Nobu Masaru Konishi, Narihiro Takashi, Liu Miaomiao, Kuroda Kyohei, Mei Ran, Liu Wen-Tso
Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Ave, Urbana, IL 61801, USA.
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan.
Environ Microbiol. 2017 Nov;19(11):4576-4586. doi: 10.1111/1462-2920.13922. Epub 2017 Oct 2.
Specialized organotrophic Bacteria 'syntrophs' and methanogenic Archaea 'methanogens' form a unique metabolic interaction to accomplish cooperative mineralization of organic compounds to CH and CO . Due to challenges in cultivation of syntrophs, mechanisms for how their organotrophic catabolism circumvents thermodynamic restrictions remain unclear. In this study, we investigate two communities hosting diverse syntrophic aromatic compound metabolizers (Syntrophus, Syntrophorhabdus, Pelotomaculum and an uncultivated Syntrophorhabdacaeae member) to uncover their catabolic diversity and flexibility. Although syntrophs have been generally presumed to metabolize aromatic compounds to acetate, CO , H and formate, combined metagenomics and metatranscriptomics show that uncultured syntrophs utilize unconventional alternative metabolic pathways in situ producing butyrate, cyclohexanecarboxylate and benzoate as catabolic byproducts. In addition, we also find parallel utilization of diverse H and formate generating pathways to facilitate interactions with partner methanogens. Based on thermodynamic calculations, these pathways may enable syntrophs to combat thermodynamic restrictions. In addition, when fed with specific substrates (i.e., benzoate, terephthalate or trimellitate), each syntroph population expresses different pathways, suggesting ecological diversification among syntrophs. These findings suggest we may be drastically underestimating the biochemical capabilities, strategies and diversity of syntrophic bacteria thriving at the thermodynamic limit.
专门的有机营养细菌“互营菌”和产甲烷古菌“产甲烷菌”形成了一种独特的代谢相互作用，以实现有机化合物向CH₄和CO₂的协同矿化。由于互营菌培养方面的挑战，其有机营养分解代谢如何规避热力学限制的机制仍不清楚。在本研究中，我们调查了两个包含多种互营芳香化合物代谢菌（互营杆菌属、互营栖热菌属、泥杆菌属以及一个未培养的互营栖热菌科成员）的群落，以揭示它们的分解代谢多样性和灵活性。尽管一般认为互营菌会将芳香化合物代谢为乙酸盐、CO₂、H₂和甲酸盐，但宏基因组学和宏转录组学相结合的研究表明，未培养的互营菌在原位利用非常规的替代代谢途径，产生丁酸盐、环己烷羧酸盐和苯甲酸盐作为分解代谢副产物。此外，我们还发现了多种产生H₂和甲酸盐途径的平行利用，以促进与伙伴产甲烷菌的相互作用。基于热力学计算，这些途径可能使互营菌能够应对热力学限制。此外，当以特定底物（即苯甲酸盐、对苯二甲酸盐或偏苯三酸盐）为食时，每个互营菌种群会表达不同的途径，这表明互营菌之间存在生态多样性。这些发现表明，我们可能严重低估了在热力学极限下蓬勃生长的互营细菌的生化能力、策略和多样性。
