Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts.
Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts.
Biotechnol Bioeng. 2018 Jun;115(6):1450-1464. doi: 10.1002/bit.26576. Epub 2018 Mar 24.
Harnessing the metabolic potential of uncultured microbial communities is a compelling opportunity for the biotechnology industry, an approach that would vastly expand the portfolio of usable feedstocks. Methane is particularly promising because it is abundant and energy-rich, yet the most efficient methane-activating metabolic pathways involve mixed communities of anaerobic methanotrophic archaea and sulfate reducing bacteria. These communities oxidize methane at high catabolic efficiency and produce chemically reduced by-products at a comparable rate and in near-stoichiometric proportion to methane consumption. These reduced compounds can be used for feedstock and downstream chemical production, and at the production rates observed in situ they are an appealing, cost-effective prospect. Notably, the microbial constituents responsible for this bioconversion are most prominent in select deep-sea sediments, and while they can be kept active at surface pressures, they have not yet been cultured in the lab. In an industrial capacity, deep-sea sediments could be periodically recovered and replenished, but the associated technical challenges and substantial costs make this an untenable approach for full-scale operations. In this study, we present a novel method for incorporating methanotrophic communities into bioindustrial processes through abstraction onto low mass, easily transportable carbon cloth artificial substrates. Using Gulf of Mexico methane seep sediment as inoculum, optimal physicochemical parameters were established for methane-oxidizing, sulfide-generating mesocosm incubations. Metabolic activity required >∼40% seawater salinity, peaking at 100% salinity and 35 °C. Microbial communities were successfully transferred to a carbon cloth substrate, and rates of methane-dependent sulfide production increased more than threefold per unit volume. Phylogenetic analyses indicated that carbon cloth-based communities were substantially streamlined and were dominated by Desulfotomaculum geothermicum. Fluorescence in situ hybridization microscopy with carbon cloth fibers revealed a novel spatial arrangement of anaerobic methanotrophs and sulfate reducing bacteria suggestive of an electronic coupling enabled by the artificial substrate. This system: 1) enables a more targeted manipulation of methane-activating microbial communities using a low-mass and sediment-free substrate; 2) holds promise for the simultaneous consumption of a strong greenhouse gas and the generation of usable downstream products; and 3) furthers the broader adoption of uncultured, mixed microbial communities for biotechnological use.
利用未培养微生物群落的代谢潜力是生物技术产业的一个诱人机会，这种方法将极大地扩展可用原料的组合。甲烷特别有前景，因为它丰富且富含能量，但最有效的甲烷激活代谢途径涉及厌氧甲烷营养古菌和硫酸盐还原菌的混合群落。这些群落以高代谢效率氧化甲烷，并以可比的速率和近乎化学计量的比例产生化学还原的副产物。这些还原化合物可用于原料和下游化学品生产，并且以原位观察到的生产速率，它们是一种有吸引力且具有成本效益的前景。值得注意的是，负责这种生物转化的微生物成分在选定的深海沉积物中最为突出，虽然它们可以在表面压力下保持活性，但尚未在实验室中培养。在工业规模上，深海沉积物可以定期回收和补充，但相关的技术挑战和巨大成本使得这种方法无法用于全面运作。在这项研究中，我们提出了一种通过将甲烷营养菌群抽象到低质量、易于运输的碳纤维人工基质中来纳入生物工业过程的新方法。使用墨西哥湾甲烷渗漏沉积物作为接种物，为甲烷氧化、硫化物生成中观培养建立了最佳的物理化学参数。代谢活性需要 >∼40%的海水盐度，在 100%盐度和 35°C 时达到峰值。微生物群落成功转移到碳纤维基质上，单位体积的甲烷依赖性硫化物产生速率增加了三倍以上。系统发育分析表明，碳纤维基群落得到了极大的简化，并且以脱硫产甲烷菌属为主。用碳纤维纤维进行荧光原位杂交显微镜分析显示，厌氧甲烷营养菌和硫酸盐还原菌的一种新的空间排列方式暗示了人工基质允许的电子偶联。该系统：1）使用低质量和无沉积物的基质更有针对性地操纵激活甲烷的微生物群落；2）有望同时消耗一种强温室气体并产生可用的下游产品；3）进一步推动未培养的混合微生物群落更广泛地用于生物技术。
