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

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.

Proteobacteria Acts as a Pathogenic Risk-Factor for Chronic Abdominal Pain and Diarrhea in Post-Cholecystectomy Syndrome Patients: A Gut Microbiome Metabolomics Study

“…Among these bacterial species, the Proteobacteria had the highest degree of enhancement. Therefore, compared to traditional bacterial culture methods, the 16S-rDNA PCR amplification technology exhibited a few remarkable merits in screening and identifying bacteria, including explicit and existent bacterial colonies, relatively higher abundance, undifferentiated bacterial colony growth, and higher efficacy [27].…”

Diversity and the role of endophytic bacteria: A review

“…They are found in both monocotyledon and dicotyledon species (Ryan et al 2008). The colonisation of endophytic bacteria in ferns, algae and bryophytes has already been described (Colombo 1978;Hollants et al 2011;Shcherbakov et al 2013;Liu et al 2014;Das et al 2017a;Tian & Li 2017;Mahlangu & Serepa-Dlamini 2018). All groups of plants ranging from seagrasses (Marhaeni et al 2011;Garcias-Bonet et al 2012) to large trees (Shen & Fulthorpe 2015;Puri et al 2017) harbour endophytic bacteria.…”

The Substitution of Sphagnum for Peat as a Culture Substrate Reduces N2O Emissions from Vegetable Production Systems

“…As the proportion of sphagnum replacing peat increases, Massilia gradually supplanted Dokdonella as the predominant denitrifying bacterial genus. Previous studies have identified Rhodanobacter as a genus with a fully denitrifying capacity that is present in a variety of habitats [35,36], while Massilia is the common dominant genus among all the mosses tested based on the previous library of research [37]. Therefore, the substitution of peat with sphagnum can alter the structure and composition of microbial communities in the substrate and enhance the denitrification potential through increasing the dominance of Massilia.…”