Strategies for Enhancing in vitro Degradation of Linuron by Variovorax sp. Strain SRS 16 Under the Guidance of Metabolic Modeling.

Kusum Dhakar,Radi Aly,Hanan Eizenberg,Basak Öztürk,Shlomit Medina,Zeev Ronen,Raphy Zarecki,Nadav Knossow,Daniella Van Bommel,Shiri Freilich

doi:10.3389/fbioe.2021.602464

Abstract

Phenyl urea herbicides are being extensively used for weed control in both agricultural and non-agricultural applications. Linuron is one of the key herbicides in this family and is in wide use. Like other phenyl urea herbicides, it is known to have toxic effects as a result of its persistence in the environment. The natural removal of linuron from the environment is mainly carried through microbial biodegradation. Some microorganisms have been reported to mineralize linuron completely and utilize it as a carbon and nitrogen source. Variovorax sp. strain SRS 16 is one of the known efficient degraders with a recently sequenced genome. The genomic data provide an opportunity to use a genome-scale model for improving biodegradation. The aim of our study is the construction of a genome-scale metabolic model following automatic and manual protocols and its application for improving its metabolic potential through iterative simulations. Applying flux balance analysis (FBA), growth and degradation performances of SRS 16 in different media considering the influence of selected supplements (potential carbon and nitrogen sources) were simulated. Outcomes are predictions for the suitable media modification, allowing faster degradation of linuron by SRS 16. Seven metabolites were selected for in vitro validation of the predictions through laboratory experiments confirming the degradation-promoting effect of specific amino acids (glutamine and asparagine) on linuron degradation and SRS 16 growth. Overall, simulations are shown to be efficient in predicting the degradation potential of SRS 16 in the presence of specific supplements. The generated information contributes to the understanding of the biochemistry of linuron degradation and can be further utilized for the development of new cleanup solutions without any genetic manipulation.

Highlights

Phenyl urea herbicides are among the most widely used herbicides for weed control in several crops through their pre- or post-emergence applications
The present study aims to elucidate the effect of nutritional supplements on linuron degradation by Variovorax SRS 16 and estimate their potential usage as biostimulants in order to harness the full potential of indigenous degraders
The composition of the biomass reaction summarizes the fractional contribution of generalized microbial biomass precursors to the synthesis of a new cell and is similar to the previously published genome-scale reconstruction of Escherichia coli strain K-12 (Monk et al, 2017)

Summary

Introduction

Phenyl urea herbicides are among the most widely used herbicides for weed control in several crops (mostly cereals) through their pre- or post-emergence applications These substances interrupt electron transfer in photosystem II, leading to the formation of reactive oxygen species and resulting in cell damage (Liu, 2010). The increased rate of application of xenobiotics such as the phenyl urea herbicides in recent years enhanced their burden to the environment due to their persistence in the surroundings (Hasanuzzaman et al, 2020). These compounds are consistently found to have negative effects on the ecosystem, including hazards to human health (de Souza et al, 2020; Garcês et al, 2020). The selection of the amendments is mostly based on trial and error

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