TY - JOUR
T1 - “Candidatus Nealsonbacteria” Are Likely Biomass Recycling Ectosymbionts of Methanogenic Archaea in a Stable Benzene-Degrading Enrichment Culture
AU - Chen, Xu
AU - Molenda, Olivia
AU - Brown, Christopher T.
AU - Toth, Courtney R.A.
AU - Guo, Shen
AU - Luo, Fei
AU - Howe, Jane
AU - Nesbø, Camilla L.
AU - He, Christine
AU - Montabana, Elizabeth A.
AU - Cate, Jamie H.D.
AU - Banfield, Jillian F.
AU - Edwards, Elizabeth A.
N1 - Funding Information:
This study was funded by Genomic Application Partnership Program (GAPP) grants awarded to E.A.E. (project IDs OGI-102 and OGI-173), which were supported by Genome Canada, Ontario Genomics, the Government of Ontario, Mitacs Canada, SiREM, Alberta Innovates, Federated Co-operatives Limited, and Imperial Oil.
Funding Information:
This study was funded by Genomic Application Partnership Program (GAPP) grants awarded to E.A.E. (project IDs OGI-102 and OGI-173), which were supported by Genome Canada, Ontario Genomics, the Government of Ontario, Mitacs Canada, SiREM, Alberta Innovates, Federated Co-operatives Limited, and Imperial Oil. We thank SiREM (Guelph, Ontario, Canada) for supplying culture for testing. We also acknowledge the laboratories of Neil Thomson (University of Waterloo), Ania Ulrich (University of Alberta), SiREM, and Innotech Alberta (Edmonton, Alberta, Canada) for providing feedback and intellectual contributions to this study during weekly GAPP consortium meetings. All authors made research and substantial intellectual contributions to the completion of this study. X.C. and E.A.E. conceived and designed the study, and X.C. carried out all experiments and data analysis and interpretation and drafted and revised the manuscript. O.M. assembled the OD1 genome with help of C.L.N. and C.T.B. E.A.M. performed the cryo-TEM data acquisition and analysis. C.R.A.T. helped with data analysis and revised the manuscript. S.G. helped to maintain the culture, performed qPCR data acquisition and analysis, and revised the manuscript. F.L. enriched the culture, extracted DNA, and performed the initial metagenome analysis. J.H. assisted with ionic liquid-SEM data acquisition and analysis. C.H. performed the OD1 taxonomy classification and phylogenetic tree and OD1 genome annotation. J.H.D.C. and J.F.B. provided critical research guidance and manuscript revisions.
Publisher Copyright:
Copyright © 2023 American Society for Microbiology. All Rights Reserved.
PY - 2023/5
Y1 - 2023/5
N2 - The Candidate Phyla Radiation (CPR), also referred to as superphylum Patescibacteria, is a very large group of bacteria with no pure culture representatives discovered by 16S rRNA sequencing or genome-resolved metagenomic analyses of environmental samples. Within the CPR, candidate phylum Parcubacteria, previously referred to as OD1, is prevalent in anoxic sediments and groundwater. Previously, we had identified a specific member of the Parcubacteria (referred to as DGGOD1a) as an important member of a methanogenic benzene-degrading consortium. Phylogenetic analyses herein place DGGOD1a within the clade “Candidatus Nealsonbacteria.” Because of its persistence over many years, we hypothesized that “Ca. Nealsonbacteria” DGGOD1a must play an important role in sustaining anaerobic benzene metabolism in the consortium. To try to identify its growth substrate, we amended the culture with a variety of defined compounds (pyruvate, acetate, hydrogen, DNA, and phospholipid), as well as crude culture lysate and three subfractions thereof. We observed the greatest (10-fold) increase in the absolute abundance of “Ca. Nealsonbacteria” DGGOD1a only when the consortium was amended with crude cell lysate. These results implicate “Ca. Nealsonbacteria” in biomass recycling. Fluorescence in situ hybridization and cryogenic transmission electron microscope images revealed that “Ca. Nealsonbacteria” DGGOD1a cells were attached to larger archaeal Methanothrix cells. This apparent epibiont lifestyle was supported by metabolic predictions from a manually curated complete genome. This is one of the first examples of bacterial-archaeal episymbiosis and may be a feature of other “Ca. Nealsonbacteria” found in anoxic environments.
AB - The Candidate Phyla Radiation (CPR), also referred to as superphylum Patescibacteria, is a very large group of bacteria with no pure culture representatives discovered by 16S rRNA sequencing or genome-resolved metagenomic analyses of environmental samples. Within the CPR, candidate phylum Parcubacteria, previously referred to as OD1, is prevalent in anoxic sediments and groundwater. Previously, we had identified a specific member of the Parcubacteria (referred to as DGGOD1a) as an important member of a methanogenic benzene-degrading consortium. Phylogenetic analyses herein place DGGOD1a within the clade “Candidatus Nealsonbacteria.” Because of its persistence over many years, we hypothesized that “Ca. Nealsonbacteria” DGGOD1a must play an important role in sustaining anaerobic benzene metabolism in the consortium. To try to identify its growth substrate, we amended the culture with a variety of defined compounds (pyruvate, acetate, hydrogen, DNA, and phospholipid), as well as crude culture lysate and three subfractions thereof. We observed the greatest (10-fold) increase in the absolute abundance of “Ca. Nealsonbacteria” DGGOD1a only when the consortium was amended with crude cell lysate. These results implicate “Ca. Nealsonbacteria” in biomass recycling. Fluorescence in situ hybridization and cryogenic transmission electron microscope images revealed that “Ca. Nealsonbacteria” DGGOD1a cells were attached to larger archaeal Methanothrix cells. This apparent epibiont lifestyle was supported by metabolic predictions from a manually curated complete genome. This is one of the first examples of bacterial-archaeal episymbiosis and may be a feature of other “Ca. Nealsonbacteria” found in anoxic environments.
KW - anaerobes
KW - anaerobic
KW - benzene
KW - biomass recycling
KW - Candidate Phyla Radiation
KW - cryo-EM
KW - electron microscopy
KW - episymbiosis
KW - fluorescence in situ hybridization
KW - genome-resolved metagenomics
KW - genomics
KW - methanogenic benzene biodegradation
KW - Methanothrix
KW - microbial growth
KW - “Candidatus Nealsonbacteria”
UR - http://www.scopus.com/inward/record.url?scp=85160965022&partnerID=8YFLogxK
U2 - 10.1128/aem.00025-23
DO - 10.1128/aem.00025-23
M3 - Article
C2 - 37098974
AN - SCOPUS:85160965022
SN - 0099-2240
VL - 89
JO - Applied and Environmental Microbiology
JF - Applied and Environmental Microbiology
IS - 5
M1 - e00025-23
ER -