Metagenomic insights into effects of spent engine oil perturbation on the microbial community composition and function in a tropical agricultural soil

Abstract

Analyzing the microbial community structure and functions become imperative for ecological processes. To understand the impact of spent engine oil (SEO) contamination on microbial community structure of an agricultural soil, soil microcosms designated 1S (agricultural soil) and AB1 (agricultural soil polluted with SEO) were set up. Metagenomic DNA extracted from the soil microcosms and sequenced using Miseq Illumina sequencing were analyzed for their taxonomic and functional properties. Taxonomic profiling of the two microcosms by MG-RAST revealed the dominance of Actinobacteria (23.36%) and Proteobacteria (52.46%) phyla in 1S and AB1 with preponderance of Streptomyces (12.83%) and Gemmatimonas (10.20%) in 1S and Geodermatophilus (26.24%), Burkholderia (15.40%), and Pseudomonas (12.72%) in AB1, respectively. Our results showed that soil microbial diversity significantly decreased in AB1. Further assignment of the metagenomic reads to MG-RAST, Cluster of Orthologous Groups (COG) of proteins, Kyoto Encyclopedia of Genes and Genomes (KEGG), GhostKOALA, and NCBI's CDD hits revealed diverse metabolic potentials of the autochthonous microbial community. It also revealed the adaptation of the community to various environmental stressors such as hydrocarbon hydrophobicity, heavy metal toxicity, oxidative stress, nutrient starvation, and C/N/P imbalance. To the best of our knowledge, this is the first study that investigates the effect of SEO perturbation on soil microbial communities through Illumina sequencing. The results indicated that SEO contamination significantly affects soil microbial community structure and functions leading to massive loss of nonhydrocarbon degrading indigenous microbiota and enrichment of hydrocarbonoclastic organisms such as members of Proteobacteria and Actinobacteria.

Mercury contamination imposes structural shift on the microbial community of an agricultural soil

“…The predominance of the phyla Proteobacteria and Firmicutes in the agricultural soil is expected as these phyla are replete with members that are well adapted to agricultural soils (Cheema et al 2015;Trivedi et al 2016;Salam et al 2017;Yin et al 2017). This is due to their huge physiological, morphological, and metabolic diversity; ability to survive in oligotrophic environments; ability to utilize diverse low molecular weight and high molecular weight recalcitrant carbon compounds prevalent in soils; and ability to survive adverse environmental conditions and resist desiccation caused by sharp variation in soil surface temperature (Fierer et al 2007;Spain et al 2009;Eilers et al 2010;Goldfarb et al 2011;Aislabie and Deslippe 2013;Montecchia et al 2015).…”

Detection of carbohydrate-active enzymes and genes in a spent engine oil-perturbed agricultural soil

“…The coordinates of the sampling site were latitude 8°29′ 11.54″ N and longitude 4°29′ 30.11″ E. The soil, which is dark-brown in color, is used to plant majorly maize and vegetables. Soil microcosm (agricultural soil, 1S; agricultural soil + SEO, AB1) set up, and incubation conditions have been described previously (Salam et al 2017). Similarly, the physicochemical properties, the residual spent engine oil (SEO), and its various constituents as well as the heavy metal content of the soil microcosms have been reported previously (Salam et al 2017).…”

“…The sequences were assembled into 2389 and 2948 unique contigs for soil microcosms 1S and AB1 with a total of 611,018 and 761,383 bp, an average length of 255 ± 63 and 258 ± 62 bp, and the GC content of 56 ± 4 and 62 ± 5%, respectively. After dereplication and quality control by the MG-RAST, the total number of sequence reads in AB1 metagenome reduced to 2828 sequence reads with 711,035 bp, an average length of 251 ± 54 bp, and a GC content of 62 ± 5% (Salam et al 2017).…”

“…Previously, we have investigated the effects of SEO perturbation on the microbial community structure and functions of an agricultural soil using Illumina NGS sequencing technique. The study particularly showed the dominance of hydrocarbonoclastic organisms due to the SEO contamination and preponderance of functional genes related to hydrocarbon degradation, heavy metal tolerance and detoxification, oxidative stress, response to nutrient starvation, and many others (Salam et al 2017). However, a curious observation is the detection of huge array of carbohydrate metabolism pathways mediated by carbohydrate-active enzymes and genes in the SEO-perturbed agricultural soil not detected in the original agricultural soil.…”

Microbiological Examination and Physicochemical Analysis of Estuary Water Used as a Point of Source Drinking Water

“…The amplified genomic DNA (15 µl) were then subjected to 1.5% gel electrophoresis after mixing with 2 µl of loading dye. These were done using as previously described by Salaam et al and Edet et al [22][23]…”