Genome-centric metagenomic insights into the role of Chloroflexi in anammox, activated sludge and methanogenic reactors
Abstract Background The phylum Chloroflexi is highly abundant in a wide variety of wastewater treatment bioreactors. It has been suggested that they play relevant roles in these ecosystems, particularly in degrading carbon compounds and on structuring flocs or granules. Nevertheless, their function...
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| Format: | Article |
| Language: | English |
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BMC
2023-02-01
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| Series: | BMC Microbiology |
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| Online Access: | https://doi.org/10.1186/s12866-023-02765-5 |
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| author | Patricia Bovio-Winkler Leandro D. Guerrero Leonardo Erijman Pía Oyarzúa María Eugenia Suárez-Ojeda Angela Cabezas Claudia Etchebehere |
| author_facet | Patricia Bovio-Winkler Leandro D. Guerrero Leonardo Erijman Pía Oyarzúa María Eugenia Suárez-Ojeda Angela Cabezas Claudia Etchebehere |
| author_sort | Patricia Bovio-Winkler |
| collection | DOAJ |
| description | Abstract Background The phylum Chloroflexi is highly abundant in a wide variety of wastewater treatment bioreactors. It has been suggested that they play relevant roles in these ecosystems, particularly in degrading carbon compounds and on structuring flocs or granules. Nevertheless, their function is not yet well understood as most species have not been isolated in axenic cultures. Here we used a metagenomic approach to investigate Chloroflexi diversity and their metabolic potential in three environmentally different bioreactors: a methanogenic full-scale reactor, a full-scale activated sludge reactor and a lab scale anammox reactor. Results Differential coverage binning approach was used to assemble the genomes of 17 new Chloroflexi species, two of which are proposed as new Candidatus genus. In addition, we recovered the first representative genome belonging to the genus ‘Ca. Villigracilis’. Even though samples analyzed were collected from bioreactors operating under different environmental conditions, the assembled genomes share several metabolic features: anaerobic metabolism, fermentative pathways and several genes coding for hydrolytic enzymes. Interestingly, genome analysis from the anammox reactor indicated a putative role of Chloroflexi in nitrogen conversion. Genes related to adhesiveness and exopolysaccharides production were also detected. Complementing sequencing analysis, filamentous morphology was detected by Fluorescent in situ hybridization. Conclusion Our results suggest that Chloroflexi participate in organic matter degradation, nitrogen removal and biofilm aggregation, playing different roles according to the environmental conditions. |
| first_indexed | 2024-04-09T23:08:52Z |
| format | Article |
| id | doaj.art-ed67b14b944142a6baf571dee02549ca |
| institution | Directory Open Access Journal |
| issn | 1471-2180 |
| language | English |
| last_indexed | 2024-04-09T23:08:52Z |
| publishDate | 2023-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Microbiology |
| spelling | doaj.art-ed67b14b944142a6baf571dee02549ca2023-03-22T10:34:34ZengBMCBMC Microbiology1471-21802023-02-0123111910.1186/s12866-023-02765-5Genome-centric metagenomic insights into the role of Chloroflexi in anammox, activated sludge and methanogenic reactorsPatricia Bovio-Winkler0Leandro D. Guerrero1Leonardo Erijman2Pía Oyarzúa3María Eugenia Suárez-Ojeda4Angela Cabezas5Claudia Etchebehere6Microbial Ecology Laboratory, Department of Microbial Biochemistry and Genomic, Biological Research Institute “Clemente Estable”Instituto de Investigaciones en Ingeniería Genética Y Biología Molecular “Dr Héctor N. Torres” (INGEBI-CONICET)Instituto de Investigaciones en Ingeniería Genética Y Biología Molecular “Dr Héctor N. Torres” (INGEBI-CONICET)GENOCOV Research Group, Department of Chemical, Biological and Environmental Engineering, Escola d’Enginyeria, Universitat Autònoma de BarcelonaGENOCOV Research Group, Department of Chemical, Biological and Environmental Engineering, Escola d’Enginyeria, Universitat Autònoma de BarcelonaInstituto Tecnológico Regional Centro Sur, Universidad Tecnológica, Francisco Antonio Maciel S/NMicrobial Ecology Laboratory, Department of Microbial Biochemistry and Genomic, Biological Research Institute “Clemente Estable”Abstract Background The phylum Chloroflexi is highly abundant in a wide variety of wastewater treatment bioreactors. It has been suggested that they play relevant roles in these ecosystems, particularly in degrading carbon compounds and on structuring flocs or granules. Nevertheless, their function is not yet well understood as most species have not been isolated in axenic cultures. Here we used a metagenomic approach to investigate Chloroflexi diversity and their metabolic potential in three environmentally different bioreactors: a methanogenic full-scale reactor, a full-scale activated sludge reactor and a lab scale anammox reactor. Results Differential coverage binning approach was used to assemble the genomes of 17 new Chloroflexi species, two of which are proposed as new Candidatus genus. In addition, we recovered the first representative genome belonging to the genus ‘Ca. Villigracilis’. Even though samples analyzed were collected from bioreactors operating under different environmental conditions, the assembled genomes share several metabolic features: anaerobic metabolism, fermentative pathways and several genes coding for hydrolytic enzymes. Interestingly, genome analysis from the anammox reactor indicated a putative role of Chloroflexi in nitrogen conversion. Genes related to adhesiveness and exopolysaccharides production were also detected. Complementing sequencing analysis, filamentous morphology was detected by Fluorescent in situ hybridization. Conclusion Our results suggest that Chloroflexi participate in organic matter degradation, nitrogen removal and biofilm aggregation, playing different roles according to the environmental conditions.https://doi.org/10.1186/s12866-023-02765-5ChloroflexiMethanogenic reactorsActivated sludgeAnammoxMetagenome assembled genomes |
| spellingShingle | Patricia Bovio-Winkler Leandro D. Guerrero Leonardo Erijman Pía Oyarzúa María Eugenia Suárez-Ojeda Angela Cabezas Claudia Etchebehere Genome-centric metagenomic insights into the role of Chloroflexi in anammox, activated sludge and methanogenic reactors BMC Microbiology Chloroflexi Methanogenic reactors Activated sludge Anammox Metagenome assembled genomes |
| title | Genome-centric metagenomic insights into the role of Chloroflexi in anammox, activated sludge and methanogenic reactors |
| title_full | Genome-centric metagenomic insights into the role of Chloroflexi in anammox, activated sludge and methanogenic reactors |
| title_fullStr | Genome-centric metagenomic insights into the role of Chloroflexi in anammox, activated sludge and methanogenic reactors |
| title_full_unstemmed | Genome-centric metagenomic insights into the role of Chloroflexi in anammox, activated sludge and methanogenic reactors |
| title_short | Genome-centric metagenomic insights into the role of Chloroflexi in anammox, activated sludge and methanogenic reactors |
| title_sort | genome centric metagenomic insights into the role of chloroflexi in anammox activated sludge and methanogenic reactors |
| topic | Chloroflexi Methanogenic reactors Activated sludge Anammox Metagenome assembled genomes |
| url | https://doi.org/10.1186/s12866-023-02765-5 |
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