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

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

doi:10.3389/fbioe.2021.602464

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

Front Bioeng Biotechnol. 2021 Apr 15:9:602464. doi: 10.3389/fbioe.2021.602464. eCollection 2021.

Authors

Kusum Dhakar^{1

2}, Raphy Zarecki^{1

2}, Daniella van Bommel³, Nadav Knossow², Shlomit Medina¹, Basak Öztürk⁴, Radi Aly¹, Hanan Eizenberg¹, Zeev Ronen², Shiri Freilich¹

Affiliations

¹ Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishai, Israel.
² Department of Environmental Hydrology & Microbiology, Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beersheba, Israel.
³ lbert Katz School for Desert Studies Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beersheba, Israel.
⁴ Junior Research Group Microbial Biotechnology, Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.

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.

Keywords: 3; 4-dichloroaniline; Variovorax sp. strain SRS 16; biodegradation; genome-scale metabolic model; linuron; phenyl urea herbicide.