Abstract
OBJECTIVE: This study aimed to study the spatial and temporal variation in archaeal-bacterial community and niche differentiation of nitrite/nitrate-dependent anaerobic methane oxidation (N-/Nr-DAMO) microbes in the sediment of aquaculture ponds. METHODS: Field sampling was carried out in May, July and September which represented different farming seasons in Northern China. The sediment samples were collected in the depth range of 0-15 cm at 5 cm intervals. The spatiotemporal distributions of sediment bacteria, archaea and N-/Nr-DAMO microbes, and characterized the niche differentiation of microbes were investigated in grass carp (Ctenopharyngodon idella) aquaculture ponds compared with a natural successional pond without human-induced practices. The copy numbers of total bacteria, total archaea, N-DAMO bacterial pmoA and Nr-DAMO archaeal mcrA were determined by qPCR, and the microbial community composition were determined by high-throughout sequencing analysis. RESULTS: Bacterial and archaeal abundances and diversities were significantly higher in aquaculture ponds than in natural succession ponds, with distinct vertical distribution patterns. Specifically, the bacterial abundance and diverse, as well as the archaeal abundance showed decreasing trends with increasing sediment depth, whereas diversities of archaea displayed an opposite trend that increased with sediment depth in May and July. Bacterial co-occurrence networks were less complex in aquaculture ponds. In the case of N-DAMO bacteria, the copy numbers of the functional gene pmoA, the relative abundance, and diversity were higher, while their occurrences in bacterial networks were lower. The archaeal co-occurrence networks were more complexity and stability in aquaculture pond sediment. In the case of Nr-DAMO archaea, their relative abundances decreased significantly, and fewer Nr-DAMO archaea were present in the archaeal co-occurrence networks. CONCLUSION: The vertical profiles, as well as the aquaculture practices impact the bacterial and archaeal community structure which were shaped mostly by ORP and nutrient availability. In aquaculture ponds, bacterial co-occurrence networks were less complex, and fewer N-DAMO bacteria were presented in the bacterial co-occurrence networks. The archaea (e.g. desulphurizor, denitrifiers, methanogens) showed negatively correlated with respect to the distribution of Nr-DAMO archaea which were fewer presented in the archaeal co-occurrence networks. These results appeared that the niches of N-/Nr-DAMO microbes were suppressed in aquaculture ponds.