(2022) Giant virus biology and diversity in the era of genome-resolved metagenomics.
Nature Reviews Microbiology , 1-16.
10.1038/s41579-022-00754-5
More Details
(2022) High-resolution mapping reveals hotspots and sex-biased recombination in Populus trichocarpa.
G3: Genes, Genomes, Genetics 13(1), jkac269.
10.1093/g3journal/jkac269
More Details
(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
More Details
(2022) Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction.
Microbiome 10(1), 183.
10.1186/s40168-022-01377-x
More Details
(2022) Cave Thiovulum (Candidatus Thiovulum stygium) differs metabolically and genomically from marine species.
The ISME Journal: Multidisciplinary Journal of Microbial Ecology , 1-14.
10.1038/s41396-022-01350-4
More Details
(2022) Phylogenomic structure and speciation in an emerging model: the Sphagnum magellanicum complex (Bryophyta).
New Phytologist 236(4), 1497-1511.
10.1111/nph.18429
More Details
(2022) The Sugar Metabolic Model of Aspergillus niger Can Only Be Reliably Transferred to Fungi of Its Phylum.
Journal of Fungi 8(12), 1315.
10.3390/jof8121315
More Details
(2022) MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters.
Nucleic Acids Research 51(D1), d603-d610.
10.1093/nar/gkac1049
More Details
(2022) Evolution of zygomycete secretomes and the origins of terrestrial fungal ecologies.
iScience 25(8), 104840.
10.1016/j.isci.2022.104840
More Details
(2022) Proteome of the Wood Decay Fungus Fomitopsis pinicola Is Altered by Substrate.
Microbiology Resource Announcements 11(9), e00586-22.
10.1128/mra.00586-22
More Details
(2022) MycoCosm, the JGI’s Fungal Genome Portal for Comparative Genomic and Multiomics Data Analyses.
2605, 271-291.
10.1007/978-1-0716-2871-3_14
More Details
(2022) High-Quality Draft Genome Sequence of Fischerella thermalis JSC-11, a Siderophilic Cyanobacterium with Bioremediation Potential.
Microbiology Resource Announcements 11(11), e00761-22.
10.1128/mra.00761-22
More Details
(2022) Population structure of an Antarctic aquatic cyanobacterium.
Microbiome 10(1), 207.
10.1186/s40168-022-01404-x
More Details
(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 .
10.1002/ldr.4549
More Details
(2022) Genome-Wide Association Studies across Environmental and Genetic Contexts Reveal Complex Genetic Architecture of Symbiotic Extended Phenotypes.
mBio 13(6), e01823-22.
10.1128/mbio.01823-22
More Details
(2022) Bioenergy sorghum stem growth regulation: intercalary meristem localization, development, and gene regulatory network analysis.
The Plant Journal 112(2), 476-492.
10.1111/tpj.15960
More Details
(2022) Increasing the Thermodynamic Driving Force of the Phosphofructokinase Reaction in Clostridium thermocellum.
Applied and Environmental Microbiology 88(22), e01258-22.
10.1128/aem.01258-22
More Details
(2022) High-quality genome of the basidiomycete yeast Dioszegia hungarica PDD-24b-2 isolated from cloud water.
G3: Genes, Genomes, Genetics 12(12), jkac282.
10.1093/g3journal/jkac282
More Details
(2022) Diploid-dominant life cycles characterize the early evolution of Fungi.
Proceedings of the National Academy of Sciences of the United States of America 119(36), e2116841119.
10.1073/pnas.2116841119
More Details
(2022) Wildfire-dependent changes in soil microbiome diversity and function.
Nature Microbiology 7(9), 1419-1430.
10.1038/s41564-022-01203-y
More Details
(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
More Details
(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
More Details
(2022) Diversity of genomic adaptations to the post‐fire environment in Pezizales fungi points to crosstalk between charcoal tolerance and sexual development.
New Phytologist 236(3), 1154-1167.
10.1111/nph.18407
More Details
(2022) Thermal Stress Has Minimal Effects on Bacterial Communities of Thermotolerant Symbiodinium Cultures.
Frontiers in Ecology and Evolution 10, 764086.
10.3389/fevo.2022.764086
More Details
(2022) Engineering of holocellulase in biomass-degrading fungi for sustainable biofuel production.
Journal of Cleaner Production 371, 133488.
10.1016/j.jclepro.2022.133488
More Details
(2022) Do Genetic Drift and Gene Flow Affect the Geographic Distribution of Female Plants in Gynodioecious Lobelia siphilitica?.
Plants 11(6), 825.
10.3390/plants11060825
More Details
(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 , 1-17.
10.1038/s41396-022-01345-1
More Details
(2022) Defensive symbiosis against giant viruses in amoebae.
Proceedings of the National Academy of Sciences of the United States of America 119(36), e2205856119.
10.1073/pnas.2205856119
More Details
(2022) Development of PCR-based markers for the identification and detection of Lophodermella needle cast pathogens on Pinus contorta var. latifolia and P. flexilis.
Journal of Microbiological Methods 200, 106546.
10.1016/j.mimet.2022.106546
More Details
(2022) Transitions of foliar mycobiota community and transcriptome in response to pathogenic conifer needle interactions.
Scientific Reports 12(1), 7832.
10.1038/s41598-022-11907-0
More Details
(2022) Enhanced terrestrial Fe(II) mobilization identified through a novel mechanism of microbially driven cave formation in Fe(III)-rich rocks.
Scientific Reports 12(1), 17062.
10.1038/s41598-022-21365-3
More Details
(2022) The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate.
Nature Microbiology 7(9), 1466-1479.
10.1038/s41564-022-01174-0
More Details
(2022) Combinatorial library design for improving isobutanol production in Saccharomyces cerevisiae.
Frontiers in Bioengineering and Biotechnology 10, 1080024.
10.3389/fbioe.2022.1080024
More Details
(2022) Coevolution of the Ess1-CTD axis in polar fungi suggests a role for phase separation in cold tolerance.
Science Advances 8(36), eabq3235.
10.1126/sciadv.abq3235
More Details
(2022) High‐throughput identification of novel heat tolerance genes via genome‐wide pooled mutant screens in the model green alga Chlamydomonas reinhardtii.
Plant Cell & Environment .
10.1111/pce.14507
More Details
(2022) Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica.
Nature Communications 13(1), 922.
10.1038/s41467-022-28540-0
More Details
(2022) Itaconic acid production is regulated by LaeA in Aspergillus pseudoterreus.
Metabolic Engineering Communications 15, e00203.
10.1016/j.mec.2022.e00203
More Details
(2022) Identifying the gluc-1 and gluc-2 mutations in Neurospora crassa by genome resequencing.
Journal of Genetics 101(2), 50.
10.1007/s12041-022-01394-7
More Details
(2022) Multiomics in the central Arctic Ocean for benchmarking biodiversity change.
PLOS Biology 20(10), e3001835.
10.1371/journal.pbio.3001835
More Details
(2022) EnZymClass: Substrate specificity prediction tool of plant acyl-ACP thioesterases based on ensemble learning.
Current Research in Biotechnology 4, 1-9.
10.1016/j.crbiot.2021.12.002
More Details
(2022) Poisson hurdle model-based method for clustering microbiome features.
Bioinformatics 39(1), btac782.
10.1093/bioinformatics/btac782
More Details
(2022) Exploring the roles of microbes in facilitating plant adaptation to climate change.
Biochemical Journal 479(3), 327-335.
10.1042/bcj20210793
More Details
(2022) Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae.
Life Science Alliance 6(3), e202201833.
10.26508/lsa.202201833
More Details
(2022) Multiple origins, one evolutionary trajectory: gradual evolution characterizes distinct lineages of allotetraploid Brachypodium..
Genetics .
10.1093/genetics/iyac146
More Details
(2022) Tissue Cultivation, Preparation, and Extraction of High Molecular Weight DNA for Single-Molecule Genome Sequencing of Plant-Associated Fungi.
2605, 79-102.
10.1007/978-1-0716-2871-3_5
More Details
(2022) Agave REVEILLE1 regulates the onset and release of seasonal dormancy in Populus..
Plant Physiology .
10.1093/plphys/kiac588
More Details
(2022) Genome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass.
Nature Communications 13(1), 7731.
10.1038/s41467-022-35507-8
More Details
(2022) The Chlamydomonas Genome Project, version 6: reference assemblies for mating type plus and minus strains reveal extensive structural mutation in the laboratory..
The Plant Cell .
10.1093/plcell/koac347
More Details
(2022) Phenotypic and genomic signatures of interspecies cooperation and conflict in naturally occurring isolates of a model plant symbiont.
Proceedings of the Royal Society B 289(1978), 20220477.
10.1098/rspb.2022.0477
More Details
(2022) Tuning of Gene Expression in Clostridium phytofermentans Using Synthetic Promoters and CRISPRi.
ACS Synthetic Biology 11(12), 4077-4088.
10.1021/acssynbio.2c00385
More Details
(2022) Complete Genome Sequences of Two Phylogenetically Distinct Nitrospina Strains Isolated from the Atlantic and Pacific Oceans.
Microbiology Resource Announcements 11(5), e00100-22.
10.1128/mra.00100-22
More Details
(2022) Multi-omics profiling of the cold tolerant Monoraphidium minutum 26B-AM in response to abiotic stress.
Algal Research 66, 102794.
10.1016/j.algal.2022.102794
More Details
(2022) Genomic Features of the Bundle-Forming Heliobacterium Heliophilum fasciatum.
Microorganisms 10(5), 869.
10.3390/microorganisms10050869
More Details
(2022) Host genotype controls ecological change in the leaf fungal microbiome.
PLOS Biology 20(8), e3001681.
10.1371/journal.pbio.3001681
More Details
(2022) Co‑cultivation of anaerobic fungi with Clostridium acetobutylicum bolsters butyrate and butanol production from cellulose and lignocellulose..
Journal of Industrial Microbiology & Biotechnology .
10.1093/jimb/kuac024
More Details
(2022) Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v.9..
Nucleic Acids Research 51(D1), d957-d963.
10.1093/nar/gkac974
More Details
(2022) Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes.
Cell Genomics 2(12), 100213.
10.1016/j.xgen.2022.100213
More Details
(2022) Multiplex knockout of trichome-regulating MYB duplicates in hybrid poplar using a single gRNA.
Plant physiology .
10.1093/plphys/kiac128
More Details
(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
More Details
(2022) Particulate and dissolved metabolite distributions along a latitudinal transect of the western Atlantic Ocean.
Limnology and Oceanography .
10.1002/lno.12275
More Details
(2022) Degradation Reduces Microbial Richness and Alters Microbial Functions in an Australian Peatland.
Microbial Ecology , 1-17.
10.1007/s00248-022-02071-z
More Details
(2022) The western redcedar genome reveals low genetic diversity in a self-compatible conifer.
Genome Research 32(10), gr.276358.121.
10.1101/gr.276358.121
More Details
(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
More Details
(2022) Structural characterization of a soil viral auxiliary metabolic gene product – a functional chitosanase.
Nature Communications 13(1), 5485.
10.1038/s41467-022-32993-8
More Details
(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
More Details
(2022) Zwartia hollandica gen. nov., sp. nov., Jezberella montanilacus gen. nov., sp. nov. and Sheuella amnicola gen. nov., comb. nov., representing the environmental GKS98 (betIII) cluster..
International Journal of Systematic and Evolutionary Microbiology 72(9).
10.1099/ijsem.0.005513
More Details
(2022) Environmental predictors of electroactive bacterioplankton in small boreal lakes.
Environmental Microbiology .
10.1111/1462-2920.16314
More Details
(2022) A Pleiotropic Flowering Time QTL Exhibits Gene-by-Environment Interaction for Fitness in a Perennial Grass.
Molecular Biology and Evolution 39(10), msac203.
10.1093/molbev/msac203
More Details
(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
More Details
(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
More Details
(2022) Pharmaceutical Biotransformation is Influenced by Photosynthesis and Microbial Nitrogen Cycling in a Benthic Wetland Biomat.
Environmental Science and Technology 56(20), 14462-14477.
10.1021/acs.est.2c03566
More Details
(2022) EARLY FLOWERING 3 and Photoperiod Sensing in Brachypodium distachyon.
Frontiers in Plant Science 12, 769194.
10.3389/fpls.2021.769194
More Details
(2022) Protist impacts on marine cyanovirocell metabolism.
ISME Communications 2(1), 94.
10.1038/s43705-022-00169-6
More Details
(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
More Details
(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
More Details
(2022) Chromosome evolution and the genetic basis of agronomically important traits in greater yam.
Nature Communications 13(1), 2001.
10.1038/s41467-022-29114-w
More Details
(2022) Phenotype to genotype in Neurospora crassa: Association of the scumbo phenotype with mutations in the gene encoding ceramide C9-methyltransferase.
Current Research in Microbial Sciences 3, 100117.
10.1016/j.crmicr.2022.100117
More Details
(2022) Enemy or ally: a genomic approach to elucidate the lifestyle of Phyllosticta citrichinaensis.
G3 (Bethesda, Md.) .
10.1093/g3journal/jkac061
More Details
(2022) Toward a data infrastructure for the Plant Cell Atlas..
Plant Physiology 191(1), 35-46.
10.1093/plphys/kiac468
More Details
(2022) Combining GWAS and population genomic analyses to characterize coevolution in a legume‐rhizobia symbiosis.
Molecular Ecology .
10.1111/mec.16602
More Details
(2022) IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata..
Nucleic Acids Research 51(D1), d733-d743.
10.1093/nar/gkac1037
More Details
(2022) Representing sex chromosomes in genome assemblies.
Cell Genomics 2(5), 100132.
10.1016/j.xgen.2022.100132
More Details
(2022) GENESPACE tracks regions of interest and gene copy number variation across multiple genomes.
eLife 11, e78526.
10.7554/elife.78526
More Details
(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
More Details
(2022) Habitat‐adapted microbial communities mediate Sphagnum peatmoss resilience to warming.
New Phytologist .
10.1111/nph.18072
More Details
(2022) Patterns of pan‐genome occupancy and gene coexpression under water‐deficit in Brachypodium distachyon.
Molecular Ecology 31(20), 5285-5306.
10.1111/mec.16661
More Details
(2022) Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea.
PLoS Biology 20(1), e3001508.
10.1371/journal.pbio.3001508
More Details
(2022) Sodalis ligni Strain 159R Isolated from an Anaerobic Lignin-Degrading Consortium.
Microbiology Spectrum 10(3), e02346-21.
10.1128/spectrum.02346-21
More Details
(2022) The IMG/M data management and analysis system v.7: content updates and new features..
Nucleic Acids Research 51(D1), d723-d732.
10.1093/nar/gkac976
More Details
(2022) Comparative genomics analysis of drought response between obligate CAM and C3 photosynthesis plants.
Journal of Plant Physiology 277, 153791.
10.1016/j.jplph.2022.153791
More Details
(2022) Genome and proteome analyses show the gaseous alkane degrader Desulfosarcina sp. strain BuS5 as an extreme metabolic specialist.
Environmental Microbiology .
10.1111/1462-2920.15956
More Details
(2022) The CC–NB–LRR protein BSR1 from Brachypodium confers resistance to Barley stripe mosaic virus in gramineous plants by recognising TGB1 movement protein.
New Phytologist .
10.1111/nph.18457
More Details
(2022) Comparative transcriptomics and metabolomics reveal specialized metabolite drought stress responses in switchgrass (Panicum virgatum).
New Phytologist 236(4), 1393-1408.
10.1111/nph.18443
More Details
(2022) Chromosomal integration of complex DNA constructs using CRAGE and CRAGE-Duet systems.
STAR Protocols 3(3), 101546.
10.1016/j.xpro.2022.101546
More Details
(2022) Cas9-Based Metabolic Engineering of Issatchenkia orientalis for Enhanced Utilization of Cellulosic Hydrolysates.
Journal of Agricultural and Food Chemistry 70(38), 12085-12094.
10.1021/acs.jafc.2c04251
More Details
(2022) Microbiome composition modulates secondary metabolism in a multispecies bacterial community.
Proceedings of the National Academy of Sciences of the United States of America 119(42), e2212930119.
10.1073/pnas.2212930119
More Details
(2022) Detailed analysis of the D-galactose catabolic pathways in Aspergillus niger reveals complexity at both metabolic and regulatory level.
Fungal Genetics and Biology 159, 103670.
10.1016/j.fgb.2022.103670
More Details
(2022) Protocol for single-cell isolation and genome amplification of environmental microbial eukaryotes for genomic analysis.
STAR Protocols 3(1), 100968.
10.1016/j.xpro.2021.100968
More Details
(2022) Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics.
Frontiers in Microbiology 13, 879116.
10.3389/fmicb.2022.879116
More Details
(2022) Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome.
Microbiome 10(1), 151.
10.1186/s40168-022-01343-7
More Details
(2022) Genome Sequencing Suggests Diverse Secondary Metabolism in Coral-Associated Aquimarina megaterium.
Microbiology Resource Announcements 11(11), e00620-22.
10.1128/mra.00620-22
More Details
(2022) Evidence of Asexual Overwintering of Melampsora paradoxa and Mapping of Stem Rust Host Resistance in Salix.
Plants 11(18), 2385.
10.3390/plants11182385
More Details
(2022) Cellular assays identify barriers impeding iron-sulfur enzyme activity in a non-native prokaryotic host.
eLife 11, e70936.
10.7554/elife.70936
More Details
(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
More Details
(2022) .
175, 179-258.
10.1016/bs.agron.2022.04.001
More Details
(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
More Details
(2022) pHBMT1, a BAHD-family monolignol acyltransferase, mediates lignin acylation in poplar.
Plant Physiology 188(2), 1014-1027.
10.1093/plphys/kiab546
More Details
(2022) Substrate availability and not thermal acclimation controls microbial temperature sensitivity response to long‐term warming.
Global Change Biology .
10.1111/gcb.16544
More Details
(2022) Virus-Host Interactions and Genetic Diversity of Antarctic Sea Ice Bacteriophages.
mBio 13(3), e00651-22.
10.1128/mbio.00651-22
More Details
(2022) Intersubunit Coupling Enables Fast CO2‑Fixation by Reductive Carboxylases.
ACS Central Science 8(8), 1091-1101.
10.1021/acscentsci.2c00057
More Details
(2022) DNA Methylation in Ensifer Species during Free-Living Growth and during Nitrogen-Fixing Symbiosis with Medicago spp.
mSystems 7(1), e01092-21.
10.1128/msystems.01092-21
More Details
(2022) The survivor strain: isolation and characterization of Phormidium yuhuli AB48, a filamentous phototactic cyanobacterium with biotechnological potential.
Frontiers in Bioengineering and Biotechnology 10, 932695.
10.3389/fbioe.2022.932695
More Details
(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
More Details
(2022) Metagenome-Assembled Genomes from a Microbiome Grown in Dairy Manure Hydrolysate.
Microbiology Resource Announcements 11(8), e00292-22.
10.1128/mra.00292-22
More Details
(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
More Details
(2022) Gene Coexpression Connectivity Predicts Gene Targets Underlying High Ionic-Liquid Tolerance in Yarrowia lipolytica.
mSystems 7(4), e00348-22.
10.1128/msystems.00348-22
More Details
(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
More Details
(2022) Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans.
Microbiome 10(1), 67.
10.1186/s40168-022-01254-7
More Details
(2022) A remarkable expansion of oligopeptide transporter genes in rust fungi (Pucciniales) suggests a specialization in nutrients acquisition for obligate biotrophy..
Phytopathology .
10.1094/phyto-04-22-0128-r
More Details
(2022) The Genome of the Acid Soil-Adapted Strain Rhizobium favelukesii OR191 Encodes Determinants for Effective Symbiotic Interaction With Both an Inverted Repeat Lacking Clade and a Phaseoloid Legume Host.
Frontiers in Microbiology 13, 735911.
10.3389/fmicb.2022.735911
More Details
(2022) Persistent memory as an effective alternative to random access memory in metagenome assembly.
BMC Bioinformatics 23(1), 513.
10.1186/s12859-022-05052-8
More Details
(2022) Discordant population structure among rhizobium divided genomes and their legume hosts.
Molecular Ecology .
10.1111/mec.16704
More Details
(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
More Details
(2022) ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria..
Microbial Genomics 8(7).
10.1099/mgen.0.000824
More Details
(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
More Details
(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
More Details
(2022) Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes.
New Phytologist 233(3), 1317-1330.
10.1111/nph.17873
More Details
(2022) Thousands of small, novel genes predicted in global phage genomes.
Cell Reports 39(12), 110984.
10.1016/j.celrep.2022.110984
More Details
(2022) Identifying candidate structured RNAs in CRISPR operons.
RNA Biology 19(1), 678-685.
10.1080/15476286.2022.2067714
More Details
(2022) Salinity tolerance mechanisms of an Arctic Pelagophyte using comparative transcriptomic and gene expression analysis.
Communications Biology 5(1), 500.
10.1038/s42003-022-03461-2
More Details
(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
More Details
(2022) Successional adaptive strategies revealed by correlating arbuscular mycorrhizal fungal abundance with host plant gene expression.
Molecular Ecology .
10.1111/mec.16343
More Details
(2022) Co-occurrence networks reveal more complexity than community composition in resistance and resilience of microbial communities.
Nature Communications 13(1), 3867.
10.1038/s41467-022-31343-y
More Details
(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
More Details
(2022) Unraveling the regulation of sugar beet pulp utilization in the industrially relevant fungus Aspergillus niger.
iScience 25(4), 104065.
10.1016/j.isci.2022.104065
More Details
(2022) Adapted laboratory evolution of Thermotoga sp. strain RQ7 under carbon starvation.
BMC Research Notes 15(1), 99.
10.1186/s13104-022-05982-9
More Details
(2022) Bioavailable iron titrations reveal oceanic Synechococcus ecotypes optimized for different iron availabilities.
ISME Communications 2(1), 54.
10.1038/s43705-022-00132-5
More Details
(2022) Sequencing and Analysis of the Entire Genome of the Mycoparasitic Bioeffector Fungus Trichoderma asperelloides Strain T 203 (Hypocreales).
Microbiology Resource Announcements 11(2), e00995-21.
10.1128/mra.00995-21
More Details
(2022) A cryptic third active site in cyanophycin synthetase creates primers for polymerization.
Nature Communications 13(1), 3923.
10.1038/s41467-022-31542-7
More Details
(2022) Rapid changes in coastal ocean microbiomes uncoupled with shifts in environmental variables.
Environmental Microbiology .
10.1111/1462-2920.16086
More Details
(2022) Applying Promiscuous RiPP Enzymes to Peptide Backbone N‑Methylation Chemistry.
ACS Chemical Biology 17(8), 2165-2178.
10.1021/acschembio.2c00293
More Details
(2022) Biochemical characterization of plant aromatic aminotransferases.
.
10.1016/bs.mie.2022.07.034
More Details
(2022) Genome‐wide CRISPR‐Cas9 screen reveals a persistent null‐hyphal phenotype that maintains high carotenoid production in Yarrowia lipolytica.
Biotechnology and Bioengineering .
10.1002/bit.28219
More Details
(2022) Microbiome engineering for sustainable agriculture: using synthetic biology to enhance nitrogen metabolism in plant-associated microbes.
Current Opinion in Microbiology 68, 102172.
10.1016/j.mib.2022.102172
More Details
(2022) Brachypodium: 20 years as a grass biology model system; the way forward?.
Trends in Plant Science .
10.1016/j.tplants.2022.04.008
More Details
(2022) Culexarchaeia, a novel archaeal class of anaerobic generalists inhabiting geothermal environments.
ISME Communications 2(1), 86.
10.1038/s43705-022-00175-8
More Details
(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
More Details
(2022) Abscisic acid supports colonization of Eucalyptus grandis roots by the mutualistic ectomycorrhizal fungus Pisolithus microcarpus.
New Phytologist 233(2), 966-982.
10.1111/nph.17825
More Details
(2022) Characterization of Streptomyces nymphaeiformis sp. nov., and its taxonomic relatedness to other polyhydroxybutyrate-degrading streptomycetes.
International journal of systematic and evolutionary microbiology 72(3).
10.1099/ijsem.0.005266
More Details
(2022) Elucidating Drought-Tolerance Mechanisms in Plant Roots through 1H NMR Metabolomics in Parallel with MALDI-MS, and NanoSIMS Imaging Techniques.
Environmental Science & Technology 56(3), 2021-2032.
10.1021/acs.est.1c06772
More Details
(2022) A sweet spot in marine ecosystems.
Nature Ecology & Evolution 6(7), 847-848.
10.1038/s41559-022-01764-5
More Details
(2022) Substrate-restricted methanogenesis and limited volatile organic compound degradation in highly diverse and heterogeneous municipal landfill microbial communities.
ISME Communications 2(1), 58.
10.1038/s43705-022-00141-4
More Details
(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
More Details
(2022) Near-Complete Genome Sequence of Zygosaccharomyces rouxii NRRL Y-64007, a Yeast Capable of Growing on Lignocellulosic Hydrolysates.
Microbiology Resource Announcements 11(5), e00050-22.
10.1128/mra.00050-22
More Details
(2022) An amoeba and a cyanobacterium walk into a bar....
Nature Reviews Microbiology 20(9), 511-511.
10.1038/s41579-022-00775-0
More Details
(2022) Development of platforms for functional characterization and production of phenazines using a multi-chassis approach via CRAGE.
Metabolic Engineering 69, 188-197.
10.1016/j.ymben.2021.11.012
More Details
(2022) Novel Viral DNA Polymerases From Metagenomes Suggest Genomic Sources of Strand-Displacing Biochemical Phenotypes.
Frontiers in Microbiology 13, 858366.
10.3389/fmicb.2022.858366
More Details
(2022) High-Quality Draft Nuclear and Mitochondrial Genome Sequence of Fusarium oxysporum f. sp. albedinis strain 9, the Causal Agent of Bayoud Disease on Date Palm..
Plant Disease 106(7), 1974-1976.
10.1094/pdis-01-22-0245-a
More Details
(2022) Genotype–phenotype correlations within the Geodermatophilaceae.
Frontiers in Microbiology 13, 975365.
10.3389/fmicb.2022.975365
More Details
(2022) DNA Sequence Analysis of an Inversion Hot Spot in Lobeliaceae Plastomes.
Plants 11(21), 2863.
10.3390/plants11212863
More Details
(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
More Details
(2022) Evolutionary Origin and Functional Diversification of Aminotransferases.
Journal of Biological Chemistry 298(8), 102122.
10.1016/j.jbc.2022.102122
More Details
(2022) N-dependent dynamics of root growth and nitrate and ammonium uptake are altered by the bacterium Herbaspirillum seropedicae in the cereal model Brachypodium distachyon..
Journal of Experimental Botany 73(15), 5306-5321.
10.1093/jxb/erac184
More Details
(2022) Faunimonas pinastri gen. nov., sp. nov., an endophyte from a pine tree of the family Pleomorphomonadaceae, class Alphaproteobacteria.
International Journal of Systematic and Evolutionary Microbiology 72(12).
10.1099/ijsem.0.005623
More Details
(2022) Transcriptomic Data Sets for Zymomonas mobilis 2032 during Fermentation of Ammonia Fiber Expansion (AFEX)-Pretreated Corn Stover and Switchgrass Hydrolysates.
Microbiology Resource Announcements 11(9), e00564-22.
10.1128/mra.00564-22
More Details
(2022) Bioenergy sorghum’s deep roots: A key to sustainable biomass production on annual cropland.
GCB Bioenergy 14(2), 132-156.
10.1111/gcbb.12907
More Details
(2022) A Single Nucleotide Change in the polC DNA Polymerase III in Clostridium thermocellum Is Sufficient To Create a Hypermutator Phenotype.
Applied and Environmental Microbiology 88(1), e01531-21.
10.1128/aem.01531-21
More Details
(2022) Comparative genomics reveals a dynamic genome evolution in the ectomycorrhizal milk‐cap (Lactarius) mushrooms.
New Phytologist 235(1), 306-319.
10.1111/nph.18143
More Details
(2022) Controlling selectivity of modular microbial biosynthesis of butyryl-CoA-derived designer esters.
Metabolic Engineering 69, 262-274.
10.1016/j.ymben.2021.12.001
More Details
(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
More Details
(2022) The Earth BioGenome Project 2020: Starting the clock.
Proceedings of the National Academy of Sciences 119(4), e2115635118.
10.1073/pnas.2115635118
More Details
(2022) Directed Evolution of Flavin-Dependent Halogenases for Site- and Atroposelective Halogenation of 3‑Aryl-4(3H)‑Quinazolinones via Kinetic or Dynamic Kinetic Resolution.
Journal of the American Chemical Society 144(36), 16676-16682.
10.1021/jacs.2c07422
More Details
(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
More Details
(2022) Silencing of Dicer‐like protein 2a restores the resistance phenotype in the rice mutant, sxi4 (suppressor of Xa21‐mediated immunity 4).
The Plant Journal .
10.1111/tpj.15692
More Details
(2022) Evolutionary transition to the ectomycorrhizal habit in the genomes of a hyperdiverse lineage of mushroom‐forming fungi.
New Phytologist .
10.1111/nph.17892
More Details
(2022) Annotation survey and life cycle transcriptomics of transcription factors in rust fungi (Pucciniales) identify a possible role for cold shock proteins in dormancy exit.
Fungal Genetics and Biology 161, 103698.
10.1016/j.fgb.2022.103698
More Details
(2022) The first complete human genome.
Nature 606(7914), 468-469.
10.1038/d41586-022-01368-w
More Details
(2022) A Synthetic Gene Library Yields a Previously Unknown Glycoside Phosphorylase That Degrades and Assembles Poly-β-1,3-GlcNAc, Completing the Suite of β‑Linked GlcNAc Polysaccharides.
ACS Central Science .
10.1021/acscentsci.1c01570
More Details
(2022) The Transcription Factor Roc1 Is a Key Regulator of Cellulose Degradation in the Wood-Decaying Mushroom Schizophyllum commune.
mBio 13(3), e00628-22.
10.1128/mbio.00628-22
More Details
(2022) Adaptive laboratory evolution for improved tolerance of isobutyl acetate in Escherichia coli.
Metabolic Engineering 69, 50-58.
10.1016/j.ymben.2021.11.002
More Details
(2022) In vivo evolution of lactic acid hyper-tolerant Clostridium thermocellum.
New Biotechnology 67, 12-22.
10.1016/j.nbt.2021.12.003
More Details
(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
More Details
(2022) GalR, GalX and AraR co‐regulate d‐galactose and l‐arabinose utilization in Aspergillus nidulans.
Microbial Biotechnology .
10.1111/1751-7915.14025
More Details
(2022) The landscape of Chlamydomonas histone H3 lysine 4 methylation reveals both constant features and dynamic changes during the diurnal cycle.
The Plant Journal 112(2), 352-368.
10.1111/tpj.15948
More Details
(2022) Critical Assessment of Metagenome Interpretation: the second round of challenges.
Nature Methods 19(4), 429-440.
10.1038/s41592-022-01431-4
More Details
(2022) Multiple sources of aerobic methane production in aquatic ecosystems include bacterial photosynthesis.
Nature Communications 13(1), 6454.
10.1038/s41467-022-34105-y
More Details
(2022) Genetic mapping and prediction of flowering time and plant height in a maize Stiff Stalk MAGIC population.
Genetics 221(2), iyac063-.
10.1093/genetics/iyac063
More Details
(2022) Comparative and pangenomic analysis of the genus Streptomyces.
Scientific Reports 12(1), 18909.
10.1038/s41598-022-21731-1
More Details
(2022) The recent evolutionary rescue of a staple crop depended on over half a century of global germplasm exchange.
Science advances 8(6), eabj4633.
10.1126/sciadv.abj4633
More Details
(2022) A generalist–specialist trade-off between switchgrass cytotypes impacts climate adaptation and geographic range.
Proceedings of the National Academy of Sciences of the United States of America 119(15), e2118879119.
10.1073/pnas.2118879119
More Details
(2022) Protocol for condition-dependent metabolite yield prediction using the TRIMER pipeline.
STAR Protocols 3(1), 101184.
10.1016/j.xpro.2022.101184
More Details
(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
More Details
(2022) RIViT-seq enables systematic identification of regulons of transcriptional machineries.
Nature Communications 13(1), 3502.
10.1038/s41467-022-31191-w
More Details
(2022) Genome Sequence and Analysis of the Flavinogenic Yeast Candida membranifaciens IST 626.
Journal of Fungi 8(3), 254.
10.3390/jof8030254
More Details
(2022) Zng1 is a GTP-dependent zinc transferase needed for activation of methionine aminopeptidase.
Cell Reports 39(7), 110834.
10.1016/j.celrep.2022.110834
More Details
(2022) Genomic Signatures of a Major Adaptive Event in the Pathogenic Fungus Melampsora larici-populina.
Genome Biology and Evolution 14(1), evab279.
10.1093/gbe/evab279
More Details
(2022) Re-evaluating the Systematics of Dendrolycopodium Using Restriction-Site Associated DNA-Sequencing.
Frontiers in Plant Science 13, 912080.
10.3389/fpls.2022.912080
More Details
(2022) Phage–host coevolution in natural populations.
Nature Microbiology 7(7), 1075-1086.
10.1038/s41564-022-01157-1
More Details
(2022) Genome Streamlining, Proteorhodopsin, and Organic Nitrogen Metabolism in Freshwater Nitrifiers.
mBio 13(3), e02379-21.
10.1128/mbio.02379-21
More Details
(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
More Details
(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
More Details
(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
More Details
(2022) Metagenomes and Metagenome-Assembled Genomes from Substrate-Amended Hot Spring Sediment Incubations from Yellowstone National Park.
Microbiology Resource Announcements , e01065-21.
10.1128/mra.01065-21
More Details
(2022) A Genomic Perspective Across Earth’s Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy.
Frontiers in Microbiology 12, 761869.
10.3389/fmicb.2021.761869
More Details
(2022) Diversity in the soil virosphere: to infinity and beyond?.
Trends in Microbiology .
10.1016/j.tim.2022.05.003
More Details
(2022) ORT: A workflow linking genome-scale metabolic models with reactive transport codes.
Bioinformatics (Oxford, England) 38(3), 778-784.
10.1093/bioinformatics/btab753
More Details
(2022) GAL08, an Uncultivated Group of Acidobacteria, Is a Dominant Bacterial Clade in a Neutral Hot Spring.
Frontiers in Microbiology 12, 787651.
10.3389/fmicb.2021.787651
More Details
(2022) Development of a Freeze-Dried CRISPR-Cas12 Sensor for Detecting Wolbachia in the Secondary Science Classroom.
ACS Synthetic Biology 11(2), 835-842.
10.1021/acssynbio.1c00503
More Details
(2022) Spacer2PAM: A computational framework to guide experimental determination of functional CRISPR-Cas system PAM sequences.
Nucleic Acids Research 50(6), 3523-3534.
10.1093/nar/gkac142
More Details
(2022) Metabolic engineering for valorization of macroalgae biomass.
Metabolic Engineering 71, 42-61.
10.1016/j.ymben.2022.01.005
More Details
(2022) Metagenome-Assembled Genomes from a Microbiome Converting Xylose to Medium-Chain Carboxylic Acids.
Microbiology Resource Announcements , e01151-21.
10.1128/mra.01151-21
More Details
(2022) Subsurface hydrocarbon degradation strategies in low- and high-sulfate coal seam communities identified with activity-based metagenomics.
npj Biofilms and Microbiomes 8(1), 7.
10.1038/s41522-022-00267-2
More Details
(2022) Weakened resilience of benthic microbial communities in the face of climate change.
ISME Communications 2(1), 21.
10.1038/s43705-022-00104-9
More Details
(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
More Details
(2022) Proteome reallocation enables the selective de novo biosynthesis of non-linear, branched-chain acetate esters.
Metabolic Engineering 73, 38-49.
10.1016/j.ymben.2022.05.003
More Details
(2022) A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants.
Developmental Cell 57(4), 543-560.e9.
10.1016/j.devcel.2022.01.008
More Details
(2022) Structure and Function of the β‑Asp-Arg Polymerase Cyanophycin Synthetase 2.
ACS Chemical Biology 17(3), 670-679.
10.1021/acschembio.1c01007
More Details
(2022) Trace metal contents of autotrophic flagellates from contrasting open‐ocean ecosystems.
Limnology and Oceanography Letters 7(4), 354-362.
10.1002/lol2.10258
More Details
(2022) Population genomics of a forest fungus reveals high gene flow and climate adaptation signatures.
Molecular Ecology 31(7), 1963-1979.
10.1111/mec.16369
More Details
(2022) An optimized ChIP‐Seq framework for profiling histone modifications in Chromochloris zofingiensis.
Plant Direct 6(3), e392.
10.1002/pld3.392
More Details
(2022) Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species.
Journal of Fungi 8(3), 311.
10.3390/jof8030311
More Details
(2022) Microbes and Climate Change: a Research Prospectus for the Future.
mBio 13(3), e00800-22.
10.1128/mbio.00800-22
More Details
(2022) On Single-Cell Enzyme Assays in Marine Microbial Ecology and Biogeochemistry.
Frontiers in Marine Science 9.
10.3389/fmars.2022.846656
More Details
(2022) SIMILE enables alignment of tandem mass spectra with statistical significance.
Nature Communications 13(1), 2510.
10.1038/s41467-022-30118-9
More Details
(2022) A toolkit for microbial community editing.
Nature Reviews Microbiology 20(7), 383-383.
10.1038/s41579-022-00747-4
More Details
(2022) Membrane Bioreactor Pretreatment of High-Salinity O&G Produced Water.
ACS ES&T Water 2(3), 484-494.
10.1021/acsestwater.1c00436
More Details
(2022) Cell-free prototyping enables implementation of optimized reverse β-oxidation pathways in heterotrophic and autotrophic bacteria.
Nature Communications 13(1), 3058.
10.1038/s41467-022-30571-6
More Details
(2022) A centimeter-long bacterium with DNA contained in metabolically active, membrane-bound organelles.
Science 376(6600), 1453-1458.
10.1126/science.abb3634
More Details
(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
More Details
(2022) Examining the Relationship Between the Testate Amoeba Hyalosphenia papilio (Arcellinida, Amoebozoa) and its Associated Intracellular Microalgae Using Molecular and Microscopic Methods.
Protist 173(1), 125853.
10.1016/j.protis.2021.125853
More Details
(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
More Details
(2022) A TXTL-Based Assay to Rapidly Identify PAMs for CRISPR-Cas Systems with Multi-Protein Effector Complexes.
, 391-411.
10.1007/978-1-0716-1998-8_24
More Details
(2022) Rapid cell-free characterization of multi-subunit CRISPR effectors and transposons.
Molecular Cell 82(6), 1210-1224.e6.
10.1016/j.molcel.2022.01.026
More Details
(2022) Kingdom-Wide Analysis of Fungal Protein-Coding and tRNA Genes Reveals Conserved Patterns of Adaptive Evolution.
Molecular Biology and Evolution 39(2), msab372.
10.1093/molbev/msab372
More Details
(2022) The ectomycorrhizal fungus Pisolithus microcarpus encodes a microRNA involved in cross-kingdom gene silencing during symbiosis.
Proceedings of the National Academy of Sciences 119(3), e2103527119.
10.1073/pnas.2103527119
More Details
(2022) Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales.
New Phytologist 233(3), 1383-1400.
10.1111/nph.17858
More Details
(2022) The role of zinc in the adaptive evolution of polar phytoplankton.
Nature Ecology & Evolution 6(7), 965-978.
10.1038/s41559-022-01750-x
More Details
(2022) Considering Strain Variation and Non-Type Strains for Yeast Metabolic Engineering Applications.
Life 12(4), 510.
10.3390/life12040510
More Details
(2022) Discovering untapped biochemistry in microorganisms from hidden corners.
Nature Reviews Microbiology 20(11), 639-639.
10.1038/s41579-022-00795-w
More Details
(2022) Community Structure and Microbial Associations in Sediment-Free Methanotrophic Enrichment Cultures from a Marine Methane Seep.
Applied and Environmental Microbiology 88(11), e02109-21.
10.1128/aem.02109-21
More Details
(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
More Details
(2022) Systems-wide analysis revealed shared and unique responses to moderate and acute high temperatures in the green alga Chlamydomonas reinhardtii.
Communications Biology 5(1), 460.
10.1038/s42003-022-03359-z
More Details