-
1
-
-
66149150877
-
Microbial community structure and its functional implications
-
COI: 1:CAS:528:DC%2BD1MXlvFShu70%3D, PID: 19444205
-
Fuhrman JA (2009) Microbial community structure and its functional implications. Nature 459:193–199. doi:10.1038/nature08058
-
(2009)
Nature
, vol.459
, pp. 193-199
-
-
Fuhrman, J.A.1
-
2
-
-
84897894862
-
Functional tradeoffs underpin salinity-driven divergence in microbial community composition
-
PID: 24586863
-
Dupont CL, Larsson J, Yooseph S, Ininbergs K, Goll J, Asplund-Samuelsson J, McCrow JP, Celepli N, Allen LZ, Ekman M, Lucas AJ, Hagstrom A, Thiagarajan M, Brindefalk B, Richter AR, Andersson AF, Tenney A, Lundin D, Tovchigrechko A, Nylander JAA, Brami D, Badger JH, Allen AE, Rusch DB, Hoffman J, Norrby E, Friedman R, Pinhassi J, Venter JC, Bergman B (2014) Functional tradeoffs underpin salinity-driven divergence in microbial community composition. PLoS One 9:e89549. doi:10.1371/journal.pone.0089549
-
(2014)
PLoS One
, vol.9
, pp. e89549
-
-
Dupont, C.L.1
Larsson, J.2
Yooseph, S.3
Ininbergs, K.4
Goll, J.5
Asplund-Samuelsson, J.6
McCrow, J.P.7
Celepli, N.8
Allen, L.Z.9
Ekman, M.10
Lucas, A.J.11
Hagstrom, A.12
Thiagarajan, M.13
Brindefalk, B.14
Richter, A.R.15
Andersson, A.F.16
Tenney, A.17
Lundin, D.18
Tovchigrechko, A.19
Nylander, J.A.A.20
Brami, D.21
Badger, J.H.22
Allen, A.E.23
Rusch, D.B.24
Hoffman, J.25
Norrby, E.26
Friedman, R.27
Pinhassi, J.28
Venter, J.C.29
Bergman, B.30
more..
-
3
-
-
80052964484
-
Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea
-
COI: 1:CAS:528:DC%2BC3MXht1WmsLjE, PID: 21472016
-
Herlemann DPR, Labrenz M, Jurgens K, Bertilsson S, Waniek JJ, Andersson AF (2011) Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J 5:1571–1579. doi:10.1038/ismej.2011.41
-
(2011)
ISME J
, vol.5
, pp. 1571-1579
-
-
Herlemann, D.P.R.1
Labrenz, M.2
Jurgens, K.3
Bertilsson, S.4
Waniek, J.J.5
Andersson, A.F.6
-
4
-
-
84884672457
-
Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin
-
COI: 1:CAS:528:DC%2BC3sXhsFenu7bL, PID: 23719153
-
Fortunato CS, Eiler A, Herfort L, Needoba JA, Peterson TD, Crump BC (2013) Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin. ISME J 7:1899–1911. doi:10.1038/ismej.2013.79
-
(2013)
ISME J
, vol.7
, pp. 1899-1911
-
-
Fortunato, C.S.1
Eiler, A.2
Herfort, L.3
Needoba, J.A.4
Peterson, T.D.5
Crump, B.C.6
-
5
-
-
1642376424
-
Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time
-
COI: 1:CAS:528:DC%2BD2cXisVKju7g%3D, PID: 15006771
-
Crump BC, Hopkinson CS, Sogin ML, Hobbie JE (2004) Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time. Appl Environ Microbiol 70:1494–1505. doi:10.1128/AEM. 70.3.1494-1505.2004
-
(2004)
Appl Environ Microbiol
, vol.70
, pp. 1494-1505
-
-
Crump, B.C.1
Hopkinson, C.S.2
Sogin, M.L.3
Hobbie, J.E.4
-
6
-
-
84872250001
-
Physiology and diversity of ammonia-oxidizing archaea
-
COI: 1:CAS:528:DC%2BC38XhsF2iur%2FE, PID: 22994489
-
Stahl DA, de la Torre JR (2012) Physiology and diversity of ammonia-oxidizing archaea. Annu Rev Microbiol 66:83–101. doi:10.1146/annurev-micro-092611-150128
-
(2012)
Annu Rev Microbiol
, vol.66
, pp. 83-101
-
-
Stahl, D.A.1
de la Torre, J.R.2
-
7
-
-
84884233716
-
Archaea in biogeochemical cycles
-
COI: 1:CAS:528:DC%2BC3sXhsleju7vO, PID: 23808334
-
Offre P, Spang A, Schleper C (2013) Archaea in biogeochemical cycles. Annu Rev Microbiol 67:437–457. doi:10.1146/annurev-micro-092412-155614
-
(2013)
Annu Rev Microbiol
, vol.67
, pp. 437-457
-
-
Offre, P.1
Spang, A.2
Schleper, C.3
-
8
-
-
39149118031
-
Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota
-
COI: 1:CAS:528:DC%2BD1cXhvFCgtLo%3D, PID: 18274537
-
Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P (2008) Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol 6:245–252. doi:10.1038/nrmicro1852
-
(2008)
Nat Rev Microbiol
, vol.6
, pp. 245-252
-
-
Brochier-Armanet, C.1
Boussau, B.2
Gribaldo, S.3
Forterre, P.4
-
9
-
-
19144373707
-
Genomic studies of uncultivated archaea
-
COI: 1:CAS:528:DC%2BD2MXksFKmsLw%3D, PID: 15931166
-
Schleper C, Jurgens G, Jonuscheit M (2005) Genomic studies of uncultivated archaea. Nat Rev Microbiol 3:479–488. doi:10.1038/nrmicro1159
-
(2005)
Nat Rev Microbiol
, vol.3
, pp. 479-488
-
-
Schleper, C.1
Jurgens, G.2
Jonuscheit, M.3
-
10
-
-
0035945618
-
Archaeal dominance in the mesopelagic zone of the Pacific Ocean
-
COI: 1:STN:280:DC%2BD3M7hvFOqsw%3D%3D, PID: 11206545
-
Karner MB, DeLong EF, Karl DM (2001) Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409:507–510. doi:10.1038/35054051
-
(2001)
Nature
, vol.409
, pp. 507-510
-
-
Karner, M.B.1
DeLong, E.F.2
Karl, D.M.3
-
11
-
-
0042853314
-
Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR
-
COI: 1:CAS:528:DC%2BD3sXnslehtr8%3D, PID: 12919414
-
Ochsenreiter T, Selezi D, Quaiser A, Bonch-Osmolovskaya L, Schleper C (2003) Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR. Environ Microbiol 5:787–797. doi:10.1046/j.1462-2920.2003.00476.x
-
(2003)
Environ Microbiol
, vol.5
, pp. 787-797
-
-
Ochsenreiter, T.1
Selezi, D.2
Quaiser, A.3
Bonch-Osmolovskaya, L.4
Schleper, C.5
-
12
-
-
33646497904
-
Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle?
-
COI: 1:CAS:528:DC%2BD28Xks1ekt7c%3D, PID: 16603359
-
Nicol GW, Schleper C (2006) Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle? Trends Microbiol 14:207–212. doi:10.1016/j.tim.2006.03.004
-
(2006)
Trends Microbiol
, vol.14
, pp. 207-212
-
-
Nicol, G.W.1
Schleper, C.2
-
13
-
-
84855281384
-
Factors influencing prokaryotic community structure composition in sub-surface coastal sediments
-
COI: 1:CAS:528:DC%2BC38XjslCiug%3D%3D
-
Molari M, Giovannelli D, d’Errico G, Manini E (2012) Factors influencing prokaryotic community structure composition in sub-surface coastal sediments. Estuar Coast Shelf Sci 97:141–148. doi:10.1016/j.ecss.2011.11.036
-
(2012)
Estuar Coast Shelf Sci
, vol.97
, pp. 141-148
-
-
Molari, M.1
Giovannelli, D.2
d’Errico, G.3
Manini, E.4
-
14
-
-
84922392302
-
Shifts in archaeaplankton community structure along ecological gradients of Pearl Estuary
-
Liu J, Yu S, Zhao M, He B, Zhang XH (2014) Shifts in archaeaplankton community structure along ecological gradients of Pearl Estuary. FEMS Microbiol Ecol. doi:10.1111/1574-6941.12404
-
(2014)
FEMS Microbiol Ecol
-
-
Liu, J.1
Yu, S.2
Zhao, M.3
He, B.4
Zhang, X.H.5
-
15
-
-
84906944377
-
Salinity-dominated change in community structure and ecological function of Archaea from the lower Pearl River to coastal South China Sea
-
COI: 1:CAS:528:DC%2BC2cXovFKnurc%3D, PID: 24880629
-
Xie W, Zhang C, Zhou X, Wang P (2014) Salinity-dominated change in community structure and ecological function of Archaea from the lower Pearl River to coastal South China Sea. Appl Microbiol Biotechnol 98:7971–7982. doi:10.1007/s00253-014-5838-9
-
(2014)
Appl Microbiol Biotechnol
, vol.98
, pp. 7971-7982
-
-
Xie, W.1
Zhang, C.2
Zhou, X.3
Wang, P.4
-
16
-
-
0034051905
-
Archaeaplankton in the Columbia River, its estuary and the adjacent coastal ocean, USA
-
COI: 1:CAS:528:DC%2BD3cXhslamurw%3D, PID: 10719204
-
Crump BC, Baross JA (2000) Archaeaplankton in the Columbia River, its estuary and the adjacent coastal ocean, USA. FEMS Microbiol Ecol 31:231–239. doi:10.1111/j.1574-6941.2000.tb00688.x
-
(2000)
FEMS Microbiol Ecol
, vol.31
, pp. 231-239
-
-
Crump, B.C.1
Baross, J.A.2
-
17
-
-
33750053594
-
Remarkably diverse and contrasting archaeal communities in a large arctic river and the coastal Arctic Ocean
-
Galand PE, Lovejoy C, Vincent WF (2006) Remarkably diverse and contrasting archaeal communities in a large arctic river and the coastal Arctic Ocean. Aquat Microb Ecol 44:115–126. doi:10.3354/ame044115
-
(2006)
Aquat Microb Ecol
, vol.44
, pp. 115-126
-
-
Galand, P.E.1
Lovejoy, C.2
Vincent, W.F.3
-
18
-
-
48849106493
-
Heterogeneous archaeal communities in the particle-rich environment of an arctic shelf ecosystem
-
Galand PE, Lovejoy C, Pouliot J, Vincent WF (2008) Heterogeneous archaeal communities in the particle-rich environment of an arctic shelf ecosystem. J Mar Syst 74:774–782. doi:10.1016/j.jmarsys.2007.12.001
-
(2008)
J Mar Syst
, vol.74
, pp. 774-782
-
-
Galand, P.E.1
Lovejoy, C.2
Pouliot, J.3
Vincent, W.F.4
-
19
-
-
84875792499
-
Stratified active archaeal communities in the sediments of Jiulong River estuary, China
-
PID: 22969752
-
Li Q, Wang F, Chen Z, Yin X, Xiao X (2012) Stratified active archaeal communities in the sediments of Jiulong River estuary, China. Front Microbiol 3:311. doi:10.3389/fmicb.2012.00311
-
(2012)
Front Microbiol
, vol.3
, pp. 311
-
-
Li, Q.1
Wang, F.2
Chen, Z.3
Yin, X.4
Xiao, X.5
-
20
-
-
84862226432
-
Distribution, fluxes and decadal changes of nutrients in the Jiulong River Estuary, Southwest Taiwan Strait
-
COI: 1:CAS:528:DC%2BC38Xos1Slsr8%3D
-
Yan XL, Zhai WD, Hong HS, Li Y, Guo WD, Huang X (2012) Distribution, fluxes and decadal changes of nutrients in the Jiulong River Estuary, Southwest Taiwan Strait. Chin Sci Bull 57:2307–2318. doi:10.1007/s11434-012-5084-4
-
(2012)
Chin Sci Bull
, vol.57
, pp. 2307-2318
-
-
Yan, X.L.1
Zhai, W.D.2
Hong, H.S.3
Li, Y.4
Guo, W.D.5
Huang, X.6
-
21
-
-
84902343876
-
Response of bacterial communities to environmental changes in a mesoscale subtropical watershed, Southeast China
-
COI: 1:CAS:528:DC%2BC2cXht1Khtrk%3D, PID: 24333997
-
Hu A, Yang X, Chen N, Hou L, Ma Y, Yu CP (2014) Response of bacterial communities to environmental changes in a mesoscale subtropical watershed, Southeast China. Sci Total Environ 472:746–756. doi:10.1016/j.scitotenv.2013.11.097
-
(2014)
Sci Total Environ
, vol.472
, pp. 746-756
-
-
Hu, A.1
Yang, X.2
Chen, N.3
Hou, L.4
Ma, Y.5
Yu, C.P.6
-
22
-
-
79953295518
-
Assessing the dynamics of chromophoric dissolved organic matter in a subtropical estuary using parallel factor analysis
-
COI: 1:CAS:528:DC%2BC3MXksVCgt7s%3D
-
Guo W, Yang L, Hong H, Stedmon CA, Wang F, Xu J, Xie Y (2011) Assessing the dynamics of chromophoric dissolved organic matter in a subtropical estuary using parallel factor analysis. Mar Chem 124:125–133. doi:10.1016/j.marchem.2011.01.003
-
(2011)
Mar Chem
, vol.124
, pp. 125-133
-
-
Guo, W.1
Yang, L.2
Hong, H.3
Stedmon, C.A.4
Wang, F.5
Xu, J.6
Xie, Y.7
-
23
-
-
80052301430
-
Bayesian community-wide culture-independent microbial source tracking
-
COI: 1:CAS:528:DC%2BC3MXovFyhu7o%3D
-
Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight R, Kelley ST (2011) Bayesian community-wide culture-independent microbial source tracking. Nat Meth 8:761–763. doi:10.1038/nmeth.1650
-
(2011)
Nat Meth
, vol.8
, pp. 761-763
-
-
Knights, D.1
Kuczynski, J.2
Charlson, E.S.3
Zaneveld, J.4
Mozer, M.C.5
Collman, R.G.6
Bushman, F.D.7
Knight, R.8
Kelley, S.T.9
-
24
-
-
23844476737
-
Modelling agricultural nitrogen contributions to the Jiulong River estuary and coastal water
-
Cao WZ, Hong HS, Yue SP (2005) Modelling agricultural nitrogen contributions to the Jiulong River estuary and coastal water. Glob Planet Chang 47:111–121. doi:10.1016/j.gloplacha.2004.10.006
-
(2005)
Glob Planet Chang
, vol.47
, pp. 111-121
-
-
Cao, W.Z.1
Hong, H.S.2
Yue, S.P.3
-
26
-
-
84862827076
-
Coastal acidification in summer bottom oxygen-depleted waters in northwestern-northern Bohai Sea from June to August in 2011
-
COI: 1:CAS:528:DC%2BC38Xjt1Gmsbg%3D
-
Zhai WD, Zhao HD, Zheng N, Xu Y (2012) Coastal acidification in summer bottom oxygen-depleted waters in northwestern-northern Bohai Sea from June to August in 2011. Chin Sci Bull 57:1062–1068. doi:10.1007/s11434-011-4949-2
-
(2012)
Chin Sci Bull
, vol.57
, pp. 1062-1068
-
-
Zhai, W.D.1
Zhao, H.D.2
Zheng, N.3
Xu, Y.4
-
27
-
-
80052888507
-
Community structure and function of planktonic Crenarchaeota: changes with depth in the South China Sea
-
COI: 1:CAS:528:DC%2BC3MXht1SitbbK, PID: 21597940
-
Hu A, Jiao N, Zhang CL (2011) Community structure and function of planktonic Crenarchaeota: changes with depth in the South China Sea. Microb Ecol 62:549–563. doi:10.1007/s00248-011-9866-z
-
(2011)
Microb Ecol
, vol.62
, pp. 549-563
-
-
Hu, A.1
Jiao, N.2
Zhang, C.L.3
-
28
-
-
0027460328
-
Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
-
COI: 1:CAS:528:DyaK3sXit1Kktrk%3D, PID: 7683183
-
Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700
-
(1993)
Appl Environ Microbiol
, vol.59
, pp. 695-700
-
-
Muyzer, G.1
de Waal, E.C.2
Uitterlinden, A.G.3
-
29
-
-
15944406459
-
Phenotypic characterization of Rice Cluster III archaea without prior isolation by applying quantitative polymerase chain reaction to an enrichment culture
-
COI: 1:CAS:528:DC%2BD2MXjsF2itb0%3D, PID: 15816932
-
Kemnitz D, Kolb S, Conrad R (2005) Phenotypic characterization of Rice Cluster III archaea without prior isolation by applying quantitative polymerase chain reaction to an enrichment culture. Environ Microbiol 7:553–565. doi:10.1111/j.1462-2920.2005.00723.x
-
(2005)
Environ Microbiol
, vol.7
, pp. 553-565
-
-
Kemnitz, D.1
Kolb, S.2
Conrad, R.3
-
30
-
-
67949086798
-
Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing
-
COI: 1:CAS:528:DC%2BD1MXnsFelt78%3D, PID: 19322244
-
Galand PE, Casamayor EO, Kirchman DL, Potvin M, Lovejoy C (2009) Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing. ISME J 3:860–869. doi:10.1038/ismej.2009.23
-
(2009)
ISME J
, vol.3
, pp. 860-869
-
-
Galand, P.E.1
Casamayor, E.O.2
Kirchman, D.L.3
Potvin, M.4
Lovejoy, C.5
-
31
-
-
79953026036
-
BIPES, a cost-effective high-throughput method for assessing microbial diversity
-
COI: 1:CAS:528:DC%2BC3MXjs1Cksro%3D, PID: 20962877
-
Zhou HW, Li DF, Tam NFY, Jiang XT, Zhang H, Sheng HF, Qin J, Liu X, Zou F (2011) BIPES, a cost-effective high-throughput method for assessing microbial diversity. ISME J 5:741–749. doi:10.1038/ismej.2010.160
-
(2011)
ISME J
, vol.5
, pp. 741-749
-
-
Zhou, H.W.1
Li, D.F.2
Tam, N.F.Y.3
Jiang, X.T.4
Zhang, H.5
Sheng, H.F.6
Qin, J.7
Liu, X.8
Zou, F.9
-
32
-
-
72949107142
-
Introducing Mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
COI: 1:CAS:528:DC%2BC3cXis1yltw%3D%3D, PID: 19801464
-
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing Mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541. doi:10.1128/AEM. 01541-09
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 7537-7541
-
-
Schloss, P.D.1
Westcott, S.L.2
Ryabin, T.3
Hall, J.R.4
Hartmann, M.5
Hollister, E.B.6
Lesniewski, R.A.7
Oakley, B.B.8
Parks, D.H.9
Robinson, C.J.10
Sahl, J.W.11
Stres, B.12
Thallinger, G.G.13
Van Horn, D.J.14
Weber, C.F.15
-
33
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
COI: 1:CAS:528:DC%2BC3cXksFalurg%3D
-
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Meth 7:335–336. doi:10.1038/nmeth.f.303
-
(2010)
Nat Meth
, vol.7
, pp. 335-336
-
-
Caporaso, J.G.1
Kuczynski, J.2
Stombaugh, J.3
Bittinger, K.4
Bushman, F.D.5
Costello, E.K.6
Fierer, N.7
Peña, A.G.8
Goodrich, J.K.9
Gordon, J.I.10
-
34
-
-
79961181125
-
UCHIME improves sensitivity and speed of chimera detection
-
COI: 1:CAS:528:DC%2BC3MXhtVSiurvL, PID: 21700674
-
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–2200. doi:10.1093/bioinformatics/btr381
-
(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
-
35
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
COI: 1:CAS:528:DC%2BC3cXht1WhtbzM, PID: 20709691
-
Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461. doi:10.1093/bioinformatics/btq461
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
36
-
-
84884904719
-
UPARSE: highly accurate OTU sequences from microbial amplicon reads
-
COI: 1:CAS:528:DC%2BC3sXht1ylsLzE
-
Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Meth 10:996–998. doi:10.1038/nmeth.2604
-
(2013)
Nat Meth
, vol.10
, pp. 996-998
-
-
Edgar, R.C.1
-
37
-
-
79959383523
-
Metagenomic biomarker discovery and explanation
-
PID: 21702898
-
Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C (2011) Metagenomic biomarker discovery and explanation. Genome Biol 12:R60. doi:10.1186/gb-2011-12-6-r60
-
(2011)
Genome Biol
, vol.12
, pp. R60
-
-
Segata, N.1
Izard, J.2
Waldron, L.3
Gevers, D.4
Miropolsky, L.5
Garrett, W.S.6
Huttenhower, C.7
-
38
-
-
79952050667
-
Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis
-
COI: 1:CAS:528:DC%2BC3MXivVymu7w%3D, PID: 21364937
-
Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR (2011) Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. PLoS ONE 6:e16626. doi:10.1371/journal.pone.0016626
-
(2011)
PLoS ONE
, vol.6
, pp. e16626
-
-
Blainey, P.C.1
Mosier, A.C.2
Potanina, A.3
Francis, C.A.4
Quake, S.R.5
-
39
-
-
38549131184
-
Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol
-
PID: 18205821
-
de la Torre JR, Walker CB, Ingalls AE, Konneke M, Stahl DA (2008) Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ Microbiol 10:810–818. doi:10.1111/j.1462-2920.2007.01506.x
-
(2008)
Environ Microbiol
, 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
-
40
-
-
41149153310
-
A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring
-
COI: 1:CAS:528:DC%2BD1cXitl2ls7o%3D, PID: 18250313
-
Hatzenpichler R, Lebedeva EV, Spieck E, Stoecker K, Richter A, Daims H, Wagner M (2008) A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc Natl Acad Sci U S A 105:2134–2139. doi:10.1073/pnas.0708857105
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 2134-2139
-
-
Hatzenpichler, R.1
Lebedeva, E.V.2
Spieck, E.3
Stoecker, K.4
Richter, A.5
Daims, H.6
Wagner, M.7
-
41
-
-
84899488485
-
Isotopic signatures of N2O produced by ammonia-oxidizing archaea from soils
-
COI: 1:CAS:528:DC%2BC2cXmvV2htLk%3D, PID: 24225887
-
Jung MY, Well R, Min D, Giesemann A, Park SJ, Kim JG, Kim SJ, Rhee SK (2014) Isotopic signatures of N2O produced by ammonia-oxidizing archaea from soils. ISME J 8:1115–1125. doi:10.1038/ismej.2013.205
-
(2014)
ISME J
, vol.8
, pp. 1115-1125
-
-
Jung, M.Y.1
Well, R.2
Min, D.3
Giesemann, A.4
Park, S.J.5
Kim, J.G.6
Kim, S.J.7
Rhee, S.K.8
-
42
-
-
25644435673
-
Isolation of an autotrophic ammonia-oxidizing marine archaeon
-
PID: 16177789
-
Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437:543–546. doi:10.1038/nature03911
-
(2005)
Nature
, vol.437
, pp. 543-546
-
-
Könneke, M.1
Bernhard, A.E.2
de la Torre, J.R.3
Walker, C.B.4
Waterbury, J.B.5
Stahl, D.A.6
-
43
-
-
84894268023
-
Enrichment and genome sequence of the group I. 1a ammonia-oxidizing Archaeon “Ca. Nitrosotenuis uzonensis” representing a clade globally distributed in thermal habitats
-
PID: 24278328
-
Lebedeva EV, Hatzenpichler R, Pelletier E, Schuster N, Hauzmayer S, Bulaev A, Grigor’eva NV, Galushko A, Schmid M, Palatinszky M, Le Paslier D, Daims H, Wagner M (2013) Enrichment and genome sequence of the group I. 1a ammonia-oxidizing Archaeon “Ca. Nitrosotenuis uzonensis” representing a clade globally distributed in thermal habitats. PLoS One 8:e80835. doi:10.1371/journal.pone.0080835
-
(2013)
PLoS One
, vol.8
, pp. e80835
-
-
Lebedeva, E.V.1
Hatzenpichler, R.2
Pelletier, E.3
Schuster, N.4
Hauzmayer, S.5
Bulaev, A.6
Grigor’eva, N.V.7
Galushko, A.8
Schmid, M.9
Palatinszky, M.10
Le Paslier, D.11
Daims, H.12
Wagner, M.13
-
44
-
-
80053158633
-
Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil
-
COI: 1:CAS:528:DC%2BC3MXht1emtbzK, PID: 21896746
-
Lehtovirta-Morley LE, Stoecker K, Vilcinskas A, Prosser JI, Nicol GW (2011) Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil. Proc Natl Acad Sci U S A 108:15892–15897. doi:10.1073/pnas.1107196108
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 15892-15897
-
-
Lehtovirta-Morley, L.E.1
Stoecker, K.2
Vilcinskas, A.3
Prosser, J.I.4
Nicol, G.W.5
-
45
-
-
84861212981
-
Genome sequence of “Candidatus Nitrosoarchaeum limnia” BG20, a low-salinity ammonia-oxidizing archaeon from the San Francisco Bay Estuary
-
COI: 1:CAS:528:DC%2BC38Xls1Sksbs%3D, PID: 22461554
-
Mosier AC, Allen EE, Kim M, Ferriera S, Francis CA (2012) Genome sequence of “Candidatus Nitrosoarchaeum limnia” BG20, a low-salinity ammonia-oxidizing archaeon from the San Francisco Bay Estuary. J Bacteriol 194:2119–2120. doi:10.1128/JB.00007-12
-
(2012)
J Bacteriol
, vol.194
, pp. 2119-2120
-
-
Mosier, A.C.1
Allen, E.E.2
Kim, M.3
Ferriera, S.4
Francis, C.A.5
-
46
-
-
84861220096
-
Genome sequence of “Candidatus Nitrosopumilus salaria” BD31, an ammonia-oxidizing archaeon from the San Francisco Bay Estuary
-
COI: 1:CAS:528:DC%2BC38Xls1Sksbk%3D, PID: 22461555
-
Mosier AC, Allen EE, Kim M, Ferriera S, Francis CA (2012) Genome sequence of “Candidatus Nitrosopumilus salaria” BD31, an ammonia-oxidizing archaeon from the San Francisco Bay Estuary. J Bacteriol 194:2121–2122. doi:10.1128/JB.00013-12
-
(2012)
J Bacteriol
, vol.194
, pp. 2121-2122
-
-
Mosier, A.C.1
Allen, E.E.2
Kim, M.3
Ferriera, S.4
Francis, C.A.5
-
47
-
-
79957684288
-
Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil
-
COI: 1:CAS:528:DC%2BC3MXmsF2jtLo%3D, PID: 21525411
-
Tourna M, Stieglmeier M, Spang A, Konneke M, Schintlmeister A, Urich T, Engel M, Schloter M, Wagner M, Richter A, Schleper C (2011) Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proc Natl Acad Sci U S A 108:8420–8425. doi:10.1073/pnas.1013488108
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 8420-8425
-
-
Tourna, M.1
Stieglmeier, M.2
Spang, A.3
Konneke, M.4
Schintlmeister, A.5
Urich, T.6
Engel, M.7
Schloter, M.8
Wagner, M.9
Richter, A.10
Schleper, C.11
-
48
-
-
84890330527
-
MEGA6: molecular evolutionary genetics analysis version 6.0
-
COI: 1:CAS:528:DC%2BC3sXhvVKhurzP, PID: 24132122
-
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729. doi:10.1093/molbev/mst197
-
(2013)
Mol Biol Evol
, vol.30
, pp. 2725-2729
-
-
Tamura, K.1
Stecher, G.2
Peterson, D.3
Filipski, A.4
Kumar, S.5
-
49
-
-
79955057814
-
Examining the global distribution of dominant archaeal populations in soil
-
COI: 1:CAS:528:DC%2BC3MXkvFahsLk%3D, PID: 21085198
-
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. doi:10.1038/ismej.2010.171
-
(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
-
50
-
-
0002154022
-
A new method for non-parametric multivariate analysis of variance
-
Anderson MJ (2001) A new method for non-parametric multivariate analysis of variance. Austral Ecol 26:32–46. doi:10.1111/j.1442-9993.2001.01070.pp.x
-
(2001)
Austral Ecol
, vol.26
, pp. 32-46
-
-
Anderson, M.J.1
-
51
-
-
0037099954
-
All-scale spatial analysis of ecological data by means of principal coordinates of neighbour matrices
-
Borcard D, Legendre P (2002) All-scale spatial analysis of ecological data by means of principal coordinates of neighbour matrices. Ecol Model 153:51–68. doi:10.1016/S0304-3800(01)00501-4
-
(2002)
Ecol Model
, vol.153
, pp. 51-68
-
-
Borcard, D.1
Legendre, P.2
-
52
-
-
33745213566
-
Spatial modelling: a comprehensive framework for principal coordinate analysis of neighbour matrices (PCNM)
-
Dray S, Legendre P, Peres-Neto PR (2006) Spatial modelling: a comprehensive framework for principal coordinate analysis of neighbour matrices (PCNM). Ecol Model 196:483–493. doi:10.1016/j.ecolmodel.2006.02.015
-
(2006)
Ecol Model
, vol.196
, pp. 483-493
-
-
Dray, S.1
Legendre, P.2
Peres-Neto, P.R.3
-
53
-
-
54549102367
-
Forward selection of explanatory variables
-
PID: 18831183
-
Blanchet FG, Legendre P, Borcard D (2008) Forward selection of explanatory variables. Ecology 89:2623–2632. doi:10.1890/07-0986.1
-
(2008)
Ecology
, vol.89
, pp. 2623-2632
-
-
Blanchet, F.G.1
Legendre, P.2
Borcard, D.3
-
54
-
-
68649113028
-
Vegan: community ecology package
-
Oksanen J, Kindt R, Legendre P, O’Hara B, Simpson G, Solymos P, Stevens M, Wagner H (2009) Vegan: community ecology package. R package version 115-2
-
(2009)
R package version
, pp. 112-115
-
-
Oksanen, J.1
Kindt, R.2
Legendre, P.3
O’Hara, B.4
Simpson, G.5
Solymos, P.6
Stevens, M.7
Wagner, H.8
-
55
-
-
84873739311
-
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
-
COI: 1:CAS:528:DC%2BC38XhvV2ksb%2FN, PID: 23193283
-
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590–D596. doi:10.1093/nar/gks1219
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D590-D596
-
-
Quast, C.1
Pruesse, E.2
Yilmaz, P.3
Gerken, J.4
Schweer, T.5
Yarza, P.6
Peplies, J.7
Glöckner, F.O.8
-
56
-
-
32944461244
-
Archaea in particle-rich waters of the Beaufort Shelf and Franklin Bay, Canadian Arctic: clues to an allochthonous origin?
-
COI: 1:CAS:528:DC%2BD28XhsFaqt7s%3D
-
Wells LE, Cordray M, Bowerman S, Miller LA, Vincent WF, Deming JW (2006) Archaea in particle-rich waters of the Beaufort Shelf and Franklin Bay, Canadian Arctic: clues to an allochthonous origin? Limnol Oceanogr 51:47–59. doi:10.4319/lo.2006.51.1.0047
-
(2006)
Limnol Oceanogr
, vol.51
, pp. 47-59
-
-
Wells, L.E.1
Cordray, M.2
Bowerman, S.3
Miller, L.A.4
Vincent, W.F.5
Deming, J.W.6
-
57
-
-
77954553749
-
Population dynamics of Crenarchaeota and Euryarchaeota in the mixing front of river and marine waters
-
Hao DM, Tashiro T, Kato M, Sohrin R, Ishibashi T, Katsuyama C, Nagaosa K, Kimura H, Thanh TD, Kato K (2010) Population dynamics of Crenarchaeota and Euryarchaeota in the mixing front of river and marine waters. Microbes Environ 25:126–132
-
(2010)
Microbes Environ
, vol.25
, pp. 126-132
-
-
Hao, D.M.1
Tashiro, T.2
Kato, M.3
Sohrin, R.4
Ishibashi, T.5
Katsuyama, C.6
Nagaosa, K.7
Kimura, H.8
Thanh, T.D.9
Kato, K.10
-
58
-
-
76349125984
-
Global ecological patterns in uncultured Archaea
-
PID: 19847207
-
Auguet JC, Barberan A, Casamayor EO (2010) Global ecological patterns in uncultured Archaea. ISME J 4:182–190. doi:10.1038/ismej.2009.109
-
(2010)
ISME J
, vol.4
, pp. 182-190
-
-
Auguet, J.C.1
Barberan, A.2
Casamayor, E.O.3
-
59
-
-
84871364582
-
Bacterial diversity, community structure and potential growth rates along an estuarine salinity gradient
-
COI: 1:CAS:528:DC%2BC38XhvVOrsbfL, PID: 22895159
-
Campbell BJ, Kirchman DL (2013) Bacterial diversity, community structure and potential growth rates along an estuarine salinity gradient. ISME J 7:210–220. doi:10.1038/ismej.2012.93
-
(2013)
ISME J
, vol.7
, pp. 210-220
-
-
Campbell, B.J.1
Kirchman, D.L.2
-
60
-
-
0034114417
-
A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces
-
COI: 1:CAS:528:DC%2BD3cXjtV2ltrw%3D, PID: 10788339
-
Massana R, DeLong EF, Pedros-Alio C (2000) A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces. Appl Environ Microbiol 66:1777–1787. doi:10.1128/AEM. 66.5.1777-1787.2000
-
(2000)
Appl Environ Microbiol
, vol.66
, pp. 1777-1787
-
-
Massana, R.1
DeLong, E.F.2
Pedros-Alio, C.3
-
61
-
-
33846053229
-
Phylogenetic diversity of planktonic Archaea in the estuarine region of East China Sea
-
COI: 1:CAS:528:DC%2BD2sXjs1Srtb4%3D, PID: 16914298
-
Zeng YH, Li HY, Jiao NZ (2007) Phylogenetic diversity of planktonic Archaea in the estuarine region of East China Sea. Microbiol Res 162:26–36. doi:10.1016/j.micres.2006.03.007
-
(2007)
Microbiol Res
, vol.162
, pp. 26-36
-
-
Zeng, Y.H.1
Li, H.Y.2
Jiao, N.Z.3
-
62
-
-
84867745042
-
Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments
-
COI: 1:CAS:528:DC%2BC38Xhtlynt7vE, PID: 22551871
-
Kubo K, Lloyd KG, Biddle JF, Amann R, Teske A, Knittel K (2012) Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments. ISME J 6:1949–1965. doi:10.1038/ismej.2012.37
-
(2012)
ISME J
, vol.6
, pp. 1949-1965
-
-
Kubo, K.1
Lloyd, K.G.2
Biddle, J.F.3
Amann, R.4
Teske, A.5
Knittel, K.6
-
63
-
-
41349083576
-
Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea
-
COI: 1:CAS:528:DC%2BD1cXlsV2rsL0%3D, PID: 18378594
-
Liu Y, Whitman WB (2008) Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann N Y Acad Sci 1125:171–189. doi:10.1196/annals.1419.019
-
(2008)
Ann N Y Acad Sci
, vol.1125
, pp. 171-189
-
-
Liu, Y.1
Whitman, W.B.2
-
64
-
-
83755195236
-
Microbial methane production in oxygenated water column of an oligotrophic lake
-
COI: 1:CAS:528:DC%2BC3MXhs1GjsbjM, PID: 22089233
-
Grossart HP, Frindte K, Dziallas C, Eckert W, Tang KW (2011) Microbial methane production in oxygenated water column of an oligotrophic lake. Proc Natl Acad Sci U S A 108:19657–19661. doi:10.1073/pnas.1110716108
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 19657-19661
-
-
Grossart, H.P.1
Frindte, K.2
Dziallas, C.3
Eckert, W.4
Tang, K.W.5
-
65
-
-
0033771975
-
Identification of novel Archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization
-
COI: 1:CAS:528:DC%2BD3cXosVyrtL8%3D, PID: 11053735
-
Jurgens G, Glockner FO, Amann R, Saano A, Montonen L, Likolammi M, Munster U (2000) Identification of novel Archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization. FEMS Microbiol Ecol 34:45–56. doi:10.1111/j.1574-6941.2000.tb00753.x
-
(2000)
FEMS Microbiol Ecol
, vol.34
, pp. 45-56
-
-
Jurgens, G.1
Glockner, F.O.2
Amann, R.3
Saano, A.4
Montonen, L.5
Likolammi, M.6
Munster, U.7
-
66
-
-
40949111460
-
A hotspot for cold crenarchaeota in the neuston of high mountain lakes
-
COI: 1:CAS:528:DC%2BD1cXkvVentbg%3D, PID: 18215160
-
Auguet JC, Casamayor EO (2008) A hotspot for cold crenarchaeota in the neuston of high mountain lakes. Environ Microbiol 10:1080–1086. doi:10.1111/j.1462-2920.2007.01498.x
-
(2008)
Environ Microbiol
, vol.10
, pp. 1080-1086
-
-
Auguet, J.C.1
Casamayor, E.O.2
-
67
-
-
67649220035
-
Diversity of Archaea and detection of crenarchaeotal amoA genes in the rivers Rhine and Têt
-
Herfort L, Kim JH, Coolen MJL, Abbas B, Schouten S, Herndl GJ, Damste JSS (2009) Diversity of Archaea and detection of crenarchaeotal amoA genes in the rivers Rhine and Têt. Aquat Microb Ecol 55:189–201. doi:10.3354/ame01294
-
(2009)
Aquat Microb Ecol
, vol.55
, pp. 189-201
-
-
Herfort, L.1
Kim, J.H.2
Coolen, M.J.L.3
Abbas, B.4
Schouten, S.5
Herndl, G.J.6
Damste, J.S.S.7
-
68
-
-
84860293674
-
Diversity of microbial plankton across the Three Gorges Dam of the Yangtze River, China
-
Wang S, Dong RM, Dong CZ, Huang L, Jiang H, Wei Y, Feng L, Liu D, Yang G, Zhang C, Dong H (2012) Diversity of microbial plankton across the Three Gorges Dam of the Yangtze River, China. Geosci Front 3:335–349. doi:10.1016/j.gsf.2011.11.013
-
(2012)
Geosci Front
, vol.3
, pp. 335-349
-
-
Wang, S.1
Dong, R.M.2
Dong, C.Z.3
Huang, L.4
Jiang, H.5
Wei, Y.6
Feng, L.7
Liu, D.8
Yang, G.9
Zhang, C.10
Dong, H.11
-
69
-
-
35148899268
-
Archaeal communities in a tropical estuarine ecosystem: Guanabara Bay, Brazil
-
PID: 17593423
-
Vieira RP, Clementino MM, Cardoso AM, Oliveira DN, Albano RM, Gonzalez AM, Paranhos R, Martins OB (2007) Archaeal communities in a tropical estuarine ecosystem: Guanabara Bay, Brazil. Microb Ecol 54:460–468. doi:10.1007/s00248-007-9261-y
-
(2007)
Microb Ecol
, vol.54
, pp. 460-468
-
-
Vieira, R.P.1
Clementino, M.M.2
Cardoso, A.M.3
Oliveira, D.N.4
Albano, R.M.5
Gonzalez, A.M.6
Paranhos, R.7
Martins, O.B.8
-
70
-
-
84866146323
-
Denaturing gradient Gel electrophoresis and barcoded pyrosequencing reveal unprecedented archaeal diversity in mangrove sediment and rhizosphere samples
-
COI: 1:CAS:528:DC%2BC38XhtFOnsrzN, PID: 22660713
-
Pires ACC, Cleary DFR, Almeida A, Cunha A, Dealtry S, Mendonca-Hagler LCS, Smalla K, Gomes NCM (2012) Denaturing gradient Gel electrophoresis and barcoded pyrosequencing reveal unprecedented archaeal diversity in mangrove sediment and rhizosphere samples. Appl Environ Microbiol 78:5520–5528. doi:10.1128/AEM. 00386-12
-
(2012)
Appl Environ Microbiol
, vol.78
, pp. 5520-5528
-
-
Pires, A.C.C.1
Cleary, D.F.R.2
Almeida, A.3
Cunha, A.4
Dealtry, S.5
Mendonca-Hagler, L.C.S.6
Smalla, K.7
Gomes, N.C.M.8
-
71
-
-
52949134066
-
Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary
-
COI: 1:CAS:528:DC%2BD1cXhtlGitrbO, PID: 18973621
-
Mosier AC, Francis CA (2008) Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary. Environ Microbiol 10:3002–3016. doi:10.1111/j.1462-2920.2008.01764.x
-
(2008)
Environ Microbiol
, vol.10
, pp. 3002-3016
-
-
Mosier, A.C.1
Francis, C.A.2
-
72
-
-
33845520639
-
Diversity of ammonia-oxidizing archaea and bacteria in the sediments of a hypernutrified subtropical estuary: Bahia del Tobari, Mexico
-
COI: 1:CAS:528:DC%2BD28XhtlWqtrbI, PID: 17012598
-
Beman JM, Francis CA (2006) Diversity of ammonia-oxidizing archaea and bacteria in the sediments of a hypernutrified subtropical estuary: Bahia del Tobari, Mexico. Appl Environ Microbiol 72:7767–7777. doi:10.1128/AEM. 00946-06
-
(2006)
Appl Environ Microbiol
, vol.72
, pp. 7767-7777
-
-
Beman, J.M.1
Francis, C.A.2
-
73
-
-
69749086719
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Infrequent marine-freshwater transitions in the microbial world
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COI: 1:CAS:528:DC%2BD1MXhtFajtrnF, PID: 19726194
-
Logares R, Brate J, Bertilsson S, Clasen JL, Shalchian-Tabrizi K, Rengefors K (2009) Infrequent marine-freshwater transitions in the microbial world. Trends Microbiol 17:414–422. doi:10.1016/j.tim.2009.05.010
-
(2009)
Trends Microbiol
, vol.17
, pp. 414-422
-
-
Logares, R.1
Brate, J.2
Bertilsson, S.3
Clasen, J.L.4
Shalchian-Tabrizi, K.5
Rengefors, K.6
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