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.
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Acknowledgements
We acknowledge Peiying Hong, Xianzheng Li and Hideyuki Tamaki for sample preparation. We thank Bernhard Schink for etymological advice on Prokaryote Candidatus nomenclature. We also thank reviewers for invaluable input. The work conducted by the US Department of Energy Joint Genome Institute is supported by the US Department of Energy Office of Science under Contract No. DE-AC02-05CH11231. This work is also supported by the US Department of Energy under Award DE-SC0006771 to the University of Illinois, Urbana–Champaign, and a grant from the Energy Biosciences Institute (EBI) at the University of Illinois Urbana-Champaign (UIUC) to WTL.
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Nobu, M., Narihiro, T., Rinke, C. et al. Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor. ISME J 9, 1710–1722 (2015). https://doi.org/10.1038/ismej.2014.256
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DOI: https://doi.org/10.1038/ismej.2014.256
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