https://doi.org/10.25678/0008YV

Data for: Making Waves: Enhancing pollutant biodegradation via rational engineering of microbial consortia

Biodegradation holds promise as an effective and sustainable process for the removal of synthetic chemical pollutants. Nevertheless, rational engineering of biodegradation for pollutant remediation remains an unfulfilled goal, while chemical pollution of waters and soils continues to advance. Efforts to (i) identify functional bacteria from aquatic and soil microbiomes, (ii) assemble them into biodegrading consortia, and (iii) identify maintenance and performance determinants, are challenged by large number of pollutants and the complexity in the enzymology and ecology of pollutant biodegradation. To overcome these challenges, approaches that leverage knowledge from environmental bio-chem-informatics and metabolic engineering are crucial. Here, we propose a novel high-throughput bio-chem-informatics pipeline, to link chemicals and their predicted biotransformation pathways with potential enzymes and bacterial strains. Our framework systematically selects the most promising candidates for the degradation of chemicals with unknown biotransformation pathways and associated enzymes from the vast array of aquatic and soil bacteria. We substantiated our perspective by validating the pipeline for two chemicals with known or predicted pathways and show that our predicted strains are consistent with strains known to biotransform those chemicals. Such pipelines can be integrated with metabolic network analysis built upon genome-scale models and ecological principles to rationally design fit-for-purpose bacterial communities for augmenting deficient biotransformation functions and study operational and design parameters that influence their structure and function. We believe that research in this direction can pave the way for achieving our long-term goal of enhancing pollutant biodegradation.

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Citation

This Data Package

Karakurt-Fischer, S., Johnson, D. R., Fenner, K., & Hafner, J. (2023). Data for: Making Waves: Enhancing pollutant biodegradation via rational engineering of microbial consortia (Version 1.0) [Data set]. Eawag: Swiss Federal Institute of Aquatic Science and Technology. https://doi.org/10.25678/0008YV

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The associated article

Karakurt-Fischer, S., Johnson, D. R., Fenner, K., & Hafner, J. (2023). Making Waves: Enhancing pollutant biodegradation via rational engineering of microbial consortia. Water Research, 120756. https://doi.org/10.1016/j.watres.2023.120756

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Publication Data Package for:

https://doi.org/10.1016/j.watres.2023.120756

Open Data

Author	Karakurt-Fischer, Sema Johnson, David R. Fenner, Kathrin Hafner, Jasmin
Keywords	bioaugmentation,environmental bioinformatics,high-throughput community assembly,microbial community engineering,pollutant biodegradation
Substances (scientific names)	1) Atrazine (InChI=1S/C8H14ClN5/c1-4-10-7-12-6(9)13-8(14-7)11-5(2)3/h5H,4H2,1-3H3,(H2,10,11,12,13,14)) 10) Dimethylcarbamic acid (InChI=1S/C3H7NO2/c1-4(2)3(5)6/h1-2H3,(H,5,6)) 11) 3,4-Dichlorocatechol (InChI=1S/C6H4Cl2O2/c7-3-1-2-4(9)6(10)5(3)8/h1-2,9-10H) 12) 2,3-Dichloromuconic acid (InChI=1S/C6H4Cl2O4/c7-3(1-2-4(9)10)5(8)6(11)12/h1-2H,(H,9,10)(H,11,12) ) 13) 2-Chlorodienelactone (InChI=1S/C6H3ClO4/c7-4-1-3(2-5(8)9)11-6(4)10/h1-2H,(H,8,9)/p-1/b3-2-) 14) 2-Chloromaleylacetic acid (InChI=1S/C6H5ClO5/c7-4(6(11)12)1-3(8)2-5(9)10/h1H,2H2,(H,9,10)(H,11,12)/p-2/b4-1+) 15) Maleylacetic acid (InChI=1S/C6H6O5/c7-4(3-6(10)11)1-2-5(8)9/h1-2H,3H2,(H,8,9)(H,10,11)/b2-1-) 2) Hydroxyatrazine (InChI=1S/C8H15N5O/c1-4-9-6-11-7(10-5(2)3)13-8(14)12-6/h5H,4H2,1-3H3,(H3,9,10,11,12,13,14)) 3) N-isopropylammelide (InChI=1S/C6H10N4O2/c1-3(2)7-4-8-5(11)10-6(12)9-4/h3H,1-2H3,(H3,7,8,9,10,11,12)) 4) Cyanuric acid (InChI=1S/C3H3N3O3/c7-1-4-2(8)6-3(9)5-1/h(H3,4,5,6,7,8,9)) 5) 1-Carboxybiuret (InChI=1S/C3H5N3O4/c4-1(7)5-2(8)6-3(9)10/h(H,9,10)(H4,4,5,6,7,8)) 6) Biuret (InChI=1S/C2H5N3O2/c3-1(6)5-2(4)7/h(H5,3,4,5,6,7)) 7) Allophanate (InChI=1S/C2H4N2O3/c3-1(5)4-2(6)7/h(H,6,7)(H3,3,4,5)) 8) Diuron (InChI=1S/C9H10Cl2N2O/c1-13(2)9(14)12-6-3-4-7(10)8(11)5-6/h3-5H,1-2H3,(H,12,14)) 9) 3,4-Dichloroaniline (InChI=1S/C6H5Cl2N/c7-5-2-1-4(9)3-6(5)8/h1-3H,9H2)
Substances (generic terms)	biotransformation products herbicide
Taxa (scientific names)	Achromobacter xylosoxidans Acinetobacter baylyi Arthrobacter aurescens TC1 Arthrobacter globiformis D47 Arthrobacter sp. AD1 Arthrobacter sp. BS2 Arthrobacter sp. DNS10 Bacillus megaterium Comamonas testesteroni Delftia acidovorans Delftia tsuruhatensis Diaphorobacter sp. LR2014-1 Hydrogenophaga sp. PBL-H3 Moorella thermoacetica ATCC 39073 Mycobacterium brisbanense JK1 Pseudomonas fluorescens Pseudomonas putida Pseudomonas sp. ADP Rhizobium leguminosarum 3841 Sphingomonas sp. SRS2 Variovorax paradoxus PBL-E5 Variovorax sp. 38R Variovorax sp. PBL-H6 Variovorax sp. SRS16
Organisms (generic terms)	bacteria
Systems	bioinformatics
Timerange	*
Review Level	none
Curator	Karakurt-Fischer, Sema
Contact	Johnson, David <David.Johnson@eawag.ch>
DOI	10.25678/0008YV