-
1
-
-
76549087358
-
Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000-year time scales in hydrothermal chimney
-
Brazelton, W., Ludwig, K., Sogin, M., Andreishcheva, E., Kelley, D., Shen, C.-C., etal. (2010) Archaea and bacteria with surprising microdiversity show shifts in dominance over 1, 000-year time scales in hydrothermal chimney. Proc Natl Acad Sci USA 107: 1612-1617.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 1612-1617
-
-
Brazelton, W.1
Ludwig, K.2
Sogin, M.3
Andreishcheva, E.4
Kelley, D.5
Shen, C.-C.6
-
2
-
-
33646827488
-
The versatile ε-proteobacteria: key players in sulphidic habitats
-
Campbell, B.J., Engel, A.S., Porter, M.L., and Takai, K. (2006) The versatile ε-proteobacteria: key players in sulphidic habitats. Nat Rev Microbiol 4: 458-468.
-
(2006)
Nat Rev Microbiol
, vol.4
, pp. 458-468
-
-
Campbell, B.J.1
Engel, A.S.2
Porter, M.L.3
Takai, K.4
-
3
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., etal. (2010a) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336.
-
(2010)
Nat Methods
, 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
-
4
-
-
75249107844
-
PyNAST: a flexible tool for aligning sequences to a template alignment
-
Caporaso, J.G., Bittinger, K., Bushman, F.D., DeSantis, T.Z., Andersen, G.L., and Knight, R. (2010b) PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26: 266-267.
-
(2010)
Bioinformatics
, vol.26
, pp. 266-267
-
-
Caporaso, J.G.1
Bittinger, K.2
Bushman, F.D.3
DeSantis, T.Z.4
Andersen, G.L.5
Knight, R.6
-
5
-
-
84980126322
-
The Chesapeake Bay Institute technique for the Winkler dissolved oxygen method
-
Carpenter, J.H. (1965) The Chesapeake Bay Institute technique for the Winkler dissolved oxygen method. Limnol Oceanogr 10: 141-143.
-
(1965)
Limnol Oceanogr
, vol.10
, pp. 141-143
-
-
Carpenter, J.H.1
-
6
-
-
84944816274
-
Spectrophotometric determination of hydrogen sulfide in natural waters
-
Cline, J. (1969) Spectrophotometric determination of hydrogen sulfide in natural waters. Limnol Oceanogr 14: 454-458.
-
(1969)
Limnol Oceanogr
, vol.14
, pp. 454-458
-
-
Cline, J.1
-
7
-
-
55949093535
-
Extreme spatial and temporal variability of hydrothermal microbial mat communities along the Mariana Island Arc and southern Mariana back-arc system
-
Davis, R.E., and Moyer, C.L. (2008) Extreme spatial and temporal variability of hydrothermal microbial mat communities along the Mariana Island Arc and southern Mariana back-arc system. J Geophys Res 113: B08S15.
-
(2008)
J Geophys Res
, vol.113
-
-
Davis, R.E.1
Moyer, C.L.2
-
8
-
-
31544483932
-
Community genomics among stratified microbial assemblages in the ocean's interior
-
DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., and Frigaard, N.U. (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
-
9
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
DeSantis, T.Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E.L., Keller, K., etal. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-5072.
-
(2006)
Appl Environ Microbiol
, vol.72
, pp. 5069-5072
-
-
DeSantis, T.Z.1
Hugenholtz, P.2
Larsen, N.3
Rojas, M.4
Brodie, E.L.5
Keller, K.6
-
10
-
-
49549107771
-
Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)
-
Dowd, S.E., Callaway, T.R., Wolcott, R.D., Sun, Y., McKeehan, T., Hagevoort, R.G., and Edrington, T.S. (2008a) Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbiol 8: 125.
-
(2008)
BMC Microbiol
, vol.8
, pp. 125
-
-
Dowd, S.E.1
Callaway, T.R.2
Wolcott, R.D.3
Sun, Y.4
McKeehan, T.5
Hagevoort, R.G.6
Edrington, T.S.7
-
11
-
-
49949095159
-
Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: bacterial diversity in the ileum of newly weaned Salmonella-infected pigs
-
Dowd, S.E., Sun, Y., Wolcott, R.D., Domingo, A., and Carroll, J.A. (2008b) Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: bacterial diversity in the ileum of newly weaned Salmonella-infected pigs. Foodborne Pathog Dis 5: 459-472.
-
(2008)
Foodborne Pathog Dis
, vol.5
, pp. 459-472
-
-
Dowd, S.E.1
Sun, Y.2
Wolcott, R.D.3
Domingo, A.4
Carroll, J.A.5
-
12
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar, R. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.1
-
13
-
-
79961169429
-
Microbial community structure of hydrothermal deposits from geochemically different vent fields along the Mid-Atlantic Ridge
-
Flores, G.E., Campbell, J.H., Kirshtein, J.D., Meneghin, J., Podar, M., Steinberg, J.I., etal. (2011) Microbial community structure of hydrothermal deposits from geochemically different vent fields along the Mid-Atlantic Ridge. Environ Microbiol 13: 2158-2171.
-
(2011)
Environ Microbiol
, vol.13
, pp. 2158-2171
-
-
Flores, G.E.1
Campbell, J.H.2
Kirshtein, J.D.3
Meneghin, J.4
Podar, M.5
Steinberg, J.I.6
-
14
-
-
84862804279
-
Inter-field variability in the microbial communities of hydrothermal vent deposits from a back-arc basin
-
Flores, G.E., Shakya, M., Meneghin, J., Yang, Z.K., Seewald, J.S., Geoff Wheat, C., etal. (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
-
15
-
-
0036253488
-
Partitioning of bacterial communities between seawater and healthy, black band diseased, and dead coral surfaces
-
Frias-Lopez, J., Zerkle, A.L., Bonheyo, G.T., and Fouke, B.W. (2002) Partitioning of bacterial communities between seawater and healthy, black band diseased, and dead coral surfaces. Appl Environ Microbiol 68: 2214-2228.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 2214-2228
-
-
Frias-Lopez, J.1
Zerkle, A.L.2
Bonheyo, G.T.3
Fouke, B.W.4
-
16
-
-
45349098022
-
Oceanospirillum and related genera
-
Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.-H., and Stackebrandt, E. (eds). New York, NY, USA: Springer-Verlag
-
Gonzalesz, J.M., and Whitman, W.B. (2006) Oceanospirillum and related genera. In The Prokaryotes. Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.-H., and Stackebrandt, E. (eds). New York, NY, USA: Springer-Verlag, pp. 887-915.
-
(2006)
The Prokaryotes
, pp. 887-915
-
-
Gonzalesz, J.M.1
Whitman, W.B.2
-
17
-
-
84856009886
-
Genome and physiology of a model Epsilonproteobacterium responsible for sulfide detoxification in marine oxygen depletion zones
-
Grote, J., Schott, T., Bruckner, C.G., Glockner, F.O., Jost, G., Teeling, H., etal. (2012) Genome and physiology of a model Epsilonproteobacterium responsible for sulfide detoxification in marine oxygen depletion zones. Proc Natl Acad Sci USA 109: 506-510.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, pp. 506-510
-
-
Grote, J.1
Schott, T.2
Bruckner, C.G.3
Glockner, F.O.4
Jost, G.5
Teeling, H.6
-
18
-
-
35148888609
-
Microbial population structures in the deep marine biosphere
-
Huber, J.A., Mark Welch, D.B., Morrison, H.G., Huse, S.M., Neal, P.R., Butterfield, D.A., and Sogin, M.L. (2007) Microbial population structures in the deep marine biosphere. Science 318: 97-100.
-
(2007)
Science
, vol.318
, pp. 97-100
-
-
Huber, J.A.1
Mark Welch, D.B.2
Morrison, H.G.3
Huse, S.M.4
Neal, P.R.5
Butterfield, D.A.6
Sogin, M.L.7
-
19
-
-
77955237112
-
Isolated communities of Epsilonproteobacteria in hydrothermal vent fluids of the Mariana Arc seamounts
-
Huber, J.A., Cantin, H.V., Huse, S.M., Welch, D.B.M., Sogin, M.L., and Butterfield, D.A. (2010) Isolated communities of Epsilonproteobacteria in hydrothermal vent fluids of the Mariana Arc seamounts. FEMS Microbiol Ecol 73: 538-549.
-
(2010)
FEMS Microbiol Ecol
, vol.73
, pp. 538-549
-
-
Huber, J.A.1
Cantin, H.V.2
Huse, S.M.3
Welch, D.B.M.4
Sogin, M.L.5
Butterfield, D.A.6
-
20
-
-
0001857117
-
16S/23S rRNA sequencing
-
Stackebrandt, E., and Goodfellow, M. (eds). Chichester, UK: John Wiley & Sons
-
Lane, D.J. (1991) 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics. Stackebrandt, E., and Goodfellow, M. (eds). Chichester, UK: John Wiley & Sons, pp. 115-175.
-
(1991)
Nucleic Acid Techniques in Bacterial Systematics
, pp. 115-175
-
-
Lane, D.J.1
-
21
-
-
30044441038
-
Variability of physico-chemical conditions in 9°50′N EPR diffuse flow vent habitats
-
LeBris, N., Govenar, B., Le Gall, C., and Fisher, C.R. (2006) Variability of physico-chemical conditions in 9°50′N EPR diffuse flow vent habitats. Mar Chem 98: 167-182.
-
(2006)
Mar Chem
, vol.98
, pp. 167-182
-
-
LeBris, N.1
Govenar, B.2
Le Gall, C.3
Fisher, C.R.4
-
22
-
-
29144464937
-
UniFrac: a new phylogenetic method for comparing microbial communities
-
Lozupone, C., and 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
-
23
-
-
37749043727
-
Geochemical constraints on source of metabolic energy for chemolithoautotrophy in ultramafic-hosted deep-sea hydrothermal systems
-
McCollom, T.M. (2007) Geochemical constraints on source of metabolic energy for chemolithoautotrophy in ultramafic-hosted deep-sea hydrothermal systems. Astrobiology 7: 933-950.
-
(2007)
Astrobiology
, vol.7
, pp. 933-950
-
-
McCollom, T.M.1
-
24
-
-
0036840287
-
RNA stable isotope probing, a novel means of linking microbial community function to phylogeny
-
Manefield, M., Whiteley, A.S., Griffiths, R.I., and Bailey, M.J. (2002) RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol 68: 5367-5373.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 5367-5373
-
-
Manefield, M.1
Whiteley, A.S.2
Griffiths, R.I.3
Bailey, M.J.4
-
25
-
-
0036324293
-
Phylogenetic approaches for describing and comparing the diversity of microbial communities
-
Martin, A.P. (2002) Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl Environ Microbiol 68: 3673-3682.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 3673-3682
-
-
Martin, A.P.1
-
26
-
-
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., and Sako, Y. (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
Sako, Y.7
-
27
-
-
34547549547
-
Deep-sea vent ε-proteobacterial genomes provide insights into emergence of pathogens
-
Nakagawa, S., Takaki, Y., Shimamura, S., Reysenbach, A.L., Takai, K., and Horikoshi, K. (2007) Deep-sea vent ε-proteobacterial genomes provide insights into emergence of pathogens. Proc Natl Acad Sci USA 104: 12146-12150.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 12146-12150
-
-
Nakagawa, S.1
Takaki, Y.2
Shimamura, S.3
Reysenbach, A.L.4
Takai, K.5
Horikoshi, K.6
-
28
-
-
59249092521
-
Comparison of microbial communities associated with phase-separation-induced hydrothermal fuids at the Yonaguni Knoll IV hydrothermal field, the Southern Okinawa Trough
-
Nanoura, T., and Takai, K. (2009) Comparison of microbial communities associated with phase-separation-induced hydrothermal fuids at the Yonaguni Knoll IV hydrothermal field, the Southern Okinawa Trough. FEMS Microbiol Ecol 67: 351-370.
-
(2009)
FEMS Microbiol Ecol
, vol.67
, pp. 351-370
-
-
Nanoura, T.1
Takai, K.2
-
29
-
-
34249999174
-
The influence of ultramafic rocks on microbial communities at the Logatchev hydrothermal field, located 15°N on the Mid-Atlantic Ridge
-
Perner, M., Kuever, J., Seifert, R., Pape, T., Koschinsky, A., Schmidt, K., etal. (2007) The influence of ultramafic rocks on microbial communities at the Logatchev hydrothermal field, located 15°N on the Mid-Atlantic Ridge. FEMS Microbiol Ecol 61: 97-109.
-
(2007)
FEMS Microbiol Ecol
, vol.61
, pp. 97-109
-
-
Perner, M.1
Kuever, J.2
Seifert, R.3
Pape, T.4
Koschinsky, A.5
Schmidt, K.6
-
30
-
-
70349661581
-
Short-term microbial and physico-chemical variability in low-temperature hydrothermal fluids near 5°S on the Mid-Atlantic Ridge
-
Perner, M., Bach, W., Hentscher, M., Koschinsky, A., Garbe-Schönberg, D., Streit, W.R., and Strauss, H. (2009) Short-term microbial and physico-chemical variability in low-temperature hydrothermal fluids near 5°S on the Mid-Atlantic Ridge. Environ Microbiol 11: 2526-2541.
-
(2009)
Environ Microbiol
, vol.11
, pp. 2526-2541
-
-
Perner, M.1
Bach, W.2
Hentscher, M.3
Koschinsky, A.4
Garbe-Schönberg, D.5
Streit, W.R.6
Strauss, H.7
-
32
-
-
84859842285
-
Driving forces behind the biotope structures in the low-temperature venting at 5°S and 9°S MAR
-
Perner, M., Hentscher, M., Rychlik, N., Seifert, R., Strauss, H., and Bach, W. (2011) Driving forces behind the biotope structures in the low-temperature venting at 5°S and 9°S MAR. Environ Microbiol Rep 3: 727-737.
-
(2011)
Environ Microbiol Rep
, vol.3
, pp. 727-737
-
-
Perner, M.1
Hentscher, M.2
Rychlik, N.3
Seifert, R.4
Strauss, H.5
Bach, W.6
-
33
-
-
77949718257
-
FastTree 2-approximately maximum-likelihood trees for large alignments
-
Price, M.N., Dehal, P.S., and Arkin, A.P. (2010) FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE 5: e9490.
-
(2010)
PLoS ONE
, vol.5
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
34
-
-
79251565226
-
Removing noise from pyrosequenced amplicons
-
Quince, C., Lanzen, A., Davenport, R.J., and Turnbaugh, P.J. (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12: 38.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 38
-
-
Quince, C.1
Lanzen, A.2
Davenport, R.J.3
Turnbaugh, P.J.4
-
35
-
-
69549129476
-
The 'rare biosphere': a reality check
-
Reeder, J., and Knight, R. (2009) The 'rare biosphere': a reality check. Nat Methods 6: 636-637.
-
(2009)
Nat Methods
, vol.6
, pp. 636-637
-
-
Reeder, J.1
Knight, R.2
-
36
-
-
0042878464
-
Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation
-
Rocap, G., Larimer, F.W., Lamerdin, J., Malfatti, S., Chain, P., Ahlgren, N.A., etal. (2003) Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424: 1042-1047.
-
(2003)
Nature
, vol.424
, pp. 1042-1047
-
-
Rocap, G.1
Larimer, F.W.2
Lamerdin, J.3
Malfatti, S.4
Chain, P.5
Ahlgren, N.A.6
-
37
-
-
37749046636
-
Temporal changes in fluid chemistry and energy profiles in the Vulcano Island hydrothermal system
-
Rogers, K.L., Amend, J.P., and Gurrieri, S. (2007) Temporal changes in fluid chemistry and energy profiles in the Vulcano Island hydrothermal system. Astrobiology 7: 905-932.
-
(2007)
Astrobiology
, vol.7
, pp. 905-932
-
-
Rogers, K.L.1
Amend, J.P.2
Gurrieri, S.3
-
38
-
-
33747073504
-
Microbial diversity in the deep sea and the underexplored 'rare biosphere'
-
Sogin, M.L., Morrison, H.G., Huber, J.A., Welch, D.M., Huse, S.M., Neal, P.R., etal. (2006) Microbial diversity in the deep sea and the underexplored 'rare biosphere'. Proc Natl Acad Sci USA 103: 12115-12120.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 12115-12120
-
-
Sogin, M.L.1
Morrison, H.G.2
Huber, J.A.3
Welch, D.M.4
Huse, S.M.5
Neal, P.R.6
-
39
-
-
2342523936
-
Two bacteria phylotypes are predominant in the Suiyo seamount hydrothermal plume
-
Sunamura, M., Higashi, Y., Miyako, C., Ishibashi, J., and 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.4
Maruyama, A.5
-
40
-
-
34548293679
-
Naive bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
Wang, Q., Garrity, G.M., Tiedje, J.M., and Cole, J.R. (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
-
41
-
-
79959921978
-
Geochemical flux and metabolic activity associated with the hydrothermal subsurface
-
Wankel, S.D., Germanovich, L.N., Lilley, M.D., Genc, G., DiPerna, C.J., Bradley, A.S., etal. (2011) Geochemical flux and metabolic activity associated with the hydrothermal subsurface. Nat Geosci 4: 461-468.
-
(2011)
Nat Geosci
, vol.4
, pp. 461-468
-
-
Wankel, S.D.1
Germanovich, L.N.2
Lilley, M.D.3
Genc, G.4
DiPerna, C.J.5
Bradley, A.S.6
-
42
-
-
80053072173
-
In situ measurements of hydrogen sulfide, oxygen, and temperature in diffuse fluids of an ultramafic-hosted hydrothermal vent field (Logatchev, 14°45′N, Mid-Atlantic Ridge): implications for chemosymbiotic bathymodiolin mussels
-
Zielinski, F..U., Gennerich, H.H., Borowski, C., Wenzhöfer, F., and Dubilier, N. (2011) In situ measurements of hydrogen sulfide, oxygen, and temperature in diffuse fluids of an ultramafic-hosted hydrothermal vent field (Logatchev, 14°45′N, Mid-Atlantic Ridge): implications for chemosymbiotic bathymodiolin mussels. G-cubed 12: Q0AE04.
-
(2011)
G-cubed
, vol.12
-
-
Zielinski, F.U.1
Gennerich, H.H.2
Borowski, C.3
Wenzhöfer, F.4
Dubilier, N.5
|