C1 compounds shape the microbial community of an abandoned century-old oil exploration well

Abstract

The search for microorganisms that degrade hydrocarbons is highly relevant because it enables the bioremediation of these substances cheaply and without dangerous by-products. In this work, we studied the microbial communities of an exploratory oil well, abandoned a century ago, located in the Cahuita National Park of Costa Rica. Cahuita well is characterized by a continuous efflux of methane and the presence of a mixture of hydrocarbons including C2-dibenzothiophene, phenanthrene or anthracene, fluoranthene pyrene, dibenzothiophene, tricyclic terpanes, pyrene, sesquiterpenes, sterane and n-alkanes. Based on the analysis of 16S rRNA gene amplicons, we detected a significant abundance of methylotrophic bacteria (Methylobacillus (6.3-26.0 % of total reads) and Methylococcus (4.1-30.6 %)) and the presence of common genera associated with hydrocarbon degradation, such as Comamonas (0.8-4.6 %), Hydrogenophaga (1.5-3.3 %) Rhodobacter (1.0-4.9 %) and Flavobacterium (1.1-6.5 %). We evidenced the presence of methane monooxygenase (MMO) activities, responsible for the first step in methane metabolism, by amplifying the pmo gene from environmental DNA. We also isolated a strain of Methylorubrum rhodesianum, which was capable of using methanol as its sole carbon source. This work represents a contribution to the understanding of the ecology of communities of microorganisms in environments with permanently high concentrations of methane and hydrocarbons, which also has biotechnological implications for the bioremediation of highly polluting petroleum components.