-
1
-
-
84871826193
-
Cross-biome metagenomic analyses of soil microbial communities and their functional attributes
-
Fierer, N. et al. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proceedings of the National Academy of Sciences of the United States of America 109, 21390-21395, https://doi. org/10. 1073/pnas. 1215210110 (2012).
-
(2012)
Proceedings of the National Academy of Sciences of the United States of America
, vol.109
, pp. 21390-21395
-
-
Fierer, N.1
-
2
-
-
20244376755
-
Comparative metagenomics of microbial communities
-
Tringe, S. G. et al. Comparative metagenomics of microbial communities. Science 308, 554-557, https://doi. org/10. 1126/ science. 1107851 (2005).
-
(2005)
Science
, vol.308
, pp. 554-557
-
-
Tringe, S.G.1
-
3
-
-
84939872332
-
Assessment and Evaluation of Soil Ecosystem Services
-
Comerford, N. et al. Assessment and Evaluation of Soil Ecosystem Services. Soil Horizons 54 (2013).
-
(2013)
Soil Horizons
, pp. 54
-
-
Comerford, N.1
-
4
-
-
0032462270
-
Geomicrobiology: Its significance for geology
-
Ehrlich, H. Geomicrobiology: its significance for geology. Earth-Science Reviews. 45, 45-60 (1998).
-
(1998)
Earth-Science Reviews.
, vol.45
, pp. 45-60
-
-
Ehrlich, H.1
-
5
-
-
0004001281
-
-
Academic Press, San Diego
-
Fenchel, T., King, G. & Blackburn, H. Bacterial Biogeochemistry: The Ecophysiology of Mineral Cycling. (Academic Press, San Diego, 1998).
-
(1998)
Bacterial Biogeochemistry: The Ecophysiology of Mineral Cycling
-
-
Fenchel, T.1
King, G.2
Blackburn, H.3
-
6
-
-
70350261490
-
What is microbial community ecology
-
Konopka, A. What is microbial community ecology The ISME journal 3, 1223-1230, https://doi. org/10. 1038/ismej. 2009. 88 (2009).
-
(2009)
The ISME Journal
, vol.3
, pp. 1223-1230
-
-
Konopka, A.1
-
7
-
-
0031662188
-
Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity
-
Hugenholtz, P., Goebel, B. M. & Pace, N. R. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. Journal of bacteriology 180, 4765-4774 (1998).
-
(1998)
Journal of Bacteriology
, vol.180
, pp. 4765-4774
-
-
Hugenholtz, P.1
Goebel, B.M.2
Pace, N.R.3
-
8
-
-
67651247607
-
Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale
-
Lauber, C. L., Hamady, M., Knight, R. & Fierer, N. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Applied and environmental microbiology 75, 5111-5120, https://doi. org/10. 1128/ AEM. 00335-09 (2009).
-
(2009)
Applied and Environmental Microbiology
, vol.75
, pp. 5111-5120
-
-
Lauber, C.L.1
Hamady, M.2
Knight, R.3
Fierer, N.4
-
10
-
-
84867717106
-
Abiotic factors influence microbial diversity in permanently cold soil horizons of a maritime-associated Antarctic Dry Valley
-
Stomeo, F. et al. Abiotic factors influence microbial diversity in permanently cold soil horizons of a maritime-associated Antarctic Dry Valley. FEMS microbiology ecology 82, 326-340, https://doi. org/10. 1111/j. 1574-6941. 2012. 01360. x (2012).
-
(2012)
FEMS Microbiology Ecology
, vol.82
, pp. 326-340
-
-
Stomeo, F.1
-
11
-
-
77950057025
-
Biogeography of soil archaea and bacteria along a steep precipitation gradient
-
Angel, R., Soares, M. I., Ungar, E. D. & Gillor, O. Biogeography of soil archaea and bacteria along a steep precipitation gradient. The ISME journal 4, 553-563, https://doi. org/10. 1038/ismej. 2009. 136 (2010).
-
(2010)
The ISME Journal
, vol.4
, pp. 553-563
-
-
Angel, R.1
Soares, M.I.2
Ungar, E.D.3
Gillor, O.4
-
12
-
-
85032301887
-
Significant Impacts of Increasing Aridity on the Arid Soil Microbiome
-
Neilson, J. W. et al. Significant Impacts of Increasing Aridity on the Arid Soil Microbiome. mSystems 2 https://doi. org/10. 1128/ mSystems. 00195-16 (2017).
-
(2017)
MSystems
, pp. 2
-
-
Neilson, J.W.1
-
13
-
-
84966263983
-
Interacting environmental mosaics drive geographic variation in mussel performance and predation vulnerability
-
Kroeker, K. J. et al. Interacting environmental mosaics drive geographic variation in mussel performance and predation vulnerability. Ecology letters 19, 771-779, https://doi. org/10. 1111/ele. 12613 (2016).
-
(2016)
Ecology Letters
, vol.19
, pp. 771-779
-
-
Kroeker, K.J.1
-
15
-
-
84960355873
-
Nitrogen cycling in an extreme hyperarid environment inferred from delta(15) N analyses of plants, soils and herbivore diet
-
Diaz, F. P., Frugone, M., Gutierrez, R. A. & Latorre, C. Nitrogen cycling in an extreme hyperarid environment inferred from delta(15) N analyses of plants, soils and herbivore diet. Scientific reports 6, 22226, https://doi. org/10. 1038/srep22226 (2016).
-
(2016)
Scientific Reports
, vol.6
, pp. 22226
-
-
Diaz, F.P.1
Frugone, M.2
Gutierrez, R.A.3
Latorre, C.4
-
16
-
-
84946829739
-
Cross-biome comparison of microbial association networks
-
Faust, K. et al. Cross-biome comparison of microbial association networks. Frontiers in microbiology 6, 1200, https://doi. org/10. 3389/ fmicb. 2015. 01200 (2015).
-
(2015)
Frontiers in Microbiology
, vol.6
, pp. 1200
-
-
Faust, K.1
-
17
-
-
84959106176
-
Correlation detection strategies in microbial data sets vary widely in sensitivity and precision
-
Weiss, S. et al. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. The ISME journal 10, 1669-1681, https://doi. org/10. 1038/ismej. 2015. 235 (2016).
-
(2016)
The ISME Journal
, vol.10
, pp. 1669-1681
-
-
Weiss, S.1
-
18
-
-
84970024430
-
Topological distortion and reorganized modular structure of gut microbial co-occurrence networks in inflammatory bowel disease
-
Baldassano, S. N. & Bassett, D. S. Topological distortion and reorganized modular structure of gut microbial co-occurrence networks in inflammatory bowel disease. Scientific reports 6, 26087, https://doi. org/10. 1038/srep26087 (2016).
-
(2016)
Scientific Reports
, vol.6
, pp. 26087
-
-
Baldassano, S.N.1
Bassett, D.S.2
-
19
-
-
84860838112
-
Life at the hyperarid margin: Novel bacterial diversity in arid soils of the Atacama Desert, Chile
-
Neilson, J. W. et al. Life at the hyperarid margin: novel bacterial diversity in arid soils of the Atacama Desert, Chile. Extremophiles: life under extreme conditions 16, 553-566, https://doi. org/10. 1007/s00792-012-0454-z (2012).
-
(2012)
Extremophiles: Life under Extreme Conditions
, vol.16
, pp. 553-566
-
-
Neilson, J.W.1
-
20
-
-
33947179096
-
Micronutrient Availability, Chemistry and Availability of Micronutrients in Soils
-
Viets, F. Micronutrient Availability, Chemistry and Availability of Micronutrients in Soils. J. Agric. Food Chem. 10, 174-178 (1962).
-
(1962)
J. Agric. Food Chem.
, vol.10
, pp. 174-178
-
-
Viets, F.1
-
21
-
-
84857122937
-
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
-
McDonald, D. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. The ISME journal 6, 610-618, https://doi. org/10. 1038/ismej. 2011. 139 (2012).
-
(2012)
The ISME Journal
, vol.6
, pp. 610-618
-
-
McDonald, D.1
-
22
-
-
84864579031
-
Microbial co-occurrence relationships in the human microbiome
-
Faust, K. et al. Microbial co-occurrence relationships in the human microbiome. PLoS computational biology 8, e1002606, https:// doi. org/10. 1371/journal. pcbi. 1002606 (2012).
-
(2012)
PLoS Computational Biology
, vol.8
, pp. e1002606
-
-
Faust, K.1
-
23
-
-
85010951420
-
CoNet app: Inference of biological association networks using Cytoscape
-
Faust, K. & Raes, J. CoNet app: inference of biological association networks using Cytoscape. F1000Research 5, 1519, https://doi. org/10. 12688/f1000research. 9050. 2 (2016).
-
(2016)
F1000Research
, vol.5
, pp. 1519
-
-
Faust, K.1
Raes, J.2
-
24
-
-
84988843641
-
How Structured is the Entangled Bank the Surprisingly Simple Organization of Multiplex Ecological Networks Leads to Increased Persistence and Resilience
-
Kefi, S., Miele, V., Wieters, E. A., Navarrete, S. A. & Berlow, E. L. How Structured Is the Entangled Bank The Surprisingly Simple Organization of Multiplex Ecological Networks Leads to Increased Persistence and Resilience. PLoS biology 14, e1002527, https:// doi. org/10. 1371/journal. pbio. 1002527 (2016).
-
(2016)
PLoS Biology
, vol.14
, pp. e1002527
-
-
Kefi, S.1
Miele, V.2
Wieters, E.A.3
Navarrete, S.A.4
Berlow, E.L.5
-
25
-
-
77956996314
-
Soil bacterial and fungal communities across a pH gradient in an arable soil
-
Rousk, J. et al. Soil bacterial and fungal communities across a pH gradient in an arable soil. The ISME journal 4, 1340-1351, https:// doi. org/10. 1038/ismej. 2010. 58 (2010).
-
(2010)
The ISME Journal
, vol.4
, pp. 1340-1351
-
-
Rousk, J.1
-
26
-
-
84908132133
-
Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally
-
Ramirez, K. S. et al. Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally. Proceedings. Biological sciences 281 https://doi. org/10. 1098/rspb. 2014. 1988 (2014).
-
(2014)
Proceedings. Biological Sciences
, pp. 281
-
-
Ramirez, K.S.1
-
27
-
-
84954459052
-
Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China
-
Ma, B. et al. Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China. The ISME journal 10, 1891-1901, https://doi. org/10. 1038/ismej. 2015. 261 (2016).
-
(2016)
The ISME Journal
, vol.10
, pp. 1891-1901
-
-
Ma, B.1
-
28
-
-
0038718854
-
The structure and function of complex networks
-
Newman, M. The structure and function of complex networks. SIAM Rev 45, 167-256 (2003).
-
(2003)
SIAM Rev
, vol.45
, pp. 167-256
-
-
Newman, M.1
-
29
-
-
84878077459
-
Ecological drivers of biogeographic patterns of soil archaeal community
-
Zheng, Y. M., Cao, P., Fu, B., Hughes, J. M. & He, J. Z. Ecological drivers of biogeographic patterns of soil archaeal community. PloS one 8, e63375, https://doi. org/10. 1371/journal. pone. 0063375 (2013).
-
(2013)
PloS One
, vol.8
, pp. e63375
-
-
Zheng, Y.M.1
Cao, P.2
Fu, B.3
Hughes, J.M.4
He, J.Z.5
-
30
-
-
1942537581
-
Algicidal bacteria in the sea and their impact on algal blooms
-
Mayali, X. & Azam, F. Algicidal bacteria in the sea and their impact on algal blooms. The Journal of eukaryotic microbiology 51, 139-144 (2004).
-
(2004)
The Journal of Eukaryotic Microbiology
, vol.51
, pp. 139-144
-
-
Mayali, X.1
Azam, F.2
-
31
-
-
10244235264
-
Challenges in the quest for keystones
-
Power, M. E. et al. Challenges in the quest for keystones. BioScience 46, 609-620 (1996).
-
(1996)
BioScience
, vol.46
, pp. 609-620
-
-
Power, M.E.1
-
32
-
-
84898968578
-
Species with a large impact on community structure
-
Smee, D. Species with a large impact on community structure. Nat Educ Knowledge 1, 18 (2010).
-
(2010)
Nat Educ Knowledge
, vol.1
, pp. 18
-
-
Smee, D.1
-
33
-
-
80053636941
-
The ecological and evolutionary implications of merging different types of networks
-
Fontaine, C. et al. The ecological and evolutionary implications of merging different types of networks. Ecology letters 14, 1170-1181, https://doi. org/10. 1111/j. 1461-0248. 2011. 01688. x (2011).
-
(2011)
Ecology Letters
, vol.14
, pp. 1170-1181
-
-
Fontaine, C.1
-
34
-
-
84936742402
-
L-GRAAL: Lagrangian graphlet-based network aligner
-
Malod-Dognin, N. & Przulj, N. L-GRAAL: Lagrangian graphlet-based network aligner. Bioinformatics 31, 2182-2189, https://doi. org/10. 1093/bioinformatics/btv130 (2015).
-
(2015)
Bioinformatics
, vol.31
, pp. 2182-2189
-
-
Malod-Dognin, N.1
Przulj, N.2
-
35
-
-
33845503055
-
Variability of precipitation in the Atacama desert: Its causes and hydrological impact
-
Houston, J. Variability of precipitation in the Atacama desert: Its causes and hydrological impact. Int. J. Climatol. 26, 2181-2198 (2006).
-
(2006)
Int. J. Climatol.
, vol.26
, pp. 2181-2198
-
-
Houston, J.1
-
36
-
-
0029892688
-
Investigation of the effect of combined variations in temperature, pH, and NaCl concentration on nisin inhibition of Listeria monocytogenes and Staphylococcus aureus
-
Thomas, L. V. & Wimpenny, J. W. Investigation of the effect of combined variations in temperature, pH, and NaCl concentration on nisin inhibition of Listeria monocytogenes and Staphylococcus aureus. Applied and environmental microbiology 62, 2006-2012 (1996).
-
(1996)
Applied and Environmental Microbiology
, vol.62
, pp. 2006-2012
-
-
Thomas, L.V.1
Wimpenny, J.W.2
-
37
-
-
85100393629
-
Salinity: Electrical conductivity and total dissolved solids
-
D. L. Sparks (ed.), Madison, WI
-
Rhoades, J. 1996. Salinity: Electrical conductivity and total dissolved solids. In D. L. Sparks (ed.) Methods of soil analysis: Chemical methods, Part 3. ASA and SSSA, Madison, WI., 417-435. (1996).
-
(1996)
Methods of Soil Analysis: Chemical Methods, Part 3. ASA and SSSA
, pp. 417-435
-
-
Rhoades, J.1
-
38
-
-
36148943584
-
Métodos de análisis recomendados para los suelos de Chile
-
Sadzawka, A. et al. Métodos de análisis recomendados para los suelos de Chile. Serie Actas INIA 163 (2006).
-
(2006)
Serie Actas INIA
, pp. 163
-
-
Sadzawka, A.1
-
39
-
-
0030070838
-
DNA recovery from soils of diverse composition
-
Zhou, J., Bruns, M. A. & Tiedje, J. M. DNA recovery from soils of diverse composition. Applied and environmental microbiology 62, 316-322 (1996).
-
(1996)
Applied and Environmental Microbiology
, vol.62
, pp. 316-322
-
-
Zhou, J.1
Bruns, M.A.2
Tiedje, J.M.3
-
40
-
-
56149104616
-
An examination of the bacteriophages and bacteria of the Namib desert
-
Prestel, E., Salamitou, S. & DuBow, M. S. An examination of the bacteriophages and bacteria of the Namib desert. Journal of microbiology 46, 364-372, https://doi. org/10. 1007/s12275-008-0007-4 (2008).
-
(2008)
Journal of Microbiology
, vol.46
, pp. 364-372
-
-
Prestel, E.1
Salamitou, S.2
DuBow, M.S.3
-
41
-
-
0033166540
-
Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis
-
Turner, S., Pryer, K. M., Miao, V. P. & Palmer, J. D. Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis. The Journal of eukaryotic microbiology 46, 327-338 (1999).
-
(1999)
The Journal of Eukaryotic Microbiology
, vol.46
, pp. 327-338
-
-
Turner, S.1
Pryer, K.M.2
Miao, V.P.3
Palmer, J.D.4
-
42
-
-
49549107771
-
Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)
-
Dowd, S. E. et al. Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC microbiology 8, 125, https://doi. org/10. 1186/1471-2180-8-125 (2008).
-
(2008)
BMC Microbiology
, vol.8
, pp. 125
-
-
Dowd, S.E.1
-
43
-
-
79953786183
-
Massive parallel 16S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats
-
Handl, S., Dowd, S. E., Garcia-Mazcorro, J. F., Steiner, J. M. & Suchodolski, J. S. Massive parallel 16S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats. FEMS microbiology ecology 76, 301-310, https://doi. org/10. 1111/j. 1574-6941. 2011. 01058. x (2011).
-
(2011)
FEMS Microbiology Ecology
, vol.76
, pp. 301-310
-
-
Handl, S.1
Dowd, S.E.2
Garcia-Mazcorro, J.F.3
Steiner, J.M.4
Suchodolski, J.S.5
-
44
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2461, https://doi. org/10. 1093/ bioinformatics/btq461 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
45
-
-
79961181125
-
UCHIME improves sensitivity and speed of chimera detection
-
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194-2200, https://doi. org/10. 1093/bioinformatics/btr381 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 2194-2200
-
-
Edgar, R.C.1
Haas, B.J.2
Clemente, J.C.3
Quince, C.4
Knight, R.5
-
46
-
-
72949107142
-
Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
Schloss, P. D. et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and environmental microbiology 75, 7537-7541, https://doi. org/10. 1128/AEM. 01541-09 (2009).
-
(2009)
Applied and Environmental Microbiology
, vol.75
, pp. 7537-7541
-
-
Schloss, P.D.1
-
47
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nature methods 7, 335-336, https:// doi. org/10. 1038/nmeth. f. 303 (2010).
-
(2010)
Nature Methods
, vol.7
, pp. 335-336
-
-
Caporaso, J.G.1
-
48
-
-
84872497741
-
Vegan: Community Ecology Package
-
Oksanen, J. Vegan: Community Ecology Package. Version 2. 0-3 (2012).
-
(2012)
Version 2. 0-3
-
-
Oksanen, J.1
-
49
-
-
0028926047
-
Energetics of bacterial growth: Balance of anabolic and catabolic reactions
-
Russell, J. B. & Cook, G. M. Energetics of bacterial growth: balance of anabolic and catabolic reactions. Microbiological reviews 59, 48-62 (1995).
-
(1995)
Microbiological Reviews
, vol.59
, pp. 48-62
-
-
Russell, J.B.1
Cook, G.M.2
-
50
-
-
15744374882
-
Metal ion homeostasis in Bacillus subtilis
-
Moore, C. M. & Helmann, J. D. Metal ion homeostasis in Bacillus subtilis. Current opinion in microbiology 8, 188-195, https://doi. org/10. 1016/j. mib. 2005. 02. 007 (2005).
-
(2005)
Current Opinion in Microbiology
, vol.8
, pp. 188-195
-
-
Moore, C.M.1
Helmann, J.D.2
-
51
-
-
84897921620
-
Iron, copper, zinc, and manganese transport and regulation in pathogenic Enterobacteria: Correlations between strains, site of infection and the relative importance of the different metal transport systems for virulence
-
Porcheron, G., Garenaux, A., Proulx, J., Sabri, M. & Dozois, C. M. Iron, copper, zinc, and manganese transport and regulation in pathogenic Enterobacteria: correlations between strains, site of infection and the relative importance of the different metal transport systems for virulence. Frontiers in cellular and infection microbiology 3, 90, https://doi. org/10. 3389/fcimb. 2013. 00090 (2013).
-
(2013)
Frontiers in Cellular and Infection Microbiology
, vol.3
, pp. 90
-
-
Porcheron, G.1
Garenaux, A.2
Proulx, J.3
Sabri, M.4
Dozois, C.M.5
-
52
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
Shannon, P. et al. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome research 13, 2498-2504, https://doi. org/10. 1101/gr. 1239303 (2003).
-
(2003)
Genome Research
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
-
53
-
-
84988369671
-
Decoupling function and taxonomy in the global ocean microbiome
-
Louca, S., Parfrey, L. W. & Doebeli, M. Decoupling function and taxonomy in the global ocean microbiome. Science 353, 1272-1277, https://doi. org/10. 1126/science. Aaf4507 (2016).
-
(2016)
Science
, vol.353
, pp. 1272-1277
-
-
Louca, S.1
Parfrey, L.W.2
Doebeli, M.3
-
54
-
-
71949100749
-
Global bathymetry and elevation data at 30 arc seconds resolution: SRTM30-PLUS
-
Becker, J. et al. Global bathymetry and elevation data at 30 arc seconds resolution: SRTM30-PLUS. Mar. Geod. 32, 355-371 (2009).
-
(2009)
Mar. Geod.
, vol.32
, pp. 355-371
-
-
Becker, J.1
-
55
-
-
0030842741
-
Global sea floor topography from satellite altimetry and ship depth soundings
-
Smith, W. & Sandwell, D. Global sea floor topography from satellite altimetry and ship depth soundings. Science 277, 1956-1962 (1997).
-
(1997)
Science
, vol.277
, pp. 1956-1962
-
-
Smith, W.1
Sandwell, D.2
|