Vertical stratification of bacteria and the chemical compounds in crude oil-contaminated soil layers of the semi-deserted Dzungharian Basin

Abstract

The largely semi-deserted and deserted Dzungharian Basin sites in the northwest of China geologically represent an extension of the Paleozoic Kazakhstan Block and were once part of an independent continent. For reasons of overdevelopment and unreasonable operations during the process of exploitation and transportation, oil pollutants that were discharged into the soil environment caused serious pollution in this weak ecosystem. To explore the bacterial community composition in detail and their possible origination and potential during the natural attenuation of petroleum contaminants in this type of ecologic niche, GC-MS and high-throughput sequencing techniques were used to resolve the organic compounds and bacterial communities in vertical soil layers. The degradation of petroleum contaminants in semi-deserted and deserted soils mainly occurred in the layer at a depth of 45-55 cm. During this process, aromatic and heterocyclic compounds were significantly enriched in soils. The bacterial communities in this basin exhibited a distinct vertical stratification from the surface layer down to the bottom soil layer. Considering the interaction between the community composition and the geochemical properties, we speculate that the degradation of petroleum contaminants in this semi-deserted and deserted soil might represent a microorganism-mediated process and mainly occur in the deeper soil layer.

Fig 1. Phenotypes of crude oil-contaminated soil samples.

Soil columns from the surface down to a depth of approximately 55 cm were divided into three layers. The green dash indicates one centimeter.

Fig 2. GC-MS analysis of the organic compounds in the three layers of petroleum-contaminated soil samples.

A. GC chromatograms of the compounds. B. Molecular structures of the aromatic compounds and heterocyclic compounds specifically denoted by arrows in the GC chromatograms. C. The heatmap indicates the profile of organic compounds with a normalized content >0.1%.

Fig 3. Dendrogram showing the similarity of bacterial communities revealed by T-RFLP analysis of the 16S rDNA from different layers of the petroleum-contaminated soils.

Samples were collected from eight sites, and three layers per sites were analyzed.

Fig 4

The rank-abundance curves (A) and rarefaction curves (B) based on the bacterial OTUs determined at 97% similarity of the sequences indicating the diversity, richness and coverage of the bacterial communities in the three layers of petroleum-contaminated soils.

Fig 5

Relative abundance of the top 10 groups classified at the level of sub-phylum and class (A), order (B), family (C) and genus (D) in communities from different soil layers.

Fig 6. Taxonomic tree of the top 10 genera among all the bacteria communities.

The pie chart indicates the ratio of communities from different soil layers. The ratio of selected taxonomic units among all bacteria communities and the ratio in the upper level taxonomic unit are listed under the taxonomic name.

Fig 7

Heatmap showing the composition of the communities from the soil layers classified at the level of class (A), order (B), family (C) and genus (D). Those units with abundant lists in the top 35 of the whole community were selected.

Fig 8. Heatmap showing the hierarchical clustering analysis of the communities from different ecological sites.

Pearson correlation distance metric and average linkage clustering methods were used to construct HCL trees of the samples and OTUs determined at 95% similarity. The reference sequences were extracted from the water column of the Clarion-Clipperton fracture zone in the Pacific Ocean (SRR1980879, SRR1980893 and SRR1980904), estuary water (ERX1529128, ERX1529080), environmental soil samples (SRR1554795, SRR1554978), and crude oil (ERR958514, ERR1039276).

Fig 9. Neighbor-joining phylogeny tree of 16S rRNA gene sequences of the representative clones of the libraries for three soil layers.

Clone from the environmental communities were selected as the references. Bootstrap values (n = 1,000) greater than 50% are indicated in the subclusters that were specifically present in Karamay ecological environments.