Diversity, abundance and distribution of amoA-encoding archaea in deep-sea methane seep sediments of the Okhotsk Sea

Abstract

The ecological characteristics of amoA-encoding archaea (AEA) in deep-sea sediments are largely unsolved. This paper aimed to study the diversity, structure, distribution and abundance of the archaeal community and especially its AEA components in the cold seep surface sediments of the Okhotsk Sea, a marginal sea harboring one of the largest methane hydrate reservoirs in the world. Diverse archaeal 16S rRNA gene sequences were identified, with the majority being related to sequences from other cold seep and methane-rich sediment environments. However, the AEA diversity and abundance were quite low as revealed by amoA gene analyses. Correlation analysis indicates that the abundance of the archaeal amoA genes was correlated with the sediment organic matter content. Thus, it is possible that the amoA-carrying archaea here might utilize organic matter for a living. The affiliation of certain archaeal amoA sequences to the GenBank sequences originally obtained from deep-sea hydrothermal vent environments indicated that the related AEA either have a wide range of temperature adaptation or they have a thermophilic evolutionary history in the modern cold deep-sea sediments of the Okhotsk Sea. The dominance of ammonia-oxidizing bacteria over AEA may indicate that bacteria play a significant role in nitrification in the Okhotsk Sea cold seep sediments.

Thaumarchaeotal Signature Gene Distribution in Sediments of the Northern South China Sea: an Indicator of the Metabolic Intersection of the Marine Carbon, Nitrogen, and Phosphorus Cycles?

“…Sediment DNA extraction, DNA concentration measurement, and thaumarchaeotal amoA gene clone library construction and analysis followed previously described procedures (7,28,31). To test the reproducibility of our experimental procedure and to identify any potential small-scale (ϳ20-cm) spatial variability of the sediment AEA community, three separate amoA gene clone libraries (A3-I, A3-II, and A3-III) were constructed for sampling station A3, each from a distinct subcore DNA sample.…”

“…To test the reproducibility of our experimental procedure and to identify any potential small-scale (ϳ20-cm) spatial variability of the sediment AEA community, three separate amoA gene clone libraries (A3-I, A3-II, and A3-III) were constructed for sampling station A3, each from a distinct subcore DNA sample. The amoA gene sequences obtained were grouped into operational taxonomic units (OTUs) based on a 0.05 sequence distance cutoff, calculated using the DOTUR program (32), to facilitate comparison with previous studies (7,20,28,31). The amoA gene sequences were translated into conceptual AmoA protein sequences, and the BLASTp program was used for retrieval of the top hit sequences from GenBank (33).…”

“…The amoA gene sequences were translated into conceptual AmoA protein sequences, and the BLASTp program was used for retrieval of the top hit sequences from GenBank (33). Phylogenetic analysis followed a previous procedure (7,28,31), with CLUSTAL X (version 2.0) for sequence alignment and PHYLIP (version 3.69) for phylogenetic-tree construction using distance neighbor-joining inference (34,35).…”

“…Deep waters may be another source of nutrient supply to the oligotrophic surface water in the SCS, which can occur via monsoonal wind driving eddies and other upwelling and vertical-mixing processes (27). The northern SCS (nSCS) includes several identified and prospective deep-sea methane hydrate reservoirs, and these areas may sustain productive methane seep-specific ecosystems, requiring a large supply or rapid recycling of nitrogenous nutrients (28,29). It is an important ecological question to identify whether and, if so, how the methane seep environments influence the community structure, spatial distribution, and biogeochemical function of the thaumarchaeota in deep-sea sediments (6).…”

Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers

“…23). In contrast, there have been very few studies of AEA-the term originally used for amoA-carrying thaumarchaeotes by Dang and colleagues (24,25)-in engineered biological treatment systems (26)(27)(28). When quantitative analyses of AOB and AEA have been conducted in some nitrifying WWTPs, the abundance of AOB has been shown to exceed that of AEA by two to three orders of magnitude.…”