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

Yuji Sekiguchi; Akiko Ohashi; Donovan H Parks; Toshihiro Yamauchi; Gene W Tyson; Philip Hugenholtz

doi:10.7717/peerj.740

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

PeerJ. 2015 Jan 27:3:e740. doi: 10.7717/peerj.740. eCollection 2015.

Authors

Yuji Sekiguchi¹, Akiko Ohashi¹, Donovan H Parks², Toshihiro Yamauchi³, Gene W Tyson⁴, Philip Hugenholtz⁵

Affiliations

¹ Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba, Ibaraki , Japan.
² Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St. Lucia, Queensland , Australia.
³ Administrative Management Department, Kubota Kasui Corporation , Minato-ku, Tokyo , Japan.
⁴ Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St. Lucia, Queensland , Australia ; Advanced Water Management Centre, The University of Queensland , St. Lucia, Queensland , Australia.
⁵ Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St. Lucia, Queensland , Australia ; Institute for Molecular Bioscience, The University of Queensland , St. Lucia, Queensland , Australia.

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.

Keywords: Anaerobic biotechnology; Candidate phylum; Filamentous bulking; KSB3 phylum; Metagenomics; Wastewater treatment.

Grants and funding

The study was supported by the Biomedical Research Institute of the National Institute of Advanced Industrial Science and Technology (AIST). Philip Hugenholtz and Donovan H. Parks were supported by an Australian Research Council (ARC) Discovery Outstanding Researcher Award (DORA) grant DP120103498. Gene W. Tyson was supported by an ARC Queen Elizabeth II Fellowship, grant DP1093175. Donovan H. Parks was also supported by the Natural Sciences and Engineering Research Council of Canada. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.