First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking

Sekiguchi, Yuji, Ohashi, Akiko, Parks, Donovan H., Yamauchi, Toshihiro, Tyson, Gene W. and Hugenholtz, Philip (2015) First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking. PeerJ, 3 e740: 1-24. doi:10.7717/peerj.740


Author Sekiguchi, Yuji
Ohashi, Akiko
Parks, Donovan H.
Yamauchi, Toshihiro
Tyson, Gene W.
Hugenholtz, Philip
Title First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking
Journal name PeerJ   Check publisher's open access policy
ISSN 2167-8359
Publication date 2015-01-27
Year available 2015
Sub-type Article (original research)
DOI 10.7717/peerj.740
Open Access Status DOI
Volume 3
Issue e740
Start page 1
End page 24
Total pages 24
Place of publication London, United Kingdom
Publisher PeerJ
Language eng
Abstract Filamentous cells belonging to the candidate bacterial phylum KSB3 were previously identified as the causative agent of fatal filament overgrowth (bulking) in a high-rate industrial anaerobic wastewater treatment bioreactor. Here, we obtained near complete genomes from two KSB3 populations in the bioreactor, including the dominant bulking filament, using differential coverage binning of metagenomic data. Fluorescence in situ hybridization with 16S rRNA-targeted probes specific for the two populations confirmed that both are filamentous organisms. Genome-based metabolic reconstruction and microscopic observation of the KSB3 filaments in the presence of sugar gradients indicate that both filament types are Gram-negative, strictly anaerobic fermenters capable of non-flagellar based gliding motility, and have a strikingly large number of sensory and response regulator genes. We propose that the KSB3 filaments are highly sensitive to their surroundings and that cellular processes, including those causing bulking, are controlled by external stimuli. The obtained genomes lay the foundation for a more detailed understanding of environmental cues used by KSB3 filaments, which may lead to more robust treatment options to prevent bulking.
Formatted abstract
Filamentous cells belonging to the candidate bacterial phylum KSB3 were previously identified as the causative agent of fatal filament overgrowth (bulking) in a high-rate industrial anaerobic wastewater treatment bioreactor. Here, we obtained near complete genomes from two KSB3 populations in the bioreactor, including the dominant bulking filament, using differential coverage binning of metagenomic data. Fluorescence in situ hybridization with 16S rRNA-targeted probes specific for the two populations confirmed that both are filamentous organisms. Genome-based metabolic reconstruction and microscopic observation of the KSB3 filaments in the presence of sugar gradients indicate that both filament types are Gram-negative, strictly anaerobic fermenters capable of non-flagellar based gliding motility, and have a strikingly large number of sensory and response regulator genes. We propose that the KSB3 filaments are highly sensitive to their surroundings and that cellular processes, including those causing bulking, are controlled by external stimuli. The obtained genomes lay the foundation for a more detailed understanding of environmental cues used by KSB3 filaments, which may lead to more robust treatment options to prevent bulking.
Keyword KSB3 phylum
Candidate phylum
Wastewater treatment
Anaerobic biotechnology
Filamentous bulking
Metagenomics
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID DP120103498
DP1093175
Institutional Status UQ

 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 20 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 31 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Fri, 06 Feb 2015, 19:36:59 EST by Mrs Louise Nimwegen on behalf of School of Chemistry & Molecular Biosciences