Ju Feng, Wang Yubo, Zhang Tong
1Environmental Biotechnology Lab, The University of Hong Kong SAR, Pokfulam Road, Hong Kong, China.
Institute of Advanced Technology, Westlake Institute for Advanced Study, Westlake University, Hangzhou, 310064 People's Republic of China.
Biotechnol Biofuels. 2018 May 11;11:135. doi: 10.1186/s13068-018-1136-6. eCollection 2018.
Methanogenic biodegradation of aromatic compounds depends on syntrophic metabolism. However, metabolic enzymes and pathways of uncultured microorganisms and their ecological interactions with methanogenic consortia are unknown because of their resistance to isolation and limited genomic information.
Genome-resolved metagenomics approaches were used to reconstruct and dissect 23 prokaryotic genomes from 37 and 20 °C methanogenic phenol-degrading reactors. Comparative genomic evidence suggests that temperature difference leads to the colonization of two distinct cooperative sub-communities that can respire sulfate/sulfite/sulfur or nitrate/nitrite compounds and compete for uptake of methanogenic substrates (e.g., acetate and hydrogen). This competition may differentiate methanogenesis. The uncultured - G1, whose close relatives have broad ecological niches including the deep-sea vents, aquifers, sediment, limestone caves, spring, and anaerobic digesters, is implicated as a -like facultative anaerobic diazotroph with metabolic versatility and remarkable environmental adaptability. We provide first genomic evidence for butyrate, alcohol, and carbohydrate utilization by a T78 clade bacterium, and phenol carboxylation and assimilatory sulfite reduction in a bacterium.
Genome-resolved metagenomics enriches our view on the differentiation of microbial community composition, metabolic pathways, and ecological interactions in temperature-differentiated methanogenic phenol-degrading bioreactors. These findings suggest optimization strategies for methanogenesis on phenol, such as temperature control, protection from light, feed desulfurization, and hydrogen sulfide removal from bioreactors. Moreover, decoding genome-borne properties (e.g., antibiotic, arsenic, and heavy metal resistance) of uncultured bacteria help to bring up alternative schemes to isolate them.
芳香族化合物的产甲烷生物降解依赖于互营代谢。然而，未培养微生物的代谢酶和途径及其与产甲烷菌群的生态相互作用尚不清楚，因为它们难以分离且基因组信息有限。
采用基因组解析宏基因组学方法，从37℃和20℃的产甲烷苯酚降解反应器中重建并剖析了23个原核生物基因组。比较基因组学证据表明，温度差异导致两个不同的协同亚群落定殖，这两个亚群落可以呼吸硫酸盐/亚硫酸盐/硫或硝酸盐/亚硝酸盐化合物，并竞争摄取产甲烷底物（如乙酸盐和氢气）。这种竞争可能会使甲烷生成产生差异。未培养的G1，其近亲具有广泛的生态位，包括深海热液喷口、含水层、沉积物、石灰岩洞穴、泉水和厌氧消化器，被认为是一种类似兼性厌氧固氮菌，具有代谢多样性和显著的环境适应性。我们首次提供了T78分支细菌利用丁酸盐、酒精和碳水化合物，以及某细菌进行苯酚羧化和同化亚硫酸盐还原的基因组证据。
基因组解析宏基因组学丰富了我们对温度分化的产甲烷苯酚降解生物反应器中微生物群落组成、代谢途径和生态相互作用差异的认识。这些发现提出了苯酚甲烷生成的优化策略，如温度控制、避光、进料脱硫和从生物反应器中去除硫化氢。此外，解码未培养细菌的基因组特性（如抗生素、砷和重金属抗性）有助于提出分离它们的替代方案。
