Long-Term Oil Contamination Alters the Molecular Ecological Networks of Soil Microbial Functional Genes

Yuting Liang,Ye Deng,Jizhong Zhou,Guanghe Li,Bo Sun,Huihui Zhao

doi:10.3389/fmicb.2016.00060

Abstract

With knowledge on microbial composition and diversity, investigation of within-community interactions is a further step to elucidate microbial ecological functions, such as the biodegradation of hazardous contaminants. In this work, microbial functional molecular ecological networks were studied in both contaminated and uncontaminated soils to determine the possible influences of oil contamination on microbial interactions and potential functions. Soil samples were obtained from an oil-exploring site located in South China, and the microbial functional genes were analyzed with GeoChip, a high-throughput functional microarray. By building random networks based on null model, we demonstrated that overall network structures and properties were significantly different between contaminated and uncontaminated soils (P < 0.001). Network connectivity, module numbers, and modularity were all reduced with contamination. Moreover, the topological roles of the genes (module hub and connectors) were altered with oil contamination. Subnetworks of genes involved in alkane and polycyclic aromatic hydrocarbon degradation were also constructed. Negative co-occurrence patterns prevailed among functional genes, thereby indicating probable competition relationships. The potential “keystone” genes, defined as either “hubs” or genes with highest connectivities in the network, were further identified. The network constructed in this study predicted the potential effects of anthropogenic contamination on microbial community co-occurrence interactions.

Highlights

Increased exploration and exploitation of oil resources have resulted in severe contamination worldwide (Kvenvolden and Cooper, 2003)
Effects of Oil Contamination on Microbial functional molecular ecological networks (fMENs) fMENs were constructed for both contaminated and uncontaminated soils to determine the effect of oil contamination on microbial functional gene co-occurrence (Table 1)
To understand the influence of oil contamination on microbial interactions further, we investigated the changes of microbial molecular ecological networks in response to oil contamination

Summary

Introduction

Increased exploration and exploitation of oil resources have resulted in severe contamination worldwide (Kvenvolden and Cooper, 2003). Hundreds of micrograms of oil per gram of soil were detected in several heavily contaminated sites (Liang et al, 2012). Oil contamination alters the biotic taxonomic composition and physical and chemical properties of an environment, posing considerable threat to the ecological systems (Kingston, 2002). Oil contamination considerably affects the structures and functional diversity of microbial communities, including bacteria, fungi, and archaea (Liang et al, 2011; Lu et al, 2012; Bell et al, 2014). Contamination Alters Microbial Community Networks microbial population diversity in oil-contaminated sites usually declines (Van Hamme et al, 2003), of those microbes participating in carbon and nitrogen cycling. The loss of microbial diversity and changes in community composition alter their functional processes. The biodegradation of refractory components of oil contaminants, such as high molecular-weight polycyclic aromatic hydrocarbons (PAHs), requires the cometabolism of several species (Nzila, 2013)

Methods

Results

Conclusion