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The Integrated Microbial Genomes & Microbiomes system (IMG/M: https://img.jgi.doe.gov/m/) at the Department of Energy (DOE) Joint Genome Institute (JGI) continues to provide support for users to perform comparative analysis of isolate and single cell genomes, metagenomes, and metatranscriptomes. In addition to datasets produced by the JGI, IMG v.7 also includes datasets imported from public sources such as NCBI Genbank, SRA, and the DOE National Microbiome Data Collaborative (NMDC), or submitted by external users. In the past couple years, we have continued our effort to help the user community by improving the annotation pipeline, upgrading the contents with new reference database versions, and adding new analysis functionalities such as advanced scaffold search, Average Nucleotide Identity (ANI) for high-quality metagenome bins, new cassette search, improved gene neighborhood display, and improvements to metatranscriptome data display and analysis. We also extended the collaboration and integration efforts with other DOE-funded projects such as NMDC and DOE Biology Knowledgebase (KBase).

The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context of a phylum-wide analysis of 6,700 genomes including public isolates and metagenome-assembled genomes (MAGs). We estimate that only 30%–50% of projected actinobacterial phylogenetic diversity possesses genomic representation via isolates and MAGs. A comparison of gene functions reveals novel determinants of host-microbe interaction as well as environment-specific adaptations such as potential antimicrobial peptides. We identify plasmids and prophages across isolates and uncover extensive prophage diversity structured mainly by host taxonomy. Analysis of >80,000 biosynthetic gene clusters reveals that horizontal gene transfer and gene loss shape secondary metabolite repertoire across taxa. Our observations illustrate the essential role of and need for high-quality isolate genome sequences. The work (proposal DOI[s]: https://doi.org/10.46936/10.25585/60001024; https://doi.org/10.46936/10.25585/60000886; https://doi.org/10.46936/10. 25585/60001401; https://doi.org/10.46936/10.25585/60001087; https:// doi.org/10.46936/10.25585/60001079; https://doi.org/10.46936/10.25585/ 60001044) conducted by the US Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the US Department of Energy operated under contract no. DE-AC02-05CH11231. Design and synthesis of peptide constructs were supported by the Biosystems Design program (DOE Office of Science contract DE-SC0018260) and the US Department of Energy Joint Genome Institute (DOE Office of Science contract DEAC02-05CH1123), respectively. Characterization of the peptide was supported by the Secured Biosystem Design project entitled ‘‘Rapid Design and Engineering of Smart and Secure Microbiological Systems’’ (DOE Office of Science contract DE-AC02-05CH1123). We thank the following researchers for their support of this study by providing free use of their public genome data: Kristen De-Angelis, Grace Pold, Mallory Choudoir, Camila Carlos-Shanley, Paul Carini, H. Corby C. Kistler, James Elkins, Javier A. Izquierdo, Dimitris Hatzinikolaou, Daniel Schachtman, Paul R. Jensen, Aindrila Mukhopadhyay, John Vogel, Carolin Frank, Paul M. D’Agostino, Ann M. Hirsch, Satoshi Yuzawa, Regina Lamendella, Bernhard Fuchs, Dale Pelletier, Laila P. Partida-Martinez, Cameron Currie, Seth De-Bolt, Jeff Dangl, David Mead, Susannah Tringe, David A. Baltrus, Seung Bum Kim, Linda Kinkel, Kelly Wrighton, William Mohn, Ludmila Christoserdova, Sarah Lebeis, Janet Janssen, Sandra Baena Garzon, and Nicholas Coleman. Special thanks to Marie Louise Ballon at the JGI Communications and Outreach office for all her help with the graphical abstract and many other details.

American burnweed is an increasingly common annual weed in wild blueberry fields in Atlantic Canada. Knowledge of susceptibility to several common herbicides used in wild blueberry, however, is lacking, and it is unclear how burnweed responds to clipping. Using greenhouse-grown plants, the objectives of this research were to evaluate burnweed susceptibility to various herbicides registered in wild blueberry and to determine the effect of clipping on burnweed lateral branch and flower production. Postemergence broadcast applications of mesotrione, flumioxazin, glufosinate, clopyralid, foramsulfuron, glyphosate, tribenuron methyl, nicosulfuron/rimsulfuron, terbacil, and hexazinone provided >90% control of burnweed. Postemergence spot applications of clopyralid, glyphosate, mesotrione, and nicosulfuron/rimsulfuron to 24 ± 0.3 cm tall burnweed plants caused 60%–97% injury, but

Accurate, reliable and cost effective hindcast databases have become essential tools for the design of offshore and coastal structures. Within the Gulf of Mexico (GoM), many databases exist, which cover operational wave climates, but very few of these fully resolve the complexities of Tropical Revolving Storms (TRS) in terms of both the spatial and temporal resolution. Here, we present the results of our hindcast analysis, covering all TRS affecting the GoM from 1979 to the present. This database represents all the physical and dynamic aspects of the TRS, reproducing not only the cyclonic winds, but also how the hurricane interacts with the atmospheric mean flow in the area surrounding the eyewall. The Weather Research and Forecasting model (WRF-ARW), with two nested fixed domains (18 km and 6 km), and uncoupled Hurricane WRF (HWRF) have been used to model the atmospheric conditions. Waves have been modeled using Wave Watch III (WW3), a third-generation wave model, driven by the 18 km WRF modeled winds. Boundary conditions from our inhouse global wave database have been used, forced by CFSR winds. Most of the existing databases produce a set of TRS based on the records of wind, track, pressure and radius of maximum speed, producing a uniform field of wind and pressure. We have developed a state of the art wind and wave database of TRS based on fully convective, non-hydrostatic numerical models. Model results have been validated against observational data from buoys, meteorological stations, airborne measurements, satellite data and against tracks from the International Best Track Archive for Climate Stewardship (IBTrACS) database. Results show that the modeled TRS are quite sensitive to the initial state, obtaining the best results when initializing the model with the vortex in a mature state. The hurricane intensification and wind distribution are well reproduced by the HWRF model, being in good agreement with both the track and measurements. This approach provides a realistic, cost effective and up to date hindcast of the wind and wave conditions during hurricane events throughout the GoM. Using cutting edge models, we have been able to reproduce hurricane conditions over the whole GoM, obtaining results that are physically representative.