Remarkable shift in structural and functional properties of an animal charcoal-polluted soil accentuated by inorganic nutrient amendment

Abstract

Background Soils polluted with animal charcoal from skin and hide cottage industries harbour extremely toxic and carcinogenic hydrocarbon pollutants and thus require a bio-based eco-friendly strategy for their depuration. The effects of carbon-free mineral medium (CFMM) amendment on hydrocarbon degradation and microbial community structure and function in an animal charcoal-polluted soil was monitored for 6 weeks in field moist microcosms consisting of CFMM-treated soil (FN4) and an untreated control (FN1). Hydrocarbon degradation was monitored using gas chromatography-flame ionization detector (GC-FID), and changes in microbial community structure were monitored using Kraken, while functional annotation of putative open reading frames (ORFs) was done using KEGG KofamKOALA and NCBI’s conserved domain database (CDD). Results Gas chromatographic analysis of hydrocarbon fractions revealed the removal of 84.02% and 82.38% aliphatic and 70.09% and 70.14% aromatic fractions in FN4 and FN1 microcosms in 42 days. Shotgun metagenomic analysis of the two metagenomes revealed a remarkable shift in the microbial community structure. In the FN4 metagenome, 92.97% of the population belong to the phylum Firmicutes and its dominant representative genera Anoxybacillus (64.58%), Bacillus (21.47%) and Solibacillus (2.39%). In untreated FN1 metagenome, the phyla Proteobacteria (56.12%), Actinobacteria (23.79%) and Firmicutes (11.20%), and the genera Xanthobacter (9.73%), Rhizobium (7.49%) and Corynebacterium (7.35%), were preponderant. Functional annotation of putative ORFs from the two metagenomes revealed the detection of degradation genes for aromatic hydrocarbons, benzoate, xylene, chlorocyclohexane/chlorobenzene, toluene and several others in FN1 metagenome. In the FN4 metagenome, only seven hydrocarbon degradation genes were detected. Conclusion This study revealed that though CFMM amendment slightly increases the rate of hydrocarbon degradation, it negatively impacts the structural and functional properties of the animal charcoal-polluted soil. It also revealed that intrinsic bioremediation of the polluted soil could be enhanced via addition of water and aeration.

Deciphering the cytochrome P450 genes in the microbiome of a chronically polluted soil with history of agricultural activities

“…With a total of 45 out of 72 bacterial CYP families affiliated to Bacillus, Streptomyces, and Mycobacterium, these genera are the most represented in the CYPome. This may be attributed to the fact that they are members of the phyla Firmicutes and Actinobacteria which have consistently been reported to assume dominance in soils contaminated with petroleum hydrocarbons, attribute accounted for by their resilience to stressors and extreme conditions, including oligotrophy (Leahy and Colwell 1990;Kanaly and Harayama 2010;Salam and Obayori 2020). The Actinobacteria are particularly notable for their metabolic plasticity and possession of diverse gene batteries encoding enzymes with broad specificities (Salam and Obayori 2020).…”

“…It is extremely difficult to find a polluted soil with a single pollutant. The presence of these pollutants imposes selective pressure on the microbial community, alters soil physicochemistry, reduces inorganic nutrients bioavailability, and potentiates changes in the direction of alternative metabolism and secondary metabolism, including bioactive compounds and toxicity and stress-induced resistances (Salam 2020;Salam and Obayori 2020;Salam et al 2021). Understanding the potential of pollutants to disrupt community structure and functions has undergone a shift in the past decade or two from culture-dependent to culture-independent method, with more emphasis placed on metagenomic approach.…”