Genes and genome‐resolved metagenomics reveal the microbial functional make up of Amazon peatlands under geochemical gradients

• Published in: Environmental microbiology 2023-11, Vol.25 (11), p.2388-2403
• Main Authors: Pavia, Michael J., Finn, Damien, Macedo‐Tafur, Franco, Tello‐Espinoza, Rodil, Penaccio, Christa, Bouskill, Nicholas, Cadillo‐Quiroz, Hinsby
• Format: Article
• Language: English
• Subjects: Abundance; Anaerobic microorganisms; Antibodies; Antitoxins; Biodegradation; CRISPR; Gene editing; Genes; Genomes; Geochemistry; Metagenomics; Microbial activity; Microbiomes; Microorganisms; Nitric oxide; Nitrous oxide; Organic carbon; Organic matter; Peatlands; Populations; Sulfate reduction; Sulphate reduction; Toxins; Toxins and antitoxins
• ISSN: 1462-2912; 1462-2920
• DOI: 10.1111/1462-2920.16469

The Pastaza‐Marañón Foreland Basin (PMFB) holds the most extensive tropical peatland area in South America. PMFB peatlands store ~7.07 Gt of organic carbon interacting with multiple microbial heterotrophic, methanogenic, and other aerobic/anaerobic respirations. Little is understood about the contribution of distinct microbial community members inhabiting tropical peatlands. Here, we studied the metagenomes of three geochemically distinct peatlands spanning minerotrophic, mixed, and ombrotrophic conditions. Using gene‐ and genome‐centric approaches, we evaluate the functional potential of the underlying microbial communities. Abundance analyses show significant differences in C, N, P, and S acquisition genes. Furthermore, community interactions mediated by toxin–antitoxin and CRISPR‐Cas systems were enriched in oligotrophic soils, suggesting that non‐metabolic interactions may exert additional controls in low‐nutrient environments. Additionally, we reconstructed 519 metagenome‐assembled genomes spanning 28 phyla. Our analyses detail key differences across the geochemical gradient in the predicted microbial populations involved in degradation of organic matter, and the cycling of N and S. Notably, we observed differences in the nitric oxide (NO) reduction strategies between sites with high and low N2O fluxes and found phyla putatively capable of both NO and sulfate reduction. Our findings detail how gene abundances and microbial populations are influenced by geochemical differences in tropical peatlands. This work explores how environmental conditions within tropical peatlands strongly influence the landscape of microbial processes responsible for cycling elements such as C, N, and S. In addition, we provide hundreds of new metagenome‐assembled genomes and explore their potential function in tropical peatlands. This information is vital for advancing the understanding of the processes occurring in tropical peatlands and their potential response to climate change.