Nobu Masaru K, Narihiro Takashi, Rinke Christian, Kamagata Yoichi, Tringe Susannah G, Woyke Tanja, Liu Wen-Tso
Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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.
ISME J. 2015 Aug;9(8):1710-22. doi: 10.1038/ismej.2014.256. Epub 2015 Jan 23.
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.
对一个降解对苯二甲酸（TA）的产甲烷生物反应器进行生态基因组学研究，有助于阐明未培养微生物的复杂协同网络，包括来自尚无培养代表菌株的候选门的微生物。我们之前的宏基因组学研究提出，泥杆菌属和产甲烷菌可能与未培养的生物体相互作用以降解TA；然而，由于过去的技术限制，群落中的许多成员仍未得到研究。在进一步的研究中，本研究采用了最先进的组学工具，为跨越15个门的未培养生物体生成了基因组草图和转录组，并首次报道了在产甲烷环境中对候选门无壁菌门、氢还原菌门和海微生物菌门的基因组见解。代谢重建表明，这些生物体通过围绕H2代谢的能量守恒来进行发酵、互营和产乙酸分解代谢。其中一些生物体可以降解TA分解代谢的副产物（乙酸盐、丁酸盐和H2），并以互营方式支持泥杆菌属。其他分类群可以清除可能来自TA降解群落产生的碎屑生物质的合成代谢产物（蛋白质和脂质）。蛋白质清除者表达了互补的代谢途径，表明通过氨基酸、支链脂肪酸和丙酸盐进行互营和发酵的逐步蛋白质降解。因此，未培养的生物体可能相互作用，与泥杆菌属和产甲烷菌形成一个复杂的由互营支持的食物网，以代谢分解代谢副产物和碎屑，从而促进TA整体矿化生成CO2和CH4。
