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

Abstract

Aims: To better explore the distribution and diversity of Candidatus Methylomirabilis oxyfera (M. oxyfera)-like bacteria of NC10 phylum in soil environments.

Methods and results: The vertical distribution and diversity of NC10 phylum bacteria were investigated in an agricultural field (surface layer, 0-10 cm; subsurface layer, 20-30 cm; deep layers, 50-60 and 90-100 cm) by using Illumina-based 16S rRNA (V3-V4 region) gene sequencing of soil DNA samples and quantitative PCR assays. It was found that the NC10-related reads accounted for 0·8-4·5% of the 16S rRNA pool in each examined core sample, with greater percentage being observed in deep soils than in surface soils and subsurface soils. The recovered NC10-related reads showed 85·1-96·9% identity to the 16S rRNA gene of M. oxyfera. A high diversity of NC10 phylum bacteria was observed in the examined soil cores. A total of 115 operational taxonomic units (OTU) were detected based on 3% sequence divergence in the recovered 16S rRNA genes. Phylogenetic analysis showed that four distinct groups of NC10 phylum bacteria (groups A, B, C and D) were present in the examined soil cores, with group B members being the dominant bacteria. The group A members, which are identified as the dominant bacteria responsible for anaerobic methane oxidation (AMO) coupled to nitrite reduction, can mainly be detected at 50-60 cm. Quantitative PCR further confirmed the presence of NC10 phylum bacteria, ranging from 3·8 × 10(6) to 9·3 × 10(6) copies g(-1) soil.

Conclusions: The results showed the presence of diverse NC10 phylum bacteria in agricultural soils by using Illumina-based 16S rRNA gene sequencing and qPCR assays.

Significance and impact of the study: 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.

Keywords: Candidatus Methylomirabilis oxyfera; Illumina-based 16S rRNA gene sequencing; NC10 phylum; distribution; diversity; quantitative PCR.