(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.
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.
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(2021) The widespread IS200/605 transposon family encodes diverse programmable RNA-guided endonucleases.
Science 374(6563), 57-65.
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(2021) Wteredinibacter haidensis sp. Nov., teredinibacter purpureus sp. nov. and teredinibacter franksiae sp. nov., marine, cellulolytic endosymbiotic bacteria isolated from the gills of the wood-boring mollusc bankia setacea (bivalvia: Teredinidae) and emended description of the genus teredinibacter.
International Journal of Systematic and Evolutionary Microbiology 71(2), 1-11.
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(2021) Dynamic genome evolution in a model fern.
Nature Plants 8(9), 1038-1051.
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(2021) Morphological and Genomic Features of the New Klosneuvirinae Isolate Fadolivirus IHUMI-VV54.
Frontiers in Microbiology 12, 719703.
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(2021) Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes.
Nucleic Acids Research , gkab1115.
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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) Three mutations repurpose a plant karrikin receptor to a strigolactone receptor.
Proceedings of the National Academy of Sciences of the United States of America 118(30).
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(2021) Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress.
Nature Communications 12.
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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 .
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(2021) Genomics Characterization of an Engineered Corynebacterium glutamicum in Bioreactor Cultivation Under Ionic Liquid Stress.
Frontiers in Bioengineering and Biotechnology 9, 766674.
10.3389/fbioe.2021.766674
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(2021) Cultivating the Bacterial Microbiota of Populus Roots.
mSystems 6(3), e01306-20.
10.1128/msystems.01306-20
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(2021) The leucine-rich repeats in allelic barley MLA immune receptors define specificity towards sequence-unrelated powdery mildew avirulence effectors with a predicted common RNase-like fold.
Plos Pathogens 17(2), 36.
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(2021) Persistence and plasticity in bacterial gene regulation.
Nature Methods 18(12), 1499-1505.
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(2021) Changing expression patterns of TonB-dependent transporters suggest shifts in polysaccharide consumption over the course of a spring phytoplankton bloom.
Isme Journal , 15.
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(2021) Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions.
Isme Journal , 16.
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(2021) Extreme dimensions — how big (or small) can tailed phages be?.
Nature Reviews Microbiology 19(7), 407.
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(2021) Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage.
Microbiome 9(1).
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(2021) iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology.
ISME Communications 1(1), 77.
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(2021) Editorial: Cell Free Biocatalysis for the Production of Bioproducts.
Frontiers in Energy Research 9, 781552.
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(2021) Genomic variation within the maize stiff-stalk heterotic germplasm pool.
Plant Genome .
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(2021) Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution.
The ISME Journal: Multidisciplinary Journal of Microbial Ecology , 1-11.
10.1038/s41396-021-01178-4
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(2021) Sorting for secreted molecule production using a biosensor-in-microdroplet approach.
Proceedings of the National Academy of Sciences of the United States of America 118(36).
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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.
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(2021) Seasonal dynamics of core fungi in the switchgrass phyllosphere, and co-occurrence with leaf bacteria.
Phytobiomes Journal 5(1), 60-68.
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(2021) Phosphate Availability Modulates Root Exudate Composition and Rhizosphere Microbial Community in a Teosinte and a Modern Maize Cultivar.
Phytobiomes Journal .
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(2021) High-quality draft genome sequence of the siderophilic and thermophilic leptolyngbyaceae cyanobacterium JSC-12.
Microbiology Resource Announcements 10(25).
10.1128/MRA.00495-21
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(2021) Co‑cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate lyases on specific substrates.
Biotechnology for Biofuels 14(1), 234.
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(2021) Experimental evolution of extremophile resistance to ionizing radiation.
Trends in Genetics .
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(2021) A multi-omic characterization of temperature stress in a halotolerant Scenedesmus strain for algal biotechnology.
Communications Biology 4(1), 15.
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(2021) Illuminating the Virosphere Through Global Metagenomics.
Annual Review of Biomedical Data Science 4(1), 369-391.
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(2021) Gene-rich UV sex chromosomes harbor conserved regulators of sexual development.
Science Advances 7(27).
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(2021) Cultivating the bacterial microbiota of populus roots.
mSystems 6(3).
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(2021) Novel metabolic interactions and environmental conditions mediate the boreal peatmoss-cyanobacteria mutualism.
The ISME Journal: Multidisciplinary Journal of Microbial Ecology , 1-12.
10.1038/s41396-021-01136-0
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(2021) High-resolution phenotyping of sorghum genotypic and phenotypic responses to low nitrogen and synthetic microbial communities.
Plant Cell and Environment 44(5), 1611-1626.
10.1111/pce.14004
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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) Genome-scale phylogenetic analyses confirm Olpidium as the closest living zoosporic fungus to the non-flagellated, terrestrial fungi.
Scientific Reports 11(1), 12.
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(2021) The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities.
Nucleic Acids Res 49(D1), D751-D763.
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(2021) Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants.
Nature Communications 12(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.
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(2021) An orthogonal metabolic framework for one-carbon utilization.
Nature Metabolism 3(10), 1385-1399.
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(2021) Revisiting a 'simple' fungal metabolic pathway reveals redundancy, complexity and diversity.
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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) A single-cell genomics pipeline for environmental microbial eukaryotes.
iScience 24(4), 102290.
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(2021) DOE JGI metagenome workflow.
mSystems 6(3).
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(2021) Global overview and major challenges of host prediction methods for uncultivated phages.
Current Opinion in Virology 49, 117-126.
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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-+.
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(2021) Plant single-cell solutions for energy and the environment.
Communications Biology 4(1).
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(2021) Different threats, same response.
Nature Plants 7(5), 544-545.
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(2021) The Roseibium album (Labrenzia alba) Genome Possesses Multiple Symbiosis Factors Possibly Underpinning Host-Microbe Relationships in the Marine Benthos.
Microbiology Resource Announcements 10(34).
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(2021) The Melampsora americana population on Salix purpurea in the Great Lakes region is highly diverse with a contributory influence of clonality.
Phytopathology .
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(2021) A global metagenomic map of urban microbiomes and antimicrobial resistance.
Cell 184(13), 3376-3393.e17.
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(2021) Cryptic genetic structure and copy-number variation in the ubiquitous forest symbiotic fungus Cenococcum geophilum.
Environmental Microbiology .
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(2021) Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways.
Nature Communications 12(1).
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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.
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(2021) Intracellular pathways for lignin catabolism in white-rot fungi.
Proceedings of the National Academy of Sciences of the United States of America 118(9), 10.
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(2021) Structural insights into bifunctional thaumarchaeal crotonyl-CoA hydratase and 3-hydroxypropionyl-CoA dehydratase from Nitrosopumilus maritimus.
Scientific Reports 11(1), 22849.
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(2021) Gamete expression of TALE class HD genes activates the diploid sporophyte program in Marchantia polymorpha.
eLife 10, e57088.
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(2021) Kinetic variation in grass phosphoenolpyruvate carboxylases provides opportunity to enhance C-4 photosynthetic efficiency.
Plant Journal 105(6), 1677-1688.
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(2021) Getting back to the grass roots: harnessing specialized metabolites for improved crop stress resilience.
Current Opinion in Biotechnology 70, 174-186.
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(2021) Perspective on taxonomic classification of uncultivated viruses.
Current Opinion in Virology 51, 207-215.
10.1016/j.coviro.2021.10.011
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(2021) Silicon-rich soil amendments impact microbial community composition and the composition of arsM bearing microbes.
Plant and Soil .
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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).
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(2021) Engineering Pseudomonas putida for efficient aromatic conversion to bioproduct using high throughput screening in a bioreactor.
Metabolic Engineering 66, 229-238.
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(2021) Transcriptional acclimation and spatial differentiation characterize drought response by the ectomycorrhizal fungus Suillus pungens.
New Phytologist .
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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) Transcriptional control of Clostridium autoethanogenum using CRISPRi.
Synthetic Biology 6(1).
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(2021) Stepping on the Gas to a Circular Economy: Accelerating Development of Carbon-Negative Chemical Production from Gas Fermentation.
Annual Review of Chemical and Biomolecular Engineering 12, 439-470.
10.1146/annurev-chembioeng-120120-021122
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(2021) Zymomonas diversity and potential for biofuel production.
Biotechnology for Biofuels 14(1).
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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) The F-box protein gene exo-1 is a target for reverse engineering enzyme hypersecretion in filamentous fungi.
Proceedings of the National Academy of Sciences 118(26), e2025689118.
10.1073/pnas.2025689118
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(2021) Widespread polycistronic gene expression in green algae.
Proceedings of the National Academy of Sciences of the United States of America 118(7), 10.
10.1073/pnas.2017714118
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(2021) Coral mucus rapidly induces chemokinesis and genome-wide transcriptional shifts toward early pathogenesis in a bacterial coral pathogen.
ISME Journal .
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(2021) Novel Extracellular Electron Transfer Channels in a Gram-Positive Thermophilic Bacterium.
Frontiers in Microbiology 11.
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(2021) Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization.
BMC Bioinformatics 22(1).
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(2021) PhycoCosm, a comparative algal genomics resource.
Nucleic Acids Res 49(D1), D1004-D1011.
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(2021) Draft genome sequences of strains CBS6241 and CBS6242 of the basidiomycetous yeast Filobasidium floriforme.
G3: Genes, Genomes, Genetics , jkab398.
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(2021) VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses.
Microbiome 9(1), 13.
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(2021) Gene family expansions and transcriptome signatures uncover fungal adaptations to wood decay.
Environmental Microbiology , 17.
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(2021) Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber.
Isme Journal 15(2), 421-434.
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(2021) Genomic characterization of three marine fungi, including Emericellopsis atlantica sp. nov. with signatures of a generalist lifestyle and marine biomass degradation.
IMA Fungus 12(1).
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(2021) The contributions from the progenitor genomes of the mesopolyploid brassiceae are evolutionarily distinct but functionally compatible.
Genome Research 31(5), 799-810.
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(2021) Draft genome sequence of Bordetella sp. strain FB-8, isolated from a former uranium mining area in Germany.
Microbiology Resource Announcements 10(14).
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(2021) Plant Metabolic Network 15: A resource of genome-wide metabolism databases for 126 plants and algae.
Journal of Integrative Plant Biology n/a(n/a).
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(2021) Pests, diseases, and aridity have shaped the genome of Corymbia citriodora.
Communications Biology 4(1).
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(2021) Evidence for Lignocellulose-Decomposing Enzymes in the Genome and Transcriptome of the Aquatic Hyphomycete Clavariopsis aquatica.
Journal of Fungi 7(10), 854.
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(2021) RNA-Seq Reveals that Light and Darkness Are Different Stimuli in Freshwater Heterotrophic Actinobacteria.
Frontiers in Microbiology 12, 739005.
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(2021) Identification of Candidate Susceptibility Genes to Puccinia graminis f. sp. tritici in Wheat.
Frontiers in Plant Science 12.
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(2021) Hybridization History and Repetitive Element Content in the Genome of a Homoploid Hybrid, Yucca gloriosa (Asparagaceae).
Frontiers in Plant Science 11, 16.
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(2021) Counting mRNA Copies in Intact Bacterial Cells by Fluctuation Localization Imaging-Based Fluorescence In Situ Hybridization (fliFISH).
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(2021) Aspects of the Neurospora crassa Sulfur Starvation Response Are Revealed by Transcriptional Profiling and DNA Affinity Purification Sequencing.
mSphere 6(5), e00564-21.
10.1128/mSphere.00564-21
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(2021) DNA affinity purification sequencing and transcriptional profiling reveal new aspects of nitrogen regulation in a filamentous fungus.
Proceedings of the National Academy of Sciences 118(13), e2009501118.
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(2021) Tiny Earth: A Big Idea for STEM Education and Antibiotic Discovery.
Mbio 12(1), 7.
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(2021) Integrative genomics reveals paths to sex dimorphism in Salix purpurea L.
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(2021) Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium.
Current Biology 31(7), 1393-1402.e5.
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(2021) Omics analyses and biochemical study of Phlebiopsis gigantea elucidate its degradation strategy of wood extractives.
Scientific Reports 11(1).
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(2021) Microfabrication of a chamber for high-resolution, in situ imaging of the whole root for plant–microbe interactions.
International Journal of Molecular Sciences 22(15).
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(2021) Vision, challenges and opportunities for a plant cell atlas.
eLife 10.
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(2021) Draft genome sequences of switchgrass diazotrophs.
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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 , 1-11.
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(2021) IMITATION SWITCH is required for normal chromatin structure and gene repression in PRC2 target domains.
Proceedings of the National Academy of Sciences of the United States of America 118(4), 9.
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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.
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(2021) Microbiome Engineering: Synthetic Biology of Plant-Associated Microbiomes in Sustainable Agriculture.
Trends in Biotechnology 39(3), 244-261.
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(2021) CRAGE-CRISPR facilitates rapid activation of secondary metabolite biosynthetic gene clusters in bacteria.
Cell Chemical Biology 29.
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(2021) Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals.
Microbiome 9(1), 21.
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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.
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(2021) A plant host, Nicotiana benthamiana, enables the production and study of fungal lignin-degrading enzymes.
Communications Biology 4(1).
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(2021) Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages.
Nature Communications 12(1).
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(2021) Virus-associated organosulfur metabolism in human and environmental systems.
Cell Reports 36(5).
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(2021) Multi-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in Rhodosporidium toruloides.
Frontiers in Bioengineering and Biotechnology 8, 16.
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(2021) Synthase-Selective Exploration of a Tunicate Microbiome by Activity-Guided Single-Cell Genomics.
ACS Chemical Biology 16(5), 813-819.
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(2021) Further engineering of R. toruloides for the production of terpenes from lignocellulosic biomass.
Biotechnology for Biofuels 14(1).
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(2021) Symbiotic nitrogen fixation in the reproductive structures of a basidiomycete fungus.
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(2021) Pangenomics reveals alternative environmental lifestyles among chlamydiae.
Nature Communications 12(1).
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(2021) Peatland microbial community responses to plant functional group and drought are depth-dependent.
Molecular Ecology 30(20), 5119-5136.
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(2021) Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups.
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(2021) Probing specificities of alcohol acyltransferases for designer ester biosynthesis with a high-throughput microbial screening platform.
Biotechnology and Bioengineering .
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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 118(32), e2105124118.
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(2021) Plant Pan-Genomics Comes of Age.
Annual Review of Plant Biology 72, 411-435.
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(2021) Metabolic patterns in Septoria canker resistant and susceptible Populus trichocarpa genotypes 24 hours post-inoculation.
Phytopathology 111.
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(2021) Long-term excess nitrogen fertilizer increases sensitivity of soil microbial community to seasonal change revealed by ecological network and metagenome analyses.
Soil Biology and Biochemistry 160.
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(2021) Genetic dissection of natural variation in oilseed traits of camelina by whole-genome resequencing and QTL mapping.
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(2021) Heterospecific Neighbor Plants Impact Root Microbiome Diversity and Molecular Function of Root Fungi.
Frontiers in Microbiology 12, 680267.
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(2021) Mercury methylation by metabolically versatile and cosmopolitan marine bacteria.
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(2021) Aromatic Dimer Dehydrogenases from Novosphingobium aromaticivorans Reduce Monoaromatic Diketones.
Applied and Environmental Microbiology 87(24), e01742-21.
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(2021) Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes.
PLOS Biology 19(11), e3001442.
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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) Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass.
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(2021) Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding.
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(2021) Current status and impending progress for cassava structural genomics.
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(2021) Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass) [version 1; peer review: 1 approved].
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(2021) Annotated genome sequence of the high-biomass-producing yellow-green alga tribonema minus.
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(2021) Revealing enzyme functional architecture via high-throughput microfluidic enzyme kinetics.
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(2021) The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole.
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(2021) Medicago root nodule microbiomes: insights into a complex ecosystem with potential candidates for plant growth promotion.
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(2021) New Insights Into the Influence of Plant and Microbial Diversity on Denitrification Rates in a Salt Marsh.
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(2021) KARRIKIN INSENSITIVE2 regulates leaf development, root system architecture and arbuscular‐mycorrhizal symbiosis in Brachypodium distachyon.
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(2021) p-Nitrophenyl esters provide new insights and applications for the thiolase enzyme OleA.
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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.
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(2021) Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes.
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