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However, attempts to understand these impacts have focused on broader community alterations or the response of specific microbial groups. Here, we recovered and characterized 69 soil bacterial and archaeal metagenome-assembled genomes (MAGs) from three forests and three pastures of the Eastern Brazilian Amazon and evaluated the impacts of land conversion on their genomic features. Pasture MAGs had significantly higher GC content (64.9% vs 60.2%), genome size (4.0 vs 3.1 Mbp), and number of coding sequences (4,058 vs 3,306) compared to forest genomes. Taxonomically, MAGs belonged to eight phyla; however, most (90%) had low similarity to previously known species, indicating potentially novel taxa at multiple levels. We also observed that the functional profiles associated with biogeochemical cycling and carbohydrate-active enzyme genes were impacted by forest conversion, with pasture MAGs exhibiting a notably higher number of both gene groups. Together, these data constitute the largest single-sourced genomic data set from upland soils of the Brazilian Amazon to date and increase the known MAG richness in these soils by 78%. Our data, therefore, not only add to a neglected yet emerging field but, importantly, highlight that land-use change has drastic impacts on the genomic characteristics and functional traits of dominant soil microbes.<\/jats:p>\n            <jats:sec>\n              <jats:title>IMPORTANCE<\/jats:title>\n              <jats:p>The Brazilian Amazon is facing unprecedented threats, including increasing deforestation and degradation, which together impact half of the original forest area. Soil microorganisms are sensitive indicators of land-use change, linked to a rise in microbial methane emissions and antibiotic-resistance genes in the Amazon. However, most Amazonian soil microbes remain unknown, and little attention has been given to their genomes. Using sequencing and bioinformatics, we recovered and characterized 69 soil bacterial and archaeal genomes (metagenome-assembled genomes). These abundant members of the microbial communities diverged across forests and pastures in terms of taxonomic and functional traits. Forest conversion favors organisms with specific genomic features \u2014 increased GC content, genome size, and gene number \u2014 selecting for microorganisms that can thrive under altered conditions. Our paper helps us understand the intricate relationships between microbes and the environment, which are crucial pieces of information for comprehensive soil health assessments and future policy formulation.<\/jats:p>\n            <\/jats:sec>\n          <\/jats:sec>","DOI":"10.1128\/spectrum.01561-24","type":"journal-article","created":{"date-parts":[[2025,3,5]],"date-time":"2025-03-05T14:05:07Z","timestamp":1741183507000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":6,"title":["Linking soil microbial genomic features to forest-to-pasture conversion in the Amazon"],"prefix":"10.1128","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5901-1658","authenticated-orcid":true,"given":"Andressa M.","family":"Venturini","sequence":"first","affiliation":[{"name":"Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of S\u00e3o Paulo","place":["Piracicaba, Brazil"]},{"name":"Department of Biology, Stanford University","place":["Stanford, USA"]},{"name":"Department of Environmental Science, American University","place":["Washington, DC, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1942-7242","authenticated-orcid":false,"given":"J\u00falia B.","family":"Gontijo","sequence":"additional","affiliation":[{"name":"Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of S\u00e3o Paulo","place":["Piracicaba, Brazil"]},{"name":"Department of Land, Air, and Water Resources, University of California-Davis","place":["Davis, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3888-9928","authenticated-orcid":true,"given":"Louis","family":"Berrios","sequence":"additional","affiliation":[{"name":"Department of Biology, Stanford University","place":["Stanford, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6446-6462","authenticated-orcid":false,"given":"Jorge L. Mazza","family":"Rodrigues","sequence":"additional","affiliation":[{"name":"Department of Land, Air, and Water Resources, University of California-Davis","place":["Davis, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7998-7412","authenticated-orcid":true,"given":"Kabir G.","family":"Peay","sequence":"additional","affiliation":[{"name":"Department of Biology, Stanford University","place":["Stanford, USA"]},{"name":"Department of Earth System Science, Stanford University","place":["Stanford, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3733-6312","authenticated-orcid":true,"given":"Siu M.","family":"Tsai","sequence":"additional","affiliation":[{"name":"Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of S\u00e3o Paulo","place":["Piracicaba, Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2304663120"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-020-0718-6"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1128\/mra.00804-22"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.01635"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1111\/1758-2229.12880"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000853"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1007\/s11056-020-09777-3"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.abp8622"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tree.2023.04.014"},{"key":"e_1_3_4_11_2","first-page":"179","volume-title":"Advances in agronomy","author":"Danielson RE","year":"2022","unstructured":"Danielson RE, Rodrigues JLM. 2022. Impacts of land-use change on soil microbial communities and their function in the Amazon Rainforest, p 179\u2013258. In Sparks DL (ed), Advances in agronomy. Vol. 175. Academic Press."},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1093\/femsmc\/xtab020"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3893"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1038\/sj.embor.7400538"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-022-01203-y"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41545-020-0057-7"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.761869"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-017-3888-y"},{"key":"e_1_3_4_19_2","doi-asserted-by":"publisher","DOI":"10.1038\/s43705-022-00209-1"},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41396-021-00944-8"},{"key":"e_1_3_4_21_2","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms11102612"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz848"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-43297-w"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.3389\/fbinf.2022.918853"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky418"},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.1111\/mec.12786"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.scitotenv.2020.139710"}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.01561-24","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.01561-24","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,4,1]],"date-time":"2025-04-01T13:09:33Z","timestamp":1743512973000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.01561-24"}},"subtitle":[],"editor":[{"given":"Noha H.","family":"Youssef","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,4]]},"references-count":26,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2025,4]]}},"alternative-id":["10.1128\/spectrum.01561-24"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.01561-24","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,4]]},"assertion":[{"value":"2024-06-28","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-01-31","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-03-05","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e01561-24"}}