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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    (PXFuel)
    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

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    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

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    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

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    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

    Read more

    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

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    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

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    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

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    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

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    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

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News & Publications
Home › News & Publications › Publications

Publications

JGI publications for calendar year 2022 appear below, listed alphabetically by author.

Abergel, Chantal et al. (2022) Giant virus biology and diversity in the era of genome-resolved metagenomics. Nature Reviews Microbiology , 1-16. 10.1038/s41579-022-00754-5
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Abeyratne, Chanaka Roshan et al. (2022) High-resolution mapping reveals hotspots and sex-biased recombination in Populus trichocarpa. G3: Genes, Genomes, Genetics 13(1), jkac269. 10.1093/g3journal/jkac269
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Acinas, Silvia G. et al. (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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Adams, Paul D. et al. (2022) Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction. Microbiome 10(1), 183. 10.1186/s40168-022-01377-x
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Aerts, Joost W. et al. (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
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Aguero, Blanka et al. (2022) Phylogenomic structure and speciation in an emerging model: the Sphagnum magellanicum complex (Bryophyta). New Phytologist 236(4), 1497-1511. 10.1111/nph.18429
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Aguilar-Pontes, Maria Victoria et al. (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
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Aguilar, César et al. (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
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Ahrendt, Steven et al. (2022) Evolution of zygomycete secretomes and the origins of terrestrial fungal ecologies. iScience 25(8), 104840. 10.1016/j.isci.2022.104840
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Ahrendt, Steven et al. (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
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Ahrendt, Steven R. et al. (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
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Alcorta, Jaime et al. (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
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Allen, Michelle A. et al. (2022) Population structure of an Antarctic aquatic cyanobacterium. Microbiome 10(1), 207. 10.1186/s40168-022-01404-x
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Allingham, Shaun M et al. (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
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Allsup, Cassandra M. et al. (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
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Altobelli, Stephen A. et al. (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
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Amador-Noguez, Daniel et al. (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
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Amato, Pierre et al. (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
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Amses, Kevin R. et al. (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
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Amundson, Kaela K. et al. (2022) Wildfire-dependent changes in soil microbiome diversity and function. Nature Microbiology 7(9), 1419-1430. 10.1038/s41564-022-01203-y
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Amundson, Kaela K. et al. (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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Anantharaman, Karthik et al. (2022) Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits. Microbiome 10(1), 241. 10.1186/s40168-022-01424-7
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Andreopoulos, Bill et al. (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
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Angel, A. M. González et al. (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
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Antoniêto, Amanda Cristina Campos et al. (2022) Engineering of holocellulase in biomass-degrading fungi for sustainable biofuel production. Journal of Cleaner Production 371, 133488. 10.1016/j.jclepro.2022.133488
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Appiah-Madson, Hannah J. et al. (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
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Arruda, Paulo et al. (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
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Arthofer, Patrick et al. (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
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Ata, Jessa P et al. (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
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Ata, Jessa P. et al. (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
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Auler, Augusto S. et al. (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
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Bachy, Charles et al. (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
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Baerwald, Justin J. et al. (2022) Combinatorial library design for improving isobutanol production in Saccharomyces cerevisiae. Frontiers in Bioengineering and Biotechnology 10, 1080024. 10.3389/fbioe.2022.1080024
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Bah, Alaji et al. (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
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Bailey, Catherine E. et al. (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
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Baisya, Dipankar et al. (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
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Baker, Scott E. et al. (2022) Itaconic acid production is regulated by LaeA in Aspergillus pseudoterreus. Metabolic Engineering Communications 15, e00203. 10.1016/j.mec.2022.e00203
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Baker, Scott E. et al. (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
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Balmonte, John-Paul et al. (2022) Multiomics in the central Arctic Ocean for benchmarking biodiversity change. PLOS Biology 20(10), e3001835. 10.1371/journal.pbio.3001835
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Banerjee, Deepro et al. (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
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Barnes, Elle et al. (2022) Poisson hurdle model-based method for clustering microbiome features. Bioinformatics 39(1), btac782. 10.1093/bioinformatics/btac782
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Barnes, Elle M. et al. (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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Barry, Kerrie et al. (2022) Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae. Life Science Alliance 6(3), e202201833. 10.26508/lsa.202201833
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Barry, Kerrie et al. (2022) Multiple origins, one evolutionary trajectory: gradual evolution characterizes distinct lineages of allotetraploid Brachypodium.. Genetics . 10.1093/genetics/iyac146
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Barry, Kerrie et al. (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
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Barry, Kerrie et al. (2022) Agave REVEILLE1 regulates the onset and release of seasonal dormancy in Populus.. Plant Physiology . 10.1093/plphys/kiac588
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Barry, Kerrie et al. (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
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Barry, Kerrie et al. (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
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Batstone, Rebecca T. et al. (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
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Baum, Chloé et al. (2022) Tuning of Gene Expression in Clostridium phytofermentans Using Synthetic Promoters and CRISPRi. ACS Synthetic Biology 11(12), 4077-4088. 10.1021/acssynbio.2c00385
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Bayer, Barbara et al. (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
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Bell, Tisza A.S. et al. (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
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Bender, Kelly S. et al. (2022) Genomic Features of the Bundle-Forming Heliobacterium Heliophilum fasciatum. Microorganisms 10(5), 869. 10.3390/microorganisms10050869
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Benucci, Gian Maria Niccolo et al. (2022) Host genotype controls ecological change in the leaf fungal microbiome. PLOS Biology 20(8), e3001681. 10.1371/journal.pbio.3001681
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Benyamin, Marcus et al. (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
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Bertsch, Jon et al. (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
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Bertsch, Jonathon et al. (2022) Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes. Cell Genomics 2(12), 100213. 10.1016/j.xgen.2022.100213
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Bewg, William P. et al. (2022) Multiplex knockout of trichome-regulating MYB duplicates in hybrid poplar using a single gRNA. Plant physiology . 10.1093/plphys/kiac128
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Bhatia, Maya P. et al. (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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Bhatia, Maya P. et al. (2022) Particulate and dissolved metabolite distributions along a latitudinal transect of the western Atlantic Ocean. Limnology and Oceanography . 10.1002/lno.12275
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Birnbaum, Christina et al. (2022) Degradation Reduces Microbial Richness and Alters Microbial Functions in an Australian Peatland. Microbial Ecology , 1-17. 10.1007/s00248-022-02071-z
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Birol, Inanc et al. (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
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Bischoff, Vera et al. (2022) New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria. Virus Evolution 8(2), veac070. 10.1093/ve/veac070
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Blaby, Ian K. et al. (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
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Blazewicz, Steven J. et al. (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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Bodelier, Paul L. E. et al. (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
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Bond, Daniel R. et al. (2022) Environmental predictors of electroactive bacterioplankton in small boreal lakes. Environmental Microbiology . 10.1111/1462-2920.16314
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Bonnette, Jason et al. (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
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Borton, Mikayla A. et al. (2022) Genome-Resolved Metaproteomics Decodes the Microbial and Viral Contributions to Coupled Carbon and Nitrogen Cycling in River Sediments. mSystems 7(4), e00516-22. 10.1128/msystems.00516-22
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Bosak, Tanja et al. (2022) Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean. Proceedings of the National Academy of Sciences of the United States of America 119(37), e2200014119. 10.1073/pnas.2200014119
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Bosworth, Lily B. et al. (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
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Bouché, Frédéric et al. (2022) EARLY FLOWERING 3 and Photoperiod Sensing in Brachypodium distachyon. Frontiers in Plant Science 12, 769194. 10.3389/fpls.2021.769194
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Bowen, Benjamin P. et al. (2022) Protist impacts on marine cyanovirocell metabolism. ISME Communications 2(1), 94. 10.1038/s43705-022-00169-6
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Boyd, Eric S. et al. (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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Brambilla, Diego et al. (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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Bredeson, Jessen V. et al. (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
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Bredeweg, Erin L. et al. (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
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Buijs, Valerie A. et al. (2022) Enemy or ally: a genomic approach to elucidate the lifestyle of Phyllosticta citrichinaensis. G3 (Bethesda, Md.) . 10.1093/g3journal/jkac061
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Burdett, Tony et al. (2022) Toward a data infrastructure for the Plant Cell Atlas.. Plant Physiology 191(1), 35-46. 10.1093/plphys/kiac468
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Burghardt, Liana T. et al. (2022) Combining GWAS and population genomic analyses to characterize coevolution in a legume‐rhizobia symbiosis. Molecular Ecology . 10.1111/mec.16602
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Call, Lee et al. (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
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Carey, Sarah B. et al. (2022) Representing sex chromosomes in genome assemblies. Cell Genomics 2(5), 100132. 10.1016/j.xgen.2022.100132
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Carlson, Joseph W et al. (2022) GENESPACE tracks regions of interest and gene copy number variation across multiple genomes. eLife 11, e78526. 10.7554/elife.78526
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Carper, Dana L. et al. (2022) Draft Metagenome Sequences of the Sphagnum (Peat Moss) Microbiome from Ambient and Warmed Environments across Europe. Microbiology Resource Announcements 11(10), e00400-22. 10.1128/mra.00400-22
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Carrell, Alyssa A. et al. (2022) Habitat‐adapted microbial communities mediate Sphagnum peatmoss resilience to warming. New Phytologist . 10.1111/nph.18072
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Catalán, Pilar et al. (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
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Chadwick, Grayson L. et al. (2022) Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea. PLoS Biology 20(1), e3001508. 10.1371/journal.pbio.3001508
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Chaput, Gina et al. (2022) Sodalis ligni Strain 159R Isolated from an Anaerobic Lignin-Degrading Consortium. Microbiology Spectrum 10(3), e02346-21. 10.1128/spectrum.02346-21
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Chen, I-Min A et al. (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
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Chen, Jin-Gui et al. (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
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Chen, Song‐Can et al. (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
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Chen, Yongxing et al. (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
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Chen, Yuxuan et al. (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
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Sun, Yi-Fei et al. (2022) Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species. Journal of Fungi 8(3), 311. 10.3390/jof8030311
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Traving, Sachia J. et al. (2022) On Single-Cell Enzyme Assays in Marine Microbial Ecology and Biogeochemistry. Frontiers in Marine Science 9. 10.3389/fmars.2022.846656
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Treen, Daniel G. C. et al. (2022) SIMILE enables alignment of tandem mass spectra with statistical significance. Nature Communications 13(1), 2510. 10.1038/s41467-022-30118-9
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Tringe, Susannah G. et al. (2022) A toolkit for microbial community editing. Nature Reviews Microbiology 20(7), 383-383. 10.1038/s41579-022-00747-4
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Van Houghton, Brett D. et al. (2022) Membrane Bioreactor Pretreatment of High-Salinity O&G Produced Water. ACS ES&T Water 2(3), 484-494. 10.1021/acsestwater.1c00436
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Ye, Naihao et al. (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
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Yi, Xiunan et al. (2022) Considering Strain Variation and Non-Type Strains for Yeast Metabolic Engineering Applications. Life 12(4), 510. 10.3390/life12040510
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Yoshikuni, Yasuo et al. (2022) Discovering untapped biochemistry in microorganisms from hidden corners. Nature Reviews Microbiology 20(11), 639-639. 10.1038/s41579-022-00795-w
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Yu, Hang et al. (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
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Zepernick, Brittany N. et al. (2022) Metatranscriptomic Sequencing of Winter and Spring Planktonic Communities from Lake Erie, a Laurentian Great Lake. Microbiology Resource Announcements 11(7), e00351-22. 10.1128/mra.00351-22
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Zhang, Ningning et al. (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
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