Toth Courtney R A, Berdugo-Clavijo Carolina, O'Farrell Corynne M, Jones Gareth M, Sheremet Andriy, Dunfield Peter F, Gieg Lisa M
Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
Microorganisms. 2018 Jul 10;6(3):65. doi: 10.3390/microorganisms6030065.
Polycyclic aromatic hydrocarbons (PAH) such as naphthalene are widespread, recalcitrant pollutants in anoxic and methanogenic environments. A mechanism catalyzing PAH activation under methanogenic conditions has yet to be discovered, and the microbial communities coordinating their metabolism are largely unknown. This is primarily due to the difficulty of cultivating PAH degraders, requiring lengthy incubations to yield sufficient biomass for biochemical analysis. Here, we sought to characterize a new methanogenic naphthalene-degrading enrichment culture using DNA-based stable isotope probing (SIP) and metagenomic analyses. 16S rRNA gene sequencing of fractionated DNA pinpointed an unclassified species as a putative naphthalene degrader after two months of SIP incubation. This finding was supported by metabolite and metagenomic evidence of genes predicted to encode for enzymes facilitating naphthalene carboxylic acid CoA-thioesterification and degradation of an unknown arylcarboxyl-CoA structure. Our findings also suggest a possible but unknown role for in naphthalene degradation. This is the first reported functional evidence of PAH biodegradation by a methanogenic consortium, and we envision that this approach could be used to assess carbon flow through other slow growing enrichment cultures and environmental samples.
多环芳烃（PAH）如萘，是缺氧和产甲烷环境中广泛存在的难降解污染物。尚未发现产甲烷条件下催化PAH活化的机制，并且协调其代谢的微生物群落也 largely unknown。这主要是由于培养PAH降解菌存在困难，需要长时间培养才能获得足够的生物量用于生化分析。在此，我们试图利用基于DNA的稳定同位素探测（SIP）和宏基因组分析来表征一种新的产甲烷萘降解富集培养物。经过两个月的SIP培养后，对分级分离的DNA进行16S rRNA基因测序，确定了一个未分类的物种为假定的萘降解菌。这一发现得到了代谢物和宏基因组证据的支持，这些证据表明存在预测编码促进萘羧酸辅酶A硫酯化和未知芳基羧基辅酶A结构降解的酶的基因。我们的研究结果还表明 在萘降解中可能存在但未知的作用。这是首次报道产甲烷菌联合体对PAH生物降解的功能证据，我们设想这种方法可用于评估通过其他生长缓慢的富集培养物和环境样品的碳流。
