Composition, diversity and abundance of Candidatus M. oxyfera-like bacteria in response to the estuary salinity gradient

“Candidatus Methylomirabilis oxyfera” (M. oxyfera) bacteria has attracted much attention recently since it plays an important role in performing methane oxidation. Most studies on M. oxyfera-like bacteria have been carried out in freshwater ecosystems, however it remains unclear about its distribution along the salinity gradient of estuarine and coastal environments. In this study, we used molecular analyses to reveal the community, diversity and abundance of M. oxyfera-like bacteria in the Yangtze estuarine and coastal sediments. Clone library analyses confirmed the wide distributions of M. oxyfera-like bacterial 16S rRNA and pmoA genes in the study area. The M. oxyfera-like bacterial 16S rRNA gene sequences were grouped into eleven separate OTUs, which were assigned to groups A and B of M. oxyfera-like bacteria. Most sequences (89.4–97.6% of total sequences) of M. oxyfera-like bacterial 16S rRNA gene were affiliated with group B, while only few clone sequences (2.4–10.6% of total sequences) were affiliated with group A. The retrieved M. oxyfera-like bacterial pmoA gene sequences were grouped into five distinct clusters. Bray–Curtis dissimilarity of M. oxyfera-like bacterial 16S rRNA and pmoA genes differed greatly among the low, middle and high salinity sites. M. oxyfera-like bacterial 16S rRNA and pmoA abundances were mainly recovered from the oligohaline sites rather than from the saline sites. In addition, the large differences in 16S rRNA and pmoA gene sequences between estuarine and land freshwater environments suggested that salinity could be able to affect the community distribution of M. oxyfera-like bacteria. Also, sediment nitrate/ammonium played an important role in affecting the M. oxyfera-like bacteria. Overall, these results indicate that salinity has a great influence on M. oxyfera-like bacteria community in estuarine environments.