title: Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor.
abstract: Ecogenomic investigation of a methanogenic bioreactor degrading terephthalate (TA) allowed elucidation of complex synergistic networks of uncultivated microorganisms, including those from candidate phyla with no cultivated representatives. Our previous metagenomic investigation proposed that Pelotomaculum and methanogens may interact with uncultivated organisms to degrade TA; however, many members of the community remained unaddressed because of past technological limitations. In further pursuit, this study employed state-of-the-art omics tools to generate draft genomes and transcriptomes for uncultivated organisms spanning 15 phyla and reports the first genomic insight into candidate phyla Atribacteria, Hydrogenedentes and Marinimicrobia in methanogenic environments. Metabolic reconstruction revealed that these organisms perform fermentative, syntrophic and acetogenic catabolism facilitated by energy conservation revolving around H2 metabolism. Several of these organisms could degrade TA catabolism by-products (acetate, butyrate and H2) and syntrophically support Pelotomaculum. Other taxa could scavenge anabolic products (protein and lipids) presumably derived from detrital biomass produced by the TA-degrading community. The protein scavengers expressed complementary metabolic pathways indicating syntrophic and fermentative step-wise protein degradation through amino acids, branched-chain fatty acids and propionate. Thus, the uncultivated organisms may interact to form an intricate syntrophy-supported food web with Pelotomaculum and methanogens to metabolize catabolic by-products and detritus, whereby facilitating holistic TA mineralization to CO2 and CH4.
authors.affiliation: Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
authors.forename: Masaru K
authors.initials: MK
authors.lastname: Nobu
authors.affiliation: 1] Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA [2] Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Narihiro
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Christian
authors.initials: C
authors.lastname: Rinke
authors.affiliation: 1] Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan [2] Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan.
authors.forename: Yoichi
authors.initials: Y
authors.lastname: Kamagata
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Susannah G
authors.initials: SG
authors.lastname: Tringe
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.affiliation: Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
authors.forename: Wen-Tso
authors.initials: WT
authors.lastname: Liu
mesh_terms: D054378:Acetogenins / Q000378:metabolism; D001419:Bacteria / Q000235:genetics* / Q000378:metabolism; D001673:Biodegradation, Environmental; D019149:Bioreactors / Q000382:microbiology*; D002087:Butyrates / Q000378:metabolism; D004734:Energy Metabolism / Q000502:physiology; D019605:Euryarchaeota / Q000235:genetics; D005285:Fermentation / Q000502:physiology; D020869:Gene Expression Profiling; D056186:Metagenomics; D008697:Methane / Q000378:metabolism*; D010459:Peptococcaceae / Q000235:genetics; D010795:Phthalic Acids / Q000378:metabolism; D010802:Phylogeny; D011422:Propionates / Q000378:metabolism
chemical_list: D054378:Acetogenins; D002087:Butyrates; D010795:Phthalic Acids; D011422:Propionates; C011363:terephthalic acid; D008697:Methane