All Stories

  1. One Health, climate change, and infectious microbes: a joint effort between AGU and ASM to understand impacts of changing climate and microbes on human well-being across scales
  2. Multiple microbial guilds mediate soil methane cycling along a wetland salinity gradient
  3. Root-associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum
  4. Unraveling the functional dark matter through global metagenomics
  5. Conservation of beneficial microbes between the rhizosphere and the cyanosphere
  6. Metagenomics untangles metabolic adaptations of Antarctic endolithic bacteria at the fringe of habitability
  7. Long-Term Persistence of Three Microbial Wildfire Biomarkers in Forest Soils
  8. Correction: Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons
  9. Highly diverse and unknown viruses may enhance Antarctic endoliths’ adaptability
  10. Dataset of 143 metagenome-assembled genomes from the Arctic and Atlantic Oceans, including 21 for eukaryotic organisms
  11. Iodidimonas, a bacterium unable to degrade hydrocarbons, thrives in a bioreactor treating oil and gas produced water
  12. Root associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum
  13. Methyl-Based Methanogenesis: an Ecological and Genomic Review
  14. Poisson hurdle model-based method for clustering microbiome features
  15. Highly diverse and unknown viruses may enhance Antarctic endoliths’ adaptability
  16. High-Quality Draft Genome Sequence of Fischerella thermalis JSC-11, a Siderophilic Cyanobacterium with Bioremediation Potential
  17. Expansion of the global RNA virome reveals diverse clades of bacteriophages
  18. Metagenomes from Arctic Soil Microbial Communities from the Barrow Environmental Observatory, Utqiaġvik, AK, USA
  19. The role of zinc in the adaptive evolution of polar phytoplankton
  20. Thousands of small, novel genes predicted in global phage genomes
  21. A toolkit for microbial community editing
  22. Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons
  23. Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans
  24. Correction: Bueno de Mesquita et al. Methylphosphonate Degradation and Salt-Tolerance Genes of Two Novel Halophilic Marivita Metagenome-Assembled Genomes from Unrestored Solar Salterns. Genes 2022, 13, 148
  25. Defining the Sphagnum Core Microbiome across the North American Continent Reveals a Central Role for Diazotrophic Methanotrophs in the Nitrogen and Carbon Cycles of Boreal Peatland Ecosystems
  26. Membrane Bioreactor Pretreatment of High-Salinity O&G Produced Water
  27. Exploring the roles of microbes in facilitating plant adaptation to climate change
  28. Methylphosphonate Degradation and Salt-Tolerance Genes of Two Novel Halophilic Marivita Metagenome-Assembled Genomes from Unrestored Solar Salterns
  29. Restoring wetlands on intensive agricultural lands modifies nitrogen cycling microbial communities and reduces N2O production potential
  30. Methanogenesis and Salt Tolerance Genes of a Novel Halophilic Methanosarcinaceae Metagenome-Assembled Genome from a Former Solar Saltern
  31. The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole
  32. Peatland microbial community responses to plant functional group and drought are depth‐dependent
  33. Microbial drivers of methane emissions from unrestored industrial salt ponds
  34. Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization
  35. High-Quality Draft Genome Sequence of the Siderophilic and Thermophilic Leptolyngbyaceae Cyanobacterium JSC-12
  36. Different threats, same response
  37. Identification of beneficial and detrimental bacteria that impact sorghum responses to drought using multi-scale and multi-system microbiome comparisons
  38. Author Correction: A genomic catalog of Earth’s microbiomes
  39. Pre-Cambrian roots of novel Antarctic cryptoendolithic bacterial lineages
  40. Microbial Community Field Surveys Reveal Abundant Pseudomonas Population in Sorghum Rhizosphere Composed of Many Closely Related Phylotypes
  41. Author Correction: Plant–microbiome interactions: from community assembly to plant health
  42. Publisher Correction: A genomic catalog of Earth’s microbiomes
  43. A genomic catalog of Earth’s microbiomes
  44. Phototrophic Co-cultures From Extreme Environments: Community Structure and Potential Value for Fundamental and Applied Research
  45. Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber
  46. Emerging Trends in Biological Treatment of Wastewater From Unconventional Oil and Gas Extraction
  47. Plant–microbiome interactions: from community assembly to plant health
  48. Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization
  49. Metagenome-assembled genomes of phytoplankton communities across the Arctic Circle
  50. Geology and climate influence rhizobiome composition of the phenotypically diverse tropical tree Tabebuia heterophylla
  51. Metagenomes in the Borderline Ecosystems of the Antarctic Cryptoendolithic Communities
  52. Antarctic cryptoendolithic bacterial lineages of pre-Cambrian origin as proxy for Mars colonization
  53. Clades of huge phages from across Earth’s ecosystems
  54. Niche differentiation is spatially and temporally regulated in the rhizosphere
  55. Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber
  56. Microbial Community Dynamics of a Membrane Bioreactor Treating Hydraulic Fracturing Wastewater
  57. Community-Driven Metadata Standards for Agricultural Microbiome Research
  58. Unusual Metabolism and Hypervariation in the Genome of a Gracilibacterium (BD1-5) from an Oil-Degrading Community
  59. Diversity, evolution, and classification of virophages uncovered through global metagenomics
  60. Division of labor in honey bee gut microbiota for plant polysaccharide digestion
  61. Hidden diversity in the oomycete genus Olpidiopsis is a potential hazard to red algal cultivation and conservation worldwide
  62. A layered defense against plant pathogens
  63. Interactions between plants and soil shaping the root microbiome under abiotic stress
  64. Complete Genome Sequence of Agrobacterium sp. Strain 33MFTa1.1, Isolated from Thlaspi arvense Roots
  65. Metatranscriptomic Analyses of Diel Metabolic Functions During a Microcystis Bloom in Western Lake Erie (United States)
  66. Metagenomes in the borderline ecosystems of the Antarctic cryptoendolithic communities
  67. Structural dynamics and transcriptomic analysis of Dehalococcoides mccartyi within a TCE-Dechlorinating community in a completely mixed flow reactor
  68. mSphere of Influence: the View from the Microbiologists of the Future
  69. Niche differentiation is spatially and temporally regulated in the rhizosphere
  70. Unusual metabolism and hypervariation in the genome of a Gracilibacteria (BD1-5) from an oil degrading community
  71. Clades of huge phage from across Earth’s ecosystems
  72. Insight into the Bacterial Endophytic Communities of Peach Cultivars Related to Crown Gall Disease Resistance
  73. Metabolomics of sorghum roots during nitrogen stress reveals compromised metabolic capacity for salicylic acid biosynthesis
  74. Completion of an Experiment
  75. Minimum Information about an Uncultivated Virus Genome (MIUViG)
  76. Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils
  77. Phototrophic co-cultures from extreme environments: community structure and potential value for fundamental and applied research
  78. Meta-omics survey of [NiFe]-hydrogenase genes fails to capture drastic variations in H2-oxidation activity measured in three soils exposed to H2
  79. Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States
  80. New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes
  81. Erratum: California voters and CIRM—will lightning strike twice?
  82. Large-scale replicated field study of maize rhizosphere identifies heritable microbes
  83. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy
  84. Discovery of enzymes for toluene synthesis from anoxic microbial communities
  85. Peatland Acidobacteria with a dissimilatory sulfur metabolism
  86. Landscape topography structures the soil microbiome in arctic polygonal tundra
  87. Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil
  88. An overview of a book devoted to metagenomics methods and applications
  89. Genomic features of bacterial adaptation to plants
  90. Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations
  91. Metagenomic analysis of intertidal hypersaline microbial mats from Elkhorn Slough, California, grown with and without molybdate
  92. A compendium of multi-omic sequence information from the Saanich Inlet water column
  93. Taxonomic and Functional Diversity of a Quercus pyrenaica Willd. Rhizospheric Microbiome in the Mediterranean Mountains
  94. PeatlandAcidobacteriawith a dissimilatory sulfur metabolism
  95. Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes
  96. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
  97. A genomic perspective on stoichiometric regulation of soil carbon cycling
  98. Microbiome of burned holm-oak: Arthrobacter's role
  99. Single-cell genomics for the masses
  100. Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism
  101. Patterns and drivers of fungal community depth stratification in Sphagnum peat
  102. Ecophysiology of freshwater Verrucomicrobia inferred from metagenome-assembled genomes
  103. Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach
  104. Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems
  105. The Tale of a Neglected Energy Source: Elevated Hydrogen Exposure Affects both Microbial Diversity and Function in Soil
  106. Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation
  107. Optimizing genome bins with DAS Tool
  108. Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions
  109. Conversion of Amazon rainforest to agriculture alters community traits of methane-cycling organisms
  110. Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems
  111. Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems
  112. Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone
  113. Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations
  114. Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone
  115. In vitro Characterization of Phenylacetate Decarboxylase, a Novel Enzyme Catalyzing Toluene Biosynthesis in an Anaerobic Microbial Community
  116. Host genotype and age shape the leaf and root microbiomes of a wild perennial plant
  117. ‘Candidatus Adiutrix intracellularis’, an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria and a putative homoacetogen
  118. Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms
  119. H2-saturation of high affinity H2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups
  120. Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines
  121. Assembly and Succession of Iron Oxide Microbial Mat Communities in Acidic Geothermal Springs
  122. The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity
  123. High-resolution phylogenetic microbial community profiling
  124. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations
  125. Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis
  126. Comparative metagenomics reveals impact of contaminants on groundwater microbiomes
  127. Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community
  128. Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species
  129. Primer and platform effects on 16S rRNA tag sequencing
  130. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa
  131. Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous ‘streamer’ community
  132. The Joint Genome Institute Offers Resources Beyond a Core Facility
  133. Patterns in Wetland Microbial Community Composition and Functional Gene Repertoire Associated with Methane Emissions
  134. Elviz – exploration of metagenome assemblies with an interactive visualization tool
  135. Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling
  136. Diverse uncultivated ultra-small bacterial cells in groundwater
  137. Accurate, multi-kb reads resolve complex populations and detect rare microorganisms
  138. Aquifer environment selects for microbial species cohorts in sediment and groundwater
  139. High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats
  140. Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor
  141. Genome Portal, Joint Genome Institute
  142. Corrigendum to Wagneret al.: Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative
  143. Metagenomes from two microbial consortia associated with Santa Barbara seep oil
  144. Convergent Bacterial Microbiotas in the Fungal Agricultural Systems of Insects
  145. Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk
  146. FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus
  147. Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling
  148. Erratum: Microbial ecology of an Antarctic hypersaline lake: genomic assessment of ecophysiology among dominant haloarchaea
  149. Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance
  150. Rearrangement of a Large Novel Pseudomonas aeruginosa Gene Island in Strains Isolated from a Patient Developing Ventilator-Associated Pneumonia
  151. Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative
  152. Correction for Howe et al., Tackling soil diversity with the assembly of large, complex metagenomes
  153. Tackling soil diversity with the assembly of large, complex metagenomes
  154. Microbial ecology of an Antarctic hypersaline lake: genomic assessment of ecophysiology among dominant haloarchaea
  155. Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California
  156. MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm
  157. Predominant Acidilobus-Like Populations from Geothermal Environments in Yellowstone National Park Exhibit Similar Metabolic Potential in Different Hypoxic Microbial Communities
  158. IMG/M 4 version of the integrated metagenome comparative analysis system
  159. High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake
  160. Metagenomic Profiling Reveals Lignocellulose Degrading System in a Microbial Community Associated with a Wood-Feeding Beetle
  161. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment
  162. Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill
  163. Comparative genomics of two ‘Candidatus Accumulibacter’ clades performing biological phosphorus removal
  164. Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass
  165. Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage
  166. Leucoagaricus gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-Cutter Ant Fungus Gardens
  167. Comparative Metagenomic and Metatranscriptomic Analysis of Hindgut Paunch Microbiota in Wood- and Dung-Feeding Higher Termites
  168. Diversity and heritability of the maize rhizosphere microbiome under field conditions
  169. A metagenomic insight into freshwater methane-utilizing communities and evidence for cooperation between theMethylococcaceaeand theMethylophilaceae
  170. Community-wide plasmid gene mobilization and selection
  171. Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes
  172. Genome Portal, Joint Genome Institute
  173. Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry
  174. Community Structure and Function of High-Temperature Chlorophototrophic Microbial Mats Inhabiting Diverse Geothermal Environments
  175. The epsomitic phototrophic microbial mat of Hot Lake, Washington: community structural responses to seasonal cycling
  176. Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling
  177. Metagenome Sequence Analysis of Filamentous Microbial Communities Obtained from Geochemically Distinct Geothermal Channels Reveals Specialization of Three Aquificales Lineages
  178. The YNP metagenome project: environmental parameters responsible for microbial distribution in the Yellowstone geothermal ecosystem
  179. Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics
  180. Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park
  181. Relationship between Abundance and Specific Activity of Bacterioplankton in Open Ocean Surface Waters
  182. Global distribution of a wild alga revealed by targeted metagenomics
  183. Defining the core Arabidopsis thaliana root microbiome
  184. Mesophilic and Thermophilic Conditions Select for Unique but Highly Parallel Microbial Communities to Perform Carboxylate Platform Biomass Conversion
  185. Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill
  186. Deep‐sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill
  187. The Metagenome of an Anaerobic Microbial Community Decomposing Poplar Wood Chips
  188. The metagenome of the marine anammox bacterium ‘CandidatusScalindua profunda’ illustrates the versatility of this globally important nitrogen cycle bacterium
  189. Metagenomic analysis of a stable trichloroethene-degrading microbial community
  190. Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens
  191. The metagenomic basis of anammox metabolism inCandidatus‘Brocadia fulgida’
  192. Microbial Iron Cycling in Acidic Geothermal Springs of Yellowstone National Park: Integrating Molecular Surveys, Geochemical Processes, and Isolation of Novel Fe-Active Microorganisms
  193. Bioprospecting Metagenomics for New Glycoside Hydrolases
  194. Hydrazine Synthase, a Unique Phylomarker with Which To Study the Presence and Biodiversity of Anammox Bacteria
  195. The metagenomic basis of anammox metabolism inCandidatus‘Brocadia fulgida’
  196. Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome
  197. Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows
  198. Isolation of Succinivibrionaceae Implicated in Low Methane Emissions from Tammar Wallabies
  199. The Enduring Legacy of Small Subunit rRNA in Microbiology
  200. Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen
  201. Bioprospecting metagenomics of decaying wood: mining for new glycoside hydrolases
  202. An Insect Herbivore Microbiome with High Plant Biomass-Degrading Capacity
  203. Validation of two ribosomal RNA removal methods for microbial metatranscriptomics
  204. Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium
  205. Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production
  206. Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton
  207. Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores
  208. Comparative Metagenomics of Freshwater Microbial Communities
  209. A call for standardized classification of metagenome projects
  210. Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community
  211. Metagenome of a Versatile Chemolithoautotroph from Expanding Oceanic Dead Zones
  212. Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities
  213. Susannah Tringe at the DOE JGI 2009 User Meeting
  214. A renaissance for the pioneering 16S rRNA gene
  215. High-resolution metagenomics targets specific functional types in complex microbial communities
  216. The Airborne Metagenome in an Indoor Urban Environment
  217. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
  218. Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments
  219. The WTM Genes in Budding Yeast Amplify Expression of the Stress-Inducible Gene RNR3
  220. Metagenomics: DNA sequencing of environmental samples
  221. Comparative Metagenomics of Microbial Communities
  222. p53 Checkpoint-Defective Cells Are Sensitive to X Rays, but Not Hypoxia
  223. PlanarXY-model dynamics in a nematic liquid crystal system
  224. Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic