Comparative analysis of bacteria associated with different mosses by 16S rRNA and 16S rDNA sequencing

J Basic Microbiol. 2017 Jan;57(1):57-67. doi: 10.1002/jobm.201600358. Epub 2016 Aug 12.

Abstract

To understand the differences of the bacteria associated with different mosses, a phylogenetic study of bacterial communities in three mosses was carried out based on 16S rDNA and 16S rRNA sequencing. The mosses used were Hygroamblystegium noterophilum, Entodon compressus and Grimmia montana, representing hygrophyte, shady plant and xerophyte, respectively. In total, the operational taxonomic units (OTUs), richness and diversity were different regardless of the moss species and the library level. All the examined 1183 clones were assigned to 248 OTUs, 56 genera were assigned in rDNA libraries and 23 genera were determined at the rRNA level. Proteobacteria and Bacteroidetes were considered as the most dominant phyla in all the libraries, whereas abundant Actinobacteria and Acidobacteria were detected in the rDNA library of Entodon compressus and approximately 24.7% clones were assigned to Candidate division TM7 in Grimmia montana at rRNA level. The heatmap showed the bacterial profiles derived from rRNA and rDNA were partly overlapping. However, the principle component analysis of all the profiles derived from rDNA showed sharper differences between the different mosses than that of rRNA-based profiles. This suggests that the metabolically active bacterial compositions in different mosses were more phylogenetically similar and the differences of the bacteria associated with different mosses were mainly detected at the rDNA level. Obtained results clearly demonstrate that combination of 16S rDNA and 16S rRNA sequencing is preferred approach to have a good understanding on the constitution of the microbial communities in mosses.

Keywords: Bacterial community; Diversity; Moss; rDNA; rRNA.

Publication types

  • Comparative Study

MeSH terms

  • Actinobacteria / genetics
  • Bacteria / classification*
  • Bacteria / genetics*
  • Bacteria / isolation & purification
  • Bacteroidetes / genetics
  • Biodiversity
  • Bryophyta / microbiology*
  • DNA, Ribosomal
  • Gene Library
  • Microbial Consortia* / genetics
  • Phylogeny
  • Proteobacteria / genetics
  • RNA, Ribosomal, 16S
  • Sequence Analysis, DNA / methods
  • Sequence Analysis, RNA

Substances

  • DNA, Ribosomal
  • RNA, Ribosomal, 16S