-
1
-
-
31544448331
-
Microbial biogeography: Putting microorganisms on the map
-
Martiny JBH, Bohannan BJM, Brown J, Colwell R, Fuhrman J, Green J, Horner-Devine M, Kane M, Krumins J, Kuske C, Morin P, Naeem S, Ovreas L, Reysenbach A, Smith V, Staley J (2006) Microbial biogeography: putting microorganisms on the map. Nature Rev Microbiol 4:102-112.
-
(2006)
Nature Rev Microbiol
, vol.4
, pp. 102-112
-
-
Martiny, J.B.H.1
Bohannan, B.J.M.2
Brown, J.3
Colwell, R.4
Fuhrman, J.5
Green, J.6
Horner-Devine, M.7
Kane, M.8
Krumins, J.9
Kuske, C.10
Morin, P.11
Naeem, S.12
Ovreas, L.13
Reysenbach, A.14
Smith, V.15
Staley, J.16
-
2
-
-
44449118067
-
Microbial biogeography: From taxonomy to traits
-
Green JL, Bohannan BJM, Whitaker RJ (2008) Microbial biogeography: From taxonomy to traits. Science 320:1039-1043.
-
(2008)
Science
, vol.320
, pp. 1039-1043
-
-
Green, J.L.1
Bohannan, B.J.M.2
Whitaker, R.J.3
-
4
-
-
0034775280
-
Ammonia-oxidizing bacteria: A model for molecular microbial ecology
-
Kowalchuk GA, Stephen JR (2001) Ammonia-oxidizing bacteria: A model for molecular microbial ecology. Ann Rev Microbiol 55:485.
-
(2001)
Ann Rev Microbiol
, vol.55
, pp. 485
-
-
Kowalchuk, G.A.1
Stephen, J.R.2
-
5
-
-
0141502465
-
16 S rRNA and amoA-based phylogeny of 12 novel betaproteobacterial ammonia-oxidizing isolates: Extension of the dataset and proposal of a new lineage within the nitrosomonads
-
Purkhold U, Wagner M, Timmermann G, Pommerening-Roser A, Koops HP (2003) 16 S rRNA and amoA-based phylogeny of 12 novel betaproteobacterial ammonia-oxidizing isolates: extension of the dataset and proposal of a new lineage within the nitrosomonads. Int J Syst Evol Microbiol 53:1485-1494.
-
(2003)
Int J Syst Evol Microbiol
, vol.53
, pp. 1485-1494
-
-
Purkhold, U.1
Wagner, M.2
Timmermann, G.3
Pommerening-Roser, A.4
Koops, H.P.5
-
6
-
-
33747479446
-
Archaea predominate among ammonia-oxidizing prokaryotes in soils
-
Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol G, Prosser J, Schuster S, Schleper C (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
Nicol, G.6
Prosser, J.7
Schuster, S.8
Schleper, C.9
-
7
-
-
52949113790
-
Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment
-
Prosser J, Nicol G (2008) Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. Environ Microbiol 10:2931-2941.
-
(2008)
Environ Microbiol
, vol.10
, pp. 2931-2941
-
-
Prosser, J.1
Nicol, G.2
-
8
-
-
17844403255
-
Links between ammonia oxidizer species composition, functional diversity and nitrification kinetics in grassland soils
-
Webster G, Embley TM, Freitag TE, Smith Z, Prosser JI (2005) Links between ammonia oxidizer species composition, functional diversity and nitrification kinetics in grassland soils. Environ Microbiol 7:676-684.
-
(2005)
Environ Microbiol
, vol.7
, pp. 676-684
-
-
Webster, G.1
Embley, T.M.2
Freitag, T.E.3
Smith, Z.4
Prosser, J.I.5
-
9
-
-
52949087143
-
Community composition of ammonia-oxidizing bacteria and archaea in soils under stands of red alder and Douglas fir in Oregon
-
Boyle-Yarwood S, Bottomley P, Myrold D (2008) Community composition of ammonia-oxidizing bacteria and archaea in soils under stands of red alder and Douglas fir in Oregon. Environ Microbiol 10:2956-2965.
-
(2008)
Environ Microbiol
, vol.10
, pp. 2956-2965
-
-
Boyle-Yarwood, S.1
Bottomley, P.2
Myrold, D.3
-
10
-
-
3843094830
-
Diversity and composition of tropical soil nitrifiers across a plant diversity gradient and among land-use types
-
Carney KM, Matson PA, Bohannan BJM (2004) Diversity and composition of tropical soil nitrifiers across a plant diversity gradient and among land-use types. Ecol Lett 7:684-694.
-
(2004)
Ecol Lett
, vol.7
, pp. 684-694
-
-
Carney, K.M.1
Matson, P.A.2
Bohannan, B.J.M.3
-
11
-
-
0038656384
-
Ammonia-oxidizing bacteria along meadow-to-forest transects in the oregon cascade mountains
-
Mintie AT, Heichen RS, Cromack K, Myrold DD, Bottomley PJ (2003) Ammonia-oxidizing bacteria along meadow-to-forest transects in the oregon cascade mountains. Appl Environ Microbiol 69:3129-3136.
-
(2003)
Appl Environ Microbiol
, vol.69
, pp. 3129-3136
-
-
Mintie, A.T.1
Heichen, R.S.2
Cromack, K.3
Myrold, D.D.4
Bottomley, P.J.5
-
12
-
-
43449114462
-
Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam
-
Shen J, Zhang L, Zhu Y, Zhang J, He J (2008) Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam. Environ Microbiol 10:1601-1611.
-
(2008)
Environ Microbiol
, vol.10
, pp. 1601-1611
-
-
Shen, J.1
Zhang, L.2
Zhu, Y.3
Zhang, J.4
He, J.5
-
13
-
-
0042197522
-
Effects of temperature and fertilizer on activity and community structure of soil ammonia oxidizers
-
Avrahami S, Liesack W, Conrad R (2003) Effects of temperature and fertilizer on activity and community structure of soil ammonia oxidizers. Environ Microbiol 5:691-705.
-
(2003)
Environ Microbiol
, vol.5
, pp. 691-705
-
-
Avrahami, S.1
Liesack, W.2
Conrad, R.3
-
15
-
-
0034548634
-
Changes in the community structure of ammonia-oxidizing bacteria during secondary succession of calcareous grasslands
-
Kowalchuk GA, Stienstra AW, Heilig GHJ, Stephen JR, Woldendorp JW (2000) Changes in the community structure of ammonia-oxidizing bacteria during secondary succession of calcareous grasslands. Environ Microbiol 2:99-110.
-
(2000)
Environ Microbiol
, vol.2
, pp. 99-110
-
-
Kowalchuk, G.A.1
Stienstra, A.W.2
Heilig, G.H.J.3
Stephen, J.R.4
Woldendorp, J.W.5
-
16
-
-
33846459656
-
Community structure of ammonia-oxidizing bacteria under long-term application of mineral fertilizer and organic manure in a sandy loam soil
-
Chu HY, Fujii T, Morimoto S, Lin XG, Yagi K, Hu JL, Zhang JB (2007) Community structure of ammonia-oxidizing bacteria under long-term application of mineral fertilizer and organic manure in a sandy loam soil. Appl Environ Microbiol 73:485-491.
-
(2007)
Appl Environ Microbiol
, vol.73
, pp. 485-491
-
-
Chu, H.Y.1
Fujii, T.2
Morimoto, S.3
Lin, X.G.4
Yagi, K.5
Hu, J.L.6
Zhang, J.B.7
-
17
-
-
14944355944
-
Responses of nitrification and ammonia-oxidizing bacteria to reciprocal transfers of soil between adjacent coniferous forest and meadow vegetation in the Cascade Mountains of Oregon
-
Bottomley PJ, Taylor AE, Boyle SA, McMahon SK, Rich JJ, Cromack K, Myrold DD (2004) Responses of nitrification and ammonia-oxidizing bacteria to reciprocal transfers of soil between adjacent coniferous forest and meadow vegetation in the Cascade Mountains of Oregon. Microbial Ecol 48:500-508.
-
(2004)
Microbial Ecol
, vol.48
, pp. 500-508
-
-
Bottomley, P.J.1
Taylor, A.E.2
Boyle, S.A.3
McMahon, S.K.4
Rich, J.J.5
Cromack, K.6
Myrold, D.D.7
-
18
-
-
29144510139
-
Cold-temperate climate: A factor for selection of ammonia oxidizers in upland soil?
-
Avrahami S, Conrad R (2005) Cold-temperate climate: a factor for selection of ammonia oxidizers in upland soil? Can J Microbiol 51:709-714.
-
(2005)
Can J Microbiol
, vol.51
, pp. 709-714
-
-
Avrahami, S.1
Conrad, R.2
-
19
-
-
0035487280
-
Numerical analysis of grassland bacterial community structure under different land management regimens by using 16 S ribosomal DNA sequence data and denaturing gradient gel electrophoresis banding patterns
-
McCaig AE, Glover LA, Prosser JI (2001) Numerical analysis of grassland bacterial community structure under different land management regimens by using 16 S ribosomal DNA sequence data and denaturing gradient gel electrophoresis banding patterns. Appl Environ Microbiol 67:4554-4559.
-
(2001)
Appl Environ Microbiol
, vol.67
, pp. 4554-4559
-
-
McCaig, A.E.1
Glover, L.A.2
Prosser, J.I.3
-
20
-
-
0033015223
-
Comparative diversity of ammonia oxidizer 16 S rRNA gene sequences in native, tilled, and successional soils
-
Bruns MA, Stephen JR, Kowalchuk GA, Prosser JI, Paul EA (1999) Comparative diversity of ammonia oxidizer 16 S rRNA gene sequences in native, tilled, and successional soils. Appl Environ Microbiol 65:2994-3000.
-
(1999)
Appl Environ Microbiol
, vol.65
, pp. 2994-3000
-
-
Bruns, M.A.1
Stephen, J.R.2
Kowalchuk, G.A.3
Prosser, J.I.4
Paul, E.A.5
-
21
-
-
0036135250
-
Grassland management regimens reduce small-scale heterogeneity and species diversity of beta-proteobacterial ammonia oxidizer populations
-
Webster G, Embley TM, Prosser JI (2002) Grassland management regimens reduce small-scale heterogeneity and species diversity of beta-proteobacterial ammonia oxidizer populations. Appl Environ Microbiol 68:20-30.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 20-30
-
-
Webster, G.1
Embley, T.M.2
Prosser, J.I.3
-
22
-
-
31444447130
-
The diversity and biogeography of soil bacterial communities
-
Fierer N, Jackson R (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103:626-631.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 626-631
-
-
Fierer, N.1
Jackson, R.2
-
23
-
-
0028240270
-
Molecular analysis of enrichment cultures of marine ammonia oxidizers
-
McCaig AE, Embley TM, Prosser JI (1994) Molecular analysis of enrichment cultures of marine ammonia oxidizers. FEMS Microbiol Lett 120:363-367.
-
(1994)
FEMS Microbiol Lett
, vol.120
, pp. 363-367
-
-
McCaig, A.E.1
Embley, T.M.2
Prosser, J.I.3
-
24
-
-
0030901922
-
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 16 S ribosomal DNA fragments
-
Kowalchuk GA, Stephen JR, DeBoer 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 16 S ribosomal DNA fragments. Appl Environ Microbiol 63:1489-1497.
-
(1997)
Appl Environ Microbiol
, vol.63
, pp. 1489-1497
-
-
Kowalchuk, G.A.1
Stephen, J.R.2
DeBoer, W.3
Prosser, J.I.4
Embley, T.M.5
Woldendorp, J.W.6
-
25
-
-
33747827586
-
NAST: A multiple sequence alignment server for comparative analysis of 16 S rRNA genes
-
DeSantis T, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, Andersen GL (2006) NAST: a multiple sequence alignment server for comparative analysis of 16 S rRNA genes. Nucleic Acids Res 34:W394-399.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
DeSantis, T.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
-
26
-
-
14644397888
-
RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees
-
Stamatakis A, Ludwig T, Meier H (2005) RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21:456-463.
-
(2005)
Bioinformatics
, vol.21
, pp. 456-463
-
-
Stamatakis, A.1
Ludwig, T.2
Meier, H.3
-
27
-
-
33644606606
-
FastGroupII: A web-based bioinformatics platform for analyses of large 16 S rDNA libraries
-
Yu Y, Breitbart M, McNairnie P, Rohwer F (2006) FastGroupII: A web-based bioinformatics platform for analyses of large 16 S rDNA libraries. BMC Bioinformatics 7:57.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 57
-
-
Yu, Y.1
Breitbart, M.2
McNairnie, P.3
Rohwer, F.4
-
29
-
-
0026499429
-
Conservation evaluation and phylogenetic diversity
-
Faith DP (1992) Conservation evaluation and phylogenetic diversity. Biol Conserv 61:1-10.
-
(1992)
Biol Conserv
, vol.61
, pp. 1-10
-
-
Faith, D.P.1
-
31
-
-
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 Bioinform 7:371.
-
(2006)
BMC Bioinform
, vol.7
, pp. 371
-
-
Lozupone, C.1
Hamady, M.2
Knight, R.3
-
32
-
-
29144464937
-
UniFrac: A new phylogenetic method for comparing microbial communities
-
Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71:8228-8235.
-
(2005)
Appl Environ Microbiol
, vol.71
, pp. 8228-8235
-
-
Lozupone, C.1
Knight, R.2
-
33
-
-
34547781750
-
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
-
Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molec Biol Evol 24:1596-1599.
-
(2007)
Molec Biol Evol
, vol.24
, pp. 1596-1599
-
-
Tamura, K.1
Dudley, J.2
Nei, M.3
Kumar, S.4
-
34
-
-
70350374890
-
-
Systat for Windows, Richmond: Systat Software
-
Systat for Windows (2004) Systat Software version 11. Systat Software, Richmond.
-
(2004)
Systat Software Version 11
-
-
-
36
-
-
33847216554
-
Response of Nitrosospira sp strain AF-Like ammonia oxidizers to changes in temperature, soil moisture content, and fertilizer concentration
-
Avrahami S, Bohannan BJA (2007) Response of Nitrosospira sp strain AF-Like ammonia oxidizers to changes in temperature, soil moisture content, and fertilizer concentration. Appl Environ Microbiol 73:1166-1173.
-
(2007)
Appl Environ Microbiol
, vol.73
, pp. 1166-1173
-
-
Avrahami, S.1
Bohannan, B.J.A.2
-
37
-
-
22044454258
-
Presence of Nitrosospira cluster 2 bacteria corresponds to N transformation rates in nine acid Scots pine forest soils
-
Nugroho RA, Roling WFM, Laverman AM, Zoomer HR, Verhoef HA (2005) Presence of Nitrosospira cluster 2 bacteria corresponds to N transformation rates in nine acid Scots pine forest soils. FEMS Microbiol Ecol 53:473-481.
-
(2005)
FEMS Microbiol Ecol
, vol.53
, pp. 473-481
-
-
Nugroho, R.A.1
Roling, W.F.M.2
Laverman, A.M.3
Zoomer, H.R.4
Verhoef, H.A.5
-
38
-
-
0035211790
-
Species diversity of uncultured and cultured populations of soil and marine ammonia oxidizing bacteria
-
Smith Z, McCaig AE, Stephen JR, Embley TM, Prosser JI (2001) Species diversity of uncultured and cultured populations of soil and marine ammonia oxidizing bacteria. Microbial Ecol 42:228-237.
-
(2001)
Microbial Ecol
, vol.42
, pp. 228-237
-
-
Smith, Z.1
McCaig, A.E.2
Stephen, J.R.3
Embley, T.M.4
Prosser, J.I.5
-
39
-
-
0034009793
-
Molecular analysis of ammonia-oxidising bacteria in soil of successional grasslands of the Drentsche A (The Netherlands)
-
Kowalchuk GA, Stienstra AW, Heilig GHJ, Stephen JR, Woldendorp JW (2000) Molecular analysis of ammonia-oxidising bacteria in soil of successional grasslands of the Drentsche A (The Netherlands). FEMS Microbiol Ecol 31:207-215.
-
(2000)
FEMS Microbiol Ecol
, vol.31
, pp. 207-215
-
-
Kowalchuk, G.A.1
Stienstra, A.W.2
Heilig, G.H.J.3
Stephen, J.R.4
Woldendorp, J.W.5
-
40
-
-
0034010942
-
Analysis of ammonia-oxidizing bacteria populations in acid forest soil during conditions of moisture limitation
-
Hastings RC, Butler C, Singleton I, Saunders JR, McCarthy AJ (2000) Analysis of ammonia-oxidizing bacteria populations in acid forest soil during conditions of moisture limitation. Lett Appl Microbiol 30:14-18.
-
(2000)
Lett Appl Microbiol
, vol.30
, pp. 14-18
-
-
Hastings, R.C.1
Butler, C.2
Singleton, I.3
Saunders, J.R.4
McCarthy, A.J.5
-
41
-
-
0034868585
-
Distribution and ecophysiology of the nitrifying bacteria emphasizing cultured species
-
Koops HP, Pommerening-Roser A (2001) Distribution and ecophysiology of the nitrifying bacteria emphasizing cultured species. FEMS Microbiol Ecol 37:1-9.
-
(2001)
FEMS Microbiol Ecol
, vol.37
, pp. 1-9
-
-
Koops, H.P.1
Pommerening-Roser, A.2
-
42
-
-
0030790950
-
Direct molecular biological analysis of ammonia oxidising bacteria populations in cultivated soil plots treated with swine manure
-
Hastings RC, Ceccherini MT, Miclaus N, Saunders JR, Bazzicalupo M, McCarthy AJ (1997) Direct molecular biological analysis of ammonia oxidising bacteria populations in cultivated soil plots treated with swine manure. FEMS Microbiol Ecol 23:45-54.
-
(1997)
FEMS Microbiol Ecol
, vol.23
, pp. 45-54
-
-
Hastings, R.C.1
Ceccherini, M.T.2
Miclaus, N.3
Saunders, J.R.4
Bazzicalupo, M.5
McCarthy, A.J.6
-
43
-
-
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
-
45
-
-
38949149446
-
Low temperature decreases the phylogenetic diversity of ammonia-oxidizing archaea and bacteria in aquarium biofiltration systems
-
Urakawa H, Tajima Y, Numata Y, Tsuneda S (2008) Low temperature decreases the phylogenetic diversity of ammonia-oxidizing archaea and bacteria in aquarium biofiltration systems. Appl Environ Microbiol 74:894-900.
-
(2008)
Appl Environ Microbiol
, vol.74
, pp. 894-900
-
-
Urakawa, H.1
Tajima, Y.2
Numata, Y.3
Tsuneda, S.4
-
46
-
-
0142040853
-
Patterns of community change among ammonia oxidizers in meadow soils upon long-term incubation at different temperatures
-
Avrahami S, Conrad R (2003) Patterns of community change among ammonia oxidizers in meadow soils upon long-term incubation at different temperatures. Appl Environ Microbiol 69:6152-6164.
-
(2003)
Appl Environ Microbiol
, vol.69
, pp. 6152-6164
-
-
Avrahami, S.1
Conrad, R.2
-
47
-
-
0032878687
-
Comparison of Nitrosospira strains isolated from terrestrial environments
-
Jiang QQ, Bakken LR (1999) Comparison of Nitrosospira strains isolated from terrestrial environments. FEMS Microbiol Ecol 30:171-186.
-
(1999)
FEMS Microbiol Ecol
, vol.30
, pp. 171-186
-
-
Jiang, Q.Q.1
Bakken, L.R.2
-
49
-
-
0030250971
-
Kinetic characteristics of ammonium-oxidizer communities in a California oak woodland-annual grassland
-
Stark JM, Firestone MK (1996) Kinetic characteristics of ammonium-oxidizer communities in a California oak woodland-annual grassland. Soil Biol Biochem 28:1307-1317.
-
(1996)
Soil Biol Biochem
, vol.28
, pp. 1307-1317
-
-
Stark, J.M.1
Firestone, M.K.2
-
50
-
-
0036240150
-
Temperature responses of net nitrogen mineralization and nitrification in conifer forest soils incubated under standard laboratory conditions
-
Dalias P, Anderson JM, Bottner P, Couteaux MM (2002) Temperature responses of net nitrogen mineralization and nitrification in conifer forest soils incubated under standard laboratory conditions. Soil Biol Biochem 34:691-701.
-
(2002)
Soil Biol Biochem
, vol.34
, pp. 691-701
-
-
Dalias, P.1
Anderson, J.M.2
Bottner, P.3
Couteaux, M.M.4
-
51
-
-
0001331898
-
Temperature dependence of oxygen respiration, nitrogen mineralization, and nitrification in Arctic sediments
-
Thamdrup B, Fleischer S (1998) Temperature dependence of oxygen respiration, nitrogen mineralization, and nitrification in Arctic sediments. Aquatic Microb Ecol 15:191-199.
-
(1998)
Aquatic Microb Ecol
, vol.15
, pp. 191-199
-
-
Thamdrup, B.1
Fleischer, S.2
|