Genome-resolved metagenomics reveals microbial potential for CO2 and CH4 emissions in prawn ponds

Abstract

Recognizing the central role of microorganisms in greenhouse gas (GHG) cycling in aquaculture systems, we provide a genome- and gene-centric perspective on the metabolic potential for CO₂ and CH₄ cycling in prawn aquaculture ponds across seasons and contrasting culture practices. Using TaxVAMB, we recovered 78 high- and medium-quality metagenome-assembled genomes (MAGs), including previously underappreciated taxa such as Bathyarchaeia and Terriglobia. Metabolic profiling revealed that CO₂ and CH₄ cycling constitute a minor fraction of the pond’s metabolic potential, dominated instead by heterotrophic processes such as fermentation, oxygen metabolism, and iron reduction. The relative metabolic weight of these carbon-cycling pathways was lower than that reported for permafrost, wetland, peatland, deep-sea, and human gut microbiomes. An integrated metabolic network suggested that genetic potential for CO₂ production is primarily driven by pyruvate and acetyl-CoA oxidation, while methanogenesis and methane oxidation genes together encode the potential for internal carbon-recycling loops via canonical archaeal and bacterial pathways. Seasonal dynamics, rather than management treatment, strongly influenced functional gene abundances, with CO₂ fixation and CH4 oxidation genes increasing toward the late season. Bathyarchaeia emerged as the most versatile taxon for CO₂ cycling and methanogenesis, with stable relative abundance across seasons and treatments. This study underscores the role of seasonally evolving microbial networks in regulating carbon turnover and the potential for CO2 and CH4 emissions in prawn aquaculture ponds.