Presence of diverse Candidatus Methylomirabilis oxyfera -like bacteria of NC10 phylum in agricultural soils

Abstract

The greatest level of diversity of NC10 phylum bacteria was reported to date in this study, which improved our understanding of the distribution of NC10 phylum bacterial communities in soil environments.

Comparison of community structures of Candidatus Methylomirabilis oxyfera-like bacteria of NC10 phylum in different freshwater habitats

“…High-throughput sequencing of bacterial 16S rRNA genes was performed on the Illumina MiSeq platform (Hangzhou Guhe Information and Technology Co., Ltd., Zhejiang, China). Briefly, the V3-V4 region of bacterial 16S rRNA genes was amplified by the primer 319f (5′-ACTCCTACGGGAGGCAGCAG-3′) and primer 806r (5′-GGACTACHVGGGTWTCTAAT-3′) as previously described 23 30 . Briefly, PCRs were performed in a 30 μl mixture containing 0.5 μl Dimethyl sulfoxide, 1.0 μl forward primer (10 mM), 1.0 μl reverse primer (10 mM), 5.0 μl DNA template, and 15.0 μl Phusion High-Fidelity PCR Master Mix with HF Buffer (NEB).…”

“…Briefly, PCRs were performed in a 30 μl mixture containing 0.5 μl Dimethyl sulfoxide, 1.0 μl forward primer (10 mM), 1.0 μl reverse primer (10 mM), 5.0 μl DNA template, and 15.0 μl Phusion High-Fidelity PCR Master Mix with HF Buffer (NEB). The thermal program was as follows 23 30 : 98 °C for 30 s; 30 cycles of 98 °C for 15 s, 58 °C for 15 s, and 72 °C for 15 s; and a final extension at 72 °C for 1 min. PCR products were purified using an agarose gel DNA purification kit (Qiagen, Chatsworth, California, USA) and then were subjected to Illumina MiSeq sequencing (2 × 300 bp).…”

“…Analysis of Mi-Seq sequencing data was conducted using Quantitative Insights Into Microbial Ecology (QIIME, www.qiime.org ) according to Shen et al . 30 31 . High-quality NC10 phylum bacterial sequences were further confirmed by aligning these sequences with the reported NC10 sequences deposited in GenBank using the BLAST search engine 30 .…”

“… 29 and Shen et al . 30 have applied Illumina-based 16S rRNA gene sequencing technology to examine the community structures of NC10 bacteria, and the latter showed an unexpected high diversity of NC10 bacteria at species level in agricultural soils. To the best of our knowledge, no study has used this technique to compare the community composition and diversity of NC10 bacteria between different natural habitats.…”

Key Physiology of a Nitrite-Dependent Methane-Oxidizing Enrichment Culture

“…Since nitrite-AOM was first discovered and the important role of Methylomirabilislike bacteria in anaerobic oxidation of methane became apparent, molecular tools based on 16S rRNA and pmoA gene amplification were developed to survey this group of bacteria (11,12). Consequently, ribosomal 16S rRNA and pmoA gene sequences related to this clade have been reported from diverse environments, such as coastal aquifers (13), wastewater treatment plants (14,15), sediments from freshwater and saline lakes (16)(17)(18)(19), peat soil from minerotrophic peatlands (20), agricultural lands and paddy field soils (21)(22)(23)(24), marine oxygen minimum zones, sediments (25,26), and rumen fluid samples (27). Methylomirabilis-like bacteria appear to be present in a wide variety of environments; however, their contribution to global nitrogen and methane fluxes is not yet fully understood (28).…”