-
1
-
-
44449137093
-
The microbial engines that drive Earth's biogeochemical cycles
-
P.G. Falkowski, T. Fenchel, and E.F. Delong The microbial engines that drive Earth's biogeochemical cycles Science 320 2008 1034 1039
-
(2008)
Science
, vol.320
, pp. 1034-1039
-
-
Falkowski, P.G.1
Fenchel, T.2
Delong, E.F.3
-
2
-
-
66149119261
-
The microbial ocean from genomes to biomes
-
E.F. DeLong The microbial ocean from genomes to biomes Nature 459 2009 200 206
-
(2009)
Nature
, vol.459
, pp. 200-206
-
-
Delong, E.F.1
-
3
-
-
80053289210
-
Eukaryotic picoplankton in surface oceans
-
R. Massana Eukaryotic picoplankton in surface oceans Annu. Rev. Microbiol. 65 2011 91 110
-
(2011)
Annu. Rev. Microbiol.
, vol.65
, pp. 91-110
-
-
Massana, R.1
-
4
-
-
83655192943
-
Marine protistan diversity
-
D. Caron, P. Countway, A. Jones, D. Kim, and A. Schnetzer Marine protistan diversity Ann Rev Mar Sci. 4 2012 467 493
-
(2012)
Ann Rev Mar Sci.
, vol.4
, pp. 467-493
-
-
Caron, D.1
Countway, P.2
Jones, A.3
Kim, D.4
Schnetzer, A.5
-
5
-
-
33748782244
-
Does the global microbiota consist of a few cosmopolitan species?
-
R. Logares Does the global microbiota consist of a few cosmopolitan species? Ecología Austral 16 2006 85 90
-
(2006)
Ecología Austral
, vol.16
, pp. 85-90
-
-
Logares, R.1
-
6
-
-
31544448331
-
Microbial biogeography: Putting microorganisms on the map
-
J.B. Martiny, B.J. Bohannan, J.H. Brown, R.K. Colwell, J.A. Fuhrman, J.L. Green, M.C. Horner-Devine, M. Kane, J.A. Krumins, and C.R. Kuske et al. Microbial biogeography: putting microorganisms on the map Nat. Rev. Microbiol. 4 2006 102 112
-
(2006)
Nat. Rev. Microbiol.
, vol.4
, pp. 102-112
-
-
Martiny, J.B.1
Bohannan, B.J.2
Brown, J.H.3
Colwell, R.K.4
Fuhrman, J.A.5
Green, J.L.6
Horner-Devine, M.C.7
Kane, M.8
Krumins, J.A.9
Kuske, C.R.10
-
7
-
-
25144475996
-
Marine microorganisms and global nutrient cycles
-
K.R. Arrigo Marine microorganisms and global nutrient cycles Nature 437 2005 349 355
-
(2005)
Nature
, vol.437
, pp. 349-355
-
-
Arrigo, K.R.1
-
8
-
-
33744745905
-
Marine microbial diversity: Can it be determined?
-
C. Pedrós-Alió Marine microbial diversity: can it be determined? Trends Microbiol. 14 2006 257 263
-
(2006)
Trends Microbiol.
, vol.14
, pp. 257-263
-
-
Pedrós-Alió, C.1
-
9
-
-
83655191007
-
The rare bacterial biosphere
-
C. Pedrós-Alió The rare bacterial biosphere Annu. Rev. Mar. Sci. 4 2012 449 466
-
(2012)
Annu. Rev. Mar. Sci.
, vol.4
, pp. 449-466
-
-
Pedrós-Alió, C.1
-
11
-
-
33747073504
-
Microbial diversity in the deep sea and the underexplored "rare biosphere"
-
M.L. Sogin, H.G. Morrison, J.A. Huber, D. Mark Welch, S.M. Huse, P.R. Neal, J.M. Arrieta, and G.J. Herndl Microbial diversity in the deep sea and the underexplored "rare biosphere" Proc. Natl. Acad. Sci. USA 103 2006 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
Mark Welch, D.4
Huse, S.M.5
Neal, P.R.6
Arrieta, J.M.7
Herndl, G.J.8
-
12
-
-
84865285541
-
Environmental microbiology through the lens of high-throughput DNA sequencing: Synopsis of current platforms and bioinformatics approaches
-
R. Logares, T.H. Haverkamp, S. Kumar, A. Lanzén, A.J. Nederbragt, C. Quince, and H. Kauserud Environmental microbiology through the lens of high-throughput DNA sequencing: synopsis of current platforms and bioinformatics approaches J. Microbiol. Methods 91 2012 106 113
-
(2012)
J. Microbiol. Methods
, vol.91
, pp. 106-113
-
-
Logares, R.1
Haverkamp, T.H.2
Kumar, S.3
Lanzén, A.4
Nederbragt, A.J.5
Quince, C.6
Kauserud, H.7
-
13
-
-
73449089058
-
Hypotheses on the role of the protistan rare biosphere in a changing world
-
D. Caron, and P. Countway Hypotheses on the role of the protistan rare biosphere in a changing world Aquat. Microb. Ecol. 57 2009 227 238
-
(2009)
Aquat. Microb. Ecol.
, vol.57
, pp. 227-238
-
-
Caron, D.1
Countway, P.2
-
14
-
-
77950526876
-
Dormancy contributes to the maintenance of microbial diversity
-
S.E. Jones, and J.T. Lennon Dormancy contributes to the maintenance of microbial diversity Proc. Natl. Acad. Sci. USA 107 2010 5881 5886
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 5881-5886
-
-
Jones, S.E.1
Lennon, J.T.2
-
16
-
-
84857065812
-
Recruitment of members from the rare biosphere of marine bacterioplankton communities after an environmental disturbance
-
J. Sjöstedt, P. Koch-Schmidt, M. Pontarp, B. Canbäck, A. Tunlid, P. Lundberg, A. Hagström, and L. Riemann Recruitment of members from the rare biosphere of marine bacterioplankton communities after an environmental disturbance Appl. Environ. Microbiol. 78 2012 1361 1369
-
(2012)
Appl. Environ. Microbiol.
, vol.78
, pp. 1361-1369
-
-
Sjöstedt, J.1
Koch-Schmidt, P.2
Pontarp, M.3
Canbäck, B.4
Tunlid, A.5
Lundberg, P.6
Hagström, A.7
Riemann, L.8
-
18
-
-
78649448174
-
A 'rare biosphere' microorganism contributes to sulfate reduction in a peatland
-
M. Pester, N. Bittner, P. Deevong, M. Wagner, and A. Loy A 'rare biosphere' microorganism contributes to sulfate reduction in a peatland ISME J. 4 2010 1591 1602
-
(2010)
ISME J.
, vol.4
, pp. 1591-1602
-
-
Pester, M.1
Bittner, N.2
Deevong, P.3
Wagner, M.4
Loy, A.5
-
19
-
-
84876822224
-
Biogeography of bacterial communities exposed to progressive long-term environmental change
-
R. Logares, E.S. Lindström, S. Langenheder, J.B. Logue, H. Paterson, J. Laybourn-Parry, K. Rengefors, L. Tranvik, and S. Bertilsson Biogeography of bacterial communities exposed to progressive long-term environmental change ISME J. 7 2013 937 948
-
(2013)
ISME J.
, vol.7
, pp. 937-948
-
-
Logares, R.1
Lindström, E.S.2
Langenheder, S.3
Logue, J.B.4
Paterson, H.5
Laybourn-Parry, J.6
Rengefors, K.7
Tranvik, L.8
Bertilsson, S.9
-
20
-
-
58049112704
-
Protists are microbes too: A perspective
-
D.A. Caron, A.Z. Worden, P.D. Countway, E. Demir, and K.B. Heidelberg Protists are microbes too: a perspective ISME J. 3 2009 4 12
-
(2009)
ISME J.
, vol.3
, pp. 4-12
-
-
Caron, D.A.1
Worden, A.Z.2
Countway, P.D.3
Demir, E.4
Heidelberg, K.B.5
-
21
-
-
70749095743
-
Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities
-
T. Stoeck, A. Behnke, R. Christen, L. Amaral-Zettler, M.J. Rodriguez-Mora, A. Chistoserdov, W. Orsi, and V.P. Edgcomb Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities BMC Biol. 7 2009 72
-
(2009)
BMC Biol.
, vol.7
, pp. 72
-
-
Stoeck, T.1
Behnke, A.2
Christen, R.3
Amaral-Zettler, L.4
Rodriguez-Mora, M.J.5
Chistoserdov, A.6
Orsi, W.7
Edgcomb, V.P.8
-
22
-
-
77954834182
-
Composition and genetic diversity of picoeukaryotes in subtropical coastal waters as revealed by 454 pyrosequencing
-
M.K. Cheung, C.H. Au, K.H. Chu, H.S. Kwan, and C.K. Wong Composition and genetic diversity of picoeukaryotes in subtropical coastal waters as revealed by 454 pyrosequencing ISME J. 4 2010 1053 1059
-
(2010)
ISME J.
, vol.4
, pp. 1053-1059
-
-
Cheung, M.K.1
Au, C.H.2
Chu, K.H.3
Kwan, H.S.4
Wong, C.K.5
-
23
-
-
77954557093
-
Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity
-
V. Nolte, R.V. Pandey, S. Jost, R. Medinger, B. Ottenwälder, J. Boenigk, and C. Schlötterer Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity Mol. Ecol. 19 2010 2908 2915
-
(2010)
Mol. Ecol.
, vol.19
, pp. 2908-2915
-
-
Nolte, V.1
Pandey, R.V.2
Jost, S.3
Medinger, R.4
Ottenwälder, B.5
Boenigk, J.6
Schlötterer, C.7
-
24
-
-
77951908579
-
Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water
-
T. Stoeck, D. Bass, M. Nebel, R. Christen, M.D. Jones, H.W. Breiner, and T.A. Richards Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water Mol. Ecol. 19 Suppl 1 2010 21 31
-
(2010)
Mol. Ecol.
, vol.19
, Issue.SUPPL. 1
, pp. 21-31
-
-
Stoeck, T.1
Bass, D.2
Nebel, M.3
Christen, R.4
Jones, M.D.5
Breiner, H.W.6
Richards, T.A.7
-
25
-
-
84878628851
-
Short-term dynamics of diversity patterns: Evidence of continual reassembly within lacustrine small eukaryotes
-
J.F. Mangot, I. Domaizon, N. Taib, N. Marouni, E. Duffaud, G. Bronner, and D. Debroas Short-term dynamics of diversity patterns: evidence of continual reassembly within lacustrine small eukaryotes Environ. Microbiol. 15 2013 1745 1758
-
(2013)
Environ. Microbiol.
, vol.15
, pp. 1745-1758
-
-
Mangot, J.F.1
Domaizon, I.2
Taib, N.3
Marouni, N.4
Duffaud, E.5
Bronner, G.6
Debroas, D.7
-
26
-
-
84986841026
-
Pelagic ecosystem structure: Heterotrophic compartments of the plankton and their relationship to plankton size fractions
-
J.M. Sieburth, V. Smetacek, and J. Lenz Pelagic ecosystem structure: heterotrophic compartments of the plankton and their relationship to plankton size fractions Limnol. Oceanogr. 23 1978 1256 1263
-
(1978)
Limnol. Oceanogr.
, vol.23
, pp. 1256-1263
-
-
Sieburth, J.M.1
Smetacek, V.2
Lenz, J.3
-
27
-
-
73349110099
-
Wrinkles in the rare biosphere: Pyrosequencing errors can lead to artificial inflation of diversity estimates
-
V. Kunin, A. Engelbrektson, H. Ochman, and P. Hugenholtz Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates Environ. Microbiol. 12 2010 118 123
-
(2010)
Environ. Microbiol.
, vol.12
, pp. 118-123
-
-
Kunin, V.1
Engelbrektson, A.2
Ochman, H.3
Hugenholtz, P.4
-
29
-
-
0016355478
-
A new look at the statistical model identification
-
H. Akaike A new look at the statistical model identification IEEE Trans. Automat. Contr. 19 1974 716 723
-
(1974)
IEEE Trans. Automat. Contr.
, vol.19
, pp. 716-723
-
-
Akaike, H.1
-
30
-
-
0001572401
-
The commonness, and rarity, of species
-
F.W. Preston The commonness, and rarity, of species Ecology 29 1948 254 283
-
(1948)
Ecology
, vol.29
, pp. 254-283
-
-
Preston, F.W.1
-
31
-
-
0026499429
-
Conservation evaluation and phylogenetic diversity
-
D. Faith Conservation evaluation and phylogenetic diversity Biol. Conserv. 61 1992 1 10
-
(1992)
Biol. Conserv.
, vol.61
, pp. 1-10
-
-
Faith, D.1
-
34
-
-
0000521518
-
A theoretical ecological model of size distributions among species of animals
-
G.E. Hutchinson, and R.H. MacArthur A theoretical ecological model of size distributions among species of animals Am. Nat. 93 1959 117 125
-
(1959)
Am. Nat.
, vol.93
, pp. 117-125
-
-
Hutchinson, G.E.1
MacArthur, R.H.2
-
36
-
-
0043141693
-
An experimentally-derived map of community assembly space
-
Y. Bar-Yam and A. Minai, eds
-
Zimmermann, C.R., Fukami, T., and Drake, J.A. (2003). An experimentally-derived map of community assembly space. Y. Bar-Yam and A. Minai, eds. Unifying Themes in Complex Systems II: Proceedings of the Second International Conference on Complex Systems, 427-436.
-
(2003)
Unifying Themes in Complex Systems II: Proceedings of the Second International Conference on Complex Systems
, pp. 427-436
-
-
Zimmermann, C.R.1
Fukami, T.2
Drake, J.A.3
-
37
-
-
0023509845
-
Community diversity: Relative roles of local and regional processes
-
R.E. Ricklefs Community diversity: relative roles of local and regional processes Science 235 1987 167 171
-
(1987)
Science
, vol.235
, pp. 167-171
-
-
Ricklefs, R.E.1
-
38
-
-
84857121817
-
Diversity and dynamics of rare and of resident bacterial populations in coastal sands
-
A. Gobet, S.I. Böer, S.M. Huse, J.E. van Beusekom, C. Quince, M.L. Sogin, A. Boetius, and A. Ramette Diversity and dynamics of rare and of resident bacterial populations in coastal sands ISME J. 6 2012 542 553
-
(2012)
ISME J.
, vol.6
, pp. 542-553
-
-
Gobet, A.1
Böer, S.I.2
Huse, S.M.3
Van Beusekom, J.E.4
Quince, C.5
Sogin, M.L.6
Boetius, A.7
Ramette, A.8
-
39
-
-
84894323131
-
Monthly to interannual variability of microbial eukaryote assemblages at four depths in the eastern North Pacific
-
D.Y. Kim, P.D. Countway, A.C. Jones, A. Schnetzer, W. Yamashita, C. Tung, and D.A. Caron Monthly to interannual variability of microbial eukaryote assemblages at four depths in the eastern North Pacific ISME J. 8 2014 515 530
-
(2014)
ISME J.
, vol.8
, pp. 515-530
-
-
Kim, D.Y.1
Countway, P.D.2
Jones, A.C.3
Schnetzer, A.4
Yamashita, W.5
Tung, C.6
Caron, D.A.7
-
41
-
-
77955251092
-
Ironing out the wrinkles in the rare biosphere through improved OTU clustering
-
S.M. Huse, D.M. Welch, H.G. Morrison, and M.L. Sogin Ironing out the wrinkles in the rare biosphere through improved OTU clustering Environ. Microbiol. 12 2010 1889 1898
-
(2010)
Environ. Microbiol.
, vol.12
, pp. 1889-1898
-
-
Huse, S.M.1
Welch, D.M.2
Morrison, H.G.3
Sogin, M.L.4
-
43
-
-
84876490476
-
Eukaryotic versus prokaryotic marine picoplankton ecology
-
R. Massana, and R. Logares Eukaryotic versus prokaryotic marine picoplankton ecology Environ. Microbiol. 15 2013 1254 1261
-
(2013)
Environ. Microbiol.
, vol.15
, pp. 1254-1261
-
-
Massana, R.1
Logares, R.2
-
44
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
J.G. Caporaso, J. Kuczynski, J. Stombaugh, K. Bittinger, F.D. Bushman, E.K. Costello, N. Fierer, A.G. Peña, J.K. Goodrich, and J.I. Gordon et al. QIIME allows analysis of high-throughput community sequencing data Nat. Methods 7 2010 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
Fierer, N.7
Peña, A.G.8
Goodrich, J.K.9
Gordon, J.I.10
-
45
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
R.C. Edgar Search and clustering orders of magnitude faster than BLAST Bioinformatics 26 2010 2460 2461
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
46
-
-
79952006773
-
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
-
Human Microbiome Consortium
-
B.J. Haas, D. Gevers, A.M. Earl, M. Feldgarden, D.V. Ward, G. Giannoukos, D. Ciulla, D. Tabbaa, S.K. Highlander, E. Sodergren Human Microbiome Consortium Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons Genome Res. 21 2011 494 504
-
(2011)
Genome Res.
, vol.21
, pp. 494-504
-
-
Haas, B.J.1
Gevers, D.2
Earl, A.M.3
Feldgarden, M.4
Ward, D.V.5
Giannoukos, G.6
Ciulla, D.7
Tabbaa, D.8
Highlander, S.K.9
Sodergren, E.10
-
47
-
-
84875623291
-
The Protist Ribosomal Reference database (PR2): A catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy
-
L. Guillou, D. Bachar, S. Audic, D. Bass, C. Berney, L. Bittner, C. Boutte, G. Burgaud, C. de Vargas, and J. Decelle et al. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy Nucleic Acids Res. 41 Database issue 2013 D597 D604
-
(2013)
Nucleic Acids Res.
, vol.41
, Issue.DATABASE ISSUE
-
-
Guillou, L.1
Bachar, D.2
Audic, S.3
Bass, D.4
Berney, C.5
Bittner, L.6
Boutte, C.7
Burgaud, G.8
De Vargas, C.9
Decelle, J.10
-
48
-
-
0025183708
-
Basic local alignment search tool
-
S.F. Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipman Basic local alignment search tool J. Mol. Biol. 215 1990 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
-
49
-
-
77956304094
-
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions
-
J. Reeder, and R. Knight Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions Nat. Methods 7 2010 668 669
-
(2010)
Nat. Methods
, vol.7
, pp. 668-669
-
-
Reeder, J.1
Knight, R.2
-
51
-
-
68649113028
-
Vegan: Community ecology package
-
version 1.15-0 (Finland: University of Oulu)
-
Oksanen, J., Kindt, R., Legendre, P., O'Hara, B., Simpson, G.L., Solymos, P., Stevens, M.H.H., and Wagner, H. (2008). Vegan: community ecology package. R package version 1.15-0 (Finland: University of Oulu).
-
(2008)
R Package
-
-
Oksanen, J.1
Kindt, R.2
Legendre, P.3
O'Hara, B.4
Simpson, G.L.5
Solymos, P.6
Stevens, M.H.H.7
Wagner, H.8
-
52
-
-
77953882250
-
Picante: R tools for integrating phylogenies and ecology
-
S.W. Kembel, P.D. Cowan, M.R. Helmus, W.K. Cornwell, H. Morlon, D.D. Ackerly, S.P. Blomberg, and C.O. Webb Picante: R tools for integrating phylogenies and ecology Bioinformatics 26 2010 1463 1464
-
(2010)
Bioinformatics
, vol.26
, pp. 1463-1464
-
-
Kembel, S.W.1
Cowan, P.D.2
Helmus, M.R.3
Cornwell, W.K.4
Morlon, H.5
Ackerly, D.D.6
Blomberg, S.P.7
Webb, C.O.8
-
53
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
P. Shannon, A. Markiel, O. Ozier, N.S. Baliga, J.T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker Cytoscape: a software environment for integrated models of biomolecular interaction networks Genome Res. 13 2003 2498 2504
-
(2003)
Genome Res.
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
-
54
-
-
33750403801
-
RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
A. Stamatakis RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models Bioinformatics 22 2006 2688 2690
-
(2006)
Bioinformatics
, vol.22
, pp. 2688-2690
-
-
Stamatakis, A.1
-
55
-
-
84874311437
-
General patterns of diversity in major marine microeukaryote lineages
-
M.C. Pernice, R. Logares, L. Guillou, and R. Massana General patterns of diversity in major marine microeukaryote lineages PLoS ONE 8 2013 e57170
-
(2013)
PLoS ONE
, vol.8
, pp. 57170
-
-
Pernice, M.C.1
Logares, R.2
Guillou, L.3
Massana, R.4
-
56
-
-
1042304216
-
APE: Analyses of phylogenetics and evolution in R language
-
E. Paradis, J. Claude, and K. Strimmer APE: Analyses of phylogenetics and evolution in R language Bioinformatics 20 2004 289 290
-
(2004)
Bioinformatics
, vol.20
, pp. 289-290
-
-
Paradis, E.1
Claude, J.2
Strimmer, K.3
|