Microbial communities are the forefront drivers of Greenhouse gas (GHG) emissions in aquaculture systems, presenting both challenges and opportunities for sustainable management. However, the relationship between microbial assemblages and GHG emissions in prawn farms remains largely unexplored. To demonstrate the linkage between microbial communities and GHG emissions, we measured GHG emissions (CO₂, CH₄, and N₂O) from 35 prawn farms using the floating chamber method, characterized microbial community structures through high-resolution Illumina metabarcoding, and quantified functional genes related to GHG dynamics in aerobic sediment (AeS) and anaerobic sediment (AnS), and water using real-time qPCR technique.
The highest CO₂ emissions were observed in polyculture pattern, extensive system, and low-saline farms, whereas methane emissions peaked in high-saline and semi-intensive farms. Microbial richness correlated positively with CO₂ emissions and negatively with methane emissions. Methanogenic archaea were strongly linked with methane production, but their association with CO₂ consumption was insignificant. Methanotrophic guilds were closely associated with methane breakdown; however, the minimal role of ANME lineage in CO₂ production signifies the ANME-driven methane oxidation as a promising approach to lower the carbon footprint in prawn production. The majority of bacterial and archaeal classes were associated with N₂O consumption, though the N₂O-reducing class Chloroflexi showed a positive correlation with N₂O emissions, contrary to existing literature. The abundance of mcrA and pmoA genes was influenced by the dissolved oxygen levels. While the lowest abundance of mcrA was observed in water, it showed a significant association with methane emissions and CO₂ consumption. This suggests a broader functional capacity of mcrA beyond classical limits and warrants further investigation into its aerobic physiology. Methane breakdown was strongly associated with the presence of the pmoA gene in both AeS and water. Interestingly, the amoA gene, when present in AeS and AnS, correlated more strongly with methane consumption, despite its usual association with N₂O emissions, which was observed only in water. The anaerobic nosZ gene contributed substantially to N₂O reduction in prawn farms.
This multidisciplinary study advances our understanding of microbial associations in GHG emissions, offering evidence that simpler on-farm management practices, such as oxygen supplementation, could substantially influence microbial communities and reduce emissions.