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

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

Binghan Wang  1 , Shanshan Huang  1 , Liangmao Zhang  2 , Jianwei Zhao  1 , Guanglong Liu  1 , Yumei Hua  1 , Wenbing Zhou  1 , Duanwei Zhu  1
Affiliations

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

Binghan Wang et al. PeerJ. .

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.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1. Schematic diagram of the rhizobox (175 × 175 × 115 mm) used for cultivation of submerged P. crispus (modified from He et al., 2005).
Figure 2
Figure 2. Neighbor-joining phylogenetic tree of M. oxyfera-like bacterial 16S rRNA gene sequences in rhizosphere and non-rhizosphere sediments of P. crispus.
R and Non represent sediment samples in root compartment and non-rhizosphere, respectively. N1–N5 represent sediment samples taken from one to five mm of near-rhizosphere sub-compartments. The numbers in the brackets represent the ratio of the number of sequences out of the total number in the corresponding interlayer. The numbers at the nodes are percentages that indicate the levels of bootstrap support based on 1,000 replicates, and only percentages more than 50% are shown. The scale bar represents 1% sequence divergence.
See this image and copyright information in PMC

References

    1. Ai C, Liang GQ, Sun JW, Wang XB, He P, Zhou W. Different roles of rhizosphere effect and long-term fertilization in the activity and community structure of ammonia oxidizers in a calcareous fluvo-aquic soil. Soil Biology and Biochemistry. 2013;57:30–42. doi: 10.1016/j.soilbio.2012.08.003. - DOI
    1. Bodelier PLE. Interactions between oxygen-releasing roots and microbial processes in flooded soils and sediments. In: De Kroon H, Visser EJW, editors. Root Ecology. Berlin and Heidelberg: Springer; 2003. pp. 331–362.
    1. Chen J, Zhou Z-C, Gu J-D. Occurrence and diversity of nitrite-dependent anaerobic methane oxidation bacteria in the sediments of the South China Sea revealed by amplification of both 16S rRNA and pmoA genes. Applied Microbiology and Biotechnology. 2014;98(12):5685–5696. doi: 10.1007/s00253-014-5733-4. - DOI - PubMed
    1. Chen J, Zhou Z, Gu J-D. Complex community of nitrite-dependent anaerobic methane oxidation bacteria in coastal sediments of the Mai Po wetland by PCR amplification of both 16S rRNA and pmoA genes. Applied Microbiology and Biotechnology. 2015;99(3):1463–1473. doi: 10.1007/s00253-014-6051-6. - DOI - PubMed
    1. Chu JY, Zhang JP, Zhou XH, Liu B, Li YM. A comparison of anammox bacterial abundance and community structures in three different emerged plants-related sediments. Current Microbiology. 2015;71(3):421–427. doi: 10.1007/s00284-015-0851-5. - DOI - PubMed