Diversity of NC10 bacteria associated with sediments of submerged Potamogeton crispus (Alismatales: Potmogetonaceae)

Binghan Wang; Shanshan Huang; Liangmao Zhang; Jianwei Zhao; Guanglong Liu; Yumei Hua; Wenbing Zhou; Duanwei Zhu

doi:10.7717/peerj.6041

Diversity of NC10 bacteria associated with sediments of submerged Potamogeton crispus (Alismatales: Potmogetonaceae)

PeerJ. 2018 Dec 4:6:e6041. doi: 10.7717/peerj.6041. eCollection 2018.

Authors

Binghan Wang¹, Shanshan Huang¹, Liangmao Zhang², Jianwei Zhao¹, Guanglong Liu¹, Yumei Hua¹, Wenbing Zhou¹, Duanwei Zhu¹

Affiliations

¹ Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China.
² Laboratory of Environmental Planning and Management, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China.

Abstract

Background: The nitrite-dependent anaerobic methane oxidation (N-DAMO) pathway, which plays an important role in carbon and nitrogen cycling in aquatic ecosystems, is mediated by "Candidatus Methylomirabilis oxyfera" (M. oxyfera) of the NC10 phylum. M. oxyfera-like bacteria are widespread in nature, however, the presence, spatial heterogeneity and genetic diversity of M. oxyfera in the rhizosphere of aquatic plants has not been widely reported.

Method: In order to simulate the rhizosphere microenvironment of submerged plants, Potamogeton crispus was cultivated using the rhizobox approach. Sediments from three compartments of the rhizobox: root (R), near-rhizosphere (including five sub-compartments of one mm width, N1-N5) and non-rhizosphere (>5 mm, Non), were sampled. The 16S rRNA gene library was used to investigate the diversity of M. oxyfera-like bacteria in these sediments.

Results: Methylomirabilis oxyfera-like bacteria were found in all three sections, with all 16S rRNA gene sequences belonging to 16 operational taxonomic units (OTUs). A maximum of six OTUs was found in the N1 sub-compartment of the near-rhizosphere compartment and a minimum of four in the root compartment (R) and N5 near-rhizosphere sub-compartment. Indices of bacterial community diversity (Shannon) and richness (Chao1) were 0.73-1.16 and 4-9, respectively. Phylogenetic analysis showed that OTU1-11 were classified into group b, while OTU12 was in a new cluster of NC10.

Discussion: Our results confirmed the existence of M. oxyfera-like bacteria in the rhizosphere microenvironment of the submerged plant P. crispus. Group b of M. oxyfera-like bacteria was the dominant group in this study as opposed to previous findings that both group a and b coexist in most other environments. Our results indicate that understanding the ecophysiology of M. oxyfera-like bacteria group b may help to explain their existence in the rhizosphere sediment of aquatic plant.

Keywords: M. oxyfera-like bacteria; Microbial diversity; NC10 phylum; Nitrite-dependent anaerobic methane oxidizing; Rhizosphere; Submerged plant.

Grants and funding

This research was funded by the National Natural Science Foundation of China (No. 41371452, 40901264), and Major Science and Technology Programme for Water Pollution Control and Treatment of China (No. 2014ZX07203010). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.