-
1
-
-
84879678051
-
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
-
Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH. (2013). Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol 31: 533-538.
-
(2013)
Nat Biotechnol
, vol.31
, pp. 533-538
-
-
Albertsen, M.1
Hugenholtz, P.2
Skarshewski, A.3
Nielsen, K.L.4
Tyson, G.W.5
Nielsen, P.H.6
-
2
-
-
84872906004
-
Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean
-
Allers E, Wright JJ, Konwar KM, Howes CG, Beneze E, Hallam SJ et al. (2013). Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean. ISME J 7: 256-268.
-
(2013)
ISME J
, vol.7
, pp. 256-268
-
-
Allers, E.1
Wright, J.J.2
Konwar, K.M.3
Howes, C.G.4
Beneze, E.5
Hallam, S.J.6
-
3
-
-
50049126125
-
Resistance, resilience, and redundancy in microbial communities
-
Allison SD, Martiny JBH. (2008). Resistance, resilience, and redundancy in microbial communities. Proc Natl Acad Sci USA 105: 11512-11519.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 11512-11519
-
-
Allison, S.D.1
Martiny, J.B.H.2
-
4
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. (1990). Basic local alignment search tool. J Mol Biol 215: 403-410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
5
-
-
84871941970
-
Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria
-
Anantharaman K, Breier JA, Sheik CS, Dick GJ. (2013). Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria. Proc Natl Acad Sci USA 110: 330-335.
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, pp. 330-335
-
-
Anantharaman, K.1
Breier, J.A.2
Sheik, C.S.3
Dick, G.J.4
-
6
-
-
84900502880
-
Sulfur oxidation genes in diverse deep-sea viruses
-
Anantharaman K, Duhaime MB, Breier JA, Wendt K, Toner BM, Dick GJ. (2014). Sulfur oxidation genes in diverse deep-sea viruses. Science 344: 757-760.
-
(2014)
Science
, vol.344
, pp. 757-760
-
-
Anantharaman, K.1
Duhaime, M.B.2
Breier, J.A.3
Wendt, K.4
Toner, B.M.5
Dick, G.J.6
-
8
-
-
84871262058
-
Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume
-
Baker BJ, Lesniewski RA, Dick GJ. (2012). Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume. ISME J 6: 2269-2279.
-
(2012)
ISME J
, vol.6
, pp. 2269-2279
-
-
Baker, B.J.1
Lesniewski, R.A.2
Dick, G.J.3
-
9
-
-
84884670976
-
Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling
-
Baker BJ, Sheik CS, Taylor CA, Jain S, Bhasi A, Cavalcoli JD et al. (2013). Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling. ISME J 7: 1962-1973.
-
(2013)
ISME J
, vol.7
, pp. 1962-1973
-
-
Baker, B.J.1
Sheik, C.S.2
Taylor, C.A.3
Jain, S.4
Bhasi, A.5
Cavalcoli, J.D.6
-
11
-
-
67649658030
-
A suspended-particle rosette multi-sampler for discrete biogeochemical sampling in low-particle-density waters
-
Breier JA, Rauch CG, McCartney K, Toner BM, Fakra SC, White SN et al. (2009). A suspended-particle rosette multi-sampler for discrete biogeochemical sampling in low-particle-density waters. Deep Sea Res I 56: 1579-1589.
-
(2009)
Deep Sea Res i
, vol.56
, pp. 1579-1589
-
-
Breier, J.A.1
Rauch, C.G.2
McCartney, K.3
Toner, B.M.4
Fakra, S.C.5
White, S.N.6
-
12
-
-
84861670733
-
Sulfur, sulfides, oxides and organic matter aggregated in submarine hydrothermal plumes at 9°50N East Pacific Rise
-
Breier JA, Toner BM, Fakra SC, Marcus MA, White SN, Thurnherr AM et al. (2012). Sulfur, sulfides, oxides and organic matter aggregated in submarine hydrothermal plumes at 9°50N East Pacific Rise. Geochim Cosmochim Acta 88: 216-236.
-
(2012)
Geochim Cosmochim Acta
, vol.88
, pp. 216-236
-
-
Breier, J.A.1
Toner, B.M.2
Fakra, S.C.3
Marcus, M.A.4
White, S.N.5
Thurnherr, A.M.6
-
13
-
-
78649710753
-
A cryptic sulfur cycle in oxygen-minimum-zone waters off the Chilean coast
-
Canfield DE, Stewart FJ, Thamdrup B, De Brabandere L, Dalsgaard T, Delong EF et al. (2010). A cryptic sulfur cycle in oxygen-minimum-zone waters off the Chilean coast. Science 330: 1375-1378.
-
(2010)
Science
, vol.330
, pp. 1375-1378
-
-
Canfield, D.E.1
Stewart, F.J.2
Thamdrup, B.3
De Brabandere, L.4
Dalsgaard, T.5
Delong, E.F.6
-
14
-
-
33644700003
-
Toward automatic reconstruction of a highly resolved tree of life
-
Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. (2006). Toward automatic reconstruction of a highly resolved tree of life. Science 311: 1283-1287.
-
(2006)
Science
, vol.311
, pp. 1283-1287
-
-
Ciccarelli, F.D.1
Doerks, T.2
Von Mering, C.3
Creevey, C.J.4
Snel, B.5
Bork, P.6
-
15
-
-
0027872519
-
Methane oxidation in deep-sea hydrothermal plumes of the endeavour segment of the Juan de Fuca Ridge
-
de Angelis MA, Lilley MD, Baross JA. (1993). Methane oxidation in deep-sea hydrothermal plumes of the endeavour segment of the Juan de Fuca Ridge. Deep Sea Res I 40: 1169-1186.
-
(1993)
Deep Sea Res i
, vol.40
, pp. 1169-1186
-
-
De Angelis, M.A.1
Lilley, M.D.2
Baross, J.A.3
-
16
-
-
31544483932
-
Community genomics among stratified microbial assemblages in the ocean's interior
-
DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard NU et al. (2006). Community genomics among stratified microbial assemblages in the ocean's interior. Science 311: 496-503.
-
(2006)
Science
, vol.311
, pp. 496-503
-
-
DeLong, E.F.1
Preston, C.M.2
Mincer, T.3
Rich, V.4
Hallam, S.J.5
Frigaard, N.U.6
-
17
-
-
84885143535
-
The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria
-
Di Rienzi SC, Sharon I, Wrighton KC, Koren O, Hug LA, Thomas BC et al. (2013). The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. ELife 2: E01102.
-
(2013)
ELife
, vol.2
, pp. e01102
-
-
Di Rienzi, S.C.1
Sharon, I.2
Wrighton, K.C.3
Koren, O.4
Hug, L.A.5
Thomas, B.C.6
-
18
-
-
84884274579
-
The microbiology of deep-sea hydrothermal vent plumes: Ecological and biogeographic linkages to seafloor and water column habitats
-
Dick GJ, Anantharaman K, Baker BJ, Li M, Reed DC, Sheik CS. (2013). The microbiology of deep-sea hydrothermal vent plumes: Ecological and biogeographic linkages to seafloor and water column habitats. Front Microbiol 4: 124.
-
(2013)
Front Microbiol
, vol.4
, pp. 124
-
-
Dick, G.J.1
Anantharaman, K.2
Baker, B.J.3
Li, M.4
Reed, D.C.5
Sheik, C.S.6
-
19
-
-
70350015324
-
Community-wide analysis of microbial genome sequence signatures
-
Dick GJ, Andersson AF, Baker BJ, Simmons SL, Thomas BC, Yelton AP et al. (2009a). Community-wide analysis of microbial genome sequence signatures. Genome Biol 10: R85.
-
(2009)
Genome Biol
, vol.10
, pp. R85
-
-
Dick, G.J.1
Andersson, A.F.2
Baker, B.J.3
Simmons, S.L.4
Thomas, B.C.5
Yelton, A.P.6
-
20
-
-
70349177696
-
Enzymatic microbial Mn(II) oxidation and Mn biooxide production in the Guaymas Basin deep-sea hydrothermal plume
-
Dick GJ, Clement BG, Webb SM, Fodrie FJ, Bargar JR, Tebo BM. (2009b). Enzymatic microbial Mn(II) oxidation and Mn biooxide production in the Guaymas Basin deep-sea hydrothermal plume. Geochim Cosmochim Acta 73: 6517-6530.
-
(2009)
Geochim Cosmochim Acta
, vol.73
, pp. 6517-6530
-
-
Dick, G.J.1
Clement, B.G.2
Webb, S.M.3
Fodrie, F.J.4
Bargar, J.R.5
Tebo, B.M.6
-
21
-
-
77953555505
-
Microbial diversity and biogeochemistry of the Guaymas Basin deep-sea hydrothermal plume
-
Dick GJ, Tebo BM. (2010). Microbial diversity and biogeochemistry of the Guaymas Basin deep-sea hydrothermal plume. Environ Microbiol 12: 1334-1347.
-
(2010)
Environ Microbiol
, vol.12
, pp. 1334-1347
-
-
Dick, G.J.1
Tebo, B.M.2
-
22
-
-
0024022987
-
Sulfur-oxidizing bacterial endosymbionts: Analysis of phylogeny and specificity by 16S rRNA sequences
-
Distel DL, Lane DJ, Olsen GJ, Giovannoni SJ, Pace B, Pace NR et al. (1988). Sulfur-oxidizing bacterial endosymbionts: Analysis of phylogeny and specificity by 16S rRNA sequences. J Bacterioll 170: 2506-2510.
-
(1988)
J Bacterioll
, vol.170
, pp. 2506-2510
-
-
Distel, D.L.1
Lane, D.J.2
Olsen, G.J.3
Giovannoni, S.J.4
Pace, B.5
Pace, N.R.6
-
23
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar RC. (2004). MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
24
-
-
4644285309
-
Neutrophilic iron-oxidizing bacteria in the ocean: Their habitats, diversity, and roles in mineral deposition, rock alteration, and biomass production in the deepsea
-
Edwards KJ, Bach W, McCollom TM, Rogers DR. (2004). Neutrophilic iron-oxidizing bacteria in the ocean: Their habitats, diversity, and roles in mineral deposition, rock alteration, and biomass production in the deepsea. Geomicrobiol J 21: 393-404.
-
(2004)
Geomicrobiol J
, vol.21
, pp. 393-404
-
-
Edwards, K.J.1
Bach, W.2
McCollom, T.M.3
Rogers, D.R.4
-
25
-
-
72249106123
-
Variable morphologic expression of volcanic, tectonic, and hydrothermal processes at six hydrothermal vent fields in the Lau back-arc basin
-
Ferrini VL, Tivey MK, Carbotte SM, Martinez F, Roman C. (2008). Variable morphologic expression of volcanic, tectonic, and hydrothermal processes at six hydrothermal vent fields in the Lau back-arc basin. Geochem Geophys Geosyst 9: Q07022.
-
(2008)
Geochem Geophys Geosyst
, vol.9
, pp. Q07022
-
-
Ferrini, V.L.1
Tivey, M.K.2
Carbotte, S.M.3
Martinez, F.4
Roman, C.5
-
26
-
-
84862804279
-
Inter-field variability in the microbial communities of hydrothermal vent deposits from a back-arc basin
-
Flores GE, Shakya M, Meneghin J, Yang ZK, Seewald JS, Geoff Wheat C et al. (2012). Inter-field variability in the microbial communities of hydrothermal vent deposits from a back-arc basin. Geobiology 10: 333-346.
-
(2012)
Geobiology
, vol.10
, pp. 333-346
-
-
Flores, G.E.1
Shakya, M.2
Meneghin, J.3
Yang, Z.K.4
Seewald, J.S.5
Geoff Wheat, C.6
-
27
-
-
77956293333
-
Diverse styles of submarine venting on the ultraslow spreading Mid-Cayman Rise
-
German CR, Bowen A, Coleman ML, Honig DL, Huber JA, Jakuba MV et al. (2010). Diverse styles of submarine venting on the ultraslow spreading Mid-Cayman Rise. Proc Natl Acad Sci USA 107: 14020-14025.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 14020-14025
-
-
German, C.R.1
Bowen, A.2
Coleman, M.L.3
Honig, D.L.4
Huber, J.A.5
Jakuba, M.V.6
-
29
-
-
0030302730
-
Abundance of viruses in deep oceanic waters
-
Hara S, Koike I, Terauchi K, Kamiya H, Tanoue E. (1996). Abundance of viruses in deep oceanic waters. Marine Ecol Prog Ser 145: 269-277.
-
(1996)
Marine Ecol Prog ser
, vol.145
, pp. 269-277
-
-
Hara, S.1
Koike, I.2
Terauchi, K.3
Kamiya, H.4
Tanoue, E.5
-
30
-
-
79953023347
-
Beyond the Calvin cycle: Autotrophic carbon fixation in the ocean
-
Hügler M, Sievert SM. (2010). Beyond the Calvin cycle: Autotrophic carbon fixation in the ocean. Annu Rev Marine Sci 3: 261-289.
-
(2010)
Annu Rev Marine Sci
, vol.3
, pp. 261-289
-
-
Hügler, M.1
Sievert, S.M.2
-
31
-
-
0021335011
-
Formation of massive sulfide deposits on oceanic ridge crests-incremental reaction models for mixing between hydrothermal solutions and seawater
-
Janecky DR, Seyfried WE. (1984). Formation of massive sulfide deposits on oceanic ridge crests-incremental reaction models for mixing between hydrothermal solutions and seawater. Geochim Cosmochim Acta 48: 2723-2738.
-
(1984)
Geochim Cosmochim Acta
, vol.48
, pp. 2723-2738
-
-
Janecky, D.R.1
Seyfried, W.E.2
-
32
-
-
0022197949
-
Geomicrobiology of deepsea hydrothermal vents
-
Jannasch HW, Mottl MJ. (1985). Geomicrobiology of deepsea hydrothermal vents. Science 229: 717-725.
-
(1985)
Science
, vol.229
, pp. 717-725
-
-
Jannasch, H.W.1
Mottl, M.J.2
-
33
-
-
84355162257
-
Community genomic analysis of an extremely acidophilic sulfur-oxidizing biofilm
-
Jones DS, Albrecht HL, Dawson KS, Schaperdoth I, Freeman KH, Pi Y et al. (2012). Community genomic analysis of an extremely acidophilic sulfur-oxidizing biofilm. ISME J 6: 158-170.
-
(2012)
ISME J
, vol.6
, pp. 158-170
-
-
Jones, D.S.1
Albrecht, H.L.2
Dawson, K.S.3
Schaperdoth, I.4
Freeman, K.H.5
Pi, Y.6
-
34
-
-
84899518211
-
InterProScan 5: Genome-scale protein function classification
-
Jones P, Binns D, Chang H-Y, Fraser M, Li W, McAnulla C et al. (2014). InterProScan 5: Genome-scale protein function classification. Bioinformatics 30: 1236-1240.
-
(2014)
Bioinformatics
, vol.30
, pp. 1236-1240
-
-
Jones, P.1
Binns, D.2
Chang, H.-Y.3
Fraser, M.4
Li, W.5
McAnulla, C.6
-
35
-
-
31844455045
-
Evolution of habitat use by deep-sea mussels
-
Jones WJ, Won YJ, Maas PAY, Smith PJ, Lutz RA, Vrijenhoek RC. (2006). Evolution of habitat use by deep-sea mussels. Marine Biol 148: 841-851.
-
(2006)
Marine Biol
, vol.148
, pp. 841-851
-
-
Jones, W.J.1
Won, Y.J.2
Maas, P.A.Y.3
Smith, P.J.4
Lutz, R.A.5
Vrijenhoek, R.C.6
-
36
-
-
0027797266
-
An assessment of the effect of chemical scavenging within submarine hydrothermal plumes upon ocean geochemistry
-
Kadko D. (1993). An assessment of the effect of chemical scavenging within submarine hydrothermal plumes upon ocean geochemistry. Earth Planet Sci Lett 120: 361-374.
-
(1993)
Earth Planet Sci Lett
, vol.120
, pp. 361-374
-
-
Kadko, D.1
-
37
-
-
84887151854
-
Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla
-
Kantor RS, Wrighton KC, Handley KM, Sharon I, Hug LA, Castelle CJ et al. (2013). Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla. mBio 4: E00708.
-
(2013)
MBio
, vol.4
, pp. e00708
-
-
Kantor, R.S.1
Wrighton, K.C.2
Handley, K.M.3
Sharon, I.4
Hug, L.A.5
Castelle, C.J.6
-
38
-
-
0021613580
-
Bacterial chemolithotrophy in the ocean Is associated with sinking particles
-
Karl DM, Knauer GA, Martin JH, Ward BB. (1984). Bacterial chemolithotrophy in the ocean Is associated with sinking particles. Nature 309: 54-56.
-
(1984)
Nature
, vol.309
, pp. 54-56
-
-
Karl, D.M.1
Knauer, G.A.2
Martin, J.H.3
Ward, B.B.4
-
39
-
-
78751704176
-
A persistent oxygen anomaly reveals the fate of spilled methane in the deep Gulf of Mexico
-
Kessler JD, Valentine DL, Redmond MC, Du M, Chan EW, Mendes SD et al. (2011). A persistent oxygen anomaly reveals the fate of spilled methane in the deep Gulf of Mexico. Science 331: 312-315.
-
(2011)
Science
, vol.331
, pp. 312-315
-
-
Kessler, J.D.1
Valentine, D.L.2
Redmond, M.C.3
Du, M.4
Chan, E.W.5
Mendes, S.D.6
-
40
-
-
25644435673
-
Isolation of an autotrophic ammonia-oxidizing marine archaeon
-
Konneke 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.
-
(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
Stahl, D.A.6
-
41
-
-
0842303733
-
Autotrophic ammonia oxidation in a deep-sea hydrothermal plume
-
Lam P, Cowen JP, Jones RD. (2004). Autotrophic ammonia oxidation in a deep-sea hydrothermal plume. FEMS Microbiol Ecol 47: 191-206.
-
(2004)
FEMS Microbiol Ecol
, vol.47
, pp. 191-206
-
-
Lam, P.1
Cowen, J.P.2
Jones, R.D.3
-
42
-
-
42149146665
-
Microbial ammonia oxidation and enhanced nitrogen cycling in the Endeavour hydrothermal plume
-
Lam P, Cowen JP, Popp BN, Jones RD. (2008). Microbial ammonia oxidation and enhanced nitrogen cycling in the Endeavour hydrothermal plume. Geochim Cosmochim Acta 72: 2268-2286.
-
(2008)
Geochim Cosmochim Acta
, vol.72
, pp. 2268-2286
-
-
Lam, P.1
Cowen, J.P.2
Popp, B.N.3
Jones, R.D.4
-
43
-
-
84871274042
-
The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs
-
Lesniewski RA, Jain S, Anantharaman K, Schloss PD, Dick GJ. (2012). The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs. ISME J 6: 2257-2268.
-
(2012)
ISME J
, vol.6
, pp. 2257-2268
-
-
Lesniewski, R.A.1
Jain, S.2
Anantharaman, K.3
Schloss, P.D.4
Dick, G.J.5
-
44
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li H, Durbin R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
45
-
-
68549104404
-
The sequence Alignment/Map format and SAMtools
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N et al. (2009). The sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
-
46
-
-
84891624159
-
Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep-sea hydrocarbon plume
-
Li M, Jain S, Baker BJ, Taylor C, Dick GJ. (2014a). Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep-sea hydrocarbon plume. Environ Microbiol 16: 60-71.
-
(2014)
Environ Microbiol
, vol.16
, pp. 60-71
-
-
Li, M.1
Jain, S.2
Baker, B.J.3
Taylor, C.4
Dick, G.J.5
-
47
-
-
84893876198
-
Microbial iron uptake as a mechanism for dispersing iron from deep-sea hydrothermal vents
-
Li M, Toner BM, Baker BJ, Breier JA, Sheik CS, Dick GJ. (2014b). Microbial iron uptake as a mechanism for dispersing iron from deep-sea hydrothermal vents. Nat Commun 5: 3192.
-
(2014)
Nat Commun
, vol.5
, pp. 3192
-
-
Li, M.1
Toner, B.M.2
Baker, B.J.3
Breier, J.A.4
Sheik, C.S.5
Dick, G.J.6
-
48
-
-
84875875462
-
The genome of Nitrospina gracilis illuminates the metabolism and evolution of the major marine nitrite oxidizer
-
Luecker S, Nowka B, Rattei T, Spieck E, Daims H. (2013). The genome of Nitrospina gracilis illuminates the metabolism and evolution of the major marine nitrite oxidizer. Front Microbiol 4: 27.
-
(2013)
Front Microbiol
, vol.4
, pp. 27
-
-
Luecker, S.1
Nowka, B.2
Rattei, T.3
Spieck, E.4
Daims, H.5
-
49
-
-
77955791222
-
A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria
-
Lücker S, Wagner M, Maixner F, Pelletier E, Koch H, Vacherie B et al. (2010). A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc Natl Acad Sci USA 107: 13479-13484.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 13479-13484
-
-
Lücker, S.1
Wagner, M.2
Maixner, F.3
Pelletier, E.4
Koch, H.5
Vacherie, B.6
-
50
-
-
38549139537
-
IMG/M: A data management and analysis system for metagenomes
-
Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, Dalevi D et al. (2008). IMG/M: A data management and analysis system for metagenomes. Nucleic Acids Res 36: D534-D538.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. D534-D538
-
-
Markowitz, V.M.1
Ivanova, N.N.2
Szeto, E.3
Palaniappan, K.4
Chu, K.5
Dalevi, D.6
-
51
-
-
33646511978
-
Opposing trends in crustal thickness and spreading rate along the back-arc Eastern Lau Spreading Center: Implications for controls on ridge morphology, faulting, and hydrothermal activity
-
Martinez F, Taylor B, Baker ET, Resing JA, Walker SL. (2006). Opposing trends in crustal thickness and spreading rate along the back-arc Eastern Lau Spreading Center: Implications for controls on ridge morphology, faulting, and hydrothermal activity. Earth Planet Sci Lett 245: 655-672.
-
(2006)
Earth Planet Sci Lett
, vol.245
, pp. 655-672
-
-
Martinez, F.1
Taylor, B.2
Baker, E.T.3
Resing, J.A.4
Walker, S.L.5
-
52
-
-
0033990775
-
Geochemical constraints on primary productivity in submarine hydrothermal vent plumes
-
McCollom T. (2000). Geochemical constraints on primary productivity in submarine hydrothermal vent plumes. Deep Sea Res II 47: 85-101.
-
(2000)
Deep Sea Res II
, vol.47
, pp. 85-101
-
-
McCollom, T.1
-
53
-
-
78751702322
-
Chemistry of hot springs along the Eastern Lau Spreading Center
-
Mottl MJ, Seewald JS, Wheat CG, Tivey MK, Michael PJ, Proskurowski G et al. (2011). Chemistry of hot springs along the Eastern Lau Spreading Center. Geochim Cosmochim Acta 75: 1013-1038.
-
(2011)
Geochim Cosmochim Acta
, vol.75
, pp. 1013-1038
-
-
Mottl, M.J.1
Seewald, J.S.2
Wheat, C.G.3
Tivey, M.K.4
Michael, P.J.5
Proskurowski, G.6
-
54
-
-
0029414629
-
Larvae of benthic invertebrates in hydrothermal vent plumes over Juan de Fuca Ridge
-
Mullineaux LS, Wiebe PH, Baker ET. (1995). Larvae of benthic invertebrates in hydrothermal vent plumes over Juan de Fuca Ridge. Marine Biol 122: 585-596.
-
(1995)
Marine Biol
, vol.122
, pp. 585-596
-
-
Mullineaux, L.S.1
Wiebe, P.H.2
Baker, E.T.3
-
55
-
-
25144503993
-
Distribution, phylogenetic diversity and physiological characteristics of epsilon-Proteobacteria in a deep-sea hydrothermal field
-
Nakagawa S, Takai K, Inagaki F, Hirayama H, Nunoura T, Horikoshi K et al. (2005). Distribution, phylogenetic diversity and physiological characteristics of epsilon-Proteobacteria in a deep-sea hydrothermal field. Environ Microbiol 7: 1619-1632.
-
(2005)
Environ Microbiol
, vol.7
, pp. 1619-1632
-
-
Nakagawa, S.1
Takai, K.2
Inagaki, F.3
Hirayama, H.4
Nunoura, T.5
Horikoshi, K.6
-
56
-
-
84867397631
-
MetaVelvet: An extension of Velvet assembler to de novo metagenome assembly from short sequence reads
-
Namiki T, Hachiya T, Tanaka H, Sakakibara Y. (2012). MetaVelvet: An extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res 40: E155.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. e155
-
-
Namiki, T.1
Hachiya, T.2
Tanaka, H.3
Sakakibara, Y.4
-
57
-
-
84861760530
-
IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
-
Peng Y, Leung HCM, Yiu SM, Chin FYL. (2012). IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28: 1420-1428.
-
(2012)
Bioinformatics
, vol.28
, pp. 1420-1428
-
-
Peng, Y.1
Leung, H.C.M.2
Yiu, S.M.3
Chin, F.Y.L.4
-
58
-
-
80051674235
-
Hydrogen is an energy source for hydrothermal vent symbioses
-
Petersen JM, Zielinski FU, Pape T, Seifert R, Moraru C, Amann R et al. (2011). Hydrogen is an energy source for hydrothermal vent symbioses. Nature 476: 176-180.
-
(2011)
Nature
, vol.476
, pp. 176-180
-
-
Petersen, J.M.1
Zielinski, F.U.2
Pape, T.3
Seifert, R.4
Moraru, C.5
Amann, R.6
-
59
-
-
33748591589
-
Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing
-
Pinard R, de Winter A, Sarkis GJ, Gerstein MB, Tartaro KR, Plant RN et al. (2006). Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing. BMC Genomics 7: 216.
-
(2006)
BMC Genomics
, vol.7
, pp. 216
-
-
Pinard, R.1
De Winter, A.2
Sarkis, G.J.3
Gerstein, M.B.4
Tartaro, K.R.5
Plant, R.N.6
-
60
-
-
37549027613
-
SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
-
Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J et al. (2007). SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188-7196.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 7188-7196
-
-
Pruesse, E.1
Quast, C.2
Knittel, K.3
Fuchs, B.M.4
Ludwig, W.5
Peplies, J.6
-
61
-
-
84937730809
-
Predicting the response of the deep-ocean microbiome to geochemical perturbations by hydrothermal vents
-
Reed DC, Breier JA, Jiang H, Anantharaman K, Klausmeier CA, Toner BM et al. (2015). Predicting the response of the deep-ocean microbiome to geochemical perturbations by hydrothermal vents. ISME J 9: 1857-1869.
-
(2015)
ISME J
, vol.9
, pp. 1857-1869
-
-
Reed, D.C.1
Breier, J.A.2
Jiang, H.3
Anantharaman, K.4
Klausmeier, C.A.5
Toner, B.M.6
-
62
-
-
77954212697
-
Major contribution of autotrophy to microbial carbon cycling in the deep North Atlantic's interior
-
Reinthaler T, van Aken HM, Herndl GJ. (2010). Major contribution of autotrophy to microbial carbon cycling in the deep North Atlantic's interior. Deep Sea Res II 57: 1572-1580.
-
(2010)
Deep Sea Res II
, vol.57
, pp. 1572-1580
-
-
Reinthaler, T.1
Van Aken, H.M.2
Herndl, G.J.3
-
63
-
-
84888199743
-
Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill
-
Rivers AR, Sharma S, Tringe SG, Martin J, Joye SB, Moran MA. (2013). Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill. ISME J 7: 2315-2329.
-
(2013)
ISME J
, vol.7
, pp. 2315-2329
-
-
Rivers, A.R.1
Sharma, S.2
Tringe, S.G.3
Martin, J.4
Joye, S.B.5
Moran, M.A.6
-
64
-
-
84856567776
-
Identification and removal of ribosomal RNA sequences from metatranscriptomes
-
Schmieder R, Lim YW, Edwards R. (2012). Identification and removal of ribosomal RNA sequences from metatranscriptomes. Bioinformatics 28: 433-435.
-
(2012)
Bioinformatics
, vol.28
, pp. 433-435
-
-
Schmieder, R.1
Lim, Y.W.2
Edwards, R.3
-
65
-
-
80052727912
-
Facultative methanotrophy: False leads, true results, and suggestions for future research
-
Semrau JD, DiSpirito AA, Vuilleumier S. (2011). Facultative methanotrophy: False leads, true results, and suggestions for future research. FEMS Microbiol Lett 323: 1-12.
-
(2011)
FEMS Microbiol Lett
, vol.323
, pp. 1-12
-
-
Semrau, J.D.1
DiSpirito, A.A.2
Vuilleumier, S.3
-
66
-
-
84929654044
-
Spatially resolved sampling reveals dynamic microbial communities in rising hydrothermal plumes across a back-arc basin
-
Sheik CS, Anantharaman K, Breier JA, Sylvan JB, Dick GJ. (2015). Spatially resolved sampling reveals dynamic microbial communities in rising hydrothermal plumes across a back-arc basin. ISME J 9: 1434-1445.
-
(2015)
ISME J
, vol.9
, pp. 1434-1445
-
-
Sheik, C.S.1
Anantharaman, K.2
Breier, J.A.3
Sylvan, J.B.4
Dick, G.J.5
-
67
-
-
84891624289
-
Metabolic flexibility of enigmatic SAR324 revealed through metagenomics and metatranscriptomics
-
Sheik CS, Jain S, Dick GJ. (2014). Metabolic flexibility of enigmatic SAR324 revealed through metagenomics and metatranscriptomics. Environ Microbiol 16: 304-317.
-
(2014)
Environ Microbiol
, vol.16
, pp. 304-317
-
-
Sheik, C.S.1
Jain, S.2
Dick, G.J.3
-
68
-
-
79955587314
-
Genomic potential of marinobacter aquaeolei a biogeochemical 'Opportunitroph'
-
Singer E, Webb EA, Nelson WC, Heidelberg JF, Ivanova N, Pati A et al. (2011). Genomic potential of marinobacter aquaeolei, a biogeochemical 'Opportunitroph'. Appl Environ Microbiol 77: 2763-2771.
-
(2011)
Appl Environ Microbiol
, vol.77
, pp. 2763-2771
-
-
Singer, E.1
Webb, E.A.2
Nelson, W.C.3
Heidelberg, J.F.4
Ivanova, N.5
Pati, A.6
-
69
-
-
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
-
70
-
-
2342523936
-
Two bacteria phylotypes are predominant in the Suiyo Seamount Hydrothermal Plume
-
Sunamura M, Higashi Y, Miyako C, Ishibashi J-I, Maruyama A. (2004). Two bacteria phylotypes are predominant in the Suiyo Seamount Hydrothermal Plume. Appl Environ Microbiol 70: 1190-1198.
-
(2004)
Appl Environ Microbiol
, vol.70
, pp. 1190-1198
-
-
Sunamura, M.1
Higashi, Y.2
Miyako, C.3
Ishibashi, J.-I.4
Maruyama, A.5
-
71
-
-
80052479893
-
Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean
-
Swan BK, Martinez-Garcia M, Preston CM, Sczyrba A, Woyke T, Lamy D et al. (2011). Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 333: 1296-1300.
-
(2011)
Science
, vol.333
, pp. 1296-1300
-
-
Swan, B.K.1
Martinez-Garcia, M.2
Preston, C.M.3
Sczyrba, A.4
Woyke, T.5
Lamy, D.6
-
72
-
-
84856680618
-
Time-series analysis of two hydrothermal plumes at 9°50N East Pacific Rise reveals distinct, heterogeneous bacterial populations
-
Sylvan JB, Pyenson BC, Rouxel O, German CR, Edwards KJ. (2012). Time-series analysis of two hydrothermal plumes at 9°50N East Pacific Rise reveals distinct, heterogeneous bacterial populations. Geobiology 10: 178-192.
-
(2012)
Geobiology
, vol.10
, pp. 178-192
-
-
Sylvan, J.B.1
Pyenson, B.C.2
Rouxel, O.3
German, C.R.4
Edwards, K.J.5
-
73
-
-
84903366028
-
Low temperature geomicrobiology follows host rock composition along a geochemical gradient in Lau Basin
-
Sylvan JB, Sia TY, Haddad AG, Briscoe LJ, Toner BM, Girguis PR et al. (2013). Low temperature geomicrobiology follows host rock composition along a geochemical gradient in Lau Basin. Front Microbiol 4: 61.
-
(2013)
Front Microbiol
, vol.4
, pp. 61
-
-
Sylvan, J.B.1
Sia, T.Y.2
Haddad, A.G.3
Briscoe, L.J.4
Toner, B.M.5
Girguis, P.R.6
-
74
-
-
77950535600
-
Hydrothermal contribution to the oceanic dissolved iron inventory
-
Tagliabue A, Bopp L, Dutay J-C, Bowie A, Chever F, Jean-Baptiste P et al. (2010). Hydrothermal contribution to the oceanic dissolved iron inventory. Nat Geosci 3: 252-256.
-
(2010)
Nat Geosci
, vol.3
, pp. 252-256
-
-
Tagliabue, A.1
Bopp, L.2
Dutay, J.-C.3
Bowie, A.4
Chever, F.5
Jean-Baptiste, P.6
-
75
-
-
77951498451
-
Distributions of putative aerobic methanotrophs in diverse pelagic marine environments
-
Tavormina PL, Ussler W 3rd, Joye SB, Harrison BK, Orphan VJ. (2010). Distributions of putative aerobic methanotrophs in diverse pelagic marine environments. ISME J 4: 700-710.
-
(2010)
ISME J
, vol.4
, pp. 700-710
-
-
Tavormina, P.L.1
Ussler, W.2
Joye, S.B.3
Harrison, B.K.4
Orphan, V.J.5
-
76
-
-
0036205605
-
Microbial diversity of hydrothermal sediments in the Guaymas Basin: Evidence for anaerobic methanotrophic communities
-
Teske A, Hinrichs K-U, Edgcomb V, de Vera Gomez A, Kysela D, Sylva SP et al. (2002). Microbial diversity of hydrothermal sediments in the Guaymas Basin: Evidence for anaerobic methanotrophic communities. Appl Environ Microbiol 68: 1994-2007.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 1994-2007
-
-
Teske, A.1
Hinrichs, K.-U.2
Edgcomb, V.3
De Vera Gomez, A.4
Kysela, D.5
Sylva, S.P.6
-
77
-
-
84875634162
-
Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration
-
Thorvaldsdóttir H, Robinson JT, Mesirov JP. (2013). Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration. Brief Bioinform 14: 178-192.
-
(2013)
Brief Bioinform
, vol.14
, pp. 178-192
-
-
Thorvaldsdóttir, H.1
Robinson, J.T.2
Mesirov, J.P.3
-
78
-
-
84903379168
-
Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype
-
Thrash JC, Ben T, Brandon KS, Zachary CL, Tanja W, Edward FD et al. (2014). Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype. ISME J 8: 1440-1451.
-
(2014)
ISME J
, vol.8
, pp. 1440-1451
-
-
Thrash, J.C.1
Ben, T.2
Brandon, K.S.3
Zachary, C.L.4
Tanja, W.5
Edward, F.D.6
-
79
-
-
65349131856
-
Preservation of iron(II) by carbon-rich matrices in a hydrothermal plume
-
Toner BM, Fakra SC, Manganini SJ, Santelli CM, Marcus MA, Moffett JW et al. (2009). Preservation of iron(II) by carbon-rich matrices in a hydrothermal plume. Nat Geosci 2: 197-201.
-
(2009)
Nat Geosci
, vol.2
, pp. 197-201
-
-
Toner, B.M.1
Fakra, S.C.2
Manganini, S.J.3
Santelli, C.M.4
Marcus, M.A.5
Moffett, J.W.6
-
80
-
-
35748974830
-
Occurrence, classification, and biological function of hydrogenases: An overview
-
Vignais PM, Billoud B. (2007). Occurrence, classification, and biological function of hydrogenases: An overview. Chem Rev 107: 4206-4272.
-
(2007)
Chem Rev
, vol.107
, pp. 4206-4272
-
-
Vignais, P.M.1
Billoud, B.2
-
81
-
-
70350502063
-
Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones
-
Walsh DA, Zaikova E, Howes CG, Song YC, Wright JJ, Tringe SG et al. (2009). Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones. Science 326: 578-582.
-
(2009)
Science
, vol.326
, pp. 578-582
-
-
Walsh, D.A.1
Zaikova, E.2
Howes, C.G.3
Song, Y.C.4
Wright, J.J.5
Tringe, S.G.6
-
82
-
-
0022554943
-
Microorganisms in deep-sea hydrothermal plumes
-
Winn CD, Karl DM, Massoth GJ. (1986). Microorganisms in deep-sea hydrothermal plumes. Nature 320: 744-746.
-
(1986)
Nature
, vol.320
, pp. 744-746
-
-
Winn, C.D.1
Karl, D.M.2
Massoth, G.J.3
-
84
-
-
84865988318
-
Sulfur metabolisms in epsilon-and gamma-Proteobacteria in deep-sea hydrothermal fields
-
Yamamoto M, Takai K. (2011). Sulfur metabolisms in epsilon-and gamma-Proteobacteria in deep-sea hydrothermal fields. Front Microbiol 2: 192.
-
(2011)
Front Microbiol
, vol.2
, pp. 192
-
-
Yamamoto, M.1
Takai, K.2
-
85
-
-
0003370910
-
A three-plate kinematic model for Lau Basin opening
-
Zellmer KE, Taylor B. (2001). A three-plate kinematic model for Lau Basin opening. Geochem Geophys Geosyst 2: 1020.
-
(2001)
Geochem Geophys Geosyst
, vol.2
, pp. 1020
-
-
Zellmer, K.E.1
Taylor, B.2
-
86
-
-
43149115851
-
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino DR, Birney E. (2008). Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829.
-
(2008)
Genome Res
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
|