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

Pingping Cai,Manlan Niu,Caijuan Guo,Zhuo Ning,Min Zhang,Jiansheng Shi,Ningning Zhang

doi:10.3390/microorganisms7100412

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.

Highlights

The biodegradation of petroleum plays a vital role in transforming hydrocarbons into harmless matter in the natural environment [1]
The understanding of microorganism metabolism related to biodegradation in petroleum hydrocarbon contaminated (PHC) aquifers can help us to evaluate the potential ability of biodegradation, which is the theoretical basis of bioremediation [2]
Methane generation, and other types of carbon fixation metabolism may exist in petroleum-contaminated aquifers [4,5]

Summary

Introduction

The biodegradation of petroleum plays a vital role in transforming hydrocarbons into harmless matter in the natural environment [1]. Petroleum hydrocarbons are considered to be electron donors, while dissolved oxygen (O2) and inorganic oxide, such as nitrate (NO3−), manganese (IV) (Mn4+), ferric ion (Fe3+), sulfate (SO42−), and CO2, are considered to be electron acceptors [3] In these biochemical reactions, metabolism related to organic carbon consumption, such as nitrogen and sulfur metabolism, are involved. Many functional genes, including hydrocarbon oxygenase genes (e.g., AlkB, AssA, and BssA), methanogenic genes (e.g., Mrc), and carbon fixation genes (e.g., RubisCO), as well as key genes of the nitrogen/sulfur cycle (e.g., NosZ, and Dsr) were explored [4,10,11,12,13,14,15] These studies either focused on quantifying the limited genes by quantitative PCR or taking some related genes as a whole but in qualitative ways using GeoChip. The results could give us a new knowledge about petroleum-contaminated aquifers and be helpful for the management of these contaminated sites

Site Description

Hydrochemical Characteristics of Groundwater

Sequencing Statistics

Methane Metabolism

Nitrogen Metabolism

Sulfur Metabolism