1
Hummelen, R.2
Macklaim, J.M.3
Dickson, R.J.4
Fernandes, A.D.5
MacPhee, R.6
Reid, G.7
-
33
-
-
0000803388
-
The population frequencies of species and the estimation of population parameters
-
Good IJ (1953) The population frequencies of species and the estimation of population parameters. Biometrika 40: 237-264.
-
(1953)
Biometrika
, vol.40
, pp. 237-264
-
-
Good, I.J.1
-
34
-
-
0036242973
-
Soil carbon stocks and land use change: a meta analysis
-
Guo LB & Gifford RM (2002) Soil carbon stocks and land use change: a meta analysis. Glob Change Biol 8: 345-360.
-
(2002)
Glob Change Biol
, vol.8
, pp. 345-360
-
-
Guo, L.B.1
Gifford, R.M.2
-
35
-
-
33646193540
-
ORDER III. Rhodobacterales ord. nov
-
Brenner DJ, Krieg NR, Garrity GM, eds) Springer, New York.
-
Imhoff J (2005) ORDER III. Rhodobacterales ord. nov. Bergey's Manual of Systematic Bacteriology, 1 (Brenner DJ, Krieg NR, Garrity GM et al., eds), pp. 161-167. Springer, New York.
-
(2005)
Bergey's Manual of Systematic Bacteriology
, vol.1
, pp. 161-167
-
-
Imhoff, J.1
-
36
-
-
9244220669
-
The ecology and genetics of microbial diversity
-
Kassen R & Rainey PB (2004) The ecology and genetics of microbial diversity. Annu Rev Microbiol 58: 207-231.
-
(2004)
Annu Rev Microbiol
, vol.58
, pp. 207-231
-
-
Kassen, R.1
Rainey, P.B.2
-
37
-
-
21244443807
-
Sucrose application, soil microbial respiration and evolved carbon dioxide isotope enrichment under contrasting land uses
-
Kelliher FM, Barbour MM & Hunt JE (2005) Sucrose application, soil microbial respiration and evolved carbon dioxide isotope enrichment under contrasting land uses. Plant Soil 268: 233-242.
-
(2005)
Plant Soil
, vol.268
, pp. 233-242
-
-
Kelliher, F.M.1
Barbour, M.M.2
Hunt, J.E.3
-
38
-
-
80052970135
-
Groundwater dependent ecosystems. Part I: hydroecological status and trends
-
Kløve B, Ala-aho P, Bertrand G et al. (2011) Groundwater dependent ecosystems. Part I: hydroecological status and trends. Environ Sci Policy 14: 770-781.
-
(2011)
Environ Sci Policy
, vol.14
, pp. 770-781
-
-
Kløve, B.1
Ala-aho, P.2
Bertrand, G.3
-
39
-
-
79960171178
-
Soil and plant factors driving the community of soil-borne microorganisms across chronosequences of secondary succession of chalk grasslands with neutral pH
-
Kuramae E, Gamper H, van Veen J & Kowalchuk G (2011) Soil and plant factors driving the community of soil-borne microorganisms across chronosequences of secondary succession of chalk grasslands with neutral pH. FEMS Microbiol Ecol 77: 285-294.
-
(2011)
FEMS Microbiol Ecol
, vol.77
, pp. 285-294
-
-
Kuramae, E.1
Gamper, H.2
van Veen, J.3
Kowalchuk, G.4
-
40
-
-
67651247607
-
Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale
-
Lauber CL, Hamady M, Knight R & Fierer N (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75: 5111-5120.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 5111-5120
-
-
Lauber, C.L.1
Hamady, M.2
Knight, R.3
Fierer, N.4
-
41
-
-
0032967877
-
Distance-based redundancy analysis: testing multispecies responses in multifactorial ecological experiments
-
Legendre P & Anderson MJ (1999) Distance-based redundancy analysis: testing multispecies responses in multifactorial ecological experiments. Ecol Monogr 69: 1-24.
-
(1999)
Ecol Monogr
, vol.69
, pp. 1-24
-
-
Legendre, P.1
Anderson, M.J.2
-
42
-
-
0034782218
-
Ecologically meaningful transformations for ordination of species data
-
Legendre P & Gallagher E (2001) Ecologically meaningful transformations for ordination of species data. Oecologia 129: 271-280.
-
(2001)
Oecologia
, vol.129
, pp. 271-280
-
-
Legendre, P.1
Gallagher, E.2
-
44
-
-
80052638464
-
Soil-specific limitations for access and analysis of soil microbial communities by metagenomics
-
Lombard N, Prestat E, van Elsas JD & Simonet P (2011) Soil-specific limitations for access and analysis of soil microbial communities by metagenomics. FEMS Microbiol Ecol 78: 31-49.
-
(2011)
FEMS Microbiol Ecol
, vol.78
, pp. 31-49
-
-
Lombard, N.1
Prestat, E.2
van Elsas, J.D.3
Simonet, P.4
-
45
-
-
78751650459
-
Microbial growth rate measurements reveal that land-use abandonment promotes a fungal dominance of SOM decomposition in grazed Mediterranean ecosystems
-
Lopez-Sangil L, Rousk J, Wallander H & Casals P (2011) Microbial growth rate measurements reveal that land-use abandonment promotes a fungal dominance of SOM decomposition in grazed Mediterranean ecosystems. Biol Fertil Soils 47: 129-138.
-
(2011)
Biol Fertil Soils
, vol.47
, pp. 129-138
-
-
Lopez-Sangil, L.1
Rousk, J.2
Wallander, H.3
Casals, P.4
-
46
-
-
11244324812
-
Microbial diversity in soil: ecological theories, the contribution of molecular techniques and the impact of transgenic plants and transgenic microorganisms
-
Lynch JM, Benedetti A, Insam H, Nuti MP, Smalla K, Torsvik V & Nannipieri P (2004) Microbial diversity in soil: ecological theories, the contribution of molecular techniques and the impact of transgenic plants and transgenic microorganisms. Biol Fertil Soils 40: 363-385.
-
(2004)
Biol Fertil Soils
, vol.40
, pp. 363-385
-
-
Lynch, J.M.1
Benedetti, A.2
Insam, H.3
Nuti, M.P.4
Smalla, K.5
Torsvik, V.6
Nannipieri, P.7
-
47
-
-
79954423226
-
Phylogenetic analysis of methanogens in the pig feces
-
Mao SY, Yang CF & Zhu WY (2011) Phylogenetic analysis of methanogens in the pig feces. Curr Microbiol 62: 1386-1389.
-
(2011)
Curr Microbiol
, vol.62
, pp. 1386-1389
-
-
Mao, S.Y.1
Yang, C.F.2
Zhu, W.Y.3
-
48
-
-
0028188895
-
Phosphomonoesterase, phosphodiesterase, phosphotriesterase, and inorganic pyrophosphatase activities in forest soils in an alpine area - effect of pH on enzyme-activity and extractability
-
Margesin R & Schinner F (1994) Phosphomonoesterase, phosphodiesterase, phosphotriesterase, and inorganic pyrophosphatase activities in forest soils in an alpine area - effect of pH on enzyme-activity and extractability. Biol Fertil Soils 18: 320-326.
-
(1994)
Biol Fertil Soils
, vol.18
, pp. 320-326
-
-
Margesin, R.1
Schinner, F.2
-
49
-
-
84860008730
-
Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia
-
Martinez-Garcia M, Brazel DM, Swan BK et al. (2012) Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia. PLoS ONE 7: e35314.
-
(2012)
PLoS ONE
, vol.7
-
-
Martinez-Garcia, M.1
Brazel, D.M.2
Swan, B.K.3
-
50
-
-
84857122937
-
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
-
McDonald D, Price MN, Goodrich J et al. (2012) An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6: 610-618.
-
(2012)
ISME J
, vol.6
, pp. 610-618
-
-
McDonald, D.1
Price, M.N.2
Goodrich, J.3
-
51
-
-
39449089394
-
Parallel tagged sequencing on the 454 platform
-
Meyer M, Stenzel U & Hofreiter M (2008) Parallel tagged sequencing on the 454 platform. Nat Protoc 3: 267-278.
-
(2008)
Nat Protoc
, vol.3
, pp. 267-278
-
-
Meyer, M.1
Stenzel, U.2
Hofreiter, M.3
-
52
-
-
77149121752
-
Halobacterium salinarum strain MMD047 - a low-salt adapted member of the Halobacteriaceae?
-
Oren A & Ventosa A (2009) Halobacterium salinarum strain MMD047 - a low-salt adapted member of the Halobacteriaceae? Biotechnol Bioprocess Eng 14: 869-870.
-
(2009)
Biotechnol Bioprocess Eng
, vol.14
, pp. 869-870
-
-
Oren, A.1
Ventosa, A.2
-
53
-
-
84892669795
-
Improving your data transformations: applying the Box-Cox transformation
-
Osborne JW (2010) Improving your data transformations: applying the Box-Cox transformation. Pract Ass Res Eval 15: 1-9.
-
(2010)
Pract Ass Res Eval
, vol.15
, pp. 1-9
-
-
Osborne, J.W.1
-
55
-
-
33646598649
-
Dynamics of a pig slurry microbial community during anaerobic storage and management
-
Peu P, Brugere H, Pourcher A-M, Kerouredan M, Godon J-J, Delgenes J-P & Dabert P (2006) Dynamics of a pig slurry microbial community during anaerobic storage and management. Appl Environ Microbiol 72: 3578-3585.
-
(2006)
Appl Environ Microbiol
, vol.72
, pp. 3578-3585
-
-
Peu, P.1
Brugere, H.2
Pourcher, A.-M.3
Kerouredan, M.4
Godon, J.-J.5
Delgenes, J.-P.6
Dabert, P.7
-
56
-
-
0037184270
-
Denitrifying genes in bacterial and archaeal genomes
-
Philippot L (2002) Denitrifying genes in bacterial and archaeal genomes. BBA-Gene Struct Expr 1577: 355-376.
-
(2002)
BBA-Gene Struct Expr
, vol.1577
, pp. 355-376
-
-
Philippot, L.1
-
57
-
-
2642518198
-
Isolation of haloarchaea that grow at low salinities
-
Purdy KJ, Cresswell-Maynard TD, Nedwell DB, McGenity TJ, Grant WD, Timmis KN & Embley TM (2004) Isolation of haloarchaea that grow at low salinities. Environ Microbiol 6: 591-595.
-
(2004)
Environ Microbiol
, vol.6
, pp. 591-595
-
-
Purdy, K.J.1
Cresswell-Maynard, T.D.2
Nedwell, D.B.3
McGenity, T.J.4
Grant, W.D.5
Timmis, K.N.6
Embley, T.M.7
-
58
-
-
84873739311
-
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
-
Quast C, Pruesse E, Yilmaz P et al. (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41: D590-D596.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Quast, C.1
Pruesse, E.2
Yilmaz, P.3
-
59
-
-
84885959895
-
-
R Development Core Team R: A language and environment for statistical computing, reference index version 2.14.1. R Foundation for Statistical Computing.
-
R Development Core Team 2011 R: A language and environment for statistical computing, reference index version 2.14.1. R Foundation for Statistical Computing.
-
(2011)
-
-
-
60
-
-
34547800097
-
Pyrosequencing enumerates and contrasts soil microbial diversity
-
Roesch LF, Fulthorpe RR, Riva A et al. (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1: 283-290.
-
(2007)
ISME J
, vol.1
, pp. 283-290
-
-
Roesch, L.F.1
Fulthorpe, R.R.2
Riva, A.3
-
61
-
-
62049085271
-
Contrasting soil pH effects on fungal and bacterial growth suggests functional redundancy in carbon mineralisation
-
Rousk J, Brookes PC & Baath E (2009) Contrasting soil pH effects on fungal and bacterial growth suggests functional redundancy in carbon mineralisation. Appl Environ Microbiol 75: 1589-1596.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 1589-1596
-
-
Rousk, J.1
Brookes, P.C.2
Baath, E.3
-
62
-
-
67650494989
-
Succession of bacterial populations during plant residue decomposition in rice field soil
-
Rui J, Peng J & Lu Y (2009) Succession of bacterial populations during plant residue decomposition in rice field soil. Appl Environ Microbiol 75: 4879-4886.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 4879-4886
-
-
Rui, J.1
Peng, J.2
Lu, Y.3
-
63
-
-
2942664887
-
Taxonomic heterogeneity within the Planctomycetales as derived by DNA-DNA hybridization, description of Rhodopirellula baltica gen. nov., sp. nov., transfer of Pirellula marina to the genus Blastopirellula gen. nov. as Blastopirellula marina comb. nov. and emended description of the genus Pirellula
-
Schlesner H, Rensmann C, Tindall BJ, Gade D, Rabus R, Pfeiffer S & Hirsch P (2004) Taxonomic heterogeneity within the Planctomycetales as derived by DNA-DNA hybridization, description of Rhodopirellula baltica gen. nov., sp. nov., transfer of Pirellula marina to the genus Blastopirellula gen. nov. as Blastopirellula marina comb. nov. and emended description of the genus Pirellula. Int J Syst Evol Microbiol 54: 1567-1580.
-
(2004)
Int J Syst Evol Microbiol
, vol.54
, pp. 1567-1580
-
-
Schlesner, H.1
Rensmann, C.2
Tindall, B.J.3
Gade, D.4
Rabus, R.5
Pfeiffer, S.6
Hirsch, P.7
-
64
-
-
77949495216
-
A high-throughput DNA sequence aligner for microbial ecology studies
-
Schloss PD (2009) A high-throughput DNA sequence aligner for microbial ecology studies. PLoS ONE 4: e8230.
-
(2009)
PLoS ONE
, vol.4
-
-
Schloss, P.D.1
-
65
-
-
78049240050
-
The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies
-
Schloss PD (2010) The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Schloss, P.D.1
-
67
-
-
79958196766
-
Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis
-
Schloss PD & Westcott SL (2011) Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77: 3219-3226.
-
(2011)
Appl Environ Microbiol
, vol.77
, pp. 3219-3226
-
-
Schloss, P.D.1
Westcott, S.L.2
-
68
-
-
72949107142
-
Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
Schloss PD, Westcott SL, Ryabin T et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 7537-7541
-
-
Schloss, P.D.1
Westcott, S.L.2
Ryabin, T.3
-
69
-
-
83355173006
-
Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies
-
Schloss PD, Gevers D & Westcott SL (2011) Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE 6: e27310.
-
(2011)
PLoS ONE
, vol.6
-
-
Schloss, P.D.1
Gevers, D.2
Westcott, S.L.3
-
70
-
-
0001359490
-
Equitability indices: dependence on the species count
-
Sheldon AL (1969) Equitability indices: dependence on the species count. Ecology 50: 466-467.
-
(1969)
Ecology
, vol.50
, pp. 466-467
-
-
Sheldon, A.L.1
-
71
-
-
40949149852
-
Biotic interactions, ecological knowledge and agriculture
-
Shennan C (2008) Biotic interactions, ecological knowledge and agriculture. Philos Trans R Soc Lond B Biol Sci 363: 717-739.
-
(2008)
Philos Trans R Soc Lond B Biol Sci
, vol.363
, pp. 717-739
-
-
Shennan, C.1
-
72
-
-
55949134434
-
Stoichiometry of soil enzyme activity at global scale
-
Sinsabaugh RL, Lauber CL, Weintraub MN et al. (2008) Stoichiometry of soil enzyme activity at global scale. Ecol Lett 11: 1252-1264.
-
(2008)
Ecol Lett
, vol.11
, pp. 1252-1264
-
-
Sinsabaugh, R.L.1
Lauber, C.L.2
Weintraub, M.N.3
-
73
-
-
15244351941
-
Characterisation of the microbial diversity in a pig manure storage pit using small subunit rDNA sequence analysis
-
Snell-Castro R, Godon J-J, Delgenès J-P & Dabert P (2005) Characterisation of the microbial diversity in a pig manure storage pit using small subunit rDNA sequence analysis. FEMS Microbiol Ecol 52: 229-242.
-
(2005)
FEMS Microbiol Ecol
, vol.52
, pp. 229-242
-
-
Snell-Castro, R.1
Godon, J.-J.2
Delgenès, J.-P.3
Dabert, P.4
-
74
-
-
33747073504
-
Microbial diversity in the deep sea and the underexplored 'rare biosphere'
-
Sogin ML, Morrison HG, Huber JA et al. (2006) Microbial diversity in the deep sea and the underexplored 'rare biosphere'. P Natl Acad Sci USA 103: 12115-12120.
-
(2006)
P Natl Acad Sci USA
, vol.103
, pp. 12115-12120
-
-
Sogin, M.L.1
Morrison, H.G.2
Huber, J.A.3
-
76
-
-
80052300610
-
Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering
-
Sul WJ, Cole JR, Jesus E da C, Wang Q, Farris RJ, Fish JA & Tiedje JM (2011) Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering. P Natl Acad Sci USA 108: 14637-14642.
-
(2011)
P Natl Acad Sci USA
, vol.108
, pp. 14637-14642
-
-
Sul, W.J.1
Cole, J.R.2
Jesus da, E.C.3
Wang, Q.4
Farris, R.J.5
Fish, J.A.6
Tiedje, J.M.7
-
77
-
-
67249096511
-
ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences
-
Sun Y, Cai Y, Liu L, Yu F, Farrell ML, McKendree W & Farmerie W (2009) ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Res 37: e76.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Sun, Y.1
Cai, Y.2
Liu, L.3
Yu, F.4
Farrell, M.L.5
McKendree, W.6
Farmerie, W.7
-
78
-
-
84873900715
-
Functional Assays and metagenomic analyses reveals differences between the microbial communities inhabiting the soil horizons of a Norway spruce plantation
-
Uroz S, Ioannidis P, Lengelle J, Al Cébron, Morin E, Buée M & Martin F (2013) Functional Assays and metagenomic analyses reveals differences between the microbial communities inhabiting the soil horizons of a Norway spruce plantation. PLoS ONE 8: e55929.
-
(2013)
PLoS ONE
, vol.8
-
-
Uroz, S.1
Ioannidis, P.2
Lengelle, J.3
Al, C.4
Morin, E.5
Buée, M.6
Martin, F.7
-
79
-
-
84864663408
-
Soil bacterial diversity screening using single 16S rRNA gene V regions coupled with multi-million read generating sequencing technologies
-
Vasileiadis S, Puglisi E, Arena M, Cappa F, Cocconcelli PS & Trevisan M (2012) Soil bacterial diversity screening using single 16S rRNA gene V regions coupled with multi-million read generating sequencing technologies. PLoS ONE 7: e42671.
-
(2012)
PLoS ONE
, vol.7
-
-
Vasileiadis, S.1
Puglisi, E.2
Arena, M.3
Cappa, F.4
Cocconcelli, P.S.5
Trevisan, M.6
-
80
-
-
79955948818
-
Effects of land use on the level, variation and spatial structure of soil enzyme activities and bacterial communities
-
Wallenius K, Rita H, Mikkonen A et al. (2011) Effects of land use on the level, variation and spatial structure of soil enzyme activities and bacterial communities. Soil Biol Biochem 43: 1464-1473.
-
(2011)
Soil Biol Biochem
, vol.43
, pp. 1464-1473
-
-
Wallenius, K.1
Rita, H.2
Mikkonen, A.3
-
81
-
-
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. 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
-
82
-
-
73249118051
-
Microbial community structure in anaerobic co-digestion of grass silage and cow manure in a laboratory continuously stirred tank reactor
-
Wang H, Tolvanen K, Lehtomäki A, Puhakka J & Rintala J (2010) Microbial community structure in anaerobic co-digestion of grass silage and cow manure in a laboratory continuously stirred tank reactor. Biodegradation 21: 135-146.
-
(2010)
Biodegradation
, vol.21
, pp. 135-146
-
-
Wang, H.1
Tolvanen, K.2
Lehtomäki, A.3
Puhakka, J.4
Rintala, J.5
-
83
-
-
1942421288
-
Managing soil microorganisms to improve productivity of agro-ecosystems
-
Welbaum GE, Sturz AV, Dong Z & Nowak J (2004) Managing soil microorganisms to improve productivity of agro-ecosystems. CRC Crit Rev Plant Sci 23: 175-193.
-
(2004)
CRC Crit Rev Plant Sci
, vol.23
, pp. 175-193
-
-
Welbaum, G.E.1
Sturz, A.V.2
Dong, Z.3
Nowak, J.4
|