-
1
-
-
76549087358
-
Archaea and bacteria with surprising microdiversity show shifts in dominance over 1000-year time scales in hydrothermal chimneys
-
Brazelton WJ, Ludwig KA, Sogin ML et al. (2010) Archaea and bacteria with surprising microdiversity show shifts in dominance over 1000-year time scales in hydrothermal chimneys. P Natl Acad Sci USA 107: 1612-1617.
-
(2010)
P Natl Acad Sci USA
, vol.107
, pp. 1612-1617
-
-
Brazelton, W.J.1
Ludwig, K.A.2
Sogin, M.L.3
-
2
-
-
0000640710
-
Modulation of chemical composition and other parameters of the cell by growth rate
-
Neidhardt FC, ed) ASM Press, Washington, DC.
-
Bremer H & Dennis PP (1996) Modulation of chemical composition and other parameters of the cell by growth rate. Escherichia coli and Salmonella: Cellular and Molecular Biology (Neidhardt FC, ed), pp. 1553-1569. ASM Press, Washington, DC.
-
(1996)
Escherichia coli and Salmonella: Cellular and Molecular Biology
, pp. 1553-1569
-
-
Bremer, H.1
Dennis, P.P.2
-
3
-
-
40549109538
-
Quantification of the detrimental effect of a single primer-template mismatch by real-time PCR using the 16S rRNA gene as an example
-
Bru D, Martin-Laurent F & Philippot L (2008) Quantification of the detrimental effect of a single primer-template mismatch by real-time PCR using the 16S rRNA gene as an example. Appl Environ Microb 74: 1660-1663.
-
(2008)
Appl Environ Microb
, vol.74
, pp. 1660-1663
-
-
Bru, D.1
Martin-Laurent, F.2
Philippot, L.3
-
5
-
-
0023526239
-
Estimating the population size for capture-recapture data with unequal catchability
-
Chao A (1987) Estimating the population size for capture-recapture data with unequal catchability. Biometrics 43: 783-791.
-
(1987)
Biometrics
, vol.43
, pp. 783-791
-
-
Chao, A.1
-
6
-
-
69249109724
-
Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine
-
Claesson MJ, O'Sullivan O, Wang Q et al. (2009) Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS One 4: e6669.
-
(2009)
PLoS One
, vol.4
-
-
Claesson, M.J.1
O'Sullivan, O.2
Wang, Q.3
-
7
-
-
55949093535
-
Extreme spatial and temporal variability of hydrothermal microbial mat communities along the Mariana Island Arc and southern Mariana back-arc system
-
Davis RE & Moyer CL (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
-
-
77951498638
-
Experimental factors affecting PCR-based estimates of microbial species richness and evenness
-
Engelbrektson A, Kunin V, Wrighton KC, Zvenigorodsky N, Chen F, Ochman H & Hugenholtz P (2010) Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J 4: 642-647.
-
(2010)
ISME J
, vol.4
, pp. 642-647
-
-
Engelbrektson, A.1
Kunin, V.2
Wrighton, K.C.3
Zvenigorodsky, N.4
Chen, F.5
Ochman, H.6
Hugenholtz, P.7
-
9
-
-
40149103278
-
Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex
-
Hamady M, Walker JJ, Harris JK, Gold NJ & Knight R (2008) Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods 5: 235-237.
-
(2008)
Nat Methods
, vol.5
, pp. 235-237
-
-
Hamady, M.1
Walker, J.J.2
Harris, J.K.3
Gold, N.J.4
Knight, R.5
-
10
-
-
35148888609
-
Microbial population structures in the deep marine biosphere
-
Huber JA, Welch DBM, Morrison HG, Huse SM, Neal PR, Butterfield DA & Sogin ML (2007) Microbial population structures in the deep marine biosphere. Science 318: 97-100.
-
(2007)
Science
, vol.318
, pp. 97-100
-
-
Huber, J.A.1
Welch, D.B.M.2
Morrison, H.G.3
Huse, S.M.4
Neal, P.R.5
Butterfield, D.A.6
Sogin, M.L.7
-
11
-
-
77955237112
-
Isolated communities of Epsilonproteobacteria in hydrothermal vent fluids of the Mariana Arc seamounts
-
Huber JA, Cantin HV, Huse SM, Mark Welch DB, Sogin ML & Butterfield DA (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
Mark Welch, D.B.4
Sogin, M.L.5
Butterfield, D.A.6
-
13
-
-
55849119180
-
Exilispira thermophila gen. nov., sp. nov., an anaerobic, thermophilic spirochaete isolated from a deep-sea hydrothermal vent chimney
-
Imachi H, Sakai S, Hirayama H, Nakagawa S, Nunoura T, Takai K & Horikoshi K (2008) Exilispira thermophila gen. nov., sp. nov., an anaerobic, thermophilic spirochaete isolated from a deep-sea hydrothermal vent chimney. Int J Syst Evol Micr 58: 2258-2265.
-
(2008)
Int J Syst Evol Micr
, vol.58
, pp. 2258-2265
-
-
Imachi, H.1
Sakai, S.2
Hirayama, H.3
Nakagawa, S.4
Nunoura, T.5
Takai, K.6
Horikoshi, K.7
-
14
-
-
38949127042
-
Miniprimer PCR, a new lens for viewing the microbial world
-
Isenbarger TA, Finney M, Rìos-Velázquez C, Handelsman J & Ruvkun G (2008) Miniprimer PCR, a new lens for viewing the microbial world. Appl Environ Microb 74: 840-849.
-
(2008)
Appl Environ Microb
, vol.74
, pp. 840-849
-
-
Isenbarger, T.A.1
Finney, M.2
Rìos-Velázquez, C.3
Handelsman, J.4
Ruvkun, G.5
-
15
-
-
77950526876
-
Dormancy contributes to the maintenance of microbial diversity
-
Jones SE & Lennon JT (2010) Dormancy contributes to the maintenance of microbial diversity. P Natl Acad Sci USA 107: 5881-5886.
-
(2010)
P Natl Acad Sci USA
, vol.107
, pp. 5881-5886
-
-
Jones, S.E.1
Lennon, J.T.2
-
16
-
-
0036207009
-
The ecology of Cytophaga-Flavobacteria in aquatic environments
-
Kirchman DL (2002) The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol Ecol 39: 91-100.
-
(2002)
FEMS Microbiol Ecol
, vol.39
, pp. 91-100
-
-
Kirchman, D.L.1
-
17
-
-
77953594953
-
The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes
-
Kirchman DL, Cottrell MT & Lovejoy C (2010) The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes. Environ Microbiol 12: 1132-1143.
-
(2010)
Environ Microbiol
, vol.12
, pp. 1132-1143
-
-
Kirchman, D.L.1
Cottrell, M.T.2
Lovejoy, C.3
-
18
-
-
33645454369
-
Bacterial and archaeal phylotypes associated with distinct mineralogical layers of a white smoker spire from a deep-sea hydrothermal vent site (9°N, East Pacific Rise)
-
Kormas KA, Tivey MK, Damm KV & Teske A (2006) Bacterial and archaeal phylotypes associated with distinct mineralogical layers of a white smoker spire from a deep-sea hydrothermal vent site (9°N, East Pacific Rise). Environ Microbiol 8: 909-920.
-
(2006)
Environ Microbiol
, vol.8
, pp. 909-920
-
-
Kormas, K.A.1
Tivey, M.K.2
Damm, K.V.3
Teske, A.4
-
19
-
-
0008048504
-
Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses
-
Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML & Pace NR (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. P Natl Acad Sci USA 82: 6955-6959.
-
(1985)
P Natl Acad Sci USA
, vol.82
, pp. 6955-6959
-
-
Lane, D.J.1
Pace, B.2
Olsen, G.J.3
Stahl, D.A.4
Sogin, M.L.5
Pace, N.R.6
-
21
-
-
54549106898
-
Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers
-
Liu Z, DeSantis TZ, Andersen GL & Knight R (2008) Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Res 36: e120.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Liu, Z.1
DeSantis, T.Z.2
Andersen, G.L.3
Knight, R.4
-
23
-
-
24044455869
-
Genome sequencing in microfabricated high-density picolitre reactors
-
Margulies M, Egholm M, Altman WE et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
-
(2005)
Nature
, vol.437
, pp. 376-380
-
-
Margulies, M.1
Egholm, M.2
Altman, W.E.3
-
24
-
-
78049286743
-
Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea
-
McCarren J, Becker JW, Repeta DJ et al. (2010) Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. P Natl Acad Sci USA 107: 16420-16427.
-
(2010)
P Natl Acad Sci USA
, vol.107
, pp. 16420-16427
-
-
McCarren, J.1
Becker, J.W.2
Repeta, D.J.3
-
25
-
-
0028976424
-
Phylogenetic diversity of the bacterial community from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii
-
Moyer CL, Dobbs FC & Karl DM (1995) Phylogenetic diversity of the bacterial community from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii. Appl Environ Microb 61: 1555-1562.
-
(1995)
Appl Environ Microb
, vol.61
, pp. 1555-1562
-
-
Moyer, C.L.1
Dobbs, F.C.2
Karl, D.M.3
-
27
-
-
79961171127
-
-
VEGAN: community ecology package. Available at
-
Oksanen JF, Blanchet FG, Kindt R et al. (2010) VEGAN: community ecology package. Available at
-
(2010)
-
-
Oksanen, J.F.1
Blanchet, F.G.2
Kindt, R.3
-
28
-
-
77951945504
-
Identifying biologically relevant differences between metagenomic communities
-
Parks DH & Beiko RG (2010) Identifying biologically relevant differences between metagenomic communities. Bioinformatics 26: 715-721.
-
(2010)
Bioinformatics
, vol.26
, pp. 715-721
-
-
Parks, D.H.1
Beiko, R.G.2
-
29
-
-
78650051812
-
Discovery of a black smoker vent field and vent fauna at the Arctic Mid-Ocean Ridge
-
Pedersen RB, Rapp HT, Thorseth IH et al. (2010) Discovery of a black smoker vent field and vent fauna at the Arctic Mid-Ocean Ridge. Nat Commun 1: 126.
-
(2010)
Nat Commun
, vol.1
, pp. 126
-
-
Pedersen, R.B.1
Rapp, H.T.2
Thorseth, I.H.3
-
30
-
-
33744745905
-
Marine microbial diversity
-
Trends Microbiol
-
Pedrós-Alió C (2006) Marine microbial diversity: can it be determined? Trends Microbiol 14: 257-263.
-
(2006)
can it be determined?
, vol.14
, pp. 257-263
-
-
Pedrós-Alió, C.1
-
31
-
-
34248176868
-
Microbial CO(2) fixation and sulfur cycling associated with low-temperature emissions at the Lilliput hydrothermal field, southern Mid-Atlantic Ridge (9°S)
-
Perner M, Seifert R, Weber S et al. (2007) Microbial CO(2) fixation and sulfur cycling associated with low-temperature emissions at the Lilliput hydrothermal field, southern Mid-Atlantic Ridge (9°S). Environ Microbiol 9: 1186-1201.
-
(2007)
Environ Microbiol
, vol.9
, pp. 1186-1201
-
-
Perner, M.1
Seifert, R.2
Weber, S.3
-
32
-
-
79961166339
-
-
The Republic. "Allegory of the cave" from Book VII. (Cornford FM, ed) 514A-521B. Oxford University Press, London.
-
Plato & Cornford FM (1941) The Republic. "Allegory of the cave" from Book VII. (Cornford FM, ed), pp. 514A-521B. Oxford University Press, London.
-
(1941)
-
-
Plato1
Cornford, F.M.2
-
33
-
-
0031711754
-
Bias in template-to-product ratios in multitemplate PCR
-
Polz MF & Cavanaugh CM (1998) Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microb 64: 3724-3730.
-
(1998)
Appl Environ Microb
, vol.64
, pp. 3724-3730
-
-
Polz, M.F.1
Cavanaugh, C.M.2
-
34
-
-
0027264175
-
Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms
-
Poulsen LK, Ballard G & Stahl DA (1993) Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms. Appl Environ Microb 59: 1354-1360.
-
(1993)
Appl Environ Microb
, vol.59
, pp. 1354-1360
-
-
Poulsen, L.K.1
Ballard, G.2
Stahl, D.A.3
-
35
-
-
37549027613
-
SILVA
-
Nucleic Acids Res
-
Pruesse E, Quast C, Knittle K, Fuchs BM, Ludwig W, Peplies J & Glöckner FO (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)
a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
, vol.35
, pp. 7188-7196
-
-
Pruesse, E.1
Quast, C.2
Knittle, K.3
Fuchs, B.M.4
Ludwig, W.5
Peplies, J.6
Glöckner, F.O.7
-
36
-
-
69549112742
-
Accurate determination of microbial diversity from 454 pyrosequencing data
-
Quince C, Lanzén A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF & Sloan WT (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 6: 639-641.
-
(2009)
Nat Methods
, vol.6
, pp. 639-641
-
-
Quince, C.1
Lanzén, A.2
Curtis, T.P.3
Davenport, R.J.4
Hall, N.5
Head, I.M.6
Read, L.F.7
Sloan, W.T.8
-
38
-
-
0037052564
-
Merging genomes with geochemistry in hydrothermal ecosystems
-
Reysenbach A-L & Shock E (2002) Merging genomes with geochemistry in hydrothermal ecosystems. Science 296: 1077-1082.
-
(2002)
Science
, vol.296
, pp. 1077-1082
-
-
Reysenbach, A.-L.1
Shock, E.2
-
39
-
-
57449090885
-
Spatial comparison of total vs. active bacterial populations by coupling genetic fingerprinting and clone library analyses in the NW Mediterranean Sea
-
Rodriguez-Blanco A, Ghiglione J-F, Catala P, Casamayor EO & Lebaron P (2009) Spatial comparison of total vs. active bacterial populations by coupling genetic fingerprinting and clone library analyses in the NW Mediterranean Sea. FEMS Microbiol Ecol 67: 30-42.
-
(2009)
FEMS Microbiol Ecol
, vol.67
, pp. 30-42
-
-
Rodriguez-Blanco, A.1
Ghiglione, J.-F.2
Catala, P.3
Casamayor, E.O.4
Lebaron, P.5
-
40
-
-
34547800097
-
Pyrosequencing enumerates and contrasts soil microbial diversity
-
Roesch LFW, Fulthorpe RR, Riva A et al. (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1: 283-290.
-
(2007)
ISME J
, vol.1
, pp. 283-290
-
-
Roesch, L.F.W.1
Fulthorpe, R.R.2
Riva, A.3
-
41
-
-
77951614880
-
The fauna of hydrothermal vents on the Mohn Ridge (North Atlantic)
-
Schander C, Rapp HT, Kongsrud JA et al. (2010) The fauna of hydrothermal vents on the Mohn Ridge (North Atlantic). Mar Biol Res 6: 155-171.
-
(2010)
Mar Biol Res
, vol.6
, pp. 155-171
-
-
Schander, C.1
Rapp, H.T.2
Kongsrud, J.A.3
-
42
-
-
39649088960
-
Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans
-
Sievert SM, Scott KM, Klotz MG et al. (2008) Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans. Appl Environ Microb 74: 1145-1156.
-
(2008)
Appl Environ Microb
, vol.74
, pp. 1145-1156
-
-
Sievert, S.M.1
Scott, K.M.2
Klotz, M.G.3
-
43
-
-
33344464667
-
Measurement of diversity
-
Simpson EH (1949) Measurement of diversity. Nature 163: 688.
-
(1949)
Nature
, vol.163
, pp. 688
-
-
Simpson, E.H.1
-
44
-
-
34247098019
-
Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis
-
Sipos R, Székely AJ, Palatinszky M, Révész S, Márialigeti K & Nikolausz M (2007) Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis. FEMS Microbiol Ecol 60: 341-350.
-
(2007)
FEMS Microbiol Ecol
, vol.60
, pp. 341-350
-
-
Sipos, R.1
Székely, A.J.2
Palatinszky, M.3
Révész, S.4
Márialigeti, K.5
Nikolausz, M.6
-
45
-
-
33747073504
-
Microbial diversity in the deep sea and the underexplored 'rare biosphere'
-
Sogin ML, Morrison HG, Huber JA et al. (2006) Microbial diversity in the deep sea and the underexplored 'rare biosphere'. P Natl Acad Sci USA 103: 12115-12120.
-
(2006)
P Natl Acad Sci USA
, vol.103
, pp. 12115-12120
-
-
Sogin, M.L.1
Morrison, H.G.2
Huber, J.A.3
-
46
-
-
1542328972
-
Properties of the reverse transcription reaction in mRNA quantification
-
Ståhlberg A, Håkansson J, Xian X, et al. (2004) Properties of the reverse transcription reaction in mRNA quantification. Clin Chem 50: 509-515.
-
(2004)
Clin Chem
, vol.50
, pp. 509-515
-
-
Ståhlberg, A.1
Håkansson, J.2
Xian, X.3
-
47
-
-
0030067991
-
Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR
-
Suzuki MT & Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microb 62: 625-630.
-
(1996)
Appl Environ Microb
, vol.62
, pp. 625-630
-
-
Suzuki, M.T.1
Giovannoni, S.J.2
-
48
-
-
79961166048
-
-
Fisher. Available at
-
Tang H & Pedersen B (2010) Fisher. Available at
-
(2010)
-
-
Tang, H.1
Pedersen, B.2
-
50
-
-
84920629237
-
A renaissance for the pioneering 16S rRNA gene
-
Tringe SG & Hugenholtz P (2008) A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol 11: 442-446.
-
(2008)
Curr Opin Microbiol
, vol.11
, pp. 442-446
-
-
Tringe, S.G.1
Hugenholtz, P.2
-
51
-
-
49649087440
-
Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome
-
Urich T, Lanzén A, Qi J, Huson DH, Schleper C & Schuster SC (2008) Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS One 3: e2527.
-
(2008)
PLoS One
, vol.3
-
-
Urich, T.1
Lanzén, A.2
Qi, J.3
Huson, D.H.4
Schleper, C.5
Schuster, S.C.6
-
52
-
-
77957892886
-
Ecology and biogeography of free-living nematodes associated with chemosynthetic environments in the deep sea
-
PLoS One:
-
Vanreusel A, Groote AD, Gollner S & Bright M (2010) Ecology and biogeography of free-living nematodes associated with chemosynthetic environments in the deep sea: a review. PLoS One 5: e12449.
-
(2010)
a review
, vol.5
-
-
Vanreusel, A.1
Groote, A.D.2
Gollner, S.3
Bright, M.4
-
53
-
-
34548293679
-
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
Wang Q, Garrity GM, Tiedje JM & Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microb 73: 5261-5267.
-
(2007)
Appl Environ Microb
, vol.73
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
Cole, J.R.4
-
54
-
-
67349235323
-
Quantitative effects of position and type of single mismatch on single base primer extension
-
Wu J-H, Hong P-Y & Liu W-T (2009) Quantitative effects of position and type of single mismatch on single base primer extension. J Microbiol Meth 77: 267-275.
-
(2009)
J Microbiol Meth
, vol.77
, pp. 267-275
-
-
Wu, J.-H.1
Hong, P.-Y.2
Liu, W.-T.3
-
55
-
-
77953571641
-
Molecular characterization of inorganic sulfur-compound metabolism in the deep-sea epsilonproteobacterium Sulfurovum sp. NBC37-1
-
Yamamoto M, Nakagawa S, Shimamura S, Takai K & Horikoshi K (2010) Molecular characterization of inorganic sulfur-compound metabolism in the deep-sea epsilonproteobacterium Sulfurovum sp. NBC37-1. Environ Microbiol 12: 1144-1153.
-
(2010)
Environ Microbiol
, vol.12
, pp. 1144-1153
-
-
Yamamoto, M.1
Nakagawa, S.2
Shimamura, S.3
Takai, K.4
Horikoshi, K.5
|