Spatial Distribution Of Ammonia-oxidizing Archaea And Ammonia-oxidizing Bacteria AmoA Gene In Mud Deposits Of The Yellow Sea And East China Sea

As the rate-limiting step in nitrification and central part of nitrogen biogeochemical cycling, ammonia oxidation is carried out by chemolithoautotrophic ammonia-oxidizing archaea (AOA) and bacteria (AOB). AOA and AOB are widespread in the environment, and they are different in the phylogeny and physiological ecology. The relative importance of AOA and AOB in nitrogen cycling is still under debate since significant variations in the relative abundance, community structure and activity between them under different environmental conditions were observed. Ammonia monooxygenase (AMO) is a key enzyme in ammonia oxidation which exists in both AOA and AOB. The amoA gene which encodes the a subunit of AMO has been commonly used as a phylogenetic marker to study the communities of AOA and AOB. In addition, high abundance of archaeal and bacterial amoA and potential rate of nitrification was found in the oxygen minimum zone of the ocean, the composition of AOA and AOB communities in this kind of environment may be different from that in oxic environment.In the Western Pacific region, the Yellow Sea and the East China Sea between the contiguous landmass of Korea and China with several mud areas were influenced by land and sea. Since the geographic location, sedimentary sources, sedimentation rate and influence of ocean currents of the mud areas varied, different microbial community may exist in these mud areas. Thus far, the community structures and abundance of ammonia-oxidizing prokaryotes in different mud deposits of the Yellow Sea and the East China Sea are still unknown. In addition, the vertical distribution of AOA and AOB in sediment and differences between their distribution pattern are unclear. The vertical distribution of AOA and AOB community and abundance in the mud deposits of the Yellow Sea and the East China Sea and their correlation with environmental factors were studied in this research, and AOA and AOB distribution pattern and the community of ammonia-oxidizing prokaryotes in different mud deposits were compared. It will fill the research void of horizontal and vertical distribution of ammonia-oxidizing bacteria and archaea in mud deposits of Chinese marginal seas and provide theoretical basis for the comprehensive understanding of the marine nitrogen biogeochemical cycling and the influence of environmental factors in it. In addition, this study will improve our understanding of the survival mechanism in deep hypoxic sediments.Sampling was conducted onboard the R/V Dongfanghong 2 in July,2013. Sediment cores from five sites (ECS01?ECS02?ECS3?SYS01 and SYS02) in four different mud areas of the Yellow Sea and East Chnia Sea (the Changjiang Estuary mud area, the Zhe-Min mud area, the distal Cheju Island mud area and the central South Yellow Sea mud area) were collected. Both archaeal and bacterial amoA gene clone libraries were constructed for surface, middle and bottom sediment samples in each site. A total of 613 archaeal amoA gene sequences and 549 bacterial amoA gene sequences were obtained and were classified into 83 OTUs and 36 OTUs at 5% distance cutoff, respectively. The diversity of AOA was, on the whole, higher than that of AOB. The diversity of AOA and AOB in surface sediments was higher than that in the deeper layers. Diversity of amoA gene varied in opposite trends in the shallow sediments along the western pacific shelf from north to south. Statistical analysis showed that the diversity of AOA was negatively correlated with PO43-, while NO3-, TOC% and TN% were potential contributors to the diversity of AOB. Nitrosopumilus lineage, followed by Nitrososphaera lineage, and Nitrosospira lineage, followed by Nitrosomonas lineage, dominated the AOA and AOB communities, respectively. A novel cluster in Nitrosopumilus lineage was classified and tentatively named as Cluster 17. Salinity was the decisive factor for dominant group. In addition, the transport distance and transport duration of sediments could also affect the relative abundance of Nitrososphaera lineage and Nitrosomonas lineage All archaeal and bacterial amoA sequences obtained in this study could be classified into three groups according to the sediment depth of their habitats:the first group was only discovered from surface sediments; the second group was shared by both surface and deeper sediments; the third group only appeared in deeper sediments. Oxygen play an important part in the distribution of different groups. The differences in both archaeal and bacterial amoA communities among different sites were more significant than those among different depths in one site.?15NTN, NH4+ and SiO32-,NO3- and ?13C had significant influences on the AOA and AOB communities distributions, respectively.As revealed by quantitative PCR (qPCR) analysis, bacterial amoA gene (2.34×104 to 4.31×106 copies/g sediment (wet weight)) was numerically dominant over that of archaea (8.11×103 to 6.09×105 copies/g sediment (wet weight)) in sediments collected from eight depths. The highest copy number of archaeal amoA genes was found in ECS02, while that of bacterial amoA was in ECS01. The abundance of both archaeal and bacterial amoA in the central South Yellow Sea mud area was lower than in mud deposits of the East Chnia Sea. The abundance of AOA amoA gene in surface sediment decreased with the increase of latitude in the western pacific marginal seas, but the abundance of AOB amoA gene did not change regularly. The abundance of both archaeal and bacterial amoA decreased with depth in the deeper layers (> 5 cm), and this trend for AOB is more obvious. The archaeal amoA copy numbers were positively correlated with SiO32- and negatively correlated with PO43-. The bacterial amoA copy numbers were positively correlated with NO3- and negatively correlated with SiO32-. The results of this study indicated high diversity and abundance of AOA and AOB in mud deposits of the Yellow Sea and the East China Sea and their significant correlation to environmental factors. The niche differentiation of ammonia-oxidizing prokaryotes was detected. This study will be of great significance to the knowledge of AOA and AOB in the oceanic mud deposits ecosystem.