Functional Analysis of a Polluted River Microbiome Reveals a Metabolic Potential for Bioremediation
The objective of this study is to understand the functional and metabolic potential of the microbial communities along the Apatlaco River and highlight activities related to bioremediation and its relationship with the Apatlaco’s pollutants, to enhance future design of more accurate bioremediation p...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-04-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/8/4/554 |
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| author | Luz Breton-Deval Ayixon Sanchez-Reyes Alejandro Sanchez-Flores Katy Juárez Ilse Salinas-Peralta Patricia Mussali-Galante |
| author_facet | Luz Breton-Deval Ayixon Sanchez-Reyes Alejandro Sanchez-Flores Katy Juárez Ilse Salinas-Peralta Patricia Mussali-Galante |
| author_sort | Luz Breton-Deval |
| collection | DOAJ |
| description | The objective of this study is to understand the functional and metabolic potential of the microbial communities along the Apatlaco River and highlight activities related to bioremediation and its relationship with the Apatlaco’s pollutants, to enhance future design of more accurate bioremediation processes. Water samples were collected at four sampling sites along the Apatlaco River (S1–S4) and a whole metagenome shotgun sequencing was performed to survey and understand the microbial metabolic functions with potential for bioremediation. A HMMER search was used to detect sequence homologs related to polyethylene terephthalate (PET) and polystyrene biodegradation, along with bacterial metal tolerance in Apatlaco River metagenomes. Our results suggest that pollution is a selective pressure which enriches microorganisms at polluted sites, displaying metabolic capacities to tolerate and transform the contamination. According to KEGG annotation, all sites along the river have bacteria with genes related to xenobiotic biodegradation. In particular, functions such as environmental processing, xenobiotic biodegradation and glycan biosynthesis are over-represented in polluted samples, in comparison to those in the clean water site. This suggests a functional specialization in the communities that inhabit each perturbated point. Our results can contribute to the determination of the partition in a metabolic niche among different Apatlaco River prokaryotic communities, that help to contend with and understand the effect of anthropogenic contamination. |
| first_indexed | 2024-03-10T20:30:56Z |
| format | Article |
| id | doaj.art-5bbaa64c994e466f93d621b8bcf6753c |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T20:30:56Z |
| publishDate | 2020-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-5bbaa64c994e466f93d621b8bcf6753c2023-11-19T21:25:03ZengMDPI AGMicroorganisms2076-26072020-04-018455410.3390/microorganisms8040554Functional Analysis of a Polluted River Microbiome Reveals a Metabolic Potential for BioremediationLuz Breton-Deval0Ayixon Sanchez-Reyes1Alejandro Sanchez-Flores2Katy Juárez3Ilse Salinas-Peralta4Patricia Mussali-Galante5Cátedras Conacyt - Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca 62210, Morelos, MexicoCátedras Conacyt - Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca 62210, Morelos, MexicoUnidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, MexicoInstituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Cuernavaca 62210, MexicoInstituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Cuernavaca 62210, MexicoLaboratorio de Investigaciones Ambientales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Colonia Chamilpa, Cuernavaca 62209, Morelos, MexicoThe objective of this study is to understand the functional and metabolic potential of the microbial communities along the Apatlaco River and highlight activities related to bioremediation and its relationship with the Apatlaco’s pollutants, to enhance future design of more accurate bioremediation processes. Water samples were collected at four sampling sites along the Apatlaco River (S1–S4) and a whole metagenome shotgun sequencing was performed to survey and understand the microbial metabolic functions with potential for bioremediation. A HMMER search was used to detect sequence homologs related to polyethylene terephthalate (PET) and polystyrene biodegradation, along with bacterial metal tolerance in Apatlaco River metagenomes. Our results suggest that pollution is a selective pressure which enriches microorganisms at polluted sites, displaying metabolic capacities to tolerate and transform the contamination. According to KEGG annotation, all sites along the river have bacteria with genes related to xenobiotic biodegradation. In particular, functions such as environmental processing, xenobiotic biodegradation and glycan biosynthesis are over-represented in polluted samples, in comparison to those in the clean water site. This suggests a functional specialization in the communities that inhabit each perturbated point. Our results can contribute to the determination of the partition in a metabolic niche among different Apatlaco River prokaryotic communities, that help to contend with and understand the effect of anthropogenic contamination.https://www.mdpi.com/2076-2607/8/4/554Apatlaco riverwater pollutionsuperficial waterbioremediationplastic biodegradationbiotechnology |
| spellingShingle | Luz Breton-Deval Ayixon Sanchez-Reyes Alejandro Sanchez-Flores Katy Juárez Ilse Salinas-Peralta Patricia Mussali-Galante Functional Analysis of a Polluted River Microbiome Reveals a Metabolic Potential for Bioremediation Microorganisms Apatlaco river water pollution superficial water bioremediation plastic biodegradation biotechnology |
| title | Functional Analysis of a Polluted River Microbiome Reveals a Metabolic Potential for Bioremediation |
| title_full | Functional Analysis of a Polluted River Microbiome Reveals a Metabolic Potential for Bioremediation |
| title_fullStr | Functional Analysis of a Polluted River Microbiome Reveals a Metabolic Potential for Bioremediation |
| title_full_unstemmed | Functional Analysis of a Polluted River Microbiome Reveals a Metabolic Potential for Bioremediation |
| title_short | Functional Analysis of a Polluted River Microbiome Reveals a Metabolic Potential for Bioremediation |
| title_sort | functional analysis of a polluted river microbiome reveals a metabolic potential for bioremediation |
| topic | Apatlaco river water pollution superficial water bioremediation plastic biodegradation biotechnology |
| url | https://www.mdpi.com/2076-2607/8/4/554 |
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