Metagenomic and metatranscriptomic analysis reveals enrichment for xenobiotic‐degrading bacterial specialists and xenobiotic‐degrading genes in a Canadian Prairie two‐cell biobed system

Abstract

Summary Biobeds are agriculture‐based bioremediation tools used to safely contain and microbially degrade on‐farm pesticide waste and rinsate, thereby reducing the negative environmental impacts associated with pesticide use. While these engineered ecosystems demonstrate efficient pesticide removal, the microbiomes in these environments remain largely understudied both taxonomically and functionally. This study used metagenomic and metatranscriptomic techniques to characterize the microbial community in a two‐cell Canadian biobed system before and after a field season of pesticide application. These culture‐independent approaches identified an enrichment of xenobiotic‐degrading bacteria, such as Afipia, Sphingopyxis and Pseudomonas, and enrichment and transcription of xenobiotic‐degrading genes, such as peroxidases, oxygenases, and hydroxylases, among others; we were able to directly link the transcription of these genes to Pseudomonas, Oligotropha, Mesorhizobium, Rhodopseudomonas, and Stenotrophomonas taxa.

Exploring microbial diversity responses in agricultural fields: a comparative analysis under pesticide stress and non-stress conditions

“…After metagenomic analysis of the activated sludge sample, a total of 68 subtypes of pesticide-degrading genes were identified, and out of them, dhn gene (encode dehydrogenase and degrade metamitron) was found to be dominant. Pesticide contaminates the metagenomic analysis of soil sample, revealing that as the concentration of pesticide increases in the soil, the expression and number of pesticide-biodegrading genes also increases and are mostly peroxidase, monooxydase, and cytochrome P450 (Russell et al, 2021). Hence, these studies confirmed that high-throughput techniques have enough potential to examine the microbial community and their different powerful pesticide-degrading genes under complex environments.…”

Biobeds, a Microbial-Based Remediation System for the Effective Treatment of Pesticide Residues in Agriculture

“…In a similar study, Góngora-Echeverría et al (2018) [108] identified several archaea (23), bacteria (598), and fungi (64) species in lab-scale biobed systems with the presence of a mixture of commercial pesticide formulates (2,4-D, atrazine, carbofuran, diazinon, and glyphosate). In addition, Russell et al (2021) [109] evaluated the bacterial diversity in a two-cell biobed system. After the treatment of pesticide residues, in cell one, 81 bacterial species from 58 genera were identified, while in cell two, 36 bacterial species from 33 genera were identified.…”

Degradation of Xenobiotic Pollutants: An Environmentally Sustainable Approach

“…Hence, new culture-independent approaches such as metagenomics are gaining momentum to identify non-cultivable microbes with xenobiotic degradation potential [68,69]. Few relevant xenobiotic degrading microorganisms were identified with culture-independent approaches, such as Sphingopyxis, Afipia, Oligotropha, Rhodopseudomonas, Mesorhizobium, and Stenotrophomonas [70]. The dominance of Thalassolituus and Oleispira have also been identified as vital oil-degrading bacteria through metagenomics and the metatranscriptomic approach [71].…”

“…They observed the upregulation of oxidase, hydrolase and NADPH-cytochrome P450 reductase genes for hydrolysis, oxidation and dealkylation of phoxim. Metatranscriptomic analysis of a two-cell Canadian biobed system identified diverse xenobiotic-degrading bacterial phyla such as Sphingopyxis, Mesorhizobium, Oligotropha, Stenotrophomonas, Afipia and Pseudomonas having an important role in the degradation of xenobiotics [70].…”