Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience

[1]  J. Rhoades Salinity: Electrical Conductivity and Total Dissolved Solids , 2018, SSSA Book Series.

[2]  William W. Van Treuren,et al.  Significant Impacts of Increasing Aridity on the Arid Soil Microbiome , 2017, mSystems.

[3]  M. Doebeli,et al.  Decoupling function and taxonomy in the global ocean microbiome , 2016, Science.

[4]  Sonia Kéfi,et al.  How Structured Is the Entangled Bank? The Surprisingly Simple Organization of Multiplex Ecological Networks Leads to Increased Persistence and Resilience , 2016, PLoS biology.

[5]  F. Chavez,et al.  Interacting environmental mosaics drive geographic variation in mussel performance and predation vulnerability. , 2016, Ecology letters.

[6]  Sophie J. Weiss,et al.  Correlation detection strategies in microbial data sets vary widely in sensitivity and precision , 2016, The ISME Journal.

[7]  J. Raes,et al.  CoNet app: inference of biological association networks using Cytoscape , 2016, F1000Research.

[8]  Danielle S. Bassett,et al.  Topological distortion and reorganized modular structure of gut microbial co-occurrence networks in inflammatory bowel disease , 2016, Scientific Reports.

[9]  R. Gutiérrez,et al.  Nitrogen cycling in an extreme hyperarid environment inferred from δ15N analyses of plants, soils and herbivore diet , 2016, Scientific Reports.

[10]  Yan He,et al.  Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China , 2016, The ISME Journal.

[11]  C. Huttenhower,et al.  Cross-biome comparison of microbial association networks , 2015, Front. Microbiol..

[12]  Natasa Przulj,et al.  L-GRAAL: Lagrangian graphlet-based network aligner , 2015, Bioinform..

[13]  Scott T. Bates,et al.  Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally , 2014, Proceedings of the Royal Society B: Biological Sciences.

[14]  C. Dozois,et al.  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 , 2013, Front. Cell. Infect. Microbiol..

[15]  B. Fu,et al.  Ecological Drivers of Biogeographic Patterns of Soil Archaeal Community , 2013, PloS one.

[16]  D. Markewitz,et al.  Assessment and Evaluation of Soil Ecosystem Services , 2013 .

[17]  Scott T. Bates,et al.  Cross-biome metagenomic analyses of soil microbial communities and their functional attributes , 2012, Proceedings of the National Academy of Sciences.

[18]  D. Cowan,et al.  Abiotic factors influence microbial diversity in permanently cold soil horizons of a maritime-associated Antarctic Dry Valley. , 2012, FEMS microbiology ecology.

[19]  Curtis Huttenhower,et al.  Microbial Co-occurrence Relationships in the Human Microbiome , 2012, PLoS Comput. Biol..

[20]  R. Wing,et al.  Life at the hyperarid margin: novel bacterial diversity in arid soils of the Atacama Desert, Chile , 2012, Extremophiles.

[21]  Eric P. Nawrocki,et al.  An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea , 2011, The ISME Journal.

[22]  Nicolas Loeuille,et al.  The ecological and evolutionary implications of merging different types of networks. , 2011, Ecology letters.

[23]  Rob Knight,et al.  UCHIME improves sensitivity and speed of chimera detection , 2011, Bioinform..

[24]  Scot E Dowd,et al.  Massive parallel 16S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats. , 2011, FEMS microbiology ecology.

[25]  G. Somero Comparative physiology: a "crystal ball" for predicting consequences of global change. , 2011, American journal of physiology. Regulatory, integrative and comparative physiology.

[26]  Robert C. Edgar,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2001 .

[27]  R. Knight,et al.  Soil bacterial and fungal communities across a pH gradient in an arable soil , 2010, The ISME Journal.

[28]  William A. Walters,et al.  QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.

[29]  Roey Angel,et al.  Biogeography of soil archaea and bacteria along a steep precipitation gradient , 2010, The ISME Journal.

[30]  Allan Konopka,et al.  What is microbial community ecology? , 2009, The ISME Journal.

[31]  D. Fabre,et al.  Global Bathymetry and Elevation Data at 30 Arc Seconds Resolution: SRTM30_PLUS , 2009 .

[32]  Martin Hartmann,et al.  Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities , 2009, Applied and Environmental Microbiology.

[33]  R. Knight,et al.  Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale , 2009, Applied and Environmental Microbiology.

[34]  M. Dubow,et al.  An examination of the bacteriophages and bacteria of the Namib desert , 2008, The Journal of Microbiology.

[35]  Yan Sun,et al.  Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) , 2008, BMC Microbiology.

[36]  J. Houston,et al.  Variability of precipitation in the Atacama Desert: its causes and hydrological impact , 2006 .

[37]  R. B. Jackson,et al.  The diversity and biogeography of soil bacterial communities. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[38]  J. Helmann,et al.  Metal ion homeostasis in Bacillus subtilis. , 2005, Current opinion in microbiology.

[39]  S. Tringe,et al.  Comparative Metagenomics of Microbial Communities , 2004, Science.

[40]  Farooq Azam,et al.  Algicidal Bacteria in the Sea and their Impact on Algal Blooms1 , 2004, The Journal of eukaryotic microbiology.

[41]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[42]  Mark E. J. Newman,et al.  The Structure and Function of Complex Networks , 2003, SIAM Rev..

[43]  J. Palmer,et al.  Investigating Deep Phylogenetic Relationships among Cyanobacteria and Plastids by Small Subunit rRNA Sequence Analysis 1 , 1999, The Journal of eukaryotic microbiology.

[44]  Henry L. Ehrlich,et al.  GEOMICROBIOLOGY: ITS SIGNIFICANCE FOR GEOLOGY , 1998 .

[45]  Philip Hugenholtz,et al.  Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity , 1998, Journal of bacteriology.

[46]  T. Blackburn,et al.  Bacterial Biogeochemistry: The Ecophysiology of Mineral Cycling , 1998 .

[47]  Walter H. F. Smith,et al.  Global Sea Floor Topography from Satellite Altimetry and Ship Depth Soundings , 1997 .

[48]  J. Castilla,et al.  Challenges in the Quest for Keystones , 1996 .

[49]  J. Wimpenny,et al.  Investigation of the effect of combined variations in temperature, pH, and NaCl concentration on nisin inhibition of Listeria monocytogenes and Staphylococcus aureus , 1996, Applied and environmental microbiology.

[50]  J. Tiedje,et al.  DNA recovery from soils of diverse composition , 1996, Applied and environmental microbiology.

[51]  J. Russell,et al.  Energetics of bacterial growth: balance of anabolic and catabolic reactions. , 1995, Microbiological reviews.

[52]  F. G. Viets Micronutrient Availability, Chemistry and Availability of Micronutrients in Soils , 1962 .