Systems biology approach to elucidation of contaminant biodegradation in complex samples – integration of high-resolution analytical and molecular tools

Gauchotte-Lindsay, Caroline; Aspray, Thomas J.; Knapp, Mara; Ijaz, Umer Zeeshan

doi:10.1039/c9fd00020h

Cited by 10 publications

(1 citation statement)

References 30 publications

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“…This family contains numerous genera, including Acidovorax, Brachymonas, and Comamonas, which are widely reported in contaminated soil microbiomes. Extensimonas, on the other hand, has rarely been reported in soil microbiomes, and there has only been a handful of studies on their involvement in hydrocarbon degradation (Zhang et al, 2013;Gauchotte-Lindsay et al, 2019). This soil therefore potentially presents a rich source of unusual species with potentially novel hydrocarbon-degrading abilities.…”

Section: Discussionmentioning

confidence: 99%

Soil Microbiome Structure and Function in Ecopiles Used to Remediate Petroleum-Contaminated Soil

Wang

Garrido‐Sanz

Sansegundo‐Lobato

et al. 2021

Front. Environ. Sci.

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The soil microbiome consists of a vast variety of microorganisms which contribute to essential ecosystem services including nutrient recycling, protecting soil structure, and pathogen suppression. Recalcitrant organic compounds present in soils contaminated with fuel oil can lead to a decrease in functional redundancy within soil microbiomes. Ecopiling is a passive bioremediation technique involving biostimulation of indigenous hydrocarbon degraders, bioaugmentation through inoculation with known petroleum-degrading consortia, and phytoremediation. The current study investigates the assemblage of soil microbial communities and pollutant-degrading potential in soil undergoing the Ecopiling process, through the amplicon marker gene and metagenomics analysis of the contaminated soil. The analysis of key community members including bacteria, fungi, and nematodes revealed a surprisingly diverse microbial community composition within the contaminated soil. The soil bacterial community was found to be dominated by Alphaproteobacteria (60–70%) with the most abundant genera such as Lysobacter, Dietzia, Pseudomonas, and Extensimonas. The fungal community consisted mainly of Ascomycota (50–70% relative abundance). Soil sequencing data allowed the identification of key enzymes involved in the biodegradation of hydrocarbons, providing a novel window into the function of individual bacterial groups in the Ecopile. Although the genus Lysobacter was identified as the most abundant bacterial genus (11–46%) in all of the contaminated soil samples, the metagenomic data were unable to confirm a role for this group in petrochemical degradation. Conversely, genera with relatively low abundance such as Dietzia (0.4–9.0%), Pusillimonas (0.7–2.3%), and Bradyrhizobium (0.8–1.8%) did possess genes involved in aliphatic or aromatic compound degradation.

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Section: Discussionmentioning

confidence: 99%