2024
(2024) Phylometagenomics of cycad coralloid roots reveals shared symbiotic signals. Microbial Genomics 10(3), 001207. 10.1099/mgen.0.001207
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(2024) Metagenomics untangles potential adaptations of Antarctic endolithic bacteria at the fringe of habitability. The Science of The Total Environment 917, 170290. 10.1016/j.scitotenv.2024.170290
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(2024) Targeted hypermutation of putative antigen sensors in multicellular bacteria. Proceedings of the National Academy of Sciences of the United States of America 121(9), e2316469121. 10.1073/pnas.2316469121
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(2024) Dominant nitrogen metabolisms of a warm, seasonally anoxic freshwater ecosystem revealed using genome resolved metatranscriptomics. mSystems 9(2), e01059-23. 10.1128/msystems.01059-23
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(2024) Multiple microbial guilds mediate soil methane cycling along a wetland salinity gradient. mSystems 9(1), e00936-23. 10.1128/msystems.00936-23
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(2024) Genomic profiles of four novel cyanobacteria MAGs from Lake Vanda, Antarctica: insights into photosynthesis, cold tolerance, and the circadian clock. Frontiers in Microbiology 14, 1330602. 10.3389/fmicb.2023.1330602
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(2024) Constraining the oxygen requirements for modern microbial eukaryote diversity. Proceedings of the National Academy of Sciences of the United States of America 121(2), e2303754120. 10.1073/pnas.2303754120
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(2024) Soil microbiome feedbacks during disturbance-driven forest ecosystem conversion. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 18(1), wrae047. 10.1093/ismejo/wrae047
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(2024) Whole community shotgun metagenomes of two biological soil crust types from the Mojave Desert. Microbiology Resource Announcements 13(3), e00980-23. 10.1128/mra.00980-23
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(2024) Metatranscriptomes of two biological soil crust types from the Mojave desert in response to wetting. Microbiology Resource Announcements 13(2), e01080-23. 10.1128/mra.01080-23
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(2024) Water aging and the quality of organic carbon sources drive niche partitioning of the active bathypelagic prokaryotic microbiome. Limnology and Oceanography 69(3), 562-575. 10.1002/lno.12505
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(2024) Methanolobus use unspecific methyltransferases to produce methane from dimethylsulphide in Baltic Sea sediments. Microbiome 12(1), 3. 10.1186/s40168-023-01720-w
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(2024) Viral potential to modulate microbial methane metabolism varies by habitat. Nature Communications 15(1), 1857. 10.1038/s41467-024-46109-x
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2023
(2023) Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification. Nature Biotechnology 41(7), 898-902. 10.1038/s41587-023-01844-2
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(2023) Microbial sensitivity to temperature and sulfate deposition modulates greenhouse gas emissions from peat soils. Global Change Biology 29(7), 1951-1970. 10.1111/gcb.16614
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(2023) Long-term CRISPR locus dynamics and stable host-virus co-existence in subsurface fractured shales. Current Biology . 10.1016/j.cub.2023.06.033
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(2023) Genomic Features Predict Bacterial Life History Strategies in Soil, as Identified by Metagenomic Stable Isotope Probing. mBio 14(2), e03584-22. 10.1128/mbio.03584-22
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(2023) Metagenomic stable isotope probing reveals bacteriophage participation in soil carbon cycling. Environmental Microbiology . 10.1111/1462-2920.16395
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(2023) Methane Cycling Microbial Community Characteristics: Comparing Natural, Actively Extracted, Restored and Unrestored Boreal Peatlands. Wetlands 43(7), 83. 10.1007/s13157-023-01726-y
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(2023) Distribution and abundance of tetraether lipid cyclization genes in terrestrial hot springs reflect pH. Environmental Microbiology . 10.1111/1462-2920.16375
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(2023) Life strategies for Aminicenantia in subseafloor oceanic crust. The ISME Journal: Multidisciplinary Journal of Microbial Ecology , 1-10. 10.1038/s41396-023-01454-5
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(2023) Microbial Ecology in a Changing Climate. , 289-314. 10.1201/9781003126096-18
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(2023) Mcr-dependent methanogenesis in Archaeoglobaceae enriched from a terrestrial hot spring. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 17(10), 1649-1659. 10.1038/s41396-023-01472-3
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(2023) Root-associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum. mSystems 9(1), e01190-23. 10.1128/msystems.01190-23
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(2023) Gallionellaceae in rice root plaque: metabolic roles in iron oxidation, nutrient cycling, and plant interactions. Applied and Environmental Microbiology 89(12), e00570-23. 10.1128/aem.00570-23
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(2023) Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem. Microbiome 11(1), 237. 10.1186/s40168-023-01666-z
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(2023) Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem. Microbiome 11(1), 237. 10.1186/s40168-023-01666-z
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(2023) Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem. Microbiome 11(1), 237. 10.1186/s40168-023-01666-z
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(2023) Water mass age structures the auxiliary metabolic gene content of free-living and particle-attached deep ocean viral communities. Microbiome 11(1), 118. 10.1186/s40168-023-01547-5
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(2023) Methyl-Based Methanogenesis: an Ecological and Genomic Review. Microbiology and Molecular Biology Reviews 87(1), e00024-22. 10.1128/mmbr.00024-22
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(2023) Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost. mSystems 9(1), e00698-23. 10.1128/msystems.00698-23
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(2023) Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes. Nature 618(7967), 992-999. 10.1038/s41586-023-06186-2
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(2023) Highly diverse and unknown viruses may enhance Antarctic endoliths’ adaptability. Microbiome 11(1), 103. 10.1186/s40168-023-01554-6
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(2023) Relationships between fluid mixing, biodiversity, and chemosynthetic primary productivity in Yellowstone hot springs. Environmental Microbiology 25(5), 1022-1040. 10.1111/1462-2920.16340
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(2023) Long-Term Persistence of Three Microbial Wildfire Biomarkers in Forest Soils. Forests 14(7), 1383. 10.3390/f14071383
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(2023) Identification of over ten thousand candidate structured RNAs in viruses and phages. Computational and Structural Biotechnology Journal 21, 5630-5639. 10.1016/j.csbj.2023.11.010
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(2023) Identification of over ten thousand candidate structured RNAs in viruses and phages. Computational and Structural Biotechnology Journal 21, 5630-5639. 10.1016/j.csbj.2023.11.010
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(2023) Identification of over ten thousand candidate structured RNAs in viruses and phages. Computational and Structural Biotechnology Journal 21, 5630-5639. 10.1016/j.csbj.2023.11.010
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(2023) CRISPR-resolved virus-host interactions in a municipal landfill include non-specific viruses, hyper-targeted viral populations, and interviral conflicts. Scientific Reports 13(1), 5611. 10.1038/s41598-023-32078-6
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(2023) Giant Virus Infection Signatures Are Modulated by Euphotic Zone Depth Strata and Iron Regimes of the Subantarctic Southern Ocean. mSystems 8(2), e01260-22. 10.1128/msystems.01260-22
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(2023) Metagenomic Methods for Addressing NASA’s Planetary Protection Policy Requirements on Future Missions: A Workshop Report. Astrobiology . 10.1089/ast.2022.0044
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(2023) Diversity, distribution, and expression of opsin genes in freshwater lakes. Molecular Ecology 32(11), 2798-2817. 10.1111/mec.16891
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(2023) Uncovering the dominant role of root metabolism in shaping rhizosphere metabolome under drought in tropical rainforest plants. The Science of The Total Environment 899, 165689. 10.1016/j.scitotenv.2023.165689
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(2023) Resolving the controls over the production and emission of ice-nucleating particles in sea spray. Environmental Science Atmospheres 3(6), 970-990. 10.1039/d2ea00154c
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(2023) Drought re-routes soil microbial carbon metabolism towards emission of volatile metabolites in an artificial tropical rainforest. Nature Microbiology 8(8), 1480-1494. 10.1038/s41564-023-01432-9
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(2023) Seasonal activities of the phyllosphere microbiome of perennial crops. Nature Communications 14(1), 1039. 10.1038/s41467-023-36515-y
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(2023) Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats. Nature Microbiology 8(5), 946-957. 10.1038/s41564-023-01347-5
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(2023) Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater. Nature Communications 14(1), 5380. 10.1038/s41467-023-40907-5
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(2023) Taxonomic distribution of metabolic functions in bacteria associated with Trichodesmium consortia. mSystems 8(6), e00742-23. 10.1128/msystems.00742-23
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(2023) Taxonomic distribution of metabolic functions in bacteria associated with Trichodesmium consortia. mSystems 8(6), e00742-23. 10.1128/msystems.00742-23
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(2023) Taxonomic distribution of metabolic functions in bacteria associated with Trichodesmium consortia. mSystems 8(6), e00742-23. 10.1128/msystems.00742-23
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(2023) Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean. mSystems , e00619-23. 10.1128/msystems.00619-23
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(2023) Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs. Cell 186(3), 646-661.e4. 10.1016/j.cell.2022.12.039
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(2023) Diversity and function of methyl-coenzyme M reductase-encoding archaea in Yellowstone hot springs revealed by metagenomics and mesocosm experiments. ISME Communications 3(1), 22. 10.1038/s43705-023-00225-9
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(2023) Taxonomic and functional restoration of tallgrass prairie soil microbial communities in comparison to remnant and agricultural soils. FEMS Microbiology Ecology 99(11), fiad120. 10.1093/femsec/fiad120
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(2023) Taxonomic and functional restoration of tallgrass prairie soil microbial communities in comparison to remnant and agricultural soils. FEMS Microbiology Ecology 99(11), fiad120. 10.1093/femsec/fiad120
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(2023) Taxonomic and functional restoration of tallgrass prairie soil microbial communities in comparison to remnant and agricultural soils. FEMS Microbiology Ecology 99(11), fiad120. 10.1093/femsec/fiad120
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(2023) Oxic–anoxic cycling promotes coupling between complex carbon metabolism and denitrification in woodchip bioreactors. Environmental Microbiology . 10.1111/1462-2920.16387
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(2023) Reactive iron, not fungal community, drives organic carbon oxidation potential in floodplain soils. Soil Biology and Biochemistry 178, 108962. 10.1016/j.soilbio.2023.108962
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(2023) Abiotic selection of microbial genome size in the global ocean. Nature Communications 14(1), 1384. 10.1038/s41467-023-36988-x
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(2023) Genes and genome‐resolved metagenomics reveal the microbial functional make up of Amazon peatlands under geochemical gradients. Environmental Microbiology . 10.1111/1462-2920.16469
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(2023) BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes. Microbiome 11(1), 186. 10.1186/s40168-023-01625-8
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(2023) Pelagic metagenome-assembled genomes from an estuarine salinity gradient in San Francisco Bay. Microbiology Resource Announcements 12(12), e00800-23. 10.1128/mra.00800-23
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(2023) iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria. PLOS Biology 21(4), e3002083. 10.1371/journal.pbio.3002083
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(2023) Counting dots or counting reads? Complementary approaches to estimate virus-to-microbe ratios. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 17(10), 1521-1522. 10.1038/s41396-023-01468-z
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(2023) DNA repair enzymes of the Antarctic Dry Valley metagenome. Frontiers in Microbiology 14, 1156817. 10.3389/fmicb.2023.1156817
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(2023) Long-term warming modulates diversity, vertical structuring of microbial communities, and sulfate reduction in coastal Baltic Sea sediments. Frontiers in Microbiology 14, 1099445. 10.3389/fmicb.2023.1099445
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(2023) Climate change-related warming reduces thermal sensitivity and modifies metabolic activity of coastal benthic bacterial communities. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 17(6), 855-869. 10.1038/s41396-023-01395-z
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(2023) Expression of macromolecular organic nitrogen degrading enzymes identifies potential mediators of soil organic N availability to an annual grass. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 17(7), 967-975. 10.1038/s41396-023-01402-3
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(2023) Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development. mSystems , e00315-23. 10.1128/msystems.00315-23
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(2023) Four principles to establish a universal virus taxonomy. PLOS Biology 21(2), e3001922. 10.1371/journal.pbio.3001922
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(2023) The dynamic influence of subsurface geological processes on the assembly and diversification of thermophilic microbial communities in continental hydrothermal systems. Geochimica et Cosmochimica Acta 362, 77-103. 10.1016/j.gca.2023.10.021
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(2023) The dynamic influence of subsurface geological processes on the assembly and diversification of thermophilic microbial communities in continental hydrothermal systems. Geochimica et Cosmochimica Acta 362, 77-103. 10.1016/j.gca.2023.10.021
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(2023) The dynamic influence of subsurface geological processes on the assembly and diversification of thermophilic microbial communities in continental hydrothermal systems. Geochimica et Cosmochimica Acta 362, 77-103. 10.1016/j.gca.2023.10.021
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(2023) Physiological and genomic evidence of cysteine degradation and aerobic hydrogen sulfide production in freshwater bacteria. mSystems 8(3), e00201-23. 10.1128/msystems.00201-23
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(2023) Astrovirology: how viruses enhance our understanding of life in the Universe.. International Journal of Astrobiology 22(4), 247-271. 10.1017/s1473550423000058
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(2023) Astrovirology: how viruses enhance our understanding of life in the Universe.. International Journal of Astrobiology 22(4), 247-271. 10.1017/s1473550423000058
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(2023) Astrovirology: how viruses enhance our understanding of life in the Universe.. International Journal of Astrobiology 22(4), 247-271. 10.1017/s1473550423000058
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(2023) A k-mer-Based Approach for Phylogenetic Classification of Taxa in Environmental Genomic Data. Systematic Biology 72(5), 1101-1118. 10.1093/sysbio/syad037
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(2023) A k-mer-Based Approach for Phylogenetic Classification of Taxa in Environmental Genomic Data. Systematic Biology 72(5), 1101-1118. 10.1093/sysbio/syad037
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(2023) A k-mer-Based Approach for Phylogenetic Classification of Taxa in Environmental Genomic Data. Systematic Biology 72(5), 1101-1118. 10.1093/sysbio/syad037
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(2023) Methane-Oxidizing Activity Enhances Sulfamethoxazole Biotransformation in a Benthic Constructed Wetland Biomat. Environmental Science and Technology 57(18), 7240-7253. 10.1021/acs.est.2c09314
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(2023) MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets. ISME Communications 3(1), 87. 10.1038/s43705-023-00295-9
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(2023) A standardized quantitative analysis strategy for stable isotope probing metagenomics. mSystems , e01280-22. 10.1128/msystems.01280-22
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(2023) A metagenome-level analysis of a microbial community fermenting ultra-filtered milk permeate. Frontiers in Bioengineering and Biotechnology 11, 1173656. 10.3389/fbioe.2023.1173656
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(2023) A metagenome-level analysis of a microbial community fermenting ultra-filtered milk permeate. Frontiers in Bioengineering and Biotechnology 11, 1173656. 10.3389/fbioe.2023.1173656
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(2023) A metagenome-level analysis of a microbial community fermenting ultra-filtered milk permeate. Frontiers in Bioengineering and Biotechnology 11, 1173656. 10.3389/fbioe.2023.1173656
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(2023) Synergistic interactions between anammox and dissimilatory nitrate reducing bacteria sustains reactor performance across variable nitrogen loading ratios. Frontiers in Microbiology 14, 1243410. 10.3389/fmicb.2023.1243410
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(2023) Hi-C metagenome sequencing reveals soil phage–host interactions. Nature Communications 14(1), 7666. 10.1038/s41467-023-42967-z
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(2023) Hi-C metagenome sequencing reveals soil phage–host interactions. Nature Communications 14(1), 7666. 10.1038/s41467-023-42967-z
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(2023) Hi-C metagenome sequencing reveals soil phage–host interactions. Nature Communications 14(1), 7666. 10.1038/s41467-023-42967-z
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(2023) Nitrogen and phosphorous acquisition strategies drive coexistence patterns among archaeal lineages in soil. The ISME Journal: Multidisciplinary Journal of Microbial Ecology , 1-12. 10.1038/s41396-023-01493-y
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(2023) Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils. Frontiers in Microbiology 14, 1140487. 10.3389/fmicb.2023.1140487
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(2023) Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines. Microbiome 11(1), 174. 10.1186/s40168-023-01619-6
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2022
(2022) Microbial communities and biogeochemical functioning across peatlands in the Athabasca Oil Sands region of Canada: Implications for reclamation and management. Land Degradation and Development 34(5), 1504-1521. 10.1002/ldr.4549
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(2022) Microbial colonization and persistence in deep fractured shales is guided by metabolic exchanges and viral predation. Microbiome 10(1), 5. 10.1186/s40168-021-01194-8
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(2022) Exploring the roles of microbes in facilitating plant adaptation to climate change. Biochemical Journal 479(3), 327-335. 10.1042/bcj20210793
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(2022) Degradation Reduces Microbial Richness and Alters Microbial Functions in an Australian Peatland. Microbial Ecology 85(3), 875-891. 10.1007/s00248-022-02071-z
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(2022) Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 17(3), 354-370. 10.1038/s41396-022-01345-1
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(2022) Pathway-Centric Analysis of Microbial Metabolic Potential and Expression Along Nutrient and Energy Gradients in the Western Atlantic Ocean. Frontiers in Marine Science 9, 867310. 10.3389/fmars.2022.867310
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(2022) Deep-branching acetogens in serpentinized subsurface fluids of Oman. Proceedings of the National Academy of Sciences of the United States of America 119(42), e2206845119. 10.1073/pnas.2206845119
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(2022) Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics. Frontiers in Microbiology 13, 879116. 10.3389/fmicb.2022.879116
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(2022) Impacts of land-use change on soil microbial communities and their function in the Amazon Rainforest. 175, 179-258. 10.1016/bs.agron.2022.04.001
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(2022) Methylphosphonate Degradation and Salt-Tolerance Genes of Two Novel Halophilic Marivita Metagenome-Assembled Genomes from Unrestored Solar Salterns. Genes 13(1), 148. 10.3390/genes13010148
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(2022) Virus-Host Interactions and Genetic Diversity of Antarctic Sea Ice Bacteriophages. mBio 13(3), e00651-22. 10.1128/mbio.00651-22
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(2022) Soils and sediments host Thermoplasmata archaea encoding novel copper membrane monooxygenases (CuMMOs). The ISME Journal: Multidisciplinary Journal of Microbial Ecology 16(5), 1348-1362. 10.1038/s41396-021-01177-5
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(2022) Substrate availability and not thermal acclimation controls microbial temperature sensitivity response to long‐term warming. Global Change Biology 29(6), 1574-1590. 10.1111/gcb.16544
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(2022) Ecological and genomic responses of soil microbiomes to high-severity wildfire: linking community assembly to functional potential. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 16(7), 1853-1863. 10.1038/s41396-022-01232-9
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(2022) Soil compartments (bulk soil, litter, root and rhizosphere) as main drivers of soil protistan communities distribution in forests with different nitrogen deposition. Soil Biology and Biochemistry 168, 108628. 10.1016/j.soilbio.2022.108628
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(2022) Metagenomes and Metagenome-Assembled Genomes from Microbiomes Metabolizing Thin Stillage from an Ethanol Biorefinery. Microbiology Resource Announcements 11(8), e00290-22. 10.1128/mra.00290-22
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(2022) Functional Insights of Salinity Stress-Related Pathways in Metagenome-Resolved Methanothrix Genomes. Applied and Environmental Microbiology 88(10), e02449-21. 10.1128/aem.02449-21
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(2022) Patterns and ecological drivers of viral communities in acid mine drainage sediments across Southern China. Nature Communications 13(1), 2389. 10.1038/s41467-022-30049-5
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(2022) Bioavailable iron titrations reveal oceanic Synechococcus ecotypes optimized for different iron availabilities. ISME Communications 2(1), 54. 10.1038/s43705-022-00132-5
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(2022) Rapid changes in coastal ocean microbiomes uncoupled with shifts in environmental variables. Environmental Microbiology 24(9), 4167-4177. 10.1111/1462-2920.16086
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(2022) Culexarchaeia, a novel archaeal class of anaerobic generalists inhabiting geothermal environments. ISME Communications 2(1), 86. 10.1038/s43705-022-00175-8
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(2022) Gallionella and Sulfuricella populations are dominant during the transition of boreal potential to actual acid sulfate soils. Communications Earth & Environment 3(1), 304. 10.1038/s43247-022-00642-z
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(2022) Elucidating Drought-Tolerance Mechanisms in Plant Roots through 1H NMR Metabolomics in Parallel with MALDI-MS, and NanoSIMS Imaging Techniques. Environmental Science and Technology 56(3), 2021-2032. 10.1021/acs.est.1c06772
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(2022) Metagenome-Assembled Genomes from a Microbiome Grown in Dairy Manure Hydrolysate. Microbiology Resource Announcements 11(8), e00292-22. 10.1128/mra.00292-22
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(2022) Particulate and dissolved metabolite distributions along a latitudinal transect of the western Atlantic Ocean. Limnology and Oceanography 68(2), 377-393. 10.1002/lno.12275
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(2022) Culexarchaeia, a novel archaeal class of anaerobic generalists inhabiting geothermal environments. ISME Communications 2(1), 86. 10.1038/s43705-022-00175-8
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(2022) 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. mBio 13(1), e03714-21. 10.1128/mbio.03714-21
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(2022) Propagation of viral genomes by replicating ammonia-oxidising archaea during soil nitrification. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 17(2), 309-314. 10.1038/s41396-022-01341-5
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(2022) Soil pH influences the structure of virus communities at local and global scales. Soil Biology and Biochemistry 166, 108569. 10.1016/j.soilbio.2022.108569
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(2022) Contrasting Modes of Mitochondrial Genome Evolution in Sister Taxa of Wood-Eating Marine Bivalves (Teredinidae and Xylophagaidae). Genome Biology and Evolution 14(6), evac089. 10.1093/gbe/evac089
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(2022) Adaptation to Environmental Extremes Structures Functional Traits in Biological Soil Crust and Hypolithic Microbial Communities. mSystems 7(4), e01419-21. 10.1128/msystems.01419-21
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(2022) TbasCO: trait-based comparative ‘omics identifies ecosystem-level and niche-differentiating adaptations of an engineered microbiome. ISME Communications 2(1), 111. 10.1038/s43705-022-00189-2
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(2022) Mieux connaître les virus présents sur Terre grâce aux métagénomes. Médecine/sciences 38(12), 999-1007. 10.1051/medsci/2022166
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(2022) Expansion of the global RNA virome reveals diverse clades of bacteriophages. Cell 185(21), 4023-4037.e18. 10.1016/j.cell.2022.08.023
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(2022) Metagenome-Assembled Genomes for “Candidatus Phormidium sp. Strain AB48” and Co-occurring Microorganisms from an Industrial Photobioreactor Environment. Microbiology Resource Announcements 11(12), e00447-22. 10.1128/mra.00447-22
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(2022) HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi. Microbiome 10(1), 199. 10.1186/s40168-022-01391-z
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(2022) Environmental predictors of electroactive bacterioplankton in small boreal lakes. Environmental Microbiology 25(3), 705-720. 10.1111/1462-2920.16314
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(2022) Reekeekee- and roodoodooviruses, two different Microviridae clades constituted by the smallest DNA phages. Virus Evolution 9(1), veac123. 10.1093/ve/veac123
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(2022) Mechanistic insights into consumption of the food additive xanthan gum by the human gut microbiota. Nature Microbiology 7(4), 556-569. 10.1038/s41564-022-01093-0
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(2022) Population structure of an Antarctic aquatic cyanobacterium. Microbiome 10(1), 207. 10.1186/s40168-022-01404-x
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(2022) Multiple sources of aerobic methane production in aquatic ecosystems include bacterial photosynthesis. Nature Communications 13(1), 6454. 10.1038/s41467-022-34105-y
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(2022) Microtopography Matters: Belowground CH4 Cycling Regulated by Differing Microbial Processes in Peatland Hummocks and Lawns. Journal of Geophysical Research Biogeosciences 127(8). 10.1029/2022jg006948
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(2022) Draft Metagenome Sequences of the Sphagnum (Peat Moss) Microbiome from Ambient and Warmed Environments across Europe. Microbiology Resource Announcements 11(10), e00400-22. 10.1128/mra.00400-22
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(2022) Diverse events have transferred genes for edible seaweed digestion from marine to human gut bacteria. Cell Host & Microbe 30(3), 314-328.e11. 10.1016/j.chom.2022.02.001
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(2022) Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 16(8), 1957-1969. 10.1038/s41396-022-01245-4
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(2022) Poisson hurdle model-based method for clustering microbiome features. Bioinformatics 39(1), btac782. 10.1093/bioinformatics/btac782
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(2022) Genome-Resolved Metagenomic Insights into Massive Seasonal Ammonia-Oxidizing Archaea Blooms in San Francisco Bay. mSystems 7(1), e01270-21. 10.1128/msystems.01270-21
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(2022) Genome-Resolved Metaproteomics Decodes the Microbial and Viral Contributions to Coupled Carbon and Nitrogen Cycling in River Sediments. mSystems 7(4), e00516-22. 10.1128/msystems.00516-22
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(2022) Diversity in the soil virosphere: to infinity and beyond?. Trends in Microbiology 30(11), 1025-1035. 10.1016/j.tim.2022.05.003
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(2022) Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean. Proceedings of the National Academy of Sciences of the United States of America 119(37), e2200014119. 10.1073/pnas.2200014119
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(2022) Metagenome-Assembled Genomes from a Microbiome Converting Xylose to Medium-Chain Carboxylic Acids. Microbiology Resource Announcements 11(4), e01151-21. 10.1128/mra.01151-21
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(2022) Weakened resilience of benthic microbial communities in the face of climate change. ISME Communications 2(1), 21. 10.1038/s43705-022-00104-9
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(2022) Variation in Root Exudate Composition Influences Soil Microbiome Membership and Function. Applied and Environmental Microbiology 88(11), e00226-22. 10.1128/aem.00226-22
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(2022) Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics. Microbiome 10(1), 157. 10.1186/s40168-022-01340-w
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(2022) Trace metal contents of autotrophic flagellates from contrasting open‐ocean ecosystems. Limnology and Oceanography Letters 7(4), 354-362. 10.1002/lol2.10258
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(2022) Metagenomes from Arctic Soil Microbial Communities from the Barrow Environmental Observatory, Utqiaġvik, AK, USA. Microbiology Resource Announcements 11(8), e00528-22. 10.1128/mra.00528-22
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(2022) Microbes and Climate Change: a Research Prospectus for the Future. mBio 13(3), e00800-22. 10.1128/mbio.00800-22
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(2022) Metagenomes and Metagenome-Assembled Genomes from Microbial Communities Fermenting Ultrafiltered Milk Permeate. Microbiology Resource Announcements 11(7), e00293-22. 10.1128/mra.00293-22
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(2022) Into the darkness: the ecologies of novel ‘microbial dark matter’ phyla in an Antarctic lake. Environmental Microbiology 24(5), 2576-2603. 10.1111/1462-2920.16026
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(2022) Metatranscriptomic Sequencing of Winter and Spring Planktonic Communities from Lake Erie, a Laurentian Great Lake. Microbiology Resource Announcements 11(7), e00351-22. 10.1128/mra.00351-22
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(2022) Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits. Microbiome 10(1), 241. 10.1186/s40168-022-01424-7
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(2022) New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria. Virus Evolution 8(2), veac070. 10.1093/ve/veac070
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(2021) Metagenomes, metatranscriptomes, and metagenome-assembled genomes from chesapeake and Delaware bay (USA) water samples. Microbiology Resource Announcements 10(21). 10.1128/MRA.00262-21
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(2021) Pre-Cambrian roots of novel Antarctic cryptoendolithic bacterial lineages. Microbiome 9(1), 15. 10.1186/s40168-021-01021-0
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(2021) Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance. mSystems 6(3), e00537-21. 10.1128/mSystems.00537-21
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(2021) Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress. Nature Communications 12. 10.1038/s41467-021-25950-4
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(2021) Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts. ISME Journal . 10.1038/s41396-021-00989-9
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(2021) Whole Community Metatranscriptomes and Lipidomes Reveal Diverse Responses Among Antarctic Phytoplankton to Changing Ice Conditions. Frontiers in Marine Science 8, 14. 10.3389/fmars.2021.593566
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(2021) Illuminating the Virosphere Through Global Metagenomics. Annual Review of Biomedical Data Science 4(1), 369-391. 10.1146/annurev-biodatasci-012221-095114
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(2021) Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants. Nature Communications 12(1). 10.1038/s41467-021-25678-1
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(2021) Microbial Community Field Surveys Reveal Abundant Pseudomonas Population in Sorghum Rhizosphere Composed of Many Closely Related Phylotypes. Frontiers in Microbiology 12, 17. 10.3389/fmicb.2021.598180
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(2021) Rapid response of nitrogen cycling gene transcription to labile carbon amendments in a soil microbial community. mSystems 6(3). 10.1128/mSystems.00161-21
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(2021) Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean. Nature Microbiology 6(2), 173-+. 10.1038/s41564-020-00814-7
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(2021) Different threats, same response. Nature Plants 7(5), 544-545. 10.1038/s41477-021-00915-z
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(2021) A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell 184(13), 3376-3393.e17. 10.1016/j.cell.2021.05.002
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(2021) Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways. Nature Communications 12(1). 10.1038/s41467-021-22736-6
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(2021) Methanogenesis and Salt Tolerance Genes of a Novel Halophilic Methanosarcinaceae Metagenome-Assembled Genome from a Former Solar Saltern. Genes 12(10), 1609. 10.3390/genes12101609
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(2021) Silicon-rich soil amendments impact microbial community composition and the composition of arsM bearing microbes. Plant and Soil . 10.1007/s11104-021-05103-8
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(2021) 16S rRNA gene amplicon sequencing data from flooded rice paddy mesocosms treated with different silicon-rich soil amendments. Microbiology Resource Announcements 10(27). 10.1128/MRA.00178-21
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(2021) 16S rRNA Gene Amplicon Sequencing Data from Flooded Rice Paddy Mesocosms Treated with Different Silicon-Rich Soil Amendments. Microbiology Resource Announcements 10(27), e00178-21. 10.1128/mra.00178-21
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(2021) Global Diversity and Biogeography of the Zostera marina Mycobiome. Applied and Environmental Microbiology 87(12), 1-19. 10.1128/AEM.02795-20
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(2021) Ecological Dichotomies Arise in Microbial Communities Due to Mixing of Deep Hydrothermal Waters and Atmospheric Gas in a Circumneutral Hot Spring. Applied and Environmental Microbiology 87(23), e01598-21. 10.1128/aem.01598-21
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(2021) Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber. Isme Journal 15(2), 421-434. 10.1038/s41396-020-00769-x
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(2021) Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium. Current Biology 31(7), 1393-1402.e5. 10.1016/j.cub.2021.01.018
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(2021) Viral community analysis in a marine oxygen minimum zone indicates increased potential for viral manipulation of microbial physiological state. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 16(4), 972-982. 10.1038/s41396-021-01143-1
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(2021) Restoring wetlands on intensive agricultural lands modifies nitrogen cycling microbial communities and reduces N2O production potential. Journal of Environmental Management 299. 10.1016/j.jenvman.2021.113562
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(2021) Metagenomic reconstruction of nitrogen and carbon cycling pathways in forest soil: Influence of different hardwood tree species. Soil Biology and Biochemistry 156. 10.1016/j.soilbio.2021.108226
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(2021) Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages. Nature Communications 12(1). 10.1038/s41467-021-23698-5
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(2021) Pangenomics reveals alternative environmental lifestyles among chlamydiae. Nature Communications 12(1). 10.1038/s41467-021-24294-3
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(2021) Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups. ISME Journal . 10.1038/s41396-021-01057-y
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(2021) Methane-derived carbon flows into host–virus networks at different trophic levels in soil. Proceedings of the National Academy of Sciences of the United States of America 118(32), e2105124118. 10.1073/pnas.2105124118
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(2021) Mercury methylation by metabolically versatile and cosmopolitan marine bacteria. Isme Journal , 16. 10.1038/s41396-020-00889-4
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(2021) Metabolic Potential for Reductive Acetogenesis and a Novel Energy-Converting [NiFe] Hydrogenase in Bathyarchaeia From Termite Guts – A Genome-Centric Analysis. Frontiers in Microbiology 11. 10.3389/fmicb.2020.635786
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(2021) Revealing enzyme functional architecture via high-throughput microfluidic enzyme kinetics. Science 373(6553). 10.1126/science.abf8761
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(2021) The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole. Nature Communications 12(1). 10.1038/s41467-021-25646-9
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(2021) New Insights Into the Influence of Plant and Microbial Diversity on Denitrification Rates in a Salt Marsh. Wetlands 41(2), 14. 10.1007/s13157-021-01423-8
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(2021) Decrypting bacterial polyphenol metabolism in an anoxic wetland soil. Nature Communications 12(1). 10.1038/s41467-021-22765-1
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(2021) Draft Metagenomes of Endolithic Cyanobacteria and Cohabitants from Hyper-Arid Deserts. Microbiology Resource Announcements 10(30), e00206-21. 10.1128/mra.00206-21
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(2021) Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. Nature Microbiology 6(7), 960-970. 10.1038/s41564-021-00928-6
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(2021) Atypical Divergence of SARS-CoV-2 Orf8 from Orf7a within the Coronavirus Lineage Suggests Potential Stealthy Viral Strategies in Immune Evasion. Mbio 12(1), 12. 10.1128/mBio.03014-20
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(2021) Niche dimensions of a marine bacterium are identified using invasion studies in coastal seawater. Nature Microbiology 6(4), 524-+. 10.1038/s41564-020-00851-2
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(2021) Verrucomicrobiota are specialist consumers of sulfated methyl pentoses during diatom blooms. ISME Journal . 10.1038/s41396-021-01105-7
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(2021) The Santorini Volcanic Complex as a Valuable Source of Enzymes for Bioenergy. Energies 14(5), 12. 10.3390/en14051414
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(2021) A Novel Freshwater to Marine Evolutionary Transition Revealed within Methylophilaceae Bacteria from the Arctic Ocean. mBio 12(3), e0130621. 10.1128/mBio.01306-21
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(2021) Diverse ecophysiological adaptations of subsurface Thaumarchaeota in floodplain sediments revealed through genome-resolved metagenomics. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 16(4), 1140-1152. 10.1038/s41396-021-01167-7
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(2021) Nutrient Inputs Stimulate Mercury Methylation by Syntrophs in a Subarctic Peatland. Frontiers in Microbiology 12, 741523. 10.3389/fmicb.2021.741523
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(2021) Flooding and ecological restoration promote wetland microbial communities and soil functions on former cranberry farmland. PLOS ONE 16(12), e0260933. 10.1371/journal.pone.0260933
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(2021) ORT: a workflow linking genome-scale metabolic models with reactive transport codes.. Bioinformatics 38(3), 778-784. 10.1093/bioinformatics/btab753
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(2021) Description of Candidatus Mesopelagibacter carboxydoxydans and Candidatus Anoxipelagibacter denitrificans: Nitrate-reducing SAR11 genera that dominate mesopelagic and anoxic marine zones. Systematic and Applied Microbiology 44(2), 126185. https://doi.org/10.1016/j.syapm.2021.126185
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(2021) The Rhizosphere Responds: Rich Fen Peat and Root Microbial Ecology after Long-Term Water Table Manipulation. Applied and environmental microbiology 87(12), e0024121. 10.1128/AEM.00241-21
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(2021) Contrasting Community Assembly Forces Drive Microbial Structural and Potential Functional Responses to Precipitation in an Incipient Soil System. Frontiers in Microbiology 12, 754698. 10.3389/fmicb.2021.754698
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(2021) An ancestral Matryoshka doll. Nature Reviews Microbiology 19(3), 140-140. 10.1038/s41579-021-00509-8
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(2021) Stimulation of dissimilatory sulfate reduction in response to sulfate in microcosm incubations from two contrasting temperate peatlands near Ithaca, NY, USA.. FEMS Microbiology Letters 368(21-24). 10.1093/femsle/fnab153
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(2021) Niche differentiation of bacteria and fungi in carbon and nitrogen cycling of different habitats in a temperate coniferous forest: A metaproteomic approach. Soil Biology and Biochemistry 155. 10.1016/j.soilbio.2021.108170
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(2021) Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan. Frontiers in Microbiology 12. 10.3389/fmicb.2021.632731
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(2021) Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika. Isme Journal , 16. 10.1038/s41396-021-00898-x
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(2021) Prokaryotic responses to a warm temperature anomaly in northeast subarctic Pacific waters. Communications Biology 4(1), 1217. 10.1038/s42003-021-02731-9
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(2021) New keys to unlock the treasure trove of microbial natural products. Nature Reviews Microbiology 19. 10.1038/s41579-021-00631-7
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(2021) Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics. Communications Biology 4(1), 1302. 10.1038/s42003-021-02809-4
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(2021) Natural soil microbiome variation affects spring foliar phenology with consequences for plant productivity and climate-driven range shifts. New Phytologist 232(2), 762-775. 10.1111/nph.17599
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(2021) Impacts of The Wetland Sedge Carex aquatilis on Microbial Community and Methane Metabolisms. Plant and Soil 471(1-2), 491-506. 10.1007/s11104-021-05239-7
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(2021) Metagenome sequencing to explore phylogenomics of terrestrial cyanobacteria. Microbiology Resource Announcements 10(22). 10.1128/MRA.00258-21
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(2021) Climate-driven divergence in plant-microbiome interactions generates range-wide variation in bud break phenology. Communications Biology 4(1). 10.1038/s42003-021-02244-5
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(2021) Genome Analysis of a Verrucomicrobial Endosymbiont With a Tiny Genome Discovered in an Antarctic Lake. Frontiers in Microbiology 12. 10.3389/fmicb.2021.674758
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(2021) Soil metabolome response to whole-ecosystem warming at the spruce and peatland responses under changing environments experiment. Proceedings of the National Academy of Sciences of the United States of America 118(25). 10.1073/pnas.2004192118
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(2021) Glacier ice archives nearly 15,000-year-old microbes and phages. Microbiome 9(1). 10.1186/s40168-021-01106-w
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(2021) Microbial drivers of methane emissions from unrestored industrial salt ponds. ISME Journal . 10.1038/s41396-021-01067-w
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(2020) Clades of huge phages from across Earth’s ecosystems. Nature 578(7795), 425-431. 10.1038/s41586-020-2007-4
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(2020) Polysaccharide niche partitioning of distinct Polaribacter clades during North Sea spring algal blooms. ISME J . 10.1038/s41396-020-0601-y
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(2020) The environment drives microbial trait variability in aquatic habitats. Mol Ecol 29(23), 4605-4617. 10.1111/mec.15656
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(2020) Metatranscriptomic Sequencing of a Cyanobacterial Soil-Surface Consortium with and without a Diverse Underlying Soil Microbiome. Microbiol Resour Announc 9(1). 10.1128/MRA.01361-19
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(2020) Metagenomes and Metatranscriptomes of a Glucose-Amended Agricultural Soil. Microbiol Resour Announc 9(44). 10.1128/MRA.00895-20
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(2020) Metagenomes in the Borderline Ecosystems of the Antarctic Cryptoendolithic Communities. Microbiol Resour Announc 9(10). 10.1128/MRA.01599-19
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(2020) Structure determination of the HgcAB complex using metagenome sequence data: insights into microbial mercury methylation. Commun Biol 3(1), 320. 10.1038/s42003-020-1047-5
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(2020) Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow. ISME J 14(7), 1834-1846. 10.1038/s41396-020-0655-x
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(2020) Ecological Assembly Processes Are Coordinated between Bacterial and Viral Communities in Fractured Shale Ecosystems. Msystems 5(2). 10.1128/mSystems.00098-20
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(2020) Characterization of digestate microbial community structure following thermophilic anaerobic digestion with varying levels of green and food wastes. J Ind Microbiol Biotechnol 47(12), 1031-1044. 10.1007/s10295-020-02326-z
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(2020) Functional Signatures of the Epiphytic Prokaryotic Microbiome of Agaves and Cacti. Front Microbiol 10, 3044. 10.3389/fmicb.2019.03044
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(2020) Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters. ISME J . 10.1038/s41396-020-00825-6
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(2020) A phylogenetically novel cyanobacterium most closely related to Gloeobacter. ISME J . 10.1038/s41396-020-0668-5
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(2020) A pipeline for targeted metagenomics of environmental bacteria. Microbiome 8(1), 21. 10.1186/s40168-020-0790-7
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(2020) Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites. PeerJ 8, e8614. 10.7717/peerj.8614
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(2020) Phage-specific metabolic reprogramming of virocells. ISME J 14(4), 881-895. 10.1038/s41396-019-0580-z
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(2020) The International Virus Bioinformatics Meeting 2020. Viruses 12(12). 10.3390/v12121398
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(2020) Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon. ISME J . 10.1038/s41396-020-00804-x
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(2020) Metagenomic and Metatranscriptomic Analyses Revealed Uncultured Bacteroidales Populations as the Dominant Proteolytic Amino Acid Degraders in Anaerobic Digesters. Front Microbiol 11. 10.3389/fmicb.2020.593006
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(2020) Nitrogen cycling microbiomes are structured by plant mycorrhizal associations with consequences for nitrogen oxide fluxes in forests. Glob Chang Biol . 10.1111/gcb.15439
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(2020) A genomic catalog of Earth’s microbiomes. Nat Biotechnol . 10.1038/s41587-020-0718-6
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(2020) CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nat Biotechnol . 10.1038/s41587-020-00774-7
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(2020) Niche differentiation is spatially and temporally regulated in the rhizosphere. Isme Journal 14(4), 999-1014. 10.1038/s41396-019-0582-x
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(2020) Geology and climate influence rhizobiome composition of the phenotypically diverse tropical tree Tabebuia heterophylla. PLoS One 15(4), e0231083. 10.1371/journal.pone.0231083
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(2020) Diversity and Distribution of a Novel Genus of Hyperthermophilic Aquificae Viruses Encoding a Proof-Reading Family-A DNA Polymerase. Front Microbiol 11, 583361. 10.3389/fmicb.2020.583361
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(2020) Metagenomes from Experimental Hydrologic Manipulation of Restored Coastal Plain Wetland Soils (Tyrell County, North Carolina). Microbiol Resour Announc 9(41). 10.1128/MRA.00882-20
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(2020) Lipid analysis of CO2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria. ISME J 14(6), 1547-1560. 10.1038/s41396-020-0624-4
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(2020) Temperature and Nutrient Levels Correspond with Lineage-Specific Microdiversification in the Ubiquitous and Abundant Freshwater Genus Limnohabitans. Appl Environ Microbiol 86(10). 10.1128/AEM.00140-20
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(2020) In-depth Spatiotemporal Characterization of Planktonic Archaeal and Bacterial Communities in North and South San Francisco Bay. Microb Ecol . 10.1007/s00248-020-01621-7
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(2020) Depth-Differentiation and Seasonality of Planktonic Microbial Assemblages in the Monterey Bay Upwelling System. Front Microbiol 11, 1075. 10.3389/fmicb.2020.01075
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(2020) COVID-19 pandemic reveals the peril of ignoring metadata standards. Sci Data 7(1), 188. 10.1038/s41597-020-0524-5
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(2020) Advantages and Limits of Metagenomic Assembly and Binning of a Giant Virus. mSystems 5(3). 10.1128/mSystems.00048-20
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(2020) Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome. Genome Biology 21(1). 10.1186/s13059-020-02195-w
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(2020) Phototrophic Co-cultures From Extreme Environments: Community Structure and Potential Value for Fundamental and Applied Research. Front Microbiol 11, 572131. 10.3389/fmicb.2020.572131
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(2020) In depth metagenomic analysis in contrasting oil wells reveals syntrophic bacterial and archaeal associations for oil biodegradation in petroleum reservoirs. Sci Total Environ 715, 136646. 10.1016/j.scitotenv.2020.136646
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(2020) High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant. ISME J 14(7), 1857-1872. 10.1038/s41396-020-0650-2
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(2020) Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions. FEMS Microbiol Ecol 96(5). 10.1093/femsec/fiaa050
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(2020) Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem. Microbiome 8(1), 22. 10.1186/s40168-019-0780-9
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2019
(2019) Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea. Nat Microbiol 4(4), 603-613. 10.1038/s41564-019-0363-3
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(2019) Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi. ISME J . 10.1038/s41396-018-0343-2
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(2019) Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot. Sci Data 6(1), 140. 10.1038/s41597-019-0141-3
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(2019) Carboxydotrophy potential of uncultivated Hydrothermarchaeota from the subseafloor crustal biosphere. ISME J 13(6), 1457-1468. 10.1038/s41396-019-0352-9
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(2019) Wetland Sediments Host Diverse Microbial Taxa Capable of Cycling Alcohols. Appl Environ Microbiol 85(12). 10.1128/AEM.00189-19
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(2019) Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing. Nat Microbiol 4(2), 352-361. 10.1038/s41564-018-0312-6
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(2019) Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms. Nat Microbiol . 10.1038/s41564-019-0449-y
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(2019) Candidatus Prosiliicoccus vernus, a spring phytoplankton bloom associated member of the Flavobacteriaceae. Syst Appl Microbiol 42(1), 41-53. 10.1016/j.syapm.2018.08.007
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(2019) Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops. Nat Commun 10(1), 4135. 10.1038/s41467-019-11974-4
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(2019) Unexpected host dependency of Antarctic Nanohaloarchaeota. Proc Natl Acad Sci U S A . 10.1073/pnas.1905179116
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(2019) Interactions between plants and soil shaping the root microbiome under abiotic stress. Biochem J 476(19), 2705-2724. 10.1042/BCJ20180615
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(2019) Extracellular Electron Transfer May Be an Overlooked Contribution to Pelagic Respiration in Humic-Rich Freshwater Lakes. mSphere 4(1). 10.1128/mSphere.00436-18
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(2019) Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials. Sci Data 6(1), 207. 10.1038/s41597-019-0222-3
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(2019) Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nature Biotechnology 37(6), 632-+. 10.1038/s41587-019-0100-8
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(2019) Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils. FEMS Microbiol Ecol 95(2). 10.1093/femsec/fiy230
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(2019) Spatial, Temporal, and Phylogenetic Scales of Microbial Ecology. Trends Microbiol . 10.1016/j.tim.2019.03.003
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(2019) Insight into the Bacterial Endophytic Communities of Peach Cultivars Related to Crown Gall Disease Resistance. Appl Environ Microbiol . 10.1128/AEM.02931-18
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(2019) Advancing Genome-Resolved Metagenomics beyond the Shotgun. mSystems 4(3). 10.1128/mSystems.00118-19
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(2019) Structural dynamics and transcriptomic analysis of Dehalococcoides mccartyi within a TCE-Dechlorinating community in a completely mixed flow reactor. Water Res 158, 146-156. 10.1016/j.watres.2019.04.038
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(2019) Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., comprising the four species Cryosericum septentrionale gen. nov. sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., Ca. C. terrychapinii sp. nov. Syst Appl Microbiol 42(1), 54-66. 10.1016/j.syapm.2018.12.003
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(2019) Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom. Sci Data 6(1), 129. 10.1038/s41597-019-0132-4
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(2019) Diversity, evolution, and classification of virophages uncovered through global metagenomics. Microbiome 7(1), 157. 10.1186/s40168-019-0768-5
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(2019) A Viral Ecogenomics Framework To Uncover the Secrets of Nature’s “Microbe Whisperers”. mSystems 4(3). 10.1128/mSystems.00111-19
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(2019) Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes. Nat Microbiol 4(11), 1895-1906. 10.1038/s41564-019-0510-x
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(2019) Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies. Sci Data 6(1), 285. 10.1038/s41597-019-0287-z
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(2019) Metabolomics of sorghum roots during nitrogen stress reveals compromised metabolic capacity for salicylic acid biosynthesis. Plant Direct 3(3), e00122. 10.1002/pld3.122
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(2019) SpaRC: scalable sequence clustering using Apache Spark. Bioinformatics 35(5), 760-768. 10.1093/bioinformatics/bty733
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(2019) Unusual Metabolism and Hypervariation in the Genome of a Gracilibacterium (BD1-5) from an Oil-Degrading Community. MBio 10(6). 10.1128/mBio.02128-19
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(2019) Deep-sea hydrothermal vent metagenome-assembled genomes provide insight into the phylum Nanoarchaeota. Environ Microbiol Rep 11(2), 262-270. 10.1111/1758-2229.12740
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(2019) Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils. PeerJ 7, e7265. 10.7717/peerj.7265
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(2019) Contrasting Pathways for Anaerobic Methane Oxidation in Gulf of Mexico Cold Seep Sediments. mSystems 4(1). 10.1128/mSystems.00091-18
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(2019) Genomic Characterization of Candidate Division LCP-89 Reveals an Atypical Cell Wall Structure, Microcompartment Production, and Dual Respiratory and Fermentative Capacities. Appl Environ Microbiol 85(10). 10.1128/AEM.00110-19
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2018
(2018) Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. ISME J . 10.1038/s41396-018-0078-0
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(2018) Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis. Nature 558(7710), 440-444. 10.1038/s41586-018-0207-y
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(2018) Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes. Microb Ecol 75(1), 123-139. 10.1007/s00248-017-1028-5
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(2018) New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes. Front Microbiol 9, 1635. 10.3389/fmicb.2018.01635
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(2018) Metagenomic insights into diazotrophic communities across Arctic glacier forefields. FEMS Microbiol Ecol . 10.1093/femsec/fiy114
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(2018) Large-scale replicated field study of maize rhizosphere identifies heritable microbes. Proc Natl Acad Sci U S A 115(28), 7368-7373. 10.1073/pnas.1800918115
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(2018) Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil. Nat Ecol Evol 2(3), 499-509. 10.1038/s41559-017-0463-5
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2017
(2017) Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla. Front Microbiol 8, 2264. 10.3389/fmicb.2017.02264
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(2017) Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales. mSphere 2(4). 10.1128/mSphereDirect.00257-17
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(2017) Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders. Proc Natl Acad Sci U S A . 10.1073/pnas.1703424114
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(2017) Integration of Metagenomic and Stable Carbon Isotope Evidence Reveals the Extent and Mechanisms of Carbon Dioxide Fixation in High-Temperature Microbial Communities. Front Microbiol 8, 88. 10.3389/fmicb.2017.00088
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(2017) Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems. PeerJ 5, e3134. 10.7717/peerj.3134
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2016
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(2015) Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous ‘streamer’ community. ISME J 10(1), 210-24. 10.1038/ismej.2015.83
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(2015) Unusual biology across a group comprising more than 15% of domain Bacteria. Nature 523(7559), 208-11. 10.1038/nature14486
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(2015) Elviz – exploration of metagenome assemblies with an interactive visualization tool. BMC Bioinformatics 16, 130. 10.1186/s12859-015-0566-4
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(2015) Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr Biol 25(6), 690-701. 10.1016/j.cub.2015.01.014
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(2015) The integrated microbial genome resource of analysis. Methods Mol Biol 1231, 289-95. 10.1007/978-1-4939-1720-4_18
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(2015) The Joint Genome Institute Offers Resources Beyond a Core Facility. Microbe 10(7), 289-293. 10.1128/microbe.10.289.1
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(2015) IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites. MBio 6(4). 10.1128/mBio.00932-15
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(2015) Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions. MBio 6(3), e00066-15. 10.1128/mBio.00066-15
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(2015) Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions. MBio 6(3), e00066-15. 10.1128/mBio.00066-15
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(2015) Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Front Microbiol 6, 1205. 10.3389/fmicb.2015.01205
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(2015) Lignin-modifying processes in the rhizosphere of arid land grasses. Environ Microbiol 17(12), 4965-78. 10.1111/1462-2920.13020
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(2015) Aquifer environment selects for microbial species cohorts in sediment and groundwater. ISME J . 10.1038/ismej.2015.2
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(2015) Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages. Environ Microbiol . 10.1111/1462-2920.12930
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(2015) Geomicrobiology of sublacustrine thermal vents in Yellowstone Lake: geochemical controls on microbial community structure and function. Front Microbiol 6, 1044. 10.3389/fmicb.2015.01044
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(2015) MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3, e1165. 10.7717/peerj.1165
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(2015) Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome-resolved metagenomics. Environ Microbiol . 10.1111/1462-2920.12936
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(2015) Spatial Homogeneity of Bacterial Communities Associated with the Surface Mucus Layer of the Reef-Building Coral Acropora palmata. PLoS One 10(12), e0143790. 10.1371/journal.pone.0143790
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(2015) Diverse uncultivated ultra-small bacterial cells in groundwater. Nat Commun 6, 6372. 10.1038/ncomms7372
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(2015) Ten Years of Maintaining and Expanding a Microbial Genome and Metagenome Analysis System. Trends Microbiol 23(11), 730-41. 10.1016/j.tim.2015.07.012
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(2015) Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology. Environ Microbiol . 10.1111/1462-2920.13095
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(2015) Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis. ISME J . 10.1038/ismej.2015.155
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(2015) Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans. ISME J . 10.1038/ismej.2015.170
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(2015) Insights into the bacterial community and its temporal succession during the fermentation of wine grapes. Front Microbiol 6, 809. 10.3389/fmicb.2015.00809
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(2015) Global diversity and biogeography of deep-sea pelagic prokaryotes. ISME J . 10.1038/ismej.2015.137
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(2015) Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes. Mol Ecol . 10.1111/mec.13419
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(2015) Accurate, multi-kb reads resolve complex populations and detect rare microorganisms. Genome Res 25(4), 534-43. 10.1101/gr.183012.114
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(2015) Performance evaluation and tuning of BioPig for genomic analysis. Proceedings of the 2015 International Workshop on Data-Intensive Scalable Computing Systems , 1-7. 10.1145/2831244.2831252
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(2015) Similar Microbial Communities Found on Two Distant Seafloor Basalts. Frontiers in Microbiology 6. ARTN 1409 10.3389/fmicb.2015.01409
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(2015) Metagenomic reconstructions of bacterial CRISPR loci constrain population histories. ISME J . 10.1038/ismej.2015.162
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(2015) Antarctic archaea-virus interactions: metaproteome-led analysis of invasion, evasion and adaptation. ISME J 9(9), 2094-107. 10.1038/ismej.2015.110
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(2015) A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses. Microbiome 3, 62. 10.1186/s40168-015-0129-y
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(2015) High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. MBio 6(1). 10.1128/mBio.02288-14
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2014
(2014) Convergent bacterial microbiotas in the fungal agricultural systems of insects. MBio 5(6). 10.1128/mBio.02077-14
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(2014) Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response. PLoS Genet 10(11), e1004784. 10.1371/journal.pgen.1004784
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(2014) Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance. Front Microbiol 5(283), 283. 10.3389/fmicb.2014.00283
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(2014) Metagenomic sequencing of two salton sea microbiomes. Genome Announc 2(1). 10.1128/genomeA.01208-13
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(2014) Metagenomes from two microbial consortia associated with Santa Barbara seep oil. Mar Genomics . 10.1016/j.margen.2014.06.003
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(2014) Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California. Stand Genomic Sci 9(3), 1259-74. 10.4056/sigs.5029016
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(2014) Tackling soil diversity with the assembly of large, complex metagenomes. Proc Natl Acad Sci U S A 111(13), 4904-9. 10.1073/pnas.1402564111
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(2014) The microbial ecology of permafrost. Nat Rev Microbiol 12(6), 414-25. 10.1038/nrmicro3262
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(2014) Predominant Acidilobus-like populations from geothermal environments in yellowstone national park exhibit similar metabolic potential in different hypoxic microbial communities. Appl Environ Microbiol 80(1), 294-305. 10.1128/AEM.02860-13
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(2014) Assessment of the Deepwater Horizon oil spill impact on Gulf coast microbial communities. Front Microbiol 5, 130. 10.3389/fmicb.2014.00130
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(2014) Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples. J Vis Exp (94). 10.3791/52117
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(2014) Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk. Proc Natl Acad Sci U S A 111(47), E5096-104. 10.1073/pnas.1413110111
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(2014) FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus. Nucleic Acids Res . 10.1093/nar/gku702
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(2014) The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification. Nucleic Acids Res . 10.1093/nar/gku950
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(2014) Improved assemblies using a source-agnostic pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of contigs. Sci Rep 4, 6480. 10.1038/srep06480
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(2014) A microarray for assessing transcription from pelagic marine microbial taxa. ISME J . 10.1038/ismej.2014.1
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(2014) Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw. Biotechnol Biofuels 7(1), 495. 10.1186/s13068-014-0180-0
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(2014) Rearrangement of a Large Novel Pseudomonas aeruginosa Gene Island in Strains Isolated from a Patient Developing Ventilator-Associated Pneumonia. J Clin Microbiol 52(7), 2430-8. 10.1128/JCM.01626-13
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(2014) Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest. ISME J . 10.1038/ismej.2014.36
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(2014) Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecol Lett 17(6), 717-26. 10.1111/ele.12276
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(2014) Microbial ecology of an Antarctic hypersaline lake: genomic assessment of ecophysiology among dominant haloarchaea. ISME J . 10.1038/ismej.2014.18
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(2014) An environmental bacterial taxon with a large and distinct metabolic repertoire. Nature 506(7486), 58-62. 10.1038/nature12959
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(2014) MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome 2, 26. 10.1186/2049-2618-2-26
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(2014) Recruiting human microbiome shotgun data to site-specific reference genomes. PLoS One 9(1), e84963. 10.1371/journal.pone.0084963
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2013
(2013) Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean. ISME J 7(2), 256-68. 10.1038/ismej.2012.108
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(2013) Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens. Appl Environ Microbiol 79(12), 3770-8. 10.1128/AEM.03833-12
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(2013) Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. PLoS One 8(7), e68465. 10.1371/journal.pone.0068465
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(2013) Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nat Commun 4, 1854. 10.1038/ncomms2884
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(2013) Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites. PLoS One 8(4), e61126. 10.1371/journal.pone.0061126
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(2013) Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling. Microbiome 1(1), 22. 10.1186/2049-2618-1-22.
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(2013) Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry. Front Microbiol 4, 95. 10.3389/fmicb.2013.00095
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(2013) The YNP Metagenome Project: Environmental Parameters Responsible for Microbial Distribution in the Yellowstone Geothermal Ecosystem. Front Microbiol 4, 67. 10.3389/fmicb.2013.00067
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(2013) Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments. Front Microbiol 4, 106. 10.3389/fmicb.2013.00106
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(2013) Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park. ISME J 7(3), 622-34. 10.1038/ismej.2012.132
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(2013) The epsomitic phototrophic microbial mat of Hot Lake, Washington: community structural responses to seasonal cycling. Front Microbiol 4, 323. 10.3389/fmicb.2013.00323
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(2013) Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 20(10), 714-37. 10.1089/cmb.2013.0084
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(2013) Pyrosequencing reveals high-temperature cellulolytic microbial consortia in Great Boiling Spring after in situ lignocellulose enrichment. PLoS One 8(3), e59927. 10.1371/journal.pone.0059927
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(2013) Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc Natl Acad Sci U S A 110(16), 6548-53. 10.1073/pnas.1302837110
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(2013) Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill. ISME J . 10.1038/ismej.2013.129
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(2013) Comparative genomic analysis of phylogenetically closely related Hydrogenobaculum sp. isolates from Yellowstone National Park. Appl Environ Microbiol 79(9), 2932-43. 10.1128/AEM.03591-12
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(2013) Metagenomic profiling reveals lignocellulose degrading system in a microbial community associated with a wood-feeding beetle. PLoS One 8(9), e73827. 10.1371/journal.pone.0073827
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(2013) Comparative Genomic Analysis of the Endosymbionts of Herbivorous Insects Reveals Eco-Environmental Adaptations: Biotechnology Applications. PLoS Genet 9(1). Artn E1003131Doi 10.1371/Journal.Pgen.1003131
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2012
(2012) Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens. ISME J 6(9), 1688-701. 10.1038/ismej.2012.10
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(2012) Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill. Environ Microbiol 14(9), 2405-16. 10.1111/j.1462-2920.2012.02780.x
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(2012) Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome. Environ Microbiol 14(1), 207-27. 10.1111/j.1462-2920.2011.02593.x
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(2012) Metagenomic analysis of a stable trichloroethene-degrading microbial community. ISME J 6(9), 1702-14. 10.1038/ismej.2012.15
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(2012) Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough estuary, Monterey Bay. ISME J 6(4), 863-74. 10.1038/ismej.2011.142
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(2012) Anaerobic decomposition of switchgrass by tropical soil-derived feedstock-adapted consortia. MBio 3(1). 10.1128/mBio.00249-11
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(2012) Common bacterial responses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide. Environ Microbiol 14(5), 1145-58. 10.1111/j.1462-2920.2011.02695.x
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(2012) Bacterial diversity in the cecum of the world’s largest living rodent (Hydrochoerus hydrochaeris). Microb Ecol 63(4), 719-25. 10.1007/s00248-011-9963-z
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(2012) Differences in crop bacterial community structure between hoatzins from different geographical locations. Research in Microbiology 163(3), 211-220. DOI 10.1016/j.resmic.2012.01.001
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(2012) Microbes in thawing permafrost: the unknown variable in the climate change equation. ISME J 6(4), 709-12. 10.1038/ismej.2011.163
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(2012) Hydrazine synthase, a unique phylomarker with which to study the presence and biodiversity of anammox bacteria. Appl Environ Microbiol 78(3), 752-8. 10.1128/AEM.07113-11
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(2012) Mesophilic and thermophilic conditions select for unique but highly parallel microbial communities to perform carboxylate platform biomass conversion. PLoS One 7(6), e39689. 10.1371/journal.pone.0039689
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(2012) A framework for human microbiome research. Nature 486(7402), 215-21. 10.1038/nature11209
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(2012) Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study. Environ Microbiol Rep 4(2), 248-56. 10.1111/j.1758-2229.2012.00328.x
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(2012) Coordinating Environmental Genomics and Geochemistry Reveals Metabolic Transitions in a Hot Spring Ecosystem. Plos One 7(6). ARTN e38108 DOI 10.1371/journal.pone.0038108
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(2012) The metagenome of an anaerobic microbial community decomposing poplar wood chips. PLoS One 7(5), e36740. 10.1371/journal.pone.0036740
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(2012) Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis. Isme Journal 6(7), 1427-1439. DOI 10.1038/ismej.2011.200
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(2012) Global distribution of a wild alga revealed by targeted metagenomics. Curr Biol 22(17), R675-7. 10.1016/j.cub.2012.07.054
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2011
(2011) Cellulose-degrading bacteria associated with the invasive woodwasp Sirex noctilio. ISME J 5(8), 1323-31. 10.1038/ismej.2011.14
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(2011) Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil. Plos One 6(4). ARTN e19306 DOI 10.1371/journal.pone.0019306
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(2011) Enriching public descriptions of marine phages using the Genomic Standards Consortium MIGS standard. Stand Genomic Sci 4(2), 271-85. 10.4056/sigs.621069
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(2011) Glycoside Hydrolase Activities of Thermophilic Bacterial Consortia Adapted to Switchgrass. Applied and Environmental Microbiology 77(16), 5804-5812. Doi 10.1128/Aem.00032-11
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(2011) Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma. J Allergy Clin Immunol 127(2), 372-381 e1-3. 10.1016/j.jaci.2010.10.048
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(2011) Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium. ISME J 5(1), 122-30. 10.1038/ismej.2010.125
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(2011) Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 480(7377), 368-71. 10.1038/nature10576
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(2011) ClaMS: A Classifier for Metagenomic Sequences. Stand Genomic Sci 5(2), 248-53. 10.4056/sigs.2075298
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(2011) Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies. Science 333(6042), 646-8. 10.1126/science.1205760
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(2011) Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction. Biotechnol Bioeng 108(9), 2088-98. 10.1002/bit.23176
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(2011) Phage encoded H-NS: a potential achilles heel in the bacterial defence system. PLoS One 6(5), e20095. 10.1371/journal.pone.0020095
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(2011) Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean. Science 333(6047), 1296-1300. DOI 10.1126/science.1203690
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2010
(2010) Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS One 5(1), e8812. 10.1371/journal.pone.0008812
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(2010) Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities. Bioenergy Research 3(2), 146-158. DOI 10.1007/s12155-010-9089-z
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(2010) Meeting Report: “Metagenomics, Metadata and Meta-analysis” (M3) Workshop at the Pacific Symposium on Biocomputing 2010. Stand Genomic Sci 2(3), 357-60. 10.4056/sigs.802738
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(2010) Phylogenetic and metagenomic analysis of Verrucomicrobia in former agricultural grassland soil. FEMS Microbiol Ecol 71(1), 23-33. 10.1111/j.1574-6941.2009.00785.x
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(2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12(1), 118-23. 10.1111/j.1462-2920.2009.02051.x
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(2010) Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLoS Biol 8(11), e1000546. 10.1371/journal.pbio.1000546
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(2010) Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. Proc Natl Acad Sci U S A 107(33), 14793-8. 10.1073/pnas.1005297107
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2008
(2008) Identification of ancient remains through genomic sequencing. Genome Research 18(8), 1347-1353. DOI 10.1101/gr.076091.108
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(2008) Annotation of metagenome short reads using proxygenes. Bioinformatics 24(16), I7-I13. DOI 10.1093/bioinformatics/btn276
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(2008) Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Mol Syst Biol 4, 198. 10.1038/msb.2008.35
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(2008) Assembly of viral metagenomes from yellowstone hot springs. Appl Environ Microbiol 74(13), 4164-74. 10.1128/AEM.02598-07
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(2008) A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol 11(5), 442-6. 10.1016/j.mib.2008.09.011
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(2008) The airborne metagenome in an indoor urban environment. PLoS One 3(4), e1862. 10.1371/journal.pone.0001862
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(2008) A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells. Isme Journal 2(11), 1146-1156. DOI 10.1038/ismej.2008.48
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2006
(2006) An experimental metagenome data management and analysis system. Bioinformatics 22(14), e359-67. 10.1093/bioinformatics/btl217
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