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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 › 2019 Publications

2019 Publications

Albert, R. A. et al. (2019) Bosea psychrotolerans sp. nov., a psychrotrophic alphaproteobacterium isolated from Lake Michigan water. Int J Syst Evol Microbiol 69(5), 1376-1383. 10.1099/ijsem.0.003319
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Ali, S. et al. (2019) High-density linkage map reveals QTL underlying growth traits in AP13xVS16 biparental population of switchgrass. Global Change Biology Bioenergy 11(5), 672-690. 10.1111/gcbb.12592
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Almasi, E. et al. (2019) Comparative genomics reveals unique wood-decay strategies and fruiting body development in the Schizophyllaceae. New Phytol . 10.1111/nph.16032
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Almasi, E. et al. (2019) Comparative genomics reveals unique wood-decay strategies and fruiting body development in the Schizophyllaceae. New Phytol . 10.1111/nph.16032
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Alvarez-Escribano, I. et al. (2019) Genome sequencing of evolved aspergilli populations reveals robust genomes, transversions in A. flavus, and sexual aberrancy in non-homologous end-joining mutants. BMC Biol 17(1), 88. 10.1186/s12915-019-0702-0
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Anasontzis, G. E. et al. (2019) Broad-specificity GH131 beta-glucanases are a hallmark of Fungi and Oomycetes that colonise plants. Environ Microbiol . 10.1111/1462-2920.14596
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Armaleo, D. et al. (2019) The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata. BMC Genomics 20(1), 605. 10.1186/s12864-019-5629-x
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Armstrong, Zachary et al. (2019) Systematic Screening of Synthetic Gene-Encoded Enzymes for Synthesis of Modified Glycosides. ACS Catalysis 9(4), 3219-3227. 10.1021/acscatal.8b05179
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Avontuur, J. R. et al. (2019) Genome-informed Bradyrhizobium taxonomy: where to from here?. Syst Appl Microbiol . 10.1016/j.syapm.2019.03.006
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Badis, Yacine et al. (2019) Hidden diversity in the oomycete genus Olpidiopsis is a potential hazard to red algal cultivation and conservation worldwide. European Journal of Phycology , 1-10. 10.1080/09670262.2019.1664769
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Barbi, F. et al. (2019) Fungal ecological strategies reflected in gene transcription - a case study of two litter decomposers. Environ Microbiol . 10.1111/1462-2920.14873
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Basso, V. et al. (2019) An ectomycorrhizal fungus alters sensitivity to jasmonate, salicylate, gibberellin, and ethylene in host roots. Plant Cell Environ . 10.1111/pce.13702
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Benocci, T. et al. (2019) Deletion of either the regulatory gene ara1 or metabolic gene xki1 in Trichoderma reesei leads to increased CAZyme gene expression on crude plant biomass. Biotechnol Biofuels 12, 81. 10.1186/s13068-019-1422-y
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Benocci, T. et al. (2019) Enzymatic Adaptation of Podospora anserina to Different Plant Biomass Provides Leads to Optimized Commercial Enzyme Cocktails. Biotechnol J 14(4), e1800185. 10.1002/biot.201800185
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Benucci, G. M. N. et al. (2019) Draft Genome Sequence of the Ectomycorrhizal Ascomycete Sphaerosporella brunnea. Microbiol Resour Announc 8(50). 10.1128/MRA.00857-19
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Berben, T. et al. (2019) Diversity and Distribution of Sulfur Oxidation-Related Genes in Thioalkalivibrio, a Genus of Chemolithoautotrophic and Haloalkaliphilic Sulfur-Oxidizing Bacteria. Front Microbiol 10, 160. 10.3389/fmicb.2019.00160
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Berghuis, B. A. et al. (2019) Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens. Proc Natl Acad Sci U S A 116(11), 5037-5044. 10.1073/pnas.1815631116
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Bernhardsgrutter, I. et al. (2019) Awakening the Sleeping Carboxylase Function of Enzymes: Engineering the Natural CO2-Binding Potential of Reductases. J Am Chem Soc 141(25), 9778-9782. 10.1021/jacs.9b03431
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Bertioli, D. J. et al. (2019) The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nat Genet 51(5), 877-884. 10.1038/s41588-019-0405-z
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Bewick, A. J. et al. (2019) Diversity of cytosine methylation across the fungal tree of life. Nat Ecol Evol 3(3), 479-490. 10.1038/s41559-019-0810-9
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Borrel, G. et al. (2019) Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea. Nat Microbiol 4(4), 603-613. 10.1038/s41564-019-0363-3
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Boyd, J. A. et al. (2019) Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi. ISME J . 10.1038/s41396-018-0343-2
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Brisson, V. et al. (2019) A New Method to Correct for Habitat Filtering in Microbial Correlation Networks. Frontiers in Microbiology 10. 10.3389/fmicb.2019.00585
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Brisson, V. L. et al. (2019) Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil. Sci Rep 9(1), 15611. 10.1038/s41598-019-52148-y
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Bruckbauer, S. T. et al. (2019) Experimental evolution of extreme resistance to ionizing radiation in Escherichia coli after 50 cycles of selection. J Bacteriol . 10.1128/JB.00784-18
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Brzoska, R. M. et al. (2019) Complete Genome Sequence for Asinibacterium sp. Strain OR53 and Draft Genome Sequence for Asinibacterium sp. Strain OR43, Two Bacteria Tolerant to Uranium. Microbiol Resour Announc 8(14). 10.1128/MRA.01701-18
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Bushman, T. J. et al. (2019) Draft Genome Sequence of Mn(II)-Oxidizing Bacterium Oxalobacteraceae sp. Strain AB_14. Microbiol Resour Announc 8(43). 10.1128/MRA.01024-19
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Calhoun, S. et al. (2019) Yeasts and how they came to be. Nat Rev Microbiol . 10.1038/s41579-019-0274-6
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Camargo, A. P. et al. (2019) Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot. Sci Data 6(1), 140. 10.1038/s41597-019-0141-3
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Camiolo, S. et al. (2019) An analysis of codon bias in six red yeast species. Yeast 36(1), 53-64. 10.1002/yea.3359
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Carr, S. A. et al. (2019) Carboxydotrophy potential of uncultivated Hydrothermarchaeota from the subseafloor crustal biosphere. ISME J 13(6), 1457-1468. 10.1038/s41396-019-0352-9
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Casado Lopez, S. et al. (2019) Draft Genome Sequences of Three Monokaryotic Isolates of the White-Rot Basidiomycete Fungus Dichomitus squalens. Microbiol Resour Announc 8(18). 10.1128/MRA.00264-19
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Chaput, G. et al. (2019) Complete Genome Sequence of Serratia quinivorans Strain 124R, a Facultative Anaerobe Isolated on Organosolv Lignin as a Sole Carbon Source. Microbiol Resour Announc 8(18). 10.1128/MRA.00409-19
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Chen, F. et al. (2019) Agrobacterium-Mediated Transformation of Brachypodium distachyon. Curr Protoc Plant Biol , e20088. 10.1002/cppb.20088
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Chen, F. et al. (2019) Agrobacterium-Mediated Transformation of Brachypodium distachyon. Curr Protoc Plant Biol , e20088. 10.1002/cppb.20088
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Chen, I. A. et al. (2019) IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res 47(D1), D666-D677. 10.1093/nar/gky901
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Chevrette, M. G. et al. (2019) Taxonomic and Metabolic Incongruence in the Ancient Genus Streptomyces. Front Microbiol 10, 2170. 10.3389/fmicb.2019.02170
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Chhetri, H. B. et al. (2019) Multitrait genome-wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits. New Phytol 223(1), 293-309. 10.1111/nph.15777
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Chiniquy, D. et al. (2019) PMR5, an acetylation protein at the intersection of pectin biosynthesis and defense against fungal pathogens. Plant J . 10.1111/tpj.14497
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Chiniquy, D. et al. (2019) PMR5, an acetylation protein at the intersection of pectin biosynthesis and defense against fungal pathogens. Plant J 100(5), 1022-1035. 10.1111/tpj.14497
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Close, D. M. et al. (2019) Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis. Mol Microbiol 112(6), 1784-1797. 10.1111/mmi.14393
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Cooper, E. A. et al. (2019) A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism. BMC Genomics 20(1), 420. 10.1186/s12864-019-5734-x
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Couradeau, E. et al. (2019) Probing the active fraction of soil microbiomes using BONCAT-FACS. Nat Commun 10(1), 2770. 10.1038/s41467-019-10542-0
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Crisp, P. A. et al. (2019) Variation and inheritance of small RNAs in maize inbreds and F1 hybrids. Plant Physiol . 10.1104/pp.19.00817
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Cui, J. et al. (2019) Characterization of the Clostridium thermocellum AdhE, NfnAB, ferredoxin and Pfor proteins for their ability to support high titer ethanol production in Thermoanaerobacterium saccharolyticum. Metab Eng 51, 32-42. 10.1016/j.ymben.2018.09.006
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Dalcin Martins, P. et al. (2019) Wetland Sediments Host Diverse Microbial Taxa Capable of Cycling Alcohols. Appl Environ Microbiol 85(12). 10.1128/AEM.00189-19
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Daly, P. et al. (2019) Glucose-mediated repression of plant biomass utilization in the white-rot fungus Dichomitus squalens. Appl Environ Microbiol . 10.1128/AEM.01828-19
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Daly, P. et al. (2019) Mixtures of aromatic compounds induce ligninolytic gene expression in the wood-rotting fungus Dichomitus squalens. J Biotechnol . 10.1016/j.jbiotec.2019.11.014
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Daly, R. A. et al. (2019) Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing. Nat Microbiol 4(2), 352-361. 10.1038/s41564-018-0312-6
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Davenport, E. J. et al. (2019) Metatranscriptomic Analyses of Diel Metabolic Functions During a Microcystis Bloom in Western Lake Erie (United States). Frontiers in Microbiology 10. 10.3389/fmicb.2019.02081
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Davis, W. J. et al. (2019) Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi). Mol Phylogenet Evol 133, 152-163. 10.1016/j.ympev.2019.01.006
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de Vries, M. et al. (2019) "Interrogating the grainyhead-like 2 (Grhl2) genomic locus identifies an enhancer element that regulates palatogenesis in mouse". Dev Biol . 10.1016/j.ydbio.2019.11.015
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Diamond, S. et al. (2019) Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms. Nat Microbiol . 10.1038/s41564-019-0449-y
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Ding, Yezhang et al. (2019) Multiple genes recruited from hormone pathways partition maize diterpenoid defences. Nature Plants 5(10), 1043-1056. 10.1038/s41477-019-0509-6
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Doud, D. F. R. et al. (2019) Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere. ISME J . 10.1038/s41396-019-0557-y
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Dudley, Q. M. et al. (2019) Cell-free biosynthesis of limonene using enzyme-enriched Escherichia coli lysates. Synth Biol (Oxf) 4(1), ysz003. 10.1093/synbio/ysz003
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Duell, E. R. et al. (2019) Direct pathway cloning of the sodorifen biosynthetic gene cluster and recombinant generation of its product in E. coli. Microb Cell Fact 18(1), 32. 10.1186/s12934-019-1080-6
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Dunivin, T. K. et al. (2019) A global survey of arsenic-related genes in soil microbiomes. BMC Biol 17(1), 45. 10.1186/s12915-019-0661-5
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Eloe-Fadrosh, E. A. et al. (2019) Genome gazing in ammonia-oxidizing archaea. Nat Rev Microbiol 17(9), 531. 10.1038/s41579-019-0248-8
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Eloe-Fadrosh, E. A. et al. (2019) Towards a genome-based virus taxonomy. Nat Microbiol 4(8), 1249-1250. 10.1038/s41564-019-0511-9
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Erbilgin, O. et al. (2019) MAGI: A Method for Metabolite Annotation and Gene Integration. ACS Chem Biol 14(4), 704-714. 10.1021/acschembio.8b01107
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Felczak, M. M. et al. (2019) Expression of Phosphofructokinase Is Not Sufficient to Enable Embden-Meyerhof-Parnas Glycolysis in Zymomonas mobilis ZM4. Front Microbiol 10, 2270. 10.3389/fmicb.2019.02270
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Fernandez-Bayo, J. D. et al. (2019) The initial soil microbiota impacts the potential for lignocellulose degradation during soil solarization. J Appl Microbiol 126(6), 1729-1741. 10.1111/jam.14258
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Fernandez-Pozo, N. et al. (2019) PEATmoss (Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens. Plant J . 10.1111/tpj.14607
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Fisher, B. F. et al. (2019) Site-Selective C-H Halogenation Using Flavin-Dependent Halogenases Identified via Family-Wide Activity Profiling. ACS Cent Sci 5(11), 1844-1856. 10.1021/acscentsci.9b00835
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Fleming, S. R. et al. (2019) Flexizyme-Enabled Benchtop Biosynthesis of Thiopeptides. J Am Chem Soc 141(2), 758-762. 10.1021/jacs.8b11521
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Francis, T. B. et al. (2019) Candidatus Prosiliicoccus vernus, a spring phytoplankton bloom associated member of the Flavobacteriaceae. Syst Appl Microbiol 42(1), 41-53. 10.1016/j.syapm.2018.08.007
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Frandsen, K. E. H. et al. (2019) Insights into an unusual Auxiliary Activity 9 family member lacking the histidine brace motif of lytic polysaccharide monooxygenases. J Biol Chem . 10.1074/jbc.RA119.009223
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Frandsen, K. E. H. et al. (2019) Insights into an unusual Auxiliary Activity 9 family member lacking the histidine brace motif of lytic polysaccharide monooxygenases. J Biol Chem 294(45), 17117-17130. 10.1074/jbc.RA119.009223
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Furches, A. et al. (2019) Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence. Front Plant Sci 10, 1249. 10.3389/fpls.2019.01249
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Garcia-Lopez, M. et al. (2019) Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Front Microbiol 10, 2083. 10.3389/fmicb.2019.02083
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Garcia-Lopez, M. et al. (2019) Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Front Microbiol 10, 2083. 10.3389/fmicb.2019.02083
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Glasgow, E. M. et al. (2019) Extent and Origins of Functional Diversity in a Subfamily of Glycoside Hydrolases. J Mol Biol 431(6), 1217-1233. 10.1016/j.jmb.2019.01.024
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Gordon, S. P. et al. (2019) PolyCRACKER, a robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution. BMC Genomics 20(1), 580. 10.1186/s12864-019-5828-5
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Grady, K. L. et al. (2019) Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops. Nat Commun 10(1), 4135. 10.1038/s41467-019-11974-4
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Guarnaccia, V. et al. (2019) Phyllosticta citricarpa and sister species of global importance to Citrus. Mol Plant Pathol . 10.1111/mpp.12861
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Guarnaccia, V. et al. (2019) Phyllosticta citricarpa and sister species of global importance to Citrus. Mol Plant Pathol 20(12), 1619-1635. 10.1111/mpp.12861
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Hamm, J. N. et al. (2019) Unexpected host dependency of Antarctic Nanohaloarchaeota. Proc Natl Acad Sci U S A . 10.1073/pnas.1905179116
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Handakumbura, P. P. et al. (2019) Metabotyping as a Stopover in Genome-to-Phenome Mapping. Sci Rep 9(1), 1858. 10.1038/s41598-019-38483-0
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Hartman, K. et al. (2019) Interactions between plants and soil shaping the root microbiome under abiotic stress. Biochem J 476(19), 2705-2724. 10.1042/BCJ20180615
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Hausmann, B. et al. (2019) Long-Term Transcriptional Activity at Zero Growth of a Cosmopolitan Rare Biosphere Member. MBio 10(1). 10.1128/mBio.02189-18
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He, S. et al. (2019) Extracellular Electron Transfer May Be an Overlooked Contribution to Pelagic Respiration in Humic-Rich Freshwater Lakes. mSphere 4(1). 10.1128/mSphere.00436-18
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Hoarfrost, A. et al. (2019) Global ecotypes in the ubiquitous marine clade SAR86. ISME J . 10.1038/s41396-019-0516-7
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Hogfors-Ronnholm, E. et al. (2019) Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials. Sci Data 6(1), 207. 10.1038/s41597-019-0222-3
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Huang, J. et al. (2019) Rare earth element alcohol dehydrogenases widely occur among globally distributed, numerically abundant and environmentally important microbes. ISME J . 10.1038/s41396-019-0414-z
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Hussey, S. G. et al. (2019) A Standardized Synthetic Eucalyptus Transcription Factor and Promoter Panel for Re-engineering Secondary Cell Wall Regulation in Biomass and Bioenergy Crops. ACS Synth Biol 8(2), 463-465. 10.1021/acssynbio.8b00440
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Izrael-Zivkovic, L. et al. (2019) High-quality draft genome sequence of Pseudomonas aeruginosa san ai, an environmental isolate resistant to heavy metals. Extremophiles 23(4), 399-405. 10.1007/s00792-019-01092-w
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Jain, R. et al. (2019) Genome sequence of the model rice variety KitaakeX. BMC Genomics 20(1), 905. 10.1186/s12864-019-6262-4
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Jang, H. B. et al. (2019) Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nature Biotechnology 37(6), 632-+. 10.1038/s41587-019-0100-8
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Jiang, L. R. et al. (2019) Whole-Genome Sequencing Identifies a Rice Grain Shape Mutant, gs9-1. Rice 12. 10.1186/s12284-019-0308-8
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Jimenez, D. J. et al. (2019) Defining the eco-enzymological role of the fungal strain Coniochaeta sp. 2T2.1 in a tripartite lignocellulolytic microbial consortium. FEMS Microbiol Ecol . 10.1093/femsec/fiz186
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Kang, D. W. D. et al. (2019) MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. Peerj 7. 10.7717/peerj.7359
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Karp, P. D. et al. (2019) A Comparison of Microbial Genome Web Portals. Front Microbiol 10, 208. 10.3389/fmicb.2019.00208
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Karunanithi, P. S. et al. (2019) Terpene Synthases as Metabolic Gatekeepers in the Evolution of Plant Terpenoid Chemical Diversity. Front Plant Sci 10, 1166. 10.3389/fpls.2019.01166
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Ke, J. et al. (2019) Multi-chassis engineering for heterologous production of microbial natural products. Curr Opin Biotechnol 62, 88-97. 10.1016/j.copbio.2019.09.005
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Ke, J. et al. (2019) Pathway and Gene Discovery from Natural Hosts and Organisms. Methods Mol Biol 1927, 1-9. 10.1007/978-1-4939-9142-6_1
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Wu, Z. Y. et al. (2019) Reversal of carbapenem-resistance in Shewanella algae by CRISPR/Cas9 genome editing. J Adv Res 18, 61-69. 10.1016/j.jare.2019.01.011
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Xia, Y. et al. (2019) Improved Draft Genome Sequence of Pseudomonas poae A2-S9, a Strain with Plant Growth-Promoting Activity. Microbiol Resour Announc 8(15). 10.1128/MRA.00275-19
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Youssef, N. H. et al. (2019) Genomic Characterization of Candidate Division LCP-89 Reveals an Atypical Cell Wall Structure, Microcompartment Production, and Dual Respiratory and Fermentative Capacities. Appl Environ Microbiol 85(10). 10.1128/AEM.00110-19
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Zhang, J. et al. (2019) The transcription factor ACE3 controls cellulase activities and lactose metabolism via two additional regulators in the fungus Trichoderma reesei. J Biol Chem 294(48), 18435-18450. 10.1074/jbc.RA119.008497
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Zhang, J. et al. (2019) Overexpression of a Prefoldin beta subunit gene reduces biomass recalcitrance in the bioenergy crop Populus. Plant Biotechnol J . 10.1111/pbi.13254
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Zheng, H. et al. (2019) Division of labor in honey bee gut microbiota for plant polysaccharide digestion. Proc Natl Acad Sci U S A 116(51), 25909-25916. 10.1073/pnas.1916224116
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