Journal Article

Uncovering Viable Microbiome in Anaerobic Sludge Digesters by Propidium Monoazide (PMA)-PCR

Ni, Jialing, Hatori, Shingo, Kubota, Kengo, Wang, Yin, Li, Yu-You

2020

Overview

Use of anaerobic sludge digester is a common practice around the world for solids digestion and methane generation from municipal sewage sludge. Understanding microbial community structure is vital to get better insight into the anaerobic digestion process and to gain better process control. However, selective analysis of viable microorganisms is limited by DNA-based assays. In this study, propidium monoazide (PMA)-PCR with 16S rRNA gene sequencing analysis was used to distinguish live and dead microorganisms based on cell membrane integrity. Microbial community structures of PMA-treated and PMA-untreated anaerobic digester sludge samples were compared. Quantitative PCR revealed that 5–30% of the rRNA genes were derived from inactive or dead cells in anaerobic sludge digesters. This caused a significant decrease in the numbers of operational taxonomic units and Chao1 and Shannon indices compared with that of the PMA-untreated sludge. Microbial community analysis showed that majority of the viable microbiome consisted of Euryarchaeota, Bacteroidetes, Deltaproteobacteria, Chloroflexi, Firmicutes, WWE1, Spirochaetes, Synergistetes, and Caldiserica. On the other hand, after the PMA treatment, numbers of Alphaproteobacteria and Betaproteobacteria declined. These were considered residual microbial members. The network analysis also revealed a relationship among the OTUs belonging to WWE1 and Bacteroidales. PMA-PCR-based 16S rRNA gene sequencing analysis is an effective tool for uncovering viable microbiome in complex environmental samples.

• Publisher: Springer Science + Business Media,Springer US,Springer Nature B.V
• Subject: alpha-Proteobacteria / anaerobic digesters / Anaerobic digestion / Anaerobic microorganisms / Anaerobic processes / Anaerobic treatment / Anatomical structures / Bacteroidales / beta-Proteobacteria / Biomedical and Life Sciences / Caldiserica / Cell membranes / Chloroflexi / Community structure / delta-Proteobacteria / Deoxyribonucleic acid / Digesters / Digestion / DNA / DNA sequencing / Ecology / Euryarchaeota / Firmicutes / Gene sequencing / genes / Geoecology/Natural Processes / Life Sciences / Methane generation / methane production / METHODS / microbial communities / Microbial Ecology / Microbiology / microbiome / Microbiomes / Microorganisms / Municipal wastes / Municipal wastewater / Nature Conservation / Network analysis / Nucleotide sequence / PCR / Phorbol esters / Polymerase chain reaction / Process control / Process controls / propidium / quantitative polymerase chain reaction / Refuse as fuel / ribosomal RNA / rRNA 16S / Sequence analysis / Sequencing / Sewage / Sewage sludge / Sludge / Sludge digestion / Spirochaetes / Spirochetes / Synergistetes / Water Quality/Water Pollution