Insights into Biodegradation Related Metabolism in an Abnormally Low Dissolved Inorganic Carbon (DIC) Petroleum-Contaminated Aquifer by Metagenomics Analysis

Abstract

In petroleum-contaminated aquifers, biodegradation is always associated with various types of microbial metabolism. It can be classified as autotrophic (such as methanogenic and other carbon fixation) and heterotrophic (such as nitrate/sulfate reduction and hydrocarbon consumption) metabolism. For each metabolic type, there are several key genes encoding the reaction enzymes, which can be identified by metagenomics analysis. Based on this principle, in an abnormally low dissolved inorganic carbon (DIC) petroleum-contaminated aquifer in North China, nine groundwater samples were collected along the groundwater flow, and metagenomics analysis was used to discover biodegradation related metabolism by key genes. The major new finding is that autotrophic metabolism was revealed, and, more usefully, we attempt to explain the reasons for abnormally low DIC. The results show that the methanogenesis gene, Mcr, was undetected but more carbon fixation genes than nitrate reduction and sulfate genes were found. This suggests that there may be a considerable number of autotrophic microorganisms that cause the phenomenon of low concentration of dissolved inorganic carbon in contaminated areas. The metagenomics data also revealed that most heterotrophic, sulfate, and nitrate reduction genes in the aquifer were assimilatory sulfate and dissimilatory nitrate reduction genes. Although there was limited dissolved oxygen, aerobic degrading genes AlkB and Cdo were more abundant than anaerobic degrading genes AssA and BssA. The metagenomics information can enrich our microorganic knowledge about petroleum-contaminated aquifers and provide basic data for further bioremediation.

New Frontiers of Anaerobic Hydrocarbon Biodegradation in the Multi-Omics Era

“…While the environment is anaerobic, many genes were found in the metagenomic data corresponding to aerobic biodegradation. Cai et al, 2019 16S rDNA profile and metatranscriptomics RNA seq data revealed that a group of nitrifiers insignificant in number has a rather significant impact on the metabolic pathways by supplying nitrate to the nitrate reducers in activated sludge bioreactors.…”

“…In a petroleum-contaminated aquifer, nitrate and sulfate reducers dominated the community. Although the aquifer was anaerobic, multiple aerobic biodegradation genes were found in the samples, but genes of enzymes involved in methanogenesis were lacking ( Cai et al, 2019 ). In certain environments having fluctuating levels of dissolved oxygen, both anaerobic and aerobic metabolic pathways could be detected in the metagenomes.…”

Recent Advances in Applied Microbiology: Editorial

“…Fang et al [ 18 ] studied three denitrifying bacteria and two functional genes as potential biomarkers for total nitrogen removal. Cai et al [ 19 ] used metagenomics analysis to explore the biodegradation related metabolism in an abnormally low dissolved inorganic carbon petroleum-contaminated aquifer. Algal biomass degradation by marine fungi isolated from the brown seaweed Fucus sp.…”