Genetic Diversity of Active Ammonia Oxidizing Archaea and Variation during Macrobenthic Bioremediation in Mudflats of Sansha Bay, China

Archaea are abundant and wide-spread in nature environments, and occupy one third of the prokaryotes in the oceanic ecosystem. It is reported that the ammonia oxidizing archaea (AOA) are more important ammonia oxidizers than ammonia oxidizing bacteria (AOB), since the amoA gene (encoding a subunit of the key enzyme ammonia monooxy genase) copies of archaea are far more abundant than bacterial amoA genes. Here we constructed clone libraries of amoA gene and investigated the community structure of active AOA and dynamic variations during macrobenthic bioremediation (Tegillarca granosa and Perinereis sp.) in mudflats of Sansha Bay, China. Statistical analysis of the clone libraries and phylogenetic analyses of the cloned sequences showed that the distribution of active AOA showed characteristics of seawater/marine sediments. Active AOA mainly belonged to the seawater and marine sediment derived group Cluster M, while two clones (accounting for about 0.47%) belonged to Cluster S, originating from land soil or fresh water sediments. Cluster M could be subdivided into nine clusters. Clusters 1 and 2 were dominant in all samples, occupying 35.1% and 44.4% of total clones, respectively. Cluster 3 (12.8%) and Cluster 8 (4.7%) were common groups; however, were absent in some samples. Other clusters were only detected in individual samples with low abundance (< 1%). The diversity of active AOA was maximal in the winter sample, while differences among other seasons were not significant. The bioremediation of macrobenthos tended to increase the active AOA diversity, thus benefiting Clusters 1 and 3 derived from the original natural environment, while suppressing the aquaculture-derived Cluster 2.