Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation

Abstract

Atrazine is an herbicide and a pollutant of great environmental concern that is naturally biodegraded by microbial communities. Paenarthrobacter aurescens TC1 is one of the most studied degraders of this herbicide. Here, we developed a genome scale metabolic model for P. aurescens TC1, iRZ1179, to study the atrazine degradation process at organism level. Constraint based flux balance analysis and time dependent simulations were used to explore the organism's phenotypic landscape. Simulations aimed at designing media optimized for supporting growth and enhancing degradation, by passing the need in strain design via genetic modifications. Growth and degradation simulations were carried with more than 100 compounds consumed by P. aurescens TC1. In vitro validation confirmed the predicted classification of different compounds as efficient, moderate or poor stimulators of growth. Simulations successfully captured previous reports on the use of glucose and phosphate as biostimulators of atrazine degradation, supported by in vitro validation. Model predictions can go beyond supplementing the medium with a single compound and can predict the growth outcomes for higher complexity combinations. Hence, the analysis demonstrates that the exhaustive power of the genome scale metabolic reconstruction allows capturing complexities that are beyond common biochemical expertise and knowledge and further support the importance of computational platforms for the educated design of complex media. The model presented here can potentially serve as a predictive tool towards achieving optimal biodegradation efficiencies and for the development of ecologically friendly solutions for pollutant degradation. Atrazine (2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine) is an herbicide employed to control broadleaf and grass mainly in crops such as rice, wheat, maize, and sorghum. It is also a well-known pollutant of great environmental concern. Atrazine has been shown to have negative effects such as DNA damage, gene expression shifts, cancer and endocrine disruption 1,2. Its residues are found in soil samples decades after it was last applied and were shown to chronically leach into local aquifers 3. As such, efforts are being made to limit and monitor its use 4. While atrazine was banned in the European Union and Switzerland since 2003, the United States Environmental Protection Agency still allows its wide use under monitoring 5,6. Areas contaminated with atrazine and other hazardous herbicides are rapidly increasing worldwide introducing a need in remediation approaches. Bioremediation-an environmental bioprocess in which naturally occurring organisms are used for breaking down hazardous substances into less toxic or non-toxic substances-is increasingly acknowledged as a cost-effective feasible alternative for environmental cleaning 7-9. Critical environmental bioprocesses are naturally carried out by bacteria and are related to removal of pollutants from water, soil or air 10. Thus, bacterial bioremediation is widely applied for the ...

PTCL1-EstA from Paenarthrobacter aurescens TC1, a Candidate for Industrial Application Belonging to the VIII Esterase Family

“…Microorganisms that grow in environments with extreme pH, salinity, and temperature conditions are also important sources of lipases with industrial potential [23]. Paenarthrobacter aurescens TC1 (formerly Arthrobacter aurescens TC1) is a high G+C content Gram-positive aerobic bacterium that acts as a bacterial bioremediate to degrade the herbicide atrazine and has been shown to degrade most other common amino acids [24][25][26]. Due to the presence of duplicated catabolic genes and its ability to funnel plasmid-derived intermediates into chromosomally encoded pathways, the P. aurescens strain can survive and prosper under various pressure and temperature conditions [27].…”

Modeling-Guided Amendments Lead to Enhanced Biodegradation in Soil

“…In a previous study, an Arthrobacter species (NCBI accession MG554188 ) was identified as an efficient degrader of atrazine in soil taken from a commercial field in Newe-Ya’ar, Israel ( 32 ). The native species is highly similar (98% identity) to the well-studied atrazine degrader Paenarthrobacter aurescens TC1 ( 34 , 39 , 40 ). Despite clear evidence for atrazine degradation activity in general and in the specific soil in particular, the relative abundance of the Arthrobacter species was unaffected by application of atrazine at conventional rates in commercial agricultural practices ( 32 ).…”

“…S1 ). The amino acids include serine, an efficient biostimulant among amino acids, and histidine, whose simulative effect depends on the presence of atrazine (and is more significant in its absence) ( 34 ). OCDCA, despite being a carbon-rich compound, is predicted to be a nonefficient enhancer, indicating that the number of carbons by itself is insufficient for predicting simulation efficiency ( Fig.…”

“…Although it is an effective agrochemical in increasing crop productivity, its persistence results in pollution of soil, surface water, and groundwater ( 38 ). To enhance the rate of degradation of atrazine in contaminated soils, the combination of sequencing technologies and metabolic modeling was shown efficient for designing strategies that will optimize its degradation by indigenous soil bacteria under in vitro conditions ( 32 , 33 , 34 ). Here, we pursued metabolic modeling for promoting realistic in terra solutions by simulation-based prioritization of alternative supplements as potential biostimulants, considering a collection of indigenous bacteria.…”

Impact of Paenarthrobacter ureafaciens ZF1 on the soil enzyme activity and microbial community during the bioremediation of atrazine-contaminated soils

“…Microbial remediation of contaminated soil have become a popular choice because of their relatively low application cost and minimal environmental impact [ 5 , 6 ]. At present, certain degrading bacteria have been isolated and applied in remediating atrazine – contaminated soil [ 7 , 8 ], including strains of Pseudomonas sp. [ 9 ], Rhodococcus sp .…”