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.
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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.
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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.
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(2022) Multiple sources of aerobic methane production in aquatic ecosystems include bacterial photosynthesis.
Nature Communications 13(1), 6454.
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(2022) Microtopography Matters: Belowground CH4 Cycling Regulated by Differing Microbial Processes in Peatland Hummocks and Lawns.
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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.
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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.
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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.
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(2022) Poisson hurdle model-based method for clustering microbiome features.
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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.
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(2022) Diversity in the soil virosphere: to infinity and beyond?.
Trends in Microbiology 30(11), 1025-1035.
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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.
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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.
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(2022) Weakened resilience of benthic microbial communities in the face of climate change.
ISME Communications 2(1), 21.
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(2022) Variation in Root Exudate Composition Influences Soil Microbiome Membership and Function.
Applied and Environmental Microbiology 88(11), e00226-22.
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(2022) Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics.
Microbiome 10(1), 157.
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(2022) Trace metal contents of autotrophic flagellates from contrasting open‐ocean ecosystems.
Limnology and Oceanography Letters 7(4), 354-362.
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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.
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(2022) Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction.
Microbiome 10(1), 183.
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(2022) Membrane Bioreactor Pretreatment of High-Salinity O&G Produced Water.
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(2022) Pharmaceutical Biotransformation is Influenced by Photosynthesis and Microbial Nitrogen Cycling in a Benthic Wetland Biomat.
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(2022) Metagenomes and Metagenome-Assembled Genomes from Microbial Communities Fermenting Ultrafiltered Milk Permeate.
Microbiology Resource Announcements 11(7), e00293-22.
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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.
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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.
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(2022) Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits.
Microbiome 10(1), 241.
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(2022) New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria.
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(2021) Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities.
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(2021) Metagenomes, metatranscriptomes, and metagenome-assembled genomes from chesapeake and Delaware bay (USA) water samples.
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(2021) Pre-Cambrian roots of novel Antarctic cryptoendolithic bacterial lineages.
Microbiome 9(1), 15.
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(2021) Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance.
mSystems 6(3), e00537-21.
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(2021) Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress.
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(2021) Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts.
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Nature Reviews Microbiology 19(7), 407.
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(2021) Whole Community Metatranscriptomes and Lipidomes Reveal Diverse Responses Among Antarctic Phytoplankton to Changing Ice Conditions.
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(2021) Illuminating the Virosphere Through Global Metagenomics.
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(2021) Cultivating the bacterial microbiota of populus roots.
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(2021) Microbial Community Field Surveys Reveal Abundant Pseudomonas Population in Sorghum Rhizosphere Composed of Many Closely Related Phylotypes.
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(2021) Rapid response of nitrogen cycling gene transcription to labile carbon amendments in a soil microbial community.
mSystems 6(3).
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(2021) DOE JGI metagenome workflow.
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(2021) Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean.
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Nature Plants 7(5), 544-545.
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(2021) Methanogenesis and Salt Tolerance Genes of a Novel Halophilic Methanosarcinaceae Metagenome-Assembled Genome from a Former Solar Saltern.
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(2021) Silicon-rich soil amendments impact microbial community composition and the composition of arsM bearing microbes.
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(2021) 16S rRNA gene amplicon sequencing data from flooded rice paddy mesocosms treated with different silicon-rich soil amendments.
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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.
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(2021) Global Diversity and Biogeography of the Zostera marina Mycobiome.
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Applied and Environmental Microbiology 87(23), e01598-21.
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(2021) Viral community analysis in a marine oxygen minimum zone indicates increased potential for viral manipulation of microbial physiological state.
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(2021) Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes.
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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.
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(2021) Flooding and ecological restoration promote wetland microbial communities and soil functions on former cranberry farmland.
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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.
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(2021) The Rhizosphere Responds: Rich Fen Peat and Root Microbial Ecology after Long-Term Water Table Manipulation.
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(2011) ClaMS: A Classifier for Metagenomic Sequences.
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(2011) Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies.
Science 333(6042), 646-8.
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(2011) Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction.
Biotechnol Bioeng 108(9), 2088-98.
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(2011) Phage encoded H-NS: a potential achilles heel in the bacterial defence system.
PLoS One 6(5), e20095.
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(2011) Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean.
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(2011) Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.
Nature Biotechnology 29(5), 415-420.
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2010
(2010) Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community.
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(2010) Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities.
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(2010) Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Workshop at the Pacific Symposium on Biocomputing 2010.
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(2010) Phylogenetic and metagenomic analysis of Verrucomicrobia in former agricultural grassland soil.
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(2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates.
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(2010) Evolutionary relationships of wild hominids recapitulated by gut microbial communities.
PLoS Biol 8(11), e1000546.
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(2010) Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores.
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2008
(2008) Identification of ancient remains through genomic sequencing.
Genome Research 18(8), 1347-1353.
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(2008) Annotation of metagenome short reads using proxygenes.
Bioinformatics 24(16), I7-I13.
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(2008) Toward a standards-compliant genomic and metagenomic publication record.
OMICS 12(2), 157-60.
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(2008) Microbiology - Metagenomics.
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(2008) A bacterial metapopulation adapts locally to phage predation despite global dispersal.
Genome Research 18(2), 293-297.
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(2008) Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat.
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(2008) IMG/M: a data management and analysis system for metagenomes.
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(2008) Assembly of viral metagenomes from yellowstone hot springs.
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(2008) A renaissance for the pioneering 16S rRNA gene.
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(2008) The airborne metagenome in an indoor urban environment.
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(2008) A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells.
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2006
(2006) An experimental metagenome data management and analysis system.
Bioinformatics 22(14), e359-67.
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