Metagenomic profiles revealing significant difference in the nitrification between the coastal and deep ocean sediments

Abstract

The nitrogen (N) cycle in the aquatic environment is highly influenced by anthropogenic activities. In the present study, N cycling processes in natural and modified ecosystems have been investigated by comprehensive metagenomic profiling of N cycling-related genes. Although various genes involved with different N cycling processes were found both in the coast (the Pearl River Estuary - PRE) and in the deep ocean (South China Seas - SCS) settings, significant differences between these sediments were only observed for amo, hao, and nif genes. A substantial fraction of ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) amoA genes was annotated as unculturable species. AOB amoA gene was dominant in the PRE sediments where it is closely related to the NH4 +-N concentrations from anthropogenic activities. On the other hand, the preponderance of AOA amoA gene in the SCS sediments indicated that AOA was well adapted to oligotrophic life. AOB amoA genes carried by Nitrosospira multiformis ATCC 25196 and Nitrosospira sp. Nsp 58 were prevalent in the PRE and SCS sediments, and exhibited significant relationships with the NH4 +-N level. The hao gene was well correlated with AOB amoA gene, suggesting that nitrification process requires the mutualism of AOB amoA and hao genes when the loading of NH4 +-N substrate was increased. This study reveals that anthropogenic disturbance on the NH3-N substrate can notably influence N cycling-related microbial processes in the aquatic environment in terms of the diversity and community structure of ammonium oxidation prokaryotes(AOPs), as well as its key functional genes.