Bacteriophage-mediated extracellular DNA release is important for the structural stability of aerobic granular sludge

Yi-Qiao Wang; Wei Li; Jin-Long Zhuang; Yong-di Liu; James P Shapleigh

doi:10.1016/j.scitotenv.2020.138392

Bacteriophage-mediated extracellular DNA release is important for the structural stability of aerobic granular sludge

Sci Total Environ. 2020 Jul 15:726:138392. doi: 10.1016/j.scitotenv.2020.138392. Epub 2020 Apr 11.

Authors

Yi-Qiao Wang¹, Wei Li², Jin-Long Zhuang¹, Yong-di Liu³, James P Shapleigh⁴

Affiliations

¹ State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China.
² State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China. Electronic address: wei_li@ecust.edu.cn.
³ State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China.
⁴ Department of Microbiology, Cornell University, Ithaca, USA.

PMID: 32334351
DOI: 10.1016/j.scitotenv.2020.138392

Abstract

The aim of this study was to investigate the microbial characteristics and the structural role of exDNA in different size AGSs. Metagenomic results showed that exDNA has a significantly lower GC content, ~46.0%, than the ~65.0% GC of intracellular DNA (inDNA). Taxonomic predictions showed most of the reads from the exDNA that could be taxonomically assigned were from members of the phyla Bacteroidetes (55.0-64.2% of the total exDNA reads). Assigned inDNA reads were mainly from Proteobacteria (50.9-57.8%) or Actinobacteria (18.0-28.0%). Reads mapping showed that exDNA read depths were similar across all predicted open reading frames from assembled genomes that were assigned as Bacteroidetes which is consistent with cell lysis as a source of exDNA. Enrichment of CRISPR-CAS proteins in exDNA reads and CRISPR spacers in Bacteroidetes associated draft genomes suggested that bacteriophage infection may be an important cause of lysis of these cells. A critical role for this exDNA was found using DNase I digestion experiments which showed that the exDNA was vital for the structural stability of relatively small sized AGS but not for the larger sized AGS. The characteristics of exDNA in AGSs revealed in this work provide a new perspective on AGS components and structural stability.

Keywords: Aerobic granular sludge (AGS); Bacteroidetes; Extracellular DNA; Metagenomics; Structural roles.

MeSH terms

Bacteria
Bacteriophages*
Bioreactors
DNA
Metagenome
Sewage*

Substances

Sewage
DNA