-
1
-
-
77954272855
-
TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations
-
Abascal, F., Zardoya, R., and Telford, M. J. (2010). TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Res. 38, 7-13. doi: 10.1093/nar/gkq291
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 7-13
-
-
Abascal, F.1
Zardoya, R.2
Telford, M.J.3
-
2
-
-
84901692094
-
Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria
-
Barberán, A., Ramirez, K. S., Leff, J. W., Bradford, M. A, Wall, D. H., and Fierer, N. (2014). Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria. Ecol. Lett. 17, 794-802. doi: 10.1111/ele.12282
-
(2014)
Ecol. Lett.
, vol.17
, pp. 794-802
-
-
Barberán, A.1
Ramirez, K.S.2
Leff, J.W.3
Bradford, M.A.4
Wall, D.H.5
Fierer, N.6
-
3
-
-
58449108616
-
A major clade of prokaryotes with ancient adaptations to life on land
-
Battistuzzi, F. U., and Hedges, S. B. (2009). A major clade of prokaryotes with ancient adaptations to life on land. Mol. Biol. Evol. 26, 335-343. doi: 10.1093/molbev/msn247
-
(2009)
Mol. Biol. Evol.
, vol.26
, pp. 335-343
-
-
Battistuzzi, F.U.1
Hedges, S.B.2
-
4
-
-
79952339121
-
Microbial diversity in non-sulfur, sulfur and iron geothermal steam vents
-
Benson, C. A., Bizzoco, R. W., Lipson, D. A., and Kelley, S. T. (2011). Microbial diversity in non-sulfur, sulfur and iron geothermal steam vents. FEMS Microbiol. Ecol. 76, 74-88. doi: 10.1111/j.1574-6941.2011.01047.x
-
(2011)
FEMS Microbiol. Ecol.
, vol.76
, pp. 74-88
-
-
Benson, C.A.1
Bizzoco, R.W.2
Lipson, D.A.3
Kelley, S.T.4
-
5
-
-
84856628838
-
Seasonal variability in airborne bacterial communities at a high-elevation site
-
Bowers, R. M., McCubbin, I. B., Hallar, A. G., and Fierer, N. (2012). Seasonal variability in airborne bacterial communities at a high-elevation site. Atmos. Environ. 50, 41-49. doi: 10.1016/j.atmosenv.2012.01.005
-
(2012)
Atmos. Environ.
, vol.50
, pp. 41-49
-
-
Bowers, R.M.1
McCubbin, I.B.2
Hallar, A.G.3
Fierer, N.4
-
6
-
-
0034636417
-
Detection and classification of atmospheric methane oxidizing bacteria in soil
-
Bull, I. D., Parekh, N. R., Hall, G. H., Ineson, P., and Evershed, R. P. (2000). Detection and classification of atmospheric methane oxidizing bacteria in soil. Nature 405, 175-178. doi: 10.1038/35012061
-
(2000)
Nature
, vol.405
, pp. 175-178
-
-
Bull, I.D.1
Parekh, N.R.2
Hall, G.H.3
Ineson, P.4
Evershed, R.P.5
-
7
-
-
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., et al. (2010). QIIME allows analysis of high-throughput community sequencing data. Nat. Methods. 7, 335-336. doi: 10.1038/nmeth.f.303
-
(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
-
8
-
-
3042631307
-
Genome sequence assembly using trace signals and additional sequence information
-
Chevreux, B., Wetter, T., and Suhai, S. (1999). Genome sequence assembly using trace signals and additional sequence information. Comput. Sci. Biol. 99, 45-56.
-
(1999)
Comput. Sci. Biol.
, vol.99
, pp. 45-56
-
-
Chevreux, B.1
Wetter, T.2
Suhai, S.3
-
9
-
-
84879936504
-
Actinobacteria -an ancient phylum active in volcanic rock weathering
-
Cockell, C. S., Kelly, L. C., and Marteinsson, V. (2013). Actinobacteria -an ancient phylum active in volcanic rock weathering. Geomicrobiol. J. 30, 706-720. doi: 10.1080/01490451.2012.758196
-
(2013)
Geomicrobiol. J.
, vol.30
, pp. 706-720
-
-
Cockell, C.S.1
Kelly, L.C.2
Marteinsson, V.3
-
10
-
-
0029845048
-
Soil microorganisms as controllers of atmospheric trace gases (H2,CO, CH4, OCS, N2O, and NO)
-
Conrad, R. (1996). Soil microorganisms as controllers of atmospheric trace gases (H2,CO, CH4, OCS, N2O, and NO). Microbiol. Rev. 60:609.
-
(1996)
Microbiol. Rev.
, vol.60
, pp. 609
-
-
Conrad, R.1
-
11
-
-
77950649410
-
The global methane cycle: recent advances in understanding the microbial processes involved
-
Conrad, R. (2009). The global methane cycle: recent advances in understanding the microbial processes involved. Environ. Microbiol. Rep. 1, 285-292. doi: 10.1111/j.1758-2229.2009.00038.x
-
(2009)
Environ. Microbiol. Rep.
, vol.1
, pp. 285-292
-
-
Conrad, R.1
-
12
-
-
80052722488
-
Genome data mining and soil survey for the novel group 5 [NiFe]-hydrogenase to explore the diversity and ecological importance of presumptive high-affinity H2-oxidizing bacteria
-
Constant, P., Chowdhury, S. P., Hesse, L., Pratscher, J., and Conrad, R. (2011). Genome data mining and soil survey for the novel group 5 [NiFe]-hydrogenase to explore the diversity and ecological importance of presumptive high-affinity H2-oxidizing bacteria. Appl. Environ. Microbiol. 77, 6027-6035. doi: 10.1128/AEM.00673-11
-
(2011)
Appl. Environ. Microbiol.
, vol.77
, pp. 6027-6035
-
-
Constant, P.1
Chowdhury, S.P.2
Hesse, L.3
Pratscher, J.4
Conrad, R.5
-
13
-
-
77953950338
-
Streptomycetes contributing to atmospheric molecular hydrogen soil uptake are widespread and encode a putative high-affinity [NiFe]-hydrogenase
-
Constant, P., Chowdhury, S. P., Pratscher, J., and Conrad, R. (2010). Streptomycetes contributing to atmospheric molecular hydrogen soil uptake are widespread and encode a putative high-affinity [NiFe]-hydrogenase. Environ. Microbiol. 12, 821-829. doi: 10.1111/j.1462-2920.2009.02130.x
-
(2010)
Environ. Microbiol.
, vol.12
, pp. 821-829
-
-
Constant, P.1
Chowdhury, S.P.2
Pratscher, J.3
Conrad, R.4
-
15
-
-
59649107254
-
Fumarole-supported islands of biodiversity within a hyperarid, high-elevation landscape on Socompa Volcano, Puna de Atacama
-
Costello, E. K., Halloy, S. R. P., Reed, S. C., Sowell, P., and Schmidt, S. K. (2009). Fumarole-supported islands of biodiversity within a hyperarid, high-elevation landscape on Socompa Volcano, Puna de Atacama, Andes. Appl. Environ. Microbiol. 75, 735-747. doi: 10.1128/AEM.01469-08
-
(2009)
Andes. Appl. Environ. Microbiol.
, vol.75
, pp. 735-747
-
-
Costello, E.K.1
Halloy, S.R.P.2
Reed, S.C.3
Sowell, P.4
Schmidt, S.K.5
-
16
-
-
77957151956
-
SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data
-
Cox, M. P., Peterson, D. A., and Biggs, P. J. (2010). SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 11:485. doi: 10.1186/1471-2105-11-485
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 485
-
-
Cox, M.P.1
Peterson, D.A.2
Biggs, P.J.3
-
17
-
-
70350015324
-
Community-wide analysis of microbial genome sequence signatures
-
Dick, G. J., Andersson, A. F., Baker, B. J., Simmons, S. L., Thomas, B. C., Yelton, A. P., et al. (2009). Community-wide analysis of microbial genome sequence signatures. Genome Biol. 10:R85. doi: 10.1186/gb-2009-10-8-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
-
18
-
-
41649109613
-
Functional metagenomic profiling of nine biomes
-
Dinsdale, E. A., Edwards, R. A., Hall, D., Angly, F., Breitbart, M., Brulc, J. M., et al. (2008). Functional metagenomic profiling of nine biomes. Nature 452, 629-632. doi: 10.1038/nature06810
-
(2008)
Nature
, vol.452
, pp. 629-632
-
-
Dinsdale, E.A.1
Edwards, R.A.2
Hall, D.3
Angly, F.4
Breitbart, M.5
Brulc, J.M.6
-
19
-
-
36849030274
-
Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia
-
Dunfield, P. F., Yuryev, A., Senin, P., Smirnova, A. V., Stott, M. B., Hou, S. B., et al. (2007). Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature 450, 879-882. doi: 10.1038/nature06411
-
(2007)
Nature
, vol.450
, pp. 879-882
-
-
Dunfield, P.F.1
Yuryev, A.2
Senin, P.3
Smirnova, A.V.4
Stott, M.B.5
Hou, S.B.6
-
20
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high throughput
-
Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797. doi: 10.1093/nar/gkh340
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
21
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar, R. C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2461. doi: 10.1093/bioinformatics/btq461
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
22
-
-
84871826193
-
Cross-biome metagenomic analyses of soil microbial communities and their functional attributes
-
Fierer, N., Leff, J. W., Adams, B. J., Nielsen, U. N., Thomas, S., Lauber, C. L., et al. (2012). Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc. Natl. Acad. Sci. U.S.A. 109, 21390-21395. doi: 10.1073/pnas.1215210110
-
(2012)
Proc. Natl. Acad. Sci. U. S. A.
, vol.109
, pp. 21390-21395
-
-
Fierer, N.1
Leff, J.W.2
Adams, B.J.3
Nielsen, U.N.4
Thomas, S.5
Lauber, C.L.6
-
23
-
-
84870431038
-
CD-HIT: accelerated for clustering the next-generation sequencing data
-
Fu, L., Niu, B., Zhu, Z., Wu, S., and Li, W. (2012). CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150-3152. doi: 10.1093/bioinformatics/bts565
-
(2012)
Bioinformatics
, vol.28
, pp. 3150-3152
-
-
Fu, L.1
Niu, B.2
Zhu, Z.3
Wu, S.4
Li, W.5
-
24
-
-
84904997234
-
Implications of streamlining theory for microbial ecology
-
Giovannoni, S. J., Cameron Thrash, J., and Temperton, B. (2014). Implications of streamlining theory for microbial ecology. ISME J. 8, 1553-1565. doi: 10.1038/ismej.2014.60
-
(2014)
ISME J
, vol.8
, pp. 1553-1565
-
-
Giovannoni, S.J.1
Cameron Thrash, J.2
Temperton, B.3
-
25
-
-
70350294348
-
Systematic artifacts in metagenomes from complex microbial communities
-
Gomez-Alvarez, V., Teal, T. K., and Schmidt, T. M. (2009). Systematic artifacts in metagenomes from complex microbial communities. ISME J. 3, 1314-1317. doi: 10.1038/ismej.2009.72
-
(2009)
ISME J
, vol.3
, pp. 1314-1317
-
-
Gomez-Alvarez, V.1
Teal, T.K.2
Schmidt, T.M.3
-
26
-
-
76349125221
-
"Atacama desert soil microbiology,"
-
ed P Dion and C. S. Nautiyal (Berlin; Heidelberg: Springer-Verlag)
-
Gómez-Silva, B., Rainey, F. A., Warren-Rhodes, K. A., McKay, C. P., and Navarro-González, R. (2008). "Atacama desert soil microbiology," in Microbiology of Extreme Soils, ed P. Dion and C. S. Nautiyal (Berlin; Heidelberg: Springer-Verlag), 117-132.
-
(2008)
Microbiology of Extreme Soils
, pp. 117-132
-
-
Gómez-Silva, B.1
Rainey, F.A.2
Warren-Rhodes, K.A.3
McKay, C.P.4
Navarro-González, R.5
-
27
-
-
0024978652
-
Substrate specificity of soluble methane monooxygenase
-
Green, J., and Dalton, H. (1989). Substrate specificity of soluble methane monooxygenase. J. Biol. Chem. 264, 17698-17703.
-
(1989)
J. Biol. Chem.
, vol.264
, pp. 17698-17703
-
-
Green, J.1
Dalton, H.2
-
28
-
-
84896541745
-
A soil actinobacterium scavenges atmospheric H2 using two membrane-associated, oxygen-dependent [NiFe] hydrogenases
-
Greening, C., Berney, M., Hards, K., Cook, G. M., and Conrad, R. (2014). A soil actinobacterium scavenges atmospheric H2 using two membrane-associated, oxygen-dependent [NiFe] hydrogenases. Proc. Natl. Acad. Sci. U.S.A. 111, 4257-4261. doi: 10.1073/pnas.1320586111
-
(2014)
Proc. Natl. Acad. Sci. U. S. A.
, vol.111
, pp. 4257-4261
-
-
Greening, C.1
Berney, M.2
Hards, K.3
Cook, G.M.4
Conrad, R.5
-
29
-
-
77950806408
-
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3
-
Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., and Gascuel, O. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307-321. doi: 10.1093/sysbio/syq010
-
(2010)
0. Syst. Biol.
, vol.59
, pp. 307-321
-
-
Guindon, S.1
Dufayard, J.-F.2
Lefort, V.3
Anisimova, M.4
Hordijk, W.5
Gascuel, O.6
-
30
-
-
0035434343
-
Enrichment of high-affinity CO oxidizers in Maine forest soil
-
Hardy, K. R., and King, G. M. (2001). Enrichment of high-affinity CO oxidizers in Maine forest soil. Appl. Environ. Microbiol. 67, 3671-3676. doi: 10.1128/AEM.67.8.3671-3676.2001
-
(2001)
Appl. Environ. Microbiol.
, vol.67
, pp. 3671-3676
-
-
Hardy, K.R.1
King, G.M.2
-
31
-
-
18844411420
-
150 million years of climatic stability: evidence from the Atacama Desert, northern Chile
-
Hartley, A., Chong, G., Houston, J., and Mather, A. E. (2005). 150 million years of climatic stability: evidence from the Atacama Desert, northern Chile. J. Geol. Soc. 162, 421-424. doi: 10.1144/0016-764904-071
-
(2005)
J. Geol. Soc.
, vol.162
, pp. 421-424
-
-
Hartley, A.1
Chong, G.2
Houston, J.3
Mather, A.E.4
-
32
-
-
80855164533
-
Sources and seasonality of atmospheric methanol based on tall tower measurements in the US Upper Midwest
-
Hu, L., Millet, D. B., Mohr, M. J., Wells, K. C., Griffis, T. J., and Helmig, D. (2011). Sources and seasonality of atmospheric methanol based on tall tower measurements in the US Upper Midwest. Atmos. Chem. Phys. 11, 11145-11156. doi: 10.5194/acp-11-11145-2011
-
(2011)
Atmos. Chem. Phys.
, vol.11
, pp. 11145-11156
-
-
Hu, L.1
Millet, D.B.2
Mohr, M.J.3
Wells, K.C.4
Griffis, T.J.5
Helmig, D.6
-
33
-
-
79958183390
-
Aciditerrimonas ferrireducens gen. nov., sp. nov., an iron-reducing thermoacidophilic actinobacterium isolated from a solfataric field
-
Itoh, T., Yamanoi, K., Kudo, T., Ohkuma, M., and Takashina, T. (2011). Aciditerrimonas ferrireducens gen. nov., sp. nov., an iron-reducing thermoacidophilic actinobacterium isolated from a solfataric field. Int. J. Syst. Evol. Microbiol. 61, 1281-1285. doi: 10.1099/ijs.0.023044-0
-
(2011)
Int. J. Syst. Evol. Microbiol.
, vol.61
, pp. 1281-1285
-
-
Itoh, T.1
Yamanoi, K.2
Kudo, T.3
Ohkuma, M.4
Takashina, T.5
-
34
-
-
1542350231
-
The linear pentadecapeptide gramicidin is assembled by four multimodular nonribosomal peptide synthetases that comprise 16 modules with 56 catalytic domains
-
Kessler, N., Schuhmann, H., Morneweg, S., Linne, U., and Marahiel, M. A. (2004). The linear pentadecapeptide gramicidin is assembled by four multimodular nonribosomal peptide synthetases that comprise 16 modules with 56 catalytic domains. J. Biol. Chem. 279, 7413-7419. doi: 10.1074/jbc.M309658200
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 7413-7419
-
-
Kessler, N.1
Schuhmann, H.2
Morneweg, S.3
Linne, U.4
Marahiel, M.A.5
-
35
-
-
84897945994
-
Description of Thermogemmatispora carboxidivorans sp. nov., a carbon-monoxide-oxidizing member of the class Ktedonobacteria isolated from a geothermally heated biofilm, and analysis of carbon monoxide oxidation by members of the class Ktedonobacteria
-
King, C. E., and King, G. M. (2014). Description of Thermogemmatispora carboxidivorans sp. nov., a carbon-monoxide-oxidizing member of the class Ktedonobacteria isolated from a geothermally heated biofilm, and analysis of carbon monoxide oxidation by members of the class Ktedonobacteria. Int. J. Syst. Evol. Microbiol. 64, 1244-1251. doi: 10.1099/ijs.0.059675-0
-
(2014)
Int. J. Syst. Evol. Microbiol.
, vol.64
, pp. 1244-1251
-
-
King, C.E.1
King, G.M.2
-
36
-
-
0038492780
-
Contributions of atmospheric CO and hydrogen uptake to microbial dynamics on recent hawaiian volcanic deposits
-
King, G. M. (2003a). Contributions of atmospheric CO and hydrogen uptake to microbial dynamics on recent hawaiian volcanic deposits. Appl. Environ. Microbiol. 69, 4067-4075. doi: 10.1128/AEM.69.7.4067-4075.2003
-
(2003)
Appl. Environ. Microbiol.
, vol.69
, pp. 4067-4075
-
-
King, G.M.1
-
37
-
-
2142694242
-
Uptake of carbon monoxide and hydrogen at environmentally relevant concentrations by mycobacteria
-
King, G. M. (2003b). Uptake of carbon monoxide and hydrogen at environmentally relevant concentrations by mycobacteria. Appl. Environ. Microbiol. 69, 7266-7272. doi: 10.1128/AEM.69.12.7266-7272.2003
-
(2003)
Appl. Environ. Microbiol.
, vol.69
, pp. 7266-7272
-
-
King, G.M.1
-
38
-
-
33846476676
-
Distribution, diversity and ecology of aerobic CO- oxidizing bacteria
-
King, G. M., and Weber, C. F. (2007). Distribution, diversity and ecology of aerobic CO- oxidizing bacteria. Nat. Rev. Microbiol. 5, 107-118. doi: 10.1038/nrmicro1595
-
(2007)
Nat. Rev. Microbiol.
, vol.5
, pp. 107-118
-
-
King, G.M.1
Weber, C.F.2
-
39
-
-
76649101991
-
The quest for atmospheric methane oxidizers in forest soils
-
Kolb, S. (2009). The quest for atmospheric methane oxidizers in forest soils. Environ. Microbiol. Rep. 1, 336-346. doi: 10.1111/j.1758-2229.2009.00047.x
-
(2009)
Environ. Microbiol. Rep.
, vol.1
, pp. 336-346
-
-
Kolb, S.1
-
40
-
-
84885395415
-
Prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment
-
Kolb, S., and Stacheter, A. (2013). Prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment. Front. Microbiol. 4:268. doi: 10.3389/fmicb.2013.00268
-
(2013)
Front. Microbiol.
, vol.4
, pp. 268
-
-
Kolb, S.1
Stacheter, A.2
-
41
-
-
1542327668
-
Trends between gene content and genome size in prokaryotic species with larger genomes
-
Konstantinidis, K. T., and Tiedje, J. M. (2004). Trends between gene content and genome size in prokaryotic species with larger genomes. Proc. Natl. Acad. Sci. U.S.A. 101, 3160-3165. doi: 10.1073/pnas.0308653100
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 3160-3165
-
-
Konstantinidis, K.T.1
Tiedje, J.M.2
-
42
-
-
36448991500
-
Clustal W and Clustal X version 2 0
-
Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., et al. (2007). Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948. doi: 10.1093/bioinformatics/btm404
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.P.3
Chenna, R.4
McGettigan, P.A.5
McWilliam, H.6
-
43
-
-
84864688131
-
Mapping the niche space of soil microorganisms using taxonomy and traits
-
Lennon, J. T., Aanderud, Z. T., Lehmkuhl, B. K., and Schoolmaster, D. R. (2012). Mapping the niche space of soil microorganisms using taxonomy and traits. Ecology 93, 1867-1879. doi: 10.1890/11-1745.1
-
(2012)
Ecology
, vol.93
, pp. 1867-1879
-
-
Lennon, J.T.1
Aanderud, Z.T.2
Lehmkuhl, B.K.3
Schoolmaster, D.R.4
-
44
-
-
33751403057
-
Microflora of extreme arid Atacama Desert soils
-
Lester, E. D., Satomi, M., and Ponce, A. (2007). Microflora of extreme arid Atacama Desert soils. Soil Biol. Biochem. 39, 704-708. doi: 10.1016/j.soilbio.2006.09.020
-
(2007)
Soil Biol. Biochem.
, vol.39
, pp. 704-708
-
-
Lester, E.D.1
Satomi, M.2
Ponce, A.3
-
45
-
-
84155164323
-
Regional sources of atmospheric formaldehyde and acetaldehyde and implications for atmospheric modeling
-
Luecken, D. J., Hutzell, W. T., Strum, M. L., and Pouliot, G. A. (2012). Regional sources of atmospheric formaldehyde and acetaldehyde and implications for atmospheric modeling. Atmos. Environ. 47, 477-490. doi: 10.1016/j.atmosenv.2011.10.005
-
(2012)
Atmos. Environ.
, vol.47
, pp. 477-490
-
-
Luecken, D.J.1
Hutzell, W.T.2
Strum, M.L.3
Pouliot, G.A.4
-
46
-
-
84862982952
-
The potential for microbial life in the highest elevation (>6000 m.a.s.l ) mineral soils of the Atacama region
-
Lynch, R. C., King, A. J., Farías, M. E., Sowell, P., Vitry, C., and Schmidt, S. K. (2012). The potential for microbial life in the highest elevation (>6000 m.a.s.l.) mineral soils of the Atacama region. J. Geophys. Res. 117, G02028. doi: 10.1029/2012JG001961
-
(2012)
J. Geophys. Res.
, vol.117
, pp. G02028
-
-
Lynch, R.C.1
King, A.J.2
Farías, M.E.3
Sowell, P.4
Vitry, C.5
Schmidt, S.K.6
-
47
-
-
79952592810
-
A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
-
Marçais, G., and Kingsford, C. (2011). A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764-770. doi: 10.1093/bioinformatics/btr011
-
(2011)
Bioinformatics
, vol.27
, pp. 764-770
-
-
Marçais, G.1
Kingsford, C.2
-
48
-
-
84861898310
-
IMG: the Integrated Microbial Genomes database and comparative analysis system
-
Markowitz, V. M., Chen, I.-M. A., Palaniappan, K., Chu, K., Szeto, E., Grechkin, Y., et al. (2012). IMG: the Integrated Microbial Genomes database and comparative analysis system. Nucleic Acids Res. 40, 115-122. doi: 10.1093/nar/gkr1044
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 115-122
-
-
Markowitz, V.M.1
Chen, I.-M.2
Palaniappan, K.3
Chu, K.4
Szeto, E.5
Grechkin, Y.6
-
49
-
-
84857122937
-
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
-
McDonald, D., Price, M. N., Goodrich, J., Nawrocki, E. P., DeSantis, T. Z., Probst, A., et al. (2012). An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 6, 610-618. doi: 10.1038/ismej.2011.139
-
(2012)
ISME J
, vol.6
, pp. 610-618
-
-
McDonald, D.1
Price, M.N.2
Goodrich, J.3
Nawrocki, E.P.4
DeSantis, T.Z.5
Probst, A.6
-
50
-
-
40549104438
-
Molecular ecology techniques for the study of aerobic methanotrophs
-
McDonald, I. R., Bodrossy, L., Chen, Y., and Murrell, J. C. (2008). Molecular ecology techniques for the study of aerobic methanotrophs. Appl. Environ. Microbiol. 74, 1305-1315. doi: 10.1128/AEM.02233-07
-
(2008)
Appl. Environ. Microbiol.
, vol.74
, pp. 1305-1315
-
-
McDonald, I.R.1
Bodrossy, L.2
Chen, Y.3
Murrell, J.C.4
-
51
-
-
53549118607
-
The metagenomics RAST server: a public resource for the automatic phylogenetic and functional analysis of metagenomes
-
Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E. M., Kubal, M., et al. (2008). The metagenomics RAST server: a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386. doi: 10.1186/1471-2105-9-386
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 386
-
-
Meyer, F.1
Paarmann, D.2
D'Souza, M.3
Olson, R.4
Glass, E.M.5
Kubal, M.6
-
52
-
-
5044221147
-
Long term atmospheric deposition as the source of nitrate and other salts in the Atacama Desert Chile: new evidence from mass-independent oxygen isotopic compositions
-
Michalski, G., Böhlke, J. K., and Thiemens, M. (2004). Long term atmospheric deposition as the source of nitrate and other salts in the Atacama Desert, Chile: new evidence from mass-independent oxygen isotopic compositions. Geochim. Cosmochim. Acta 68, 4023-4038. doi: 10.1016/j.gca.2004.04.009
-
(2004)
Geochim. Cosmochim. Acta
, vol.68
, pp. 4023-4038
-
-
Michalski, G.1
Böhlke, J.K.2
Thiemens, M.3
-
53
-
-
0242662483
-
Mars-like soils in the Atacama Desert, Chile and the dry limit of microbial life
-
Navarro-González, R., Rainey, F. A., Molina, P., Bagaley, D. R., Hollen, B. J., de la Rosa, J., et al. (2003). Mars-like soils in the Atacama Desert, Chile, and the dry limit of microbial life. Science 302, 1018-1021. doi: 10.1126/science.1089143
-
(2003)
Science
, vol.302
, pp. 1018-1021
-
-
Navarro-González, R.1
Rainey, F.A.2
Molina, P.3
Bagaley, D.R.4
Hollen, B.J.5
de la Rosa, J.6
-
54
-
-
84860838112
-
Life at the hyperarid margin: novel bacterial diversity in arid soils of the Atacama Desert
-
Neilson, J. W., Quade, J., Ortiz, M., Nelson, W. M., Legatzki, A., Tian, F., et al. (2012). Life at the hyperarid margin: novel bacterial diversity in arid soils of the Atacama Desert, Chile. Extremophiles 16, 553-566. doi: 10.1007/s00792-012-0454-z
-
(2012)
Chile. Extremophiles
, vol.16
, pp. 553-566
-
-
Neilson, J.W.1
Quade, J.2
Ortiz, M.3
Nelson, W.M.4
Legatzki, A.5
Tian, F.6
-
55
-
-
58949100307
-
Diversity of culturable actinomycetes in hyper-arid soils of the Atacama Desert
-
Okoro, C. K., Brown, R., Jones, A. L., Andrews, B. A., Asenjo, J. A., Goodfellow, M., et al. (2009). Diversity of culturable actinomycetes in hyper-arid soils of the Atacama Desert, Chile. Antonie Van Leeuwenhoek 95, 121-133. doi: 10.1007/s10482-008-9295-2
-
(2009)
Chile. Antonie Van Leeuwenhoek
, vol.95
, pp. 121-133
-
-
Okoro, C.K.1
Brown, R.2
Jones, A.L.3
Andrews, B.A.4
Asenjo, J.A.5
Goodfellow, M.6
-
56
-
-
25644458211
-
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
-
Overbeek, R., Begley, T., Butler, R. M., Choudhuri, J. V., Chuang, H.-Y., Cohoon, M., et al. (2005). The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 33, 5691-5702. doi: 10.1093/nar/gki866
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 5691-5702
-
-
Overbeek, R.1
Begley, T.2
Butler, R.M.3
Choudhuri, J.V.4
Chuang, H.-Y.5
Cohoon, M.6
-
57
-
-
67649327176
-
FastTree: computing large minimum evolution trees with profiles instead of a distance matrix
-
Price, M. N., Dehal, P. S., and Arkin, A. P. (2009). FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol. 26, 1641-1650. doi: 10.1093/molbev/msp077
-
(2009)
Mol. Biol. Evol.
, vol.26
, pp. 1641-1650
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
58
-
-
84864134721
-
SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes
-
Pruesse, E., Peplies, J., and Glöckner, F. O. (2012). SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28, 1823-1829. doi: 10.1093/bioinformatics/bts252
-
(2012)
Bioinformatics
, vol.28
, pp. 1823-1829
-
-
Pruesse, E.1
Peplies, J.2
Glöckner, F.O.3
-
59
-
-
84858077472
-
The Pfam protein families database
-
Punta, M., Coggill, P. C., Eberhardt, R. Y., Mistry, J., Tate, J., Boursnell, C., et al. (2012). The Pfam protein families database. Nucleic Acids Res. 40, 290-301. doi: 10.1093/nar/gkr1065
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 290-301
-
-
Punta, M.1
Coggill, P.C.2
Eberhardt, R.Y.3
Mistry, J.4
Tate, J.5
Boursnell, C.6
-
60
-
-
84873739311
-
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
-
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., et al. (2013). The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590-D596. doi: 10.1093/nar/gks1219
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D590-D596
-
-
Quast, C.1
Pruesse, E.2
Yilmaz, P.3
Gerken, J.4
Schweer, T.5
Yarza, P.6
-
61
-
-
84905120058
-
Land-use influences the distribution and activity of high affinity CO-oxidizing bacteria associated to type I-coxL genotype in soil
-
Quiza, L., Lalonde, I., Guertin, C., and Constant, P. (2014). Land-use influences the distribution and activity of high affinity CO-oxidizing bacteria associated to type I-coxL genotype in soil. Front. Microbiol. 5:271. doi: 10.3389/fmicb.2014.00271
-
(2014)
Front. Microbiol.
, vol.5
, pp. 271
-
-
Quiza, L.1
Lalonde, I.2
Guertin, C.3
Constant, P.4
-
62
-
-
0031744640
-
New dimethyl disulfide-degrading actinomycetes and emended description of the genus Pseudonocardia
-
Reichert, K., Lipski, A., Pradella, S., Stackebrandt, E., and Altendorf, K. (1998). New dimethyl disulfide-degrading actinomycetes and emended description of the genus Pseudonocardia. Int. J. Syst. Bacteriol. 48, 441-449. doi: 10.1099/00207713-48-2-441
-
(1998)
Int. J. Syst. Bacteriol.
, vol.48
, pp. 441-449
-
-
Reichert, K.1
Lipski, A.2
Pradella, S.3
Stackebrandt, E.4
Altendorf, K.5
-
63
-
-
85013728083
-
"Alpine and arctic soil microbial communities," in The Prokaryotes, eds E. Rosenberg, E. F. DeLong, E. Stackebrandt, S. Lory, and F
-
Rhodes, M., Knelman, J., Lynch, R. C., Darcy, J. L., Nemergut, D. R., and Schmidt, S. K. (2013). "Alpine and arctic soil microbial communities," in The Prokaryotes, eds E. Rosenberg, E. F. DeLong, E. Stackebrandt, S. Lory, and F. Thompson (Berlin: Springer), 44-56.
-
(2013)
Thompson (Berlin: Springer)
, pp. 44-56
-
-
Rhodes, M.1
Knelman, J.2
Lynch, R.C.3
Darcy, J.L.4
Nemergut, D.R.5
Schmidt, S.K.6
-
64
-
-
0036339474
-
Cordillera de la Atacama Das trockenste Hochgebirge der Welt
-
Richter, M., and Schmidt, D. (2002). Cordillera de la Atacama. Das trockenste Hochgebirge der Welt. Petermanns Geographische Mitteilungen 146, 48-57.
-
(2002)
Petermanns Geographische Mitteilungen
, vol.146
, pp. 48-57
-
-
Richter, M.1
Schmidt, D.2
-
65
-
-
84881138595
-
Insights into the phylogeny and coding potential of microbial dark matter
-
Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N. N., Anderson, I. J., Cheng, J.-F., et al. (2013). Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431-437. doi: 10.1038/nature12352
-
(2013)
Nature
, vol.499
, pp. 431-437
-
-
Rinke, C.1
Schwientek, P.2
Sczyrba, A.3
Ivanova, N.N.4
Anderson, I.J.5
Cheng, J.-F.6
-
66
-
-
9444225935
-
Java Treeview-extensible visualization of microarray data
-
Saldanha, A. J. (2004). Java Treeview-extensible visualization of microarray data. Bioinformatics 20, 3246-3248. doi: 10.1093/bioinformatics/bth349
-
(2004)
Bioinformatics
, vol.20
, pp. 3246-3248
-
-
Saldanha, A.J.1
-
67
-
-
84862130138
-
Fungal communities at the edge: ecological lessons from high alpine fungi
-
Schmidt, S. K., Naff, C. S., and Lynch, R. C. (2012). Fungal communities at the edge: ecological lessons from high alpine fungi. Fungal Ecol. 5, 443-452. doi: 10.1016/j.funeco.2011.10.005
-
(2012)
Fungal Ecol
, vol.5
, pp. 443-452
-
-
Schmidt, S.K.1
Naff, C.S.2
Lynch, R.C.3
-
68
-
-
70449719366
-
Microbial activity and diversity during extreme freeze-thaw cycles in periglacial soils, 5400 m elevation, Cordillera Vilcanota
-
Schmidt, S. K., Nemergut, D. R., Miller, A. E., Freeman, K. R., King, A. J., and Seimon, A. (2009). Microbial activity and diversity during extreme freeze-thaw cycles in periglacial soils, 5400 m elevation, Cordillera Vilcanota, Perú. Extremophiles 13, 807-816. doi: 10.1007/s00792-009-0268-9
-
(2009)
Perú. Extremophiles
, vol.13
, pp. 807-816
-
-
Schmidt, S.K.1
Nemergut, D.R.2
Miller, A.E.3
Freeman, K.R.4
King, A.J.5
Seimon, A.6
-
69
-
-
84255194908
-
Satellite evidence for a large source of formic acid from boreal and tropical forests
-
Stavrakou, T., Müller, J.-F., Peeters, J., Razavi, A., Clarisse, L., Clerbaux, C., et al. (2011). Satellite evidence for a large source of formic acid from boreal and tropical forests. Nat. Geosci. 5, 26-30. doi: 10.1038/ngeo1354
-
(2011)
Nat. Geosci.
, vol.5
, pp. 26-30
-
-
Stavrakou, T.1
Müller, J.-F.2
Peeters, J.3
Razavi, A.4
Clarisse, L.5
Clerbaux, C.6
-
70
-
-
78649369418
-
Frequent freeze-thaw cycles yield diminished yet resistant and responsive microbial communities in two temperate soils: a laboratory experiment
-
Stres, B., Philippot, L., Faganeli, J., and Tiedje, J. M. (2010). Frequent freeze-thaw cycles yield diminished yet resistant and responsive microbial communities in two temperate soils: a laboratory experiment. FEMS Microb. Ecol. 74, 323-335. doi: 10.1111/j.1574-6941.2010.00951.x
-
(2010)
FEMS Microb. Ecol.
, vol.74
, pp. 323-335
-
-
Stres, B.1
Philippot, L.2
Faganeli, J.3
Tiedje, J.M.4
-
71
-
-
84884608376
-
Recently deglaciated high-altitude soils of the Himalaya: diverse environments, heterogenous bacterial communities and long-range dust inputs from the upper troposphere
-
Stres, B., Sul, W. J., Murovec, B., and Tiedje, J. M. (2013). Recently deglaciated high-altitude soils of the Himalaya: diverse environments, heterogenous bacterial communities and long-range dust inputs from the upper troposphere. PLoS ONE 8:e76440. doi: 10.1371/journal.pone.0076440
-
(2013)
PLoS ONE
, vol.8
-
-
Stres, B.1
Sul, W.J.2
Murovec, B.3
Tiedje, J.M.4
-
72
-
-
84890330527
-
MEGA6: molecular evolutionary genetics analysis version 6.0
-
Tamura, K., Stecher, G., Peterson, D., Filipski, A., and Kumar, S. (2013). MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30, 2725-2729. doi: 10.1093/molbev/mst197
-
(2013)
Mol. Biol. Evol
, vol.30
, pp. 2725-2729
-
-
Tamura, K.1
Stecher, G.2
Peterson, D.3
Filipski, A.4
Kumar, S.5
-
73
-
-
0030660581
-
A genomic perspective on protein families
-
Tatusov, R. L. (1997). A genomic perspective on protein families. Science 278, 631-637. doi: 10.1126/science.278.5338.631
-
(1997)
Science
, vol.278
, pp. 631-637
-
-
Tatusov, R.L.1
-
74
-
-
21144440351
-
Facultative Methanotrophs Revisited
-
Theisen, A. R., and Murrell, J. C. (2005). Facultative Methanotrophs Revisited. J. Bacteriol. 187, 4303-4305. doi: 10.1128/JB.187.13.4303-4305.2005
-
(2005)
J. Bacteriol.
, vol.187
, pp. 4303-4305
-
-
Theisen, A.R.1
Murrell, J.C.2
-
75
-
-
35748974830
-
Occurrence, classification, and biological function of hydrogenases: an overview
-
Vignais, P. M., and Billoud, B. (2007). Occurrence, classification, and biological function of hydrogenases: an overview. Chem. Rev. 107, 4206-4272. doi: 10.1021/cr050196r
-
(2007)
Chem. Rev.
, vol.107
, pp. 4206-4272
-
-
Vignais, P.M.1
Billoud, B.2
-
76
-
-
51749095104
-
Phylocom: software for the analysis of phylogenetic community structure and trait evolution
-
Webb, C. O., Ackerly, D. D., and Kembel, S. W. (2008). Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 24, 2098-2100. doi: 10.1093/bioinformatics/btn358
-
(2008)
Bioinformatics
, vol.24
, pp. 2098-2100
-
-
Webb, C.O.1
Ackerly, D.D.2
Kembel, S.W.3
-
77
-
-
77955251806
-
Distribution and diversity of carbon monoxide-oxidizing bacteria and bulk bacterial communities across a succession gradient on a Hawaiian volcanic deposit
-
Weber, C. F., and King, G. M. (2010). Distribution and diversity of carbon monoxide-oxidizing bacteria and bulk bacterial communities across a succession gradient on a Hawaiian volcanic deposit. Environ. Microbiol. 12, 1855-1867. doi: 10.1111/j.1462-2920.2010.02190.x
-
(2010)
Environ. Microbiol.
, vol.12
, pp. 1855-1867
-
-
Weber, C.F.1
King, G.M.2
-
78
-
-
0031897964
-
Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
-
Yang, Z. (1998). Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15, 568-573. doi: 10.1093/oxfordjournals.molbev.a025957
-
(1998)
Mol. Biol. Evol.
, vol.15
, pp. 568-573
-
-
Yang, Z.1
-
79
-
-
34547803197
-
PAML 4 phylogenetic analysis by maximum likelihood
-
Yang, Z. (2007). PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586-1591. doi: 10.1093/molbev/msm088
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
-
80
-
-
78951472080
-
Gene expression analysis of methylotrophic oxidoreductases involved in the oligotrophic growth of Rhodococcus erythropolis N9T-4
-
Yoshida, N., Hayasaki, T., and Takagi, H. (2011). Gene expression analysis of methylotrophic oxidoreductases involved in the oligotrophic growth of Rhodococcus erythropolis N9T-4. Biosci. Biotechnol. Biochem. 75, 123-127. doi: 10.1271/bbb.100700
-
(2011)
Biosci. Biotechnol. Biochem.
, vol.75
, pp. 123-127
-
-
Yoshida, N.1
Hayasaki, T.2
Takagi, H.3
-
81
-
-
36448962771
-
Screening of carbon dioxide-requiring extreme oligotrophs from soil
-
Yoshida, N. Y., Hhata, N. O., Oshino, Y. Y., Atsuragi, T. K., Ani, Y. T., and Akagi, H. T. (2007). Screening of carbon dioxide-requiring extreme oligotrophs from soil. Biosci. Biotechnol. Biochem. 71, 2830-2832. doi: 10.1271/bbb.70042
-
(2007)
Biosci. Biotechnol. Biochem.
, vol.71
, pp. 2830-2832
-
-
Yoshida, N.Y.1
Hhata, N.O.2
Oshino, Y.Y.3
Atsuragi, T.K.4
Ani, Y.T.5
Akagi, H.T.6
-
82
-
-
84861157356
-
Significant role for microbial autotrophy in the sequestration of soil carbon
-
Yuan, H., Ge, T., Chen, C., O'Donnell, A. G., and Wu, J. (2012). Significant role for microbial autotrophy in the sequestration of soil carbon. Appl. Environ. Microbiol. 78, 2328-2336. doi: 10.1128/AEM.06881-11
-
(2012)
Appl. Environ. Microbiol.
, vol.78
, pp. 2328-2336
-
-
Yuan, H.1
Ge, T.2
Chen, C.3
O'Donnell, A.G.4
Wu, J.5
-
83
-
-
77955085506
-
Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives
-
Zaneveld, J. R., Lozupone, C., Gordon, J. I., and Knight, R. (2010). Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives. Nucleic Acids Res. 38, 3869-3879. doi: 10.1093/nar/gkq066
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 3869-3879
-
-
Zaneveld, J.R.1
Lozupone, C.2
Gordon, J.I.3
Knight, R.4
|