{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T00:03:58Z","timestamp":1767830638505,"version":"3.49.0"},"reference-count":41,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2021,10,7]],"date-time":"2021-10-07T00:00:00Z","timestamp":1633564800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["SFRH\/BD\/116702\/2016"],"award-info":[{"award-number":["SFRH\/BD\/116702\/2016"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["CEECIND\/02968\/2017"],"award-info":[{"award-number":["CEECIND\/02968\/2017"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["UIDB\/04423\/2020"],"award-info":[{"award-number":["UIDB\/04423\/2020"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["UIDP\/04423\/2020"],"award-info":[{"award-number":["UIDP\/04423\/2020"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","award":["NORTE-01-0145-FEDER-000064"],"award-info":[{"award-number":["NORTE-01-0145-FEDER-000064"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Epoxiconazole (EPO) and fludioxonil (FLU) are two widely used fluorinated pesticides known to be highly persistent and with high ecotoxicological potential, turning them into pollutants of concern. This work aimed to optimize two degrading bacterial consortia, previously obtained from an agricultural soil through enrichment with EPO and FLU, by characterizing the contribution of their corresponding bacterial isolates to the biodegradation of these pesticides using both culture-dependent and independent methodologies. Results showed that a co-culture of the strains Hydrogenophaga eletricum 5AE and Methylobacillus sp. 8AE was the most efficient in biodegrading EPO, being able to defluorinate ca. 80% of this pesticide in 28 days. This catabolic performance is likely the result of a commensalistic cooperation, in which H. eletricum may be the defluorinating strain and Methylobacillus sp. may assume an accessory, yet pivotal, catabolic role. Furthermore, 16S rRNA metabarcoding analysis revealed that these strains represent a minority in their original consortium, showing that the biodegradation of EPO can be driven by less abundant phylotypes in the community. On the other hand, none of the tested combinations of bacterial strains showed potential to biodegrade FLU, indicating that the key degrading strains were not successfully isolated from the original enrichment culture. Overall, this work shows, for the first time, the direct involvement of two bacterial species, namely H. eletricum and Methylobacillus sp., in the biodegradation of EPO, while also offering insight on how they might cooperate to accomplish this process. Moreover, the importance of adequate culture-dependent approaches in the engineering of microbial consortia for bioremediation purposes is also emphasized.<\/jats:p>","DOI":"10.3390\/microorganisms9102109","type":"journal-article","created":{"date-parts":[[2021,10,8]],"date-time":"2021-10-08T21:23:55Z","timestamp":1633728235000},"page":"2109","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Combining Culture-Dependent and Independent Approaches for the Optimization of Epoxiconazole and Fludioxonil-Degrading Bacterial Consortia"],"prefix":"10.3390","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9685-3435","authenticated-orcid":false,"given":"Diogo A. M.","family":"Alexandrino","sequence":"first","affiliation":[{"name":"CIIMAR\u2014Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Avenida General Norton de Matos s\/n, 4450-208 Matosinhos, Portugal"},{"name":"School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal"}]},{"given":"Ana P.","family":"Mucha","sequence":"additional","affiliation":[{"name":"CIIMAR\u2014Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Avenida General Norton de Matos s\/n, 4450-208 Matosinhos, Portugal"},{"name":"Faculty of Sciences, University of Porto (FCUP), Rua do Campo Alegre 790, 4150-171 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3255-0982","authenticated-orcid":false,"given":"Maria Paola","family":"Tomasino","sequence":"additional","affiliation":[{"name":"CIIMAR\u2014Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Avenida General Norton de Matos s\/n, 4450-208 Matosinhos, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6836-0331","authenticated-orcid":false,"given":"C. Marisa R.","family":"Almeida","sequence":"additional","affiliation":[{"name":"CIIMAR\u2014Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Avenida General Norton de Matos s\/n, 4450-208 Matosinhos, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7181-0540","authenticated-orcid":false,"given":"Maria F.","family":"Carvalho","sequence":"additional","affiliation":[{"name":"CIIMAR\u2014Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Avenida General Norton de Matos s\/n, 4450-208 Matosinhos, Portugal"},{"name":"School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2021,10,7]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1080\/07388551.2020.1853032","article-title":"Biotechnological basis of microbial consortia for the removal of pesticides from the environment","volume":"41","author":"Bhatt","year":"2021","journal-title":"Crit. Rev. Biotechnol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1038\/s41579-018-0004-5","article-title":"The social network of microorganisms\u2014How auxotrophies shape complex communities","volume":"16","author":"Zengler","year":"2018","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Borchert, E., Hammerschmidt, K., Hentschel, U., and Deines, P. (2021). Enhancing Microbial Pollutant Degradation by Integrating Eco-Evolutionary Principles with Environmental Biotechnology. Trends Microbiol.","DOI":"10.1016\/j.tim.2021.03.002"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"20190256","DOI":"10.1098\/rstb.2019.0256","article-title":"Understanding the evolution of interspecies interactions in microbial communities","volume":"375","author":"Gorter","year":"2020","journal-title":"Philos. Trans. R. Soc. B Biol. Sci."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Arias-S\u00e1nchez, F.I., Vessman, B., and Mitri, S. (2019). Artificially selecting microbial communities: If we can breed dogs, why not microbiomes?. PLoS Biol., 17.","DOI":"10.1371\/journal.pbio.3000356"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1050","DOI":"10.1080\/10807039.2015.1133242","article-title":"An international database for pesticide risk assessments and management","volume":"22","author":"Lewis","year":"2016","journal-title":"Hum. Ecol. Risk Assess. Int. J."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"122545","DOI":"10.1016\/j.jhazmat.2020.122545","article-title":"Microbial degradation of two highly persistent fluorinated fungicides\u2014Epoxiconazole and fludioxonil","volume":"394","author":"Alexandrino","year":"2020","journal-title":"J. Hazard. Mater."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"3774","DOI":"10.1007\/s11356-020-09231-z","article-title":"Biotreatment and bacterial succession in an upflow immobilized cell bioreactor fed with fludioxonil wastewater","volume":"28","author":"Mavriou","year":"2021","journal-title":"Environ. Sci. Pollut. Res."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1080\/00084433.2017.1409934","article-title":"Application of stirred mill to upgrading of graphite concentrate by flotation","volume":"57","author":"Zhang","year":"2018","journal-title":"Can. Metall. Q."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1080\/03601234.2017.1405619","article-title":"Leaching and sorption of neonicotinoid insecticides and fungicides from seed coatings","volume":"53","author":"Smalling","year":"2018","journal-title":"J. Environ. Sci. Health Part B"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1204","DOI":"10.1016\/j.scitotenv.2019.03.207","article-title":"Screening of pesticides and veterinary drugs in small streams in the European Union by liquid chromatography high resolution mass spectrometry","volume":"670","author":"Casado","year":"2019","journal-title":"Sci. Total Environ."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"127637","DOI":"10.1016\/j.chemosphere.2020.127637","article-title":"Adsorption of epoxiconazole and tebuconazole in twenty different agricultural soils in relation to their properties","volume":"261","author":"Hofman","year":"2020","journal-title":"Chemosphere"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.nbt.2017.08.005","article-title":"Biodegradation of mono-, di- and trifluoroacetate by microbial cultures with different origins","volume":"43","author":"Alexandrino","year":"2018","journal-title":"New Biotechnol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1111\/1462-2920.13023","article-title":"Every base matters: Assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples","volume":"18","author":"Parada","year":"2016","journal-title":"Environ. Microbiol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"e00127-16","DOI":"10.1128\/mSystems.00127-16","article-title":"Microbiome Helper: A Custom and Streamlined Workflow for Microbiome Research","volume":"2","author":"Comeau","year":"2017","journal-title":"mSystems"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1093\/bioinformatics\/btr026","article-title":"Quality control and preprocessing of metagenomic datasets","volume":"27","author":"Schmieder","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Schubert, M., Lindgreen, S., and Orlando, L. (2016). AdapterRemoval v2: Rapid adapter trimming, identification, and read merging. BMC Res. Notes, 9.","DOI":"10.1186\/s13104-016-1900-2"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"7537","DOI":"10.1128\/AEM.01541-09","article-title":"Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities","volume":"75","author":"Schloss","year":"2009","journal-title":"Appl Environ. Microbiol"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"D590","DOI":"10.1093\/nar\/gks1219","article-title":"The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools","volume":"41","author":"Quast","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1823","DOI":"10.1093\/bioinformatics\/bts252","article-title":"SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes","volume":"28","author":"Pruesse","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","article-title":"Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences","volume":"22","author":"Li","year":"2006","journal-title":"Bioinformatics"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T.L. (2009). BLAST+: Architecture and applications. BMC Bioinform., 10.","DOI":"10.1186\/1471-2105-10-421"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"2194","DOI":"10.1093\/bioinformatics\/btr381","article-title":"UCHIME improves sensitivity and speed of chimera detection","volume":"27","author":"Edgar","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.1007\/s11274-009-0283-0","article-title":"Biodegradation of epoxyconazole and piraclostrobin fungicides by Klebsiella sp. from soil","volume":"26","author":"Lopes","year":"2010","journal-title":"World J. Microbiol. Biotechnol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"2138","DOI":"10.1002\/etc.1928","article-title":"Assessing the metabolic potential of phototrophic communities in surface water environments: Fludioxonil as a model compound","volume":"31","author":"Thomas","year":"2012","journal-title":"Environ. Toxicol. Chem."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.nbt.2011.03.005","article-title":"Fungicides degradation in an organic biomixture: Impact on microbial diversity","volume":"29","author":"Coppola","year":"2011","journal-title":"N. Biotechnol"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"949","DOI":"10.1080\/03067319.2011.609934","article-title":"Evaluation of BiomassBed system in bio-cleaning water contaminated by fungicides applied in vineyard","volume":"92","author":"Vischetti","year":"2012","journal-title":"Int. J. Environ. Anal. Chem."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"2546","DOI":"10.1007\/s11356-012-1165-9","article-title":"The dissipation of three fungicides in a biobed organic substrate and their impact on the structure and activity of the microbial community","volume":"20","author":"Marinozzi","year":"2013","journal-title":"Environ. Sci. Pollut. Res."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1016\/j.chemosphere.2019.06.001","article-title":"Removal of triazines, triazoles and organophophates in biomixtures and application of a biopurification system for the treatment of laboratory wastewaters","volume":"233","author":"Tortella","year":"2019","journal-title":"Chemosphere"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"121951","DOI":"10.1016\/j.jhazmat.2019.121951","article-title":"Enantioselective bioactivity, toxicity, and degradation in different environmental mediums of chiral fungicide epoxiconazole","volume":"386","author":"Kaziem","year":"2020","journal-title":"J. Hazard. Mater."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"129029","DOI":"10.1016\/j.chemosphere.2020.129029","article-title":"Groundwater contamination by fluorinated aromatics: Benzotrifluoride and its derivatives","volume":"265","author":"Lava","year":"2021","journal-title":"Chemosphere"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1085\/jgp.201411243","article-title":"Bacterial fluoride resistance, Fluc channels, and the weak acid accumulation effect","volume":"144","author":"Ji","year":"2014","journal-title":"J. Gen. Physiol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1146\/annurev.micro.091208.073600","article-title":"The Expanding World of Methylotrophic Metabolism","volume":"63","author":"Chistoserdova","year":"2009","journal-title":"Annu. Rev. Microbiol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1007\/s13205-016-0524-5","article-title":"Biodegradation of endocrine disruptor dibutyl phthalate (DBP) by a newly isolated Methylobacillus sp. V29b and the DBP degradation pathway","volume":"6","author":"Kumar","year":"2016","journal-title":"3 Biotech"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"124014","DOI":"10.1016\/j.biortech.2020.124014","article-title":"The key active degrader, metabolic pathway and microbial ecology of triclosan biodegradation in an anoxic\/oxic system","volume":"317","author":"Dai","year":"2020","journal-title":"Bioresour. Technol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1038\/nrmicro2259","article-title":"Bacterial competition: Surviving and thriving in the microbial jungle","volume":"8","author":"Hibbing","year":"2010","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Pascoal, F., Magalh\u00e3es, C., and Costa, R. (2020). The Link Between the Ecology of the Prokaryotic Rare Biosphere and Its Biotechnological Potential. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.00231"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"e03321-16","DOI":"10.1128\/AEM.03321-16","article-title":"Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem","volume":"83","author":"Wang","year":"2017","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"14393","DOI":"10.1021\/acs.est.0c04483","article-title":"Microbial Cleavage of C\u2013F Bonds in Two C6 Per- and Polyfluorinated Compounds via Reductive Defluorination","volume":"54","author":"Yu","year":"2020","journal-title":"Environ. Sci. Technol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"103881","DOI":"10.1016\/j.jece.2020.103881","article-title":"Potential of bacterial consortia obtained from different environments for bioremediation of paroxetine and bezafibrate","volume":"8","author":"Fernandes","year":"2020","journal-title":"J. Environ. Chem. Eng."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/9\/10\/2109\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T07:10:07Z","timestamp":1760166607000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/9\/10\/2109"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,10,7]]},"references-count":41,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2021,10]]}},"alternative-id":["microorganisms9102109"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms9102109","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,10,7]]}}}