-
1
-
-
34548544450
-
Bridging the Rubicon: Phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms
-
Alverson AJ, Jansen RK, Theriot EC. 2007. Bridging the Rubicon: phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms. Mol Phylogenet Evol. 45:193-210
-
(2007)
Mol Phylogenet Evol.
, vol.45
, pp. 193-210
-
-
Alverson, A.J.1
Jansen, R.K.2
Theriot, E.C.3
-
2
-
-
84980877218
-
The Venice system for the classification of marine waters according to salinity
-
Anonymous
-
Anonymous. 1958. The Venice system for the classification of marine waters according to salinity. Limnol Oceanogr. 3:346-347.
-
(1958)
Limnol Oceanogr.
, vol.3
, pp. 346-347
-
-
-
3
-
-
44849083699
-
Widespread distribution of proteorhodopsins in freshwater and brackish ecosystems
-
Atamna-Ismaeel N, Sabehi G, Sharon I, Witzel KP, Labrenz M, Jurgens K, Barkay T, Stomp M, Huisman J, Beja O. 2008. Widespread distribution of proteorhodopsins in freshwater and brackish ecosystems. ISME J. 2:656-662.
-
(2008)
ISME J.
, vol.2
, pp. 656-662
-
-
Atamna-Ismaeel, N.1
Sabehi, G.2
Sharon, I.3
Witzel, K.P.4
Labrenz, M.5
Jurgens, K.6
Barkay, T.7
Stomp, M.8
Huisman, J.9
Beja, O.10
-
4
-
-
28944440027
-
Marine bacterial microdiversity as revealed by internal transcribed spacer analysis
-
Brown MV, Fuhrman JA. 2005. Marine bacterial microdiversity as revealed by internal transcribed spacer analysis. Aquat Microb Ecol. 41:15-23.
-
(2005)
Aquat Microb Ecol.
, vol.41
, pp. 15-23
-
-
Brown, M.V.1
Fuhrman, J.A.2
-
5
-
-
60749109199
-
Seasonal dynamics of SAR11 populations in the euphotic and mesopelagic zones of the northwestern Sargasso Sea
-
Carlson CA, Morris R, Parsons R, Treusch AH, Giovannoni SJ, Vergin K. 2009. Seasonal dynamics of SAR11 populations in the euphotic and mesopelagic zones of the northwestern Sargasso Sea. ISME J. 3:283-295.
-
(2009)
ISME J.
, vol.3
, pp. 283-295
-
-
Carlson, C.A.1
Morris, R.2
Parsons, R.3
Treusch, A.H.4
Giovannoni, S.J.5
Vergin, K.6
-
6
-
-
0034043778
-
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
-
Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 17:540-552.
-
(2000)
Mol Biol Evol.
, vol.17
, pp. 540-552
-
-
Castresana, J.1
-
7
-
-
0006942901
-
Ecological salinity boundaries in Poikilohaline waters
-
Dahl E. 1956. Ecological salinity boundaries in Poikilohaline waters. Oikos 7:1-21.
-
(1956)
Oikos
, vol.7
, pp. 1-21
-
-
Dahl, E.1
-
8
-
-
33747827586
-
NAST: A multiple sequence alignment server for comparative analysis of 16S rRNA genes
-
DeSantis TZ Jr., Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, Andersen GL. 2006. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res. 34:W394-W399.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
DeSantis Jr., T.Z.1
Hugenholtz, P.2
Keller, K.3
Brodie, E.L.4
Larsen, N.5
Piceno, Y.M.6
Phan, R.7
Andersen, G.L.8
-
9
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. 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
Huber, T.7
Dalevi, D.8
Hu, P.9
Andersen, G.L.10
-
10
-
-
24344510265
-
Discordant 16S and 23S rRNA gene phylogenies for the genus Helicobacter: Implications for phylogenetic inference and systematics
-
Dewhirst FE, Shen Z, Scimeca MS, Stokes LN, Boumenna T, Chen T, Paster BJ, Fox JG. 2005. Discordant 16S and 23S rRNA gene phylogenies for the genus Helicobacter: implications for phylogenetic inference and systematics. J Bacteriol. 187:6106-6118.
-
(2005)
J Bacteriol.
, vol.187
, pp. 6106-6118
-
-
Dewhirst, F.E.1
Shen, Z.2
Scimeca, M.S.3
Stokes, L.N.4
Boumenna, T.5
Chen, T.6
Paster, B.J.7
Fox, J.G.8
-
11
-
-
0031027068
-
Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria
-
Field KG, Gordon D, Wright T, Rappe M, Urback E, Vergin K, Giovannoni SJ. 1997. Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria. Appl Environ Microbiol. 63:63-70.
-
(1997)
Appl Environ Microbiol.
, vol.63
, pp. 63-70
-
-
Field, K.G.1
Gordon, D.2
Wright, T.3
Rappe, M.4
Urback, E.5
Vergin, K.6
Giovannoni, S.J.7
-
12
-
-
46749116439
-
A rare SAR11 fosmid clone confirming genetic variability in the 'Candidatus Pelagibacter ubique' genome
-
Gilbert JA, Muhling M, Joint I. 2008. A rare SAR11 fosmid clone confirming genetic variability in the 'Candidatus Pelagibacter ubique' genome. ISME J. 2:790-793.
-
(2008)
ISME J.
, vol.2
, pp. 790-793
-
-
Gilbert, J.A.1
Muhling, M.2
Joint, I.3
-
13
-
-
27744438187
-
Proteorhodopsin in the ubiquitous marine bacterium SAR11
-
12 co-authors
-
Giovannoni SJ, Bibbs L, Cho JC, et al. (12 co-authors). 2005. Proteorhodopsin in the ubiquitous marine bacterium SAR11. Nature. 438:82-85.
-
(2005)
Nature.
, vol.438
, pp. 82-85
-
-
Giovannoni, S.J.1
Bibbs, L.2
Cho, J.C.3
-
15
-
-
23844446418
-
Genome streamlining in a cosmopolitan oceanic bacterium
-
14 co-authors
-
Giovannoni SJ, Tripp HJ, Givan S, et al. (14 co-authors). 2005. Genome streamlining in a cosmopolitan oceanic bacterium. Science 309:1242-1245.
-
(2005)
Science
, vol.309
, pp. 1242-1245
-
-
Giovannoni, S.J.1
Tripp, H.J.2
Givan, S.3
-
16
-
-
3042596603
-
Upwelling-driven nearshore hypoxia signals ecosystem and oceanographic changes in the northeast Pacific
-
Grantham BA, Chan F, Nielsen KJ, Fox DS, Barth JA, Huyer A, Lubchenco J, Menge BA. 2004. Upwelling-driven nearshore hypoxia signals ecosystem and oceanographic changes in the northeast Pacific. Nature. 429:749-754.
-
(2004)
Nature.
, vol.429
, pp. 749-754
-
-
Grantham, B.A.1
Chan, F.2
Nielsen, K.J.3
Fox, D.S.4
Barth, J.A.5
Huyer, A.6
Lubchenco, J.7
Menge, B.A.8
-
17
-
-
74549134948
-
Saline lake ecosystems of the world
-
Dordrecht (The Netherlands) Dr. W. Junk Publishers Hebert PD, Remigio EA, Colbourne JK, Taylor DJ, Wilson CC Accelerated molecular evolution in halophilic crustaceans
-
Hammer T. 1986. Saline lake ecosystems of the world. Dordrecht (The Netherlands): Dr. W. Junk Publishers Hebert PD, Remigio EA, Colbourne JK, Taylor DJ, Wilson CC. 2002. Accelerated molecular evolution in halophilic crustaceans. Evolution 56:909-926.
-
(1986)
Evolution
, vol.56
, pp. 909-926
-
-
Hammer, T.1
-
18
-
-
44649159553
-
Novel estuarine bacterioplankton in rRNA operon libraries from the Chesapeake Bay
-
Kan J, Evans SE, Chen F, Suzuki MT. 2008. Novel estuarine bacterioplankton in rRNA operon libraries from the Chesapeake Bay. Aquat Microb Ecol. 51:55-66.
-
(2008)
Aquat Microb Ecol.
, vol.51
, pp. 55-66
-
-
Kan, J.1
Evans, S.E.2
Chen, F.3
Suzuki, M.T.4
-
19
-
-
45949107473
-
Recent developments in the MAFFT multiple sequence alignment program
-
Katoh K, Toh H. 2008. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 9:286-298.
-
(2008)
Brief Bioinform.
, vol.9
, pp. 286-298
-
-
Katoh, K.1
Toh, H.2
-
20
-
-
0003912769
-
Limnoecology. the ecology of lakes and streams
-
Oxford: Oxford University Press. Laybourn-Parry J, Pearce DA The biodiversity and ecology of Antarctic lakes: models for evolution
-
Lampert W, Sommer U. 2007. Limnoecology. The ecology of lakes and streams. Oxford: Oxford University Press. Laybourn-Parry J, Pearce DA. 2007. The biodiversity and ecology of Antarctic lakes: models for evolution. Philos Trans R Soc Lond B Biol Sci. 362:2273-2289.
-
(2007)
Philos Trans R Soc Lond B Biol Sci.
, vol.362
, pp. 2273-2289
-
-
Lampert, W.1
Sommer, U.2
-
21
-
-
33845873289
-
Interactive Tree of Life (iTOL): An online tool for phylogenetic tree display and annotation
-
Letunic I, Bork P. 2007. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23:127-128.
-
(2007)
Bioinformatics
, vol.23
, pp. 127-128
-
-
Letunic, I.1
Bork, P.2
-
22
-
-
69749086719
-
Infrequent marine-freshwater transitions in the microbial world
-
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.
-
(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
-
23
-
-
29144464937
-
UniFrac: A new phylogenetic method for comparing microbial communities
-
Lozupone C, Knight R. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Envir Microbiol. 71:8228-8235.
-
(2005)
Appl Envir Microbiol.
, vol.71
, pp. 8228-8235
-
-
Lozupone, C.1
Knight, R.2
-
24
-
-
0036324293
-
Phylogenetic approaches for describing and comparing the diversity of microbial communities
-
Martin AP. 2002. Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl Envir Microbiol. 68:3673-3682.
-
(2002)
Appl Envir Microbiol.
, vol.68
, pp. 3673-3682
-
-
Martin, A.P.1
-
25
-
-
53549118607
-
The metagenomics RAST server\-a public resource for the automatic phylogenetic and functional analysis of metagenomes
-
12 co-authors
-
Meyer F, Paarmann D, D'Souza M, et al. (12 co-authors). 2008. The metagenomics RAST server\-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinform. 9:386.
-
(2008)
BMC Bioinform.
, vol.9
, pp. 386
-
-
Meyer, F.1
Paarmann, D.2
D'Souza, M.3
-
26
-
-
0037180794
-
SAR11 clade dominates ocean surface bacterioplankton communities
-
Morris RM, Rappe MS, Connon SA, Vergin KL, Siebold WA, Carlson CA, Giovannoni SJ. 2002. SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420:806-810.
-
(2002)
Nature
, vol.420
, pp. 806-810
-
-
Morris, R.M.1
Rappe, M.S.2
Connon, S.A.3
Vergin, K.L.4
Siebold, W.A.5
Carlson, C.A.6
Giovannoni, S.J.7
-
27
-
-
63149143240
-
Comparison of productivity and phytoplankton in a warm (Kongsfjorden) and a cold (Hornsund) Spitsbergen fjord in midsummer 2002
-
Piwosz K, Walkusz W, Hapter R, Wieczorek P, Hop H, Wiktor J. 2009. Comparison of productivity and phytoplankton in a warm (Kongsfjorden) and a cold (Hornsund) Spitsbergen fjord in midsummer 2002. Polar Biol. 32:549-559.
-
(2009)
Polar Biol.
, vol.32
, pp. 549-559
-
-
Piwosz, K.1
Walkusz, W.2
Hapter, R.3
Wieczorek, P.4
Hop, H.5
Wiktor, J.6
-
28
-
-
74549116992
-
FigTree
-
University of Edinburgh, United Kingdom
-
Rambaut A. 2009. FigTree. Institute of Evolutionary Biology, University of Edinburgh, United Kingdom. http://tree.bio.ed. ac.uk/software/figtree/.
-
(2009)
Institute of Evolutionary Biology
-
-
Rambaut, A.1
-
29
-
-
0002364934
-
The chemical stratification and microbial communities of Ace Lake, Antarctica: A review of the characteristics of a marine-derived meromictic lake
-
Rankin LM, Gibson JAE, Franzmann PD, Burton HR. 1999. The chemical stratification and microbial communities of Ace Lake, Antarctica: a review of the characteristics of a marine-derived meromictic lake. Polarforschung. 66:33-52.
-
(1999)
Polarforschung.
, vol.66
, pp. 33-52
-
-
Rankin, L.M.1
Gibson, J.A.E.2
Franzmann, P.D.3
Burton, H.R.4
-
30
-
-
0037043731
-
Cultivation of the ubiquitous SAR11 marine bacterioplankton clade
-
Rappe MS, Connon SA, Vergin KL, Giovannoni SJ. 2002. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630-633.
-
(2002)
Nature
, vol.418
, pp. 630-633
-
-
Rappe, M.S.1
Connon, S.A.2
Vergin, K.L.3
Giovannoni, S.J.4
-
32
-
-
0002922962
-
Die brackwasserfauna
-
Remane A. 1934. Die Brackwasserfauna. Verh Deutsch Zool Ges. 36:34-74.
-
(1934)
Verh Deutsch Zool Ges.
, vol.36
, pp. 34-74
-
-
Remane, A.1
-
33
-
-
33947238287
-
The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through eastern tropical Pacific
-
40 co-authors
-
Rusch DB, Halpern AL, Sutton G, et al. (40 co-authors). 2007. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol. 5:e77.
-
(2007)
PLoS Biol.
, vol.5
-
-
Rusch, D.B.1
Halpern, A.L.2
Sutton, G.3
-
34
-
-
33947215475
-
CAMERA: A community resource for metagenomics
-
Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M. 2007. CAMERA: a community resource for metagenomics. PLoS Biol. 5:e75.
-
(2007)
PLoS Biol.
, vol.5
-
-
Seshadri, R.1
Kravitz, S.A.2
Smarr, L.3
Gilna, P.4
Frazier, M.5
-
35
-
-
51649088380
-
Diversification of unicellular eukaryotes: Cryptomonad colonizations of marine and fresh waters inferred from revised 18S rRNA phylogeny
-
Shalchian-Tabrizi K, Brate J, Logares R, Klaveness D, Berney C, Jakobsen KS. 2008. Diversification of unicellular eukaryotes: cryptomonad colonizations of marine and fresh waters inferred from revised 18S rRNA phylogeny. Environ Microbiol. 10: 2635-2644.
-
(2008)
Environ Microbiol.
, vol.10
, pp. 2635-2644
-
-
Shalchian-Tabrizi, K.1
Brate, J.2
Logares, R.3
Klaveness, D.4
Berney, C.5
Jakobsen, K.S.6
-
36
-
-
48749125472
-
It's all relative: Ranking the diversity of aquatic bacterial communities
-
Shaw AK, Halpern AL, Beeson K, Tran B, Venter JC, 2Martiny JB. 2008. It's all relative: ranking the diversity of aquatic bacterial communities. Environ Microbiol. 10:2200-2210.
-
(2008)
Environ Microbiol.
, vol.10
, pp. 2200-2210
-
-
Shaw, A.K.1
Halpern, A.L.2
Beeson, K.3
Tran, B.4
Venter, J.C.5
Martiny, J.B.6
-
37
-
-
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
-
38
-
-
34547775666
-
Improvements of high-throughput culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site
-
Stingl U, Tripp HJ, Giovannoni SJ. 2007. Improvements of high-throughput culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site. ISME J. 1: 361-371.
-
(2007)
ISME J.
, vol.1
, pp. 361-371
-
-
Stingl, U.1
Tripp, H.J.2
Giovannoni, S.J.3
-
39
-
-
42049104578
-
SAR11 marine bacteria require exogenous reduced sulphur for growth
-
Tripp HJ, Kitner JB, Schwalbach MS, Dacey JW, Wilhelm LJ, Giovannoni SJ. 2008. SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature 452:741-744.
-
(2008)
Nature
, vol.452
, pp. 741-744
-
-
Tripp, H.J.1
Kitner, J.B.2
Schwalbach, M.S.3
Dacey, J.W.4
Wilhelm, L.J.5
Giovannoni, S.J.6
-
40
-
-
34548406920
-
High intraspecific recombination rate in a native population of Candidatus pelagibacter ubique (SAR11)
-
Vergin KL, Tripp HJ, Wilhelm LJ, Denver DR, Rappe MS, Giovannoni SJ. 2007. High intraspecific recombination rate in a native population of Candidatus pelagibacter ubique (SAR11). Environ Microbiol. 9:2430-2440.
-
(2007)
Environ Microbiol.
, vol.9
, pp. 2430-2440
-
-
Vergin, K.L.1
Tripp, H.J.2
Wilhelm, L.J.3
Denver, D.R.4
Rappe, M.S.5
Giovannoni, S.J.6
-
41
-
-
38849200974
-
Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data
-
Wilhelm LJ, Tripp HJ, Givan SA, Smith DP, Giovannoni SJ. 2007. Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data. Biol Direct. 2:27.
-
(2007)
Biol Direct.
, vol.2
, pp. 27
-
-
Wilhelm, L.J.1
Tripp, H.J.2
Givan, S.A.3
Smith, D.P.4
Giovannoni, S.J.5
-
42
-
-
33747359120
-
Bacterioplankton community composition along a salinity gradient of sixteen high-mountain lakes located on the Tibetan Plateau, China
-
Wu QL, Zwart G, Schauer M, Kamst-van Agterveld MP, Hahn MW. 2006. Bacterioplankton community composition along a salinity gradient of sixteen high-mountain lakes located on the Tibetan Plateau, China. Appl Environ Microbiol. 72:5478-5485.
-
(2006)
Appl Environ Microbiol.
, vol.72
, pp. 5478-5485
-
-
Wu, Q.L.1
Zwart, G.2
Schauer, M.3
Kamst-Van Agterveld, M.P.4
Hahn, M.W.5
-
43
-
-
0037178021
-
Typical freshwater bacteria: An analysis of available 16S rRNA gene sequences from plankton of lakes and rivers
-
Zwart G, Crump BC, Agterveld MPKV, Hagen F, Han SK. 2002. Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquat Microb Ecol. 28:141-155.
-
(2002)
Aquat Microb Ecol.
, vol.28
, pp. 141-155
-
-
Zwart, G.1
Crump, B.C.2
Mpkv, A.3
Hagen, F.4
Han, S.K.5
|