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The ubiquitous and abundant distribution of ammonia-oxidizing  Thaumarchaeota  in marine environments is now well documented, and their crucial role in the global nitrogen cycle has been highlighted. However, the potential contribution of  Thaumarchaeota  in the carbon cycle remains poorly understood. Here we present for the first time a seasonal investigation on the shelf region (bathymetry≤200 m) of the East China Sea (ECS) involving analysis of both thaumarchaeal 16S rRNA and autotrophy-related genes (acetyl-CoA carboxylase gene,  accA ). Quantitative PCR results clearly showed a higher abundance of thaumarchaeal 16S and  accA  genes in late-autumn (November) than summer (August), whereas the diversity and community structure of autotrophic  Thaumarchaeota  showed no statistically significant difference between different seasons as revealed by thaumarchaeal  accA  gene clone libraries. Phylogenetic analysis indicated that shallow ecotypes dominated the autotrophic  Thaumarchaeota  in the ECS shelf (86.3% of total sequences), while a novel non-marine thaumarchaeal  accA  lineage was identified in the Changjiang estuary in summer (when freshwater plumes become larger) but not in autumn, implying that Changjiang freshwater discharge played a certain role in transporting terrestrial microorganisms to the ECS. Multivariate statistical analysis indicated that the biogeography of the autotrophic  Thaumarchaeota  in the shelf water of the ECS was influenced by complex hydrographic conditions. However, an in silico comparative analysis suggested that the diversity and abundance of the autotrophic  Thaumarchaeota  might be biased by the ‘universal’ thaumarchaeal  accA  gene primers Cren529F/Cren981R since this primer set is likely to miss some members within particular phylogenetic groups. Collectively, this study improved our understanding of the biogeographic patterns of the autotrophic  Thaumarchaeota  in temperate coastal waters, and suggested that new  accA  primers with improved coverage and sensitivity across phylogenetic groups are needed to gain a more thorough understanding of the role of the autotrophic  Thaumarchaeota  in the global carbon cycle.

Dynamics of Autotrophic Marine Planktonic Thaumarchaeota in the East China Sea