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Front. Microbiol. | doi: 10.3389/fmicb.2018.00147

Metagenomic functional potential predicts degradation rates of a model organophosphorus xenobiotic in pesticide contaminated soils

  • 1Hawkesbury Institute for the Environment, Western Sydney University, Australia
  • 2School of Science and Health, Western Sydney University, Australia

Chemical contamination of natural and agricultural habitats is an increasing global problem and a major threat to sustainability and human health. Organophosphorus (OP) compounds are one major class of contaminant and can undergo microbial degradation, however, no studies have applied system-wide ecogenomic tools to investigate OP degradation or use metagenomics to understand the underlying mechanisms of biodegradation In Situ and predict degradation potential. Thus there is a lack of knowledge regarding the functional genes and genomic potential underpinning degradation and community responses to contamination. Here we address this knowledge gap by performing shotgun sequencing of community DNA from agricultural soils with a history of pesticide usage and profiling shifts in functional genes and microbial taxa abundance. Our results showed two distinct groups of soils defined by differing functional and taxonomic profiles. Degradation assays suggested that these groups corresponded to the organophosphorus degradation potential of soils, with the fastest degrading community being defined by increases in transport and nutrient cycling pathways and enzymes potentially involved in phosphorus metabolism. This was against a backdrop of taxonomic community shifts potentially related to contamination adaptation and reflecting the legacy of exposure. Overall our results highlight the value of using holistic system-wide metagenomic approaches as a tool to predict microbial degradation in the context of the ecology of contaminated habitats.

Keywords: Metagenomics, bioremediation, Pesticides, Soil Microbiology, Biodegradation, Environmental

Received: 02 Nov 2017; Accepted: 23 Jan 2018.

Edited by:

Dimitrios G. Karpouzas, University of Thessaly, Greece

Reviewed by:

Chao LIANG, Institute of Applied Ecology (CAS), China
Mariusz Cycoń, Medical University of Silesia, Poland  

Copyright: © 2018 Jeffries, Rayu, Nielsen, Lai, Ijaz, Nazaries and Singh. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Thomas C. Jeffries, Western Sydney University, Hawkesbury Institute for the Environment, Penrith, Australia,