Community‐Level Metabolic Shifts Following Land Use Change in the Amazon Rainforest Identified by a Supervised Machine Leaning Approach

Khan, Md Abdul Wadud; Bohannan, Brendan J. M.; Meyer, Kyle M.; Womack, Ann M.; Nüsslein, Klaus; Grover, James P.; Mazza Rodrigues, Jorge L.

doi:10.1111/1758-2229.70088

Community‐Level Metabolic Shifts Following Land Use Change in the Amazon Rainforest Identified by a Supervised Machine Leaning Approach

Journal Article · Wed Apr 23 00:00:00 EDT 2025 · Environmental Microbiology Reports

DOI:https://doi.org/10.1111/1758-2229.70088· OSTI ID:2562708

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Department of Biology The University of Texas Arlington Texas USA
Institute of Ecology and Evolution University of Oregon Eugene Oregon USA
Department of Microbiology University of Massachusetts Amherst Massachusetts USA
Department of Land, Air and Water Resources University of California Davis California USA, Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley California USA

ABSTRACT

The Amazon rainforest has been subjected to high rates of deforestation, mostly for pasturelands, over the last few decades. This change in plant cover is known to alter the soil microbiome and the functions it mediates, but the genomic changes underlying this response are still unresolved. In this study, we used a combination of deep shotgun metagenomics complemented by a supervised machine learning approach to compare the metabolic strategies of tropical soil microbial communities in pristine forests and long‐term established pastures in the Amazon. Machine learning‐derived metagenome analysis indicated that microbial community structures (bacteria, archaea and viruses) and the composition of protein‐coding genes were distinct in each plant cover type environment. Forest and pasture soils had different genomic diversities for the above three taxonomic groups, characterised by their protein‐coding genes. These differences in metagenome profiles in soils under forests and pastures suggest that metabolic strategies related to carbohydrate and energy metabolisms were altered at community level. Changes were also consistent with known modifications to the C and N cycles caused by long‐term shifts in aboveground vegetation and were also associated with several soil physicochemical properties known to change with land use, such as the C/N ratio, soil temperature and exchangeable acidity. In addition, our analysis reveals that these alterations in land use can also result in changes to the composition and diversity of the soil DNA virome. Collectively, our study indicates that soil microbial communities shift their overall metabolic strategies, driven by genomic alterations observed in pristine forests and long‐term established pastures with implications for the C and N cycles.

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Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2562708

Alternate ID(s):: OSTI ID: 2567695
OSTI ID: 2570291

Journal Information:: Environmental Microbiology Reports, Journal Name: Environmental Microbiology Reports Journal Issue: 2 Vol. 17; ISSN 1758-2229

Publisher:: Wiley-BlackwellCopyright Statement

Country of Publication:: United States

Language:: English

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