A genomic catalog of Earth’s microbiomes

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes

Microbial response to copper oxide nanoparticles in soils is controlled by land use rather than copper fate

Copper (Cu) products, including copper oxide nanoparticles (nCuO), are critically important agricultural fungicides and algaecides. Foliar application onto crops and subsequent aerosol drift of these Cu products, especially nCuO, on to soil may alter nutrient cycling and microbial communities in both managed and unmanaged environments. We measured the influence of land use on soil microbial biomass and respiration in response to the addition of nCuO to an alluvial soil. Different land uses included grassland, forest and both organic and conventional managed row crops. Soil samples were amended with 1000 mg Cu per kg soil as CuCl2, 16 nm CuO (16nCuO), 42 nm CuO (42nCuO), and larger than nanoparticle sized bulk CuO (bCuO). Copper availability immediately increased in all soils following Cu addition in the order of CuCl2 > 16nCuO > 42nCuO > bCuO. After 70 days Cu availability was diminished across land uses and lowest in soils treated with bCuO. Using X-ray absorption near edge structure (XANES) spectroscopy, we determined that the relatively high availability of Cu after treatment with nanoparticle sized CuO was due to the dissolution of CuO particles and subsequent adsorption by soil materials. Respiration, an indicator of microbial activity, was suppressed by Cu additions, especially CuCl2. Copper effects on soil microbial biomass were sensitive to land use. In agricultural soils, microbial biomass was unaltered by Cu form, regardless of concentration, whereas in unmanaged soils, it decreased following exposure to CuCl2 and 42nCuO. Our results suggest that land use history has little impact on Cu chemical fate in soils, but strongly modulates microbial response to Cu exposure. These results are especially important for organic agricultural systems where copper fungicides are widely used but may suppress microbial mineralization of nutrients from soil organic matter

Author Correction: A genomic catalog of Earth’s microbiomes (Nature Biotechnology, (2021), 39, 4, (499-509), 10.1038/s41587-020-0718-6)

In the version of this article initially published, four people were missing from the alphabetical list of IMG/M Data Consortium members: Lauren V. Alteio of the Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria; Jeffrey L. Blanchard of the Biology Department, University of Massachusetts Amherst, Amherst, MA, USA; Kristen M. DeAngelis of the Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA; and William Rodriguez-Reillo of the Research Computing Division, Harvard Medical School, Boston, MA, USA. The error has been corrected in the PDF and HTML versions of the article