Publications

JGI publications for calendar year 2024 appear below, listed alphabetically by author.

• Alsup, Tyler A. et al. (2024) Characterization of UbiA terpene synthases with a precursor overproduction system in Escherichia coli. . 10.1016/bs.mie.2024.02.001
• Amusat, Oluwamayowa O et al. (2024) Automated annotation of scientific texts for ML-based keyphrase extraction and validation. Database 2024, baae093. 10.1093/database/baae093
• Aplakidou, Eleni et al. (2024) Visualizing metagenomic and metatranscriptomic data: A comprehensive review. Computational and Structural Biotechnology Journal 23, 2011-2033. 10.1016/j.csbj.2024.04.060
• Arahal, David R. et al. (2024) Judicial Opinion 129.. International Journal of Systematic and Evolutionary Microbiology 74(2). 10.1099/ijsem.0.006064
• Arahal, David R. et al. (2024) Judicial Opinion 130.. International Journal of Systematic and Evolutionary Microbiology 74(6). 10.1099/ijsem.0.006414
• Arthofer, Patrick et al. (2024) A giant virus infecting the amoeboflagellate Naegleria. Nature Communications 15(1), 3307. 10.1038/s41467-024-47308-2
• Bálint, Balázs et al. (2024) ContScout: sensitive detection and removal of contamination from annotated genomes. Nature Communications 15(1), 936. 10.1038/s41467-024-45024-5
• Baltrus, David A. et al. (2024) Luteibacter mycovicinus sp. nov., a yellow-pigmented gammaproteobacterium found as an endohyphal symbiont of endophytic Ascomycota. International Journal of Systematic and Evolutionary Microbiology 74(5), 006240. 10.1099/ijsem.0.006240
• Barnes, Elle M. et al. (2024) Abiotic stress reorganizes rhizosphere and endosphere network structure of Sorghum bicolor. Phytobiomes Journal . 10.1094/pbiomes-02-24-0012-r
• Baroncelli, Riccardo et al. (2024) Genome evolution and transcriptome plasticity is associated with adaptation to monocot and dicot plants in Colletotrichum fungi. GigaScience 13, giae036. 10.1093/gigascience/giae036
• Barros, Katharina O. et al. (2024) Oxygenation influences xylose fermentation and gene expression in the yeast genera Spathaspora and Scheffersomyces. Biotechnology for Biofuels and Bioproducts 17(1), 20. 10.1186/s13068-024-02467-8
• Bayer, Barbara et al. (2024) Metabolite release by nitrifiers facilitates metabolic interactions in the ocean. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 18(1), wrae172. 10.1093/ismejo/wrae172
• Ben Ayed, Amal et al. (2024) Genome sequencing of Porostereum spadiceum to study the degradation of levofloxacin. Ecotoxicology and Environmental Safety 270, 115808. 10.1016/j.ecoenv.2023.115808
• Berner, Keely et al. (2024) Draft genome sequences of Butyrivibrio hungatei DSM 14810 (JK 615T) and Butyrivibrio fibrisolvens DSM 3071 (D1T).. Microbiology Resource Announcements , e0051724. 10.1128/mra.00517-24
• Bhat, Aditi et al. (2024) Horizontal gene transfer of the Mer operon is associated with large effects on the transcriptome and increased tolerance to mercury in nitrogen-fixing bacteria. BMC Microbiology 24(1), 247. 10.1186/s12866-024-03391-5
• Blow, Matthew J. et al. (2024) Mapping the microbiome milieu. Nature Reviews Microbiology 22(4), 190-190. 10.1038/s41579-024-01019-z
• Bowers, Robert M et al. (2024) scMicrobe PTA: near complete genomes from single bacterial cells. ISME Communications 4(1), ycae085. 10.1093/ismeco/ycae085
• Buscaglia, Marianne et al. (2024) Adaptation strategies of giant viruses to low-temperature marine ecosystems. The ISME Journal: Multidisciplinary Journal of Microbial Ecology , wrae162. 10.1093/ismejo/wrae162
• Bustos-Diaz, Edder D. et al. (2024) Phylometagenomics of cycad coralloid roots reveals shared symbiotic signals. Microbial Genomics 10(3), 001207. 10.1099/mgen.0.001207
• Camargo, Antonio Pedro et al. (2024) Unveiling plasmid diversity in nature. Nature Reviews Microbiology 22(10), 597-597. 10.1038/s41579-024-01093-3
• Campos, Miguel et al. (2024) Repeated migration, interbreeding and bottlenecking shaped the phylogeography of the selfing grass Brachypodium stacei. Molecular Ecology 33(19), e17513. 10.1111/mec.17513
• Carhuaricra-Huaman, Dennis et al. (2024) Analysis of twelve genomes of the bacterium Kerstersia gyiorum from brown-throated sloths (Bradypus variegatus), the first from a non-human host. PeerJ 12, e17206. 10.7717/peerj.17206
• Champagne, Sarah E. et al. (2024) Biocatalytic Stereoselective Oxidation of 2‑Arylindoles. Journal of the American Chemical Society 146(4), 2728-2735. 10.1021/jacs.3c12393
• Charon, Justine et al. (2024) Consensus statement from the first RdRp Summit: advancing RNA virus discovery at scale across communities. Frontiers in Virology 4, 1371958. 10.3389/fviro.2024.1371958
• Chiarelli, Daniela Prates et al. (2024) Expression and characterization of monofunctional alcohol dehydrogenase enzymes in Clostridium thermocellum. Metabolic Engineering Communications 19, e00243. 10.1016/j.mec.2024.e00243
• Chodkowski, John L. et al. (2024) Bioactive exometabolites drive maintenance competition in simple bacterial communities. mSystems 9(4), e00064-24. 10.1128/msystems.00064-24
• Chuckran, Peter F. et al. (2024) Metatranscriptomes of California grassland soil microbial communities in response to rewetting. Microbiology Resource Announcements 13(6), e00322-24. 10.1128/mra.00322-24
• Coclet, Clément et al. (2024) MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes.. mSystems . 10.1128/msystems.00888-24
• Coleine, Claudia et al. (2024) Metagenomics untangles potential adaptations of Antarctic endolithic bacteria at the fringe of habitability. The Science of The Total Environment 917, 170290. 10.1016/j.scitotenv.2024.170290
• Colman, Daniel R. et al. (2024) Covariation of hot spring geochemistry with microbial genomic diversity, function, and evolution. Nature Communications 15(1), 7506. 10.1038/s41467-024-51841-5
• Conway, Jonathan M. et al. (2024) Arabidopsis Root Microbiome Microfluidic (ARMM) Device for Imaging Bacterial Colonization and Morphogenesis of Arabidopsis Roots. Methods in Molecular Biology 2805, 213-228. 10.1007/978-1-0716-3854-5_15
• Cook, Ryan et al. (2024) Driving through stop signs: predicting stop codon reassignment improves functional annotation of bacteriophages. ISME Communications 4(1), ycae079. 10.1093/ismeco/ycae079
• Coomey, Joshua H. et al. (2024) Mechanically induced localisation of SECONDARY WALL INTERACTING bZIP is associated with thigmomorphogenic and secondary cell wall gene expression. Quantitative Plant Biology 5, e5. 10.1017/qpb.2024.5
• Covington, Jonathan K. et al. (2024) Biochemical characterization of Fsa16295Glu from “Fervidibacter sacchari,” the first hyperthermophilic GH50 with β-1,3-endoglucanase activity and founding member of the subfamily GH50_3. Frontiers in Microbiology 15, 1355444. 10.3389/fmicb.2024.1355444
• Curry, Kristen D et al. (2024) Reference-free structural variant detection in microbiomes via long-read co-assembly graphs. Bioinformatics 40(Supplement_1), i58-i67. 10.1093/bioinformatics/btae224
• Czajka, Jeffrey J. et al. (2024) Genome-scale model development and genomic sequencing of the oleaginous clade Lipomyces. Frontiers in Bioengineering and Biotechnology 12, 1356551. 10.3389/fbioe.2024.1356551
• de Mesquita, Clifton P Bueno et al. (2024) Disentangling the effects of sulfate and other seawater ions on microbial communities and greenhouse gas emissions in a coastal forested wetland. ISME Communications 4(1), ycae040. 10.1093/ismeco/ycae040
• de Mesquita, Clifton P. Bueno et al. (2024) Fungal diversity and function in metagenomes sequenced from extreme environments. Fungal Ecology 72, 101383. 10.1016/j.funeco.2024.101383
• de Mesquita, Clifton P. Bueno et al. (2024) Microbial Ecology and Site Characteristics Underlie Differences in Salinity‐Methane Relationships in Coastal Wetlands. Journal of Geophysical Research Biogeosciences 129(6). 10.1029/2024jg008133
• DeChellis, Antonio et al. (2024) Supercharging Carbohydrate Binding Module Alone Enhances Endocellulase Thermostability, Binding, and Activity on Cellulosic Biomass. ACS Sustainable Chemistry & Engineering 12(9), 3500-3516. 10.1021/acssuschemeng.3c06266
• Denison, Elizabeth R. et al. (2024) Metatranscriptomic analysis reveals dissimilarity in viral community activity between an ice-free and ice-covered winter in Lake Erie. mSystems 9(7), e00753-24. 10.1128/msystems.00753-24
• Dieser, Markus et al. (2024) Seven genome sequences of airborne, bacterial isolates from Antarctica. Microbiology Resource Announcements 13(6), e01129-23. 10.1128/mra.01129-23
• Doré, Hugo et al. (2024) Targeted hypermutation of putative antigen sensors in multicellular bacteria. Proceedings of the National Academy of Sciences of the United States of America 121(9), e2316469121. 10.1073/pnas.2316469121
• Dziuba, Marcin K. et al. (2024) Phylogeny, morphology, virulence, ecology, and host range of Ordospora pajunii (Ordosporidae), a microsporidian symbiont of Daphnia spp.. mBio 15(6), e00582-24. 10.1128/mbio.00582-24
• Eichfeld, Ruben et al. (2024) Transcriptomics reveal a mechanism of niche defense: two beneficial root endophytes deploy an antimicrobial GH18‐CBM5 chitinase to protect their hosts. New Phytologist . 10.1111/nph.20080
• Eloe-Fadrosh, Emiley A. et al. (2024) A Practical Approach to Using the Genomic Standards Consortium MIxS Reporting Standard for Comparative Genomics and Metagenomics. Methods in Molecular Biology 2802, 587-609. 10.1007/978-1-0716-3838-5_20
• Espina, Mary Jane C. et al. (2024) Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean. The Plant Journal . 10.1111/tpj.17026
• Fadum, J. M. et al. (2024) Dominant nitrogen metabolisms of a warm, seasonally anoxic freshwater ecosystem revealed using genome resolved metatranscriptomics. mSystems 9(2), e01059-23. 10.1128/msystems.01059-23
• Feitosa-Junior, Oseias R. et al. (2024) The Exometabolome of Xylella fastidiosa in Contact with Paraburkholderia phytofirmans Supernatant Reveals Changes in Nicotinamide, Amino Acids, Biotin, and Plant Hormones. Metabolites 14(2), 82. 10.3390/metabo14020082
• Felipe Benites, L. et al. (2024) Hot springs viruses at Yellowstone National Park have ancient origins and are adapted to thermophilic hosts. Communications Biology 7(1), 312. 10.1038/s42003-024-05931-1
• Feng, Xuehuan et al. (2024) Genomes of multicellular algal sisters to land plants illuminate signaling network evolution. Nature Genetics 56(5), 1018-1031. 10.1038/s41588-024-01737-3
• Ferrinho, Scarlet et al. (2024) Compendium of Metabolomic and Genomic Datasets for Cyanobacteria: Mined the Gap. Water Research 256, 121492. 10.1016/j.watres.2024.121492
• Fong, Allison A. et al. (2024) Overview of the MOSAiC expedition: Ecosystem. Elementa: Science of the Anthropocene 12(1). 10.1525/elementa.2023.00135
• Freyria, Nastasia J. et al. (2024) Stress responses in an Arctic microalga (Pelagophyceae) following sudden salinity change revealed by gene expression analysis. Communications Biology 7(1), 1084. 10.1038/s42003-024-06765-7
• Gomez-Gutierrrez, Sandra V. et al. (2024) Comparative genomics of the extremophile Cryomyces antarcticus and other psychrophilic Dothideomycetes. Frontiers in Fungal Biology 5, 1418145. 10.3389/ffunb.2024.1418145
• Graham, Emily B. et al. (2024) A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts. Nature Microbiology 9(7), 1873-1883. 10.1038/s41564-024-01686-x
• Greenblum, Sharon et al. (2024) Microbial adaptability in changing environments. Nature Reviews Microbiology 22(6), 327-327. 10.1038/s41579-024-01046-w
• Grones, Carolin et al. (2024) Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics. The Plant Cell 36(4), 812-828. 10.1093/plcell/koae003
• Grosjean, Nicolas et al. (2024) A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria. Nature Communications 15(1), 3167. 10.1038/s41467-024-47486-z
• Haddad Momeni, Majid et al. (2024) Insights into the action of phylogenetically diverse microbial expansins on the structure of cellulose microfibrils. Biotechnology for Biofuels and Bioproducts 17(1), 56. 10.1186/s13068-024-02500-w
• Haghani, Nadia B. et al. (2024) Identification and characterization of a skin microbiome on Caenorhabditis elegans suggests environmental microbes confer cuticle protection. Microbiology Spectrum 12(8), e00169-24. 10.1128/spectrum.00169-24
• Harder, Christoffer Bugge et al. (2024) Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations. Cell Genomics 4(7), 100586. 10.1016/j.xgen.2024.100586
• Hartman, Wyatt H. et al. (2024) Multiple microbial guilds mediate soil methane cycling along a wetland salinity gradient. mSystems 9(1), e00936-23. 10.1128/msystems.00936-23
• Healey, A. L. et al. (2024) The complex polyploid genome architecture of sugarcane. Nature , 1-7. 10.1038/s41586-024-07231-4
• Hiraoka, Yoko et al. (2024) Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives. Plants 13(5), 691. 10.3390/plants13050691
• Hofmeyr, Steven et al. (2024) Exabiome: Advancing Microbial Science through Exascale Computing. Computing in Science & Engineering PP(99), 1-8. 10.1109/mcse.2024.3402546
• Howard-Varona, Cristina et al. (2024) Environment-specific virocell metabolic reprogramming. The ISME Journal: Multidisciplinary Journal of Microbial Ecology , wrae055. 10.1093/ismejo/wrae055
• Hu, Zhijuan et al. (2024) Engineered Biosynthesis and Anticancer Studies of Ring-Expanded Antimycin-Type Depsipeptides. ACS Synthetic Biology 13(5), 1562-1571. 10.1021/acssynbio.4c00193
• Jensen, Rasmus O. et al. (2024) Phylogenomics and genetic analysis of solvent-producing Clostridium species. Scientific Data 11(1), 432. 10.1038/s41597-024-03210-6
• Jiao, Jian-Yu et al. (2024) Cultivation of novel Atribacterota from oil well provides new insight into their diversity, ecology, and evolution in anoxic, carbon-rich environments. Microbiome 12(1), 123. 10.1186/s40168-024-01836-7
• Jiménez, Idoia et al. (2024) In silico analysis of the expression profile of AA9 Lytic Polysaccharide Monooxygenases (LPMOs) and the CDH Cellobiose Dehydrogenase enzyme in wood-degrader Agaricomycetes. The Pleurotus ostreatus case. Current Research in Biotechnology 8, 100244. 10.1016/j.crbiot.2024.100244
• Jo, Seohyun et al. (2024) Unlocking saponin biosynthesis in soapwort. Nature Chemical Biology , 1-12. 10.1038/s41589-024-01681-7
• Kangi, Emel et al. (2024) A multi-omic survey of black cottonwood tissues highlights coordinated transcriptomic and metabolomic mechanisms for plant adaptation to phosphorus deficiency. Frontiers in Plant Science 15, 1324608. 10.3389/fpls.2024.1324608
• Kim, Youngchang et al. (2024) Revealing reaction intermediates in one-carbon elongation by thiamine diphosphate/CoA-dependent enzyme family. Communications Chemistry 7(1), 160. 10.1038/s42004-024-01242-y
• Kohtz, Anthony J. et al. (2024) Cultivation and visualization of a methanogen of the phylum Thermoproteota. Nature 632(8027), 1118-1123. 10.1038/s41586-024-07631-6
• Koper, Kaan et al. (2024) Multisubstrate specificity shaped the complex evolution of the aminotransferase family across the tree of life. Proceedings of the National Academy of Sciences of the United States of America 121(26), e2405524121. 10.1073/pnas.2405524121
• Kraisitudomsook, Nattapol et al. (2024) On the origin of bird’s nest fungi: Phylogenomic analyses of fungi in the Nidulariaceae (Agaricales, Basidiomycota). Molecular Phylogenetics and Evolution 193, 108010. 10.1016/j.ympev.2024.108010
• Kridler, Melanie R. et al. (2024) Draft genome sequences of Arthrobacter sp. AZCC_0090 and Mycobacterium sp. AZCC_0083 isolated from oligotrophic subsurface forest soil in the Santa Catalina mountains of Southern Arizona. Microbiology Resource Announcements 13(3), e01089-23. 10.1128/mra.01089-23
• Krinos, Arianna I. et al. (2024) Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake. Microbiome 12(1), 133. 10.1186/s40168-024-01831-y
• Krukenberg, Viola et al. (2024) Methyl-reducing methanogenesis by a thermophilic culture of Korarchaeia. Nature 632(8027), 1131-1136. 10.1038/s41586-024-07829-8
• Lax, Carlos et al. (2024) Symmetric and asymmetric DNA N6-adenine methylation regulates different biological responses in Mucorales. Nature Communications 15(1), 6066. 10.1038/s41467-024-50365-2
• Lee, Ye-Gi et al. (2024) Self-Buffering system for Cost-Effective production of lactic acid from glucose and xylose using Acid-Tolerant Issatchenkia orientalis. Bioresource Technology 399, 130641. 10.1016/j.biortech.2024.130641
• Li, Cheng et al. (2024) Extraordinary preservation of gene collinearity over three hundred million years revealed in homosporous lycophytes. Proceedings of the National Academy of Sciences of the United States of America 121(4), e2312607121. 10.1073/pnas.2312607121
• Li, Li et al. (2024) Biosynthesis of Cytosporones in Leotiomycetous Filamentous Fungi. Journal of the American Chemical Society 146(9), 6189-6198. 10.1021/jacs.3c14066
• Li, Songjun et al. (2024) Baltic Sea coastal sediment-bound eukaryotes have increased year-round activities under predicted climate change related warming. Frontiers in Microbiology 15, 1369102. 10.3389/fmicb.2024.1369102
• Li, Yaoming et al. (2024) Genomic insights into redox-driven microbial processes for carbon decomposition in thawing Arctic soils and permafrost.. mSphere , e0025924. 10.1128/msphere.00259-24
• Liu, Dujuan et al. (2024) AraR plays a more dominant role than XlnR in plant biomass conversion in Penicillium subrubescens. Current Research in Biotechnology 8, 100243. 10.1016/j.crbiot.2024.100243
• Liu, Hualan et al. (2024) Bacterial barcoding facilitates plant microbiome studies. Nature Reviews Microbiology 22(8), 459-459. 10.1038/s41579-024-01069-3
• Liu, Xiao Jun A et al. (2024) Microbial responses to long-term warming differ across soil microenvironments. ISME Communications 4(1), ycae051. 10.1093/ismeco/ycae051
• Lofgren, Lotus et al. (2024) Suillus: an emerging model for the study of ectomycorrhizal ecology and evolution. New Phytologist 242(4), 1448-1475. 10.1111/nph.19700
• Lopez, Bryn N K et al. (2024) CO2 response screen in grass Brachypodium reveals the key role of a MAP kinase in CO2-triggered stomatal closure. Plant Physiology , kiae262. 10.1093/plphys/kiae262
• Louie, Tiffany S et al. (2024) Mo than meets the eye: genomic insights into molybdoenzyme diversity of Seleniivibrio woodruffii strain S4T. Letters in Applied Microbiology 77(4), ovae038. 10.1093/lambio/ovae038
• Lui, Lauren M. et al. (2024) Decomposing a San Francisco estuary microbiome using long-read metagenomics reveals species- and strain-level dominance from picoeukaryotes to viruses. mSystems 9(9), e00242-24. 10.1128/msystems.00242-24
• Lumian, Jessica et al. (2024) Genomic profiles of four novel cyanobacteria MAGs from Lake Vanda, Antarctica: insights into photosynthesis, cold tolerance, and the circadian clock. Frontiers in Microbiology 14, 1330602. 10.3389/fmicb.2023.1330602
• Ma, Xiao et al. (2024) Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment. Nature Plants 10(2), 240-255. 10.1038/s41477-023-01608-5
• Machado, Rodrigo et al. (2024) BdRCN4, a Brachypodium distachyon TFL1 homologue, is involved in regulation of apical meristem fate. Plant Molecular Biology 114(4), 81. 10.1007/s11103-024-01467-4
• Maini Rekdal, Vayu et al. (2024) Neurospora intermedia from a traditional fermented food enables waste-to-food conversion. Nature Microbiology , 1-18. 10.1038/s41564-024-01799-3
• Mantel, Samuel J. et al. (2024) Postzygotic barriers persist despite ongoing introgression in hybridizing Mimulus species. Molecular Ecology 33(4), e17261. 10.1111/mec.17261
• Marian, Ioana M et al. (2024) High phenotypic and genotypic plasticity among strains of the mushroom-forming fungus Schizophyllum commune. Fungal Genetics and Biology 173, 103913. 10.1016/j.fgb.2024.103913
• Marinos, Georgios et al. (2024) Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics.. Microbiology Spectrum 12(2), e0114423. 10.1128/spectrum.01144-23
• Markel, Kasey et al. (2024) Cynipid wasps systematically reprogram host metabolism and restructure cell walls in developing galls. Plant Physiology , kiae001. 10.1093/plphys/kiae001
• Markel, Kasey et al. (2024) Expression of a mammalian RNA demethylase increases flower number and floral stem branching in Arabidopsis thaliana. Plant Direct 8(8). 10.1002/pld3.70000
• Marqués‐Gálvez, José Eduardo et al. (2024) Populus MYC2 orchestrates root transcriptional reprogramming of defence pathway to impair Laccaria bicolor ectomycorrhizal development. New Phytologist 242(2), 658-674. 10.1111/nph.19609
• Martin, Francis M. et al. (2024) The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application. New Phytologist 242(4), 1486-1506. 10.1111/nph.19541
• Mathieu, Davis et al. (2024) Multilevel analysis between Physcomitrium patens and Mortierellaceae endophytes explores potential long‐standing interaction among land plants and fungi. The Plant Journal 118(2), 304-323. 10.1111/tpj.16605
• McGivern, Bridget B. et al. (2024) Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle. Nature Microbiology 9(6), 1454-1466. 10.1038/s41564-024-01691-0
• Messyasz, Adriana et al. (2024) Genome analysis and description of Tunturibacter gen. nov. expands the diversity of Terriglobia in tundra soils. Environmental Microbiology 26(5), e16640. 10.1111/1462-2920.16640
• Miliotis, Georgios et al. (2024) Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. nov.. mBio 15(4), e00181-24. 10.1128/mbio.00181-24
• Mills, Daniel B. et al. (2024) Constraining the oxygen requirements for modern microbial eukaryote diversity. Proceedings of the National Academy of Sciences of the United States of America 121(2), e2303754120. 10.1073/pnas.2303754120
• Miyada, Matthew G. et al. (2024) Fluorometric Analysis of Carrier-Protein-Dependent Biosynthesis through a Conformationally Sensitive Solvatochromic Pantetheinamide Probe. ACS Chemical Biology 19(7), 1416-1425. 10.1021/acschembio.4c00169
• Murali, Ranjani et al. (2024) Diversity and evolution of nitric oxide reduction in bacteria and archaea. Proceedings of the National Academy of Sciences of the United States of America 121(26), e2316422121. 10.1073/pnas.2316422121
• Navarro, David et al. (2024) Draft genome sequencing and assembly of Favolaschia claudopus CIRM-BRFM 2984 isolated from oak limbs. Journal of Genomics 12, 44-46. 10.7150/jgen.92255
• Nelson, Amelia R et al. (2024) Soil microbiome feedbacks during disturbance-driven forest ecosystem conversion. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 18(1), wrae047. 10.1093/ismejo/wrae047
• Nguyen, Thuy M. et al. (2024) Whole community shotgun metagenomes of two biological soil crust types from the Mojave Desert. Microbiology Resource Announcements 13(3), e00980-23. 10.1128/mra.00980-23
• Oliver, Tiffany et al. (2024) Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota. Scientific Data 11(1), 966. 10.1038/s41597-024-03826-8
• Pakkir Shah, Abzer K. et al. (2024) Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data. Nature Protocols , 1-71. 10.1038/s41596-024-01046-3
• Panich, Justin et al. (2024) Functional plasticity of HCO3 – uptake and CO2 fixation in Cupriavidus necator H16. Bioresource Technology 410, 131214. 10.1016/j.biortech.2024.131214
• Paterson, Andrew H et al. (2024) Genome organization and botanical diversity. The Plant Cell 36(5), 1186-1204. 10.1093/plcell/koae045
• Pellitier, Peter T et al. (2024) Potential for functional divergence in ectomycorrhizal fungal communities across a precipitation gradient. ISME Communications 4(1), ycae031. 10.1093/ismeco/ycae031
• Pena, Michelle M et al. (2024) Genetic and Functional Diversity Help Explain Pathogenic, Weakly Pathogenic, and Commensal Lifestyles in the Genus Xanthomonas. Genome Biology and Evolution 16(4), evae074. 10.1093/gbe/evae074
• Pitot, Thomas M et al. (2024) Distinct and rich assemblages of giant viruses in Arctic and Antarctic lakes. ISME Communications 4(1), ycae048. 10.1093/ismeco/ycae048
• Powell, Tyler et al. (2024) Metagenome-assembled bacterial genomes from benthic microbial mats in ice-covered Lake Vanda, Antarctica. Microbiology Resource Announcements 13(5), e01250-23. 10.1128/mra.01250-23
• Ramos, Victor M. Gonzalez et al. (2024) Transcriptional response of the white-rot fungus Dichomitus squalens to polysaccharides reveals a co-expression network of plant biomass conversion related genes. Current Research in Biotechnology 7, 100198. 10.1016/j.crbiot.2024.100198
• Rasmussen, Anna N et al. (2024) Dynamics and activity of an ammonia-oxidizing archaea bloom in South San Francisco Bay. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 18(1), wrae148. 10.1093/ismejo/wrae148
• Rasmussen, Anna N. et al. (2024) Diverse and unconventional methanogens, methanotrophs, and methylotrophs in metagenome-assembled genomes from subsurface sediments of the Slate River floodplain, Crested Butte, CO, USA. mSystems 9(7), e00314-24. 10.1128/msystems.00314-24
• Robinson, David et al. (2024) Antarctic lake viromes reveal potential virus associated influences on nutrient cycling in ice-covered lakes. Frontiers in Microbiology 15, 1422941. 10.3389/fmicb.2024.1422941
• Rodríguez-Ramos, Josué et al. (2024) Untargeted, tandem mass spectrometry metaproteome of Columbia River sediments. Microbiology Resource Announcements 13(6), e00033-24. 10.1128/mra.00033-24
• Roman, Victor A et al. (2024) Identification and recombinant expression of a cutinase from Papiliotrema laurentii that hydrolyzes natural and synthetic polyesters.. Applied and Environmental Microbiology 90(5), e0169423. 10.1128/aem.01694-23
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