Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples
| Autor(a) principal: | |
|---|---|
| Data de Publicação: | 2023 |
| Outros Autores: | , , , , , , , |
| Tipo de documento: | Artigo |
| Idioma: | eng |
| Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
| Texto Completo: | https://hdl.handle.net/1822/86538 |
Resumo: | The online version contains supplementary material available at: https://doi.org/10.1007/s00253-023-12627-9. |
| id |
RCAP_18b53c8d02a79c5b37981dd417d6d603 |
|---|---|
| oai_identifier_str |
oai:repositorium.sdum.uminho.pt:1822/86538 |
| network_acronym_str |
RCAP |
| network_name_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
| repository_id_str |
7160 |
| spelling |
Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samplesCAZymesCompostingGlycoside hydrolasesLignocelluloseMetagenomicsThe online version contains supplementary material available at: https://doi.org/10.1007/s00253-023-12627-9.The renewable, abundant, and low-cost nature of lignocellulosic biomass can play an important role in the sustainable production of bioenergy and several added-value bioproducts, thus providing alternative solutions to counteract the global energetic and industrial demands. The efficient conversion of lignocellulosic biomass greatly relies on the catalytic activity of carbohydrate-active enzymes (CAZymes). Finding novel and robust biocatalysts, capable of being active under harsh industrial conditions, is thus imperative to achieve an economically feasible process. In this study, thermophilic compost samples from three Portuguese companies were collected, and their metagenomic DNA was extracted and sequenced through shotgun sequencing. A novel multi-step bioinformatic pipeline was developed to find CAZymes and characterize the taxonomic and functional profiles of the microbial communities, using both reads and metagenome-assembled genomes (MAGs) as input. The samples' microbiome was dominated by bacteria, where the classes Gammaproteobacteria, Alphaproteobacteria, and Balneolia stood out for their higher abundance, indicating that the degradation of compost biomass is mainly driven by bacterial enzymatic activity. Furthermore, the functional studies revealed that our samples are a rich reservoir of glycoside hydrolases (GH), particularly of GH5 and GH9 cellulases, and GH3 oligosaccharide-degrading enzymes. We further constructed metagenomic fosmid libraries with the compost DNA and demonstrated that a great number of clones exhibited $\beta$-glucosidase activity. The comparison of our samples with others from the literature showed that, independently of the composition and process conditions, composting is an excellent source of lignocellulose-degrading enzymes. To the best of our knowledge, this is the first comparative study on the CAZyme abundance and taxonomic/functional profiles of Portuguese compost samples.Open access funding provided by FCT|FCCN (b-on). This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UIDB/04469/2020 unit, the projects LIGNOZYMES—Metagenomics approach to unravel the potential of lignocellulosic residues towards the discovery of novel enzymes (POCI-01–0145-FEDER-029773), and B3iS—Biodiversity and Bioprospecting of Biosurfactants in Saline Environments (PTDC/BII-BIO/5554/2020); and by RNCA Advanced Computing Project MetaLignoZymes, metagenomic analysis of lignocellulosic residues towards the discovery of novel enzymes (CPCA/A0/408464/2021).info:eu-repo/semantics/publishedVersionSpringer NatureUniversidade do MinhoPereira, Cátia Sofia SantosSousa, JoanaCosta, Ângela Maria AraújoSantos, A. O.Rito, TeresaSoares, PedroFranco-Duarte, RicardoSilvério, Sara Isabel CruzRodrigues, L. R.2023-07-072023-07-07T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/1822/86538engCátia S. Pereira; Sousa, Joana; Costa, Ângela; Santos, A. O.; Rito, Teresa; Soares, Pedro; Franco-Duarte, Ricardo; Silvério, Sara C.; Rodrigues, Lígia R., Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples. Applied Microbiology and Biotechnology, 107, 5379-5401, 20230175759810.1007/s00253-023-12627-937417976http://www.springer.com/chemistry/biotechnology/journal/253info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-12-30T01:29:15Zoai:repositorium.sdum.uminho.pt:1822/86538Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T20:30:42.130730Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
| dc.title.none.fl_str_mv |
Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples |
| title |
Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples |
| spellingShingle |
Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples Pereira, Cátia Sofia Santos CAZymes Composting Glycoside hydrolases Lignocellulose Metagenomics |
| title_short |
Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples |
| title_full |
Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples |
| title_fullStr |
Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples |
| title_full_unstemmed |
Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples |
| title_sort |
Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples |
| author |
Pereira, Cátia Sofia Santos |
| author_facet |
Pereira, Cátia Sofia Santos Sousa, Joana Costa, Ângela Maria Araújo Santos, A. O. Rito, Teresa Soares, Pedro Franco-Duarte, Ricardo Silvério, Sara Isabel Cruz Rodrigues, L. R. |
| author_role |
author |
| author2 |
Sousa, Joana Costa, Ângela Maria Araújo Santos, A. O. Rito, Teresa Soares, Pedro Franco-Duarte, Ricardo Silvério, Sara Isabel Cruz Rodrigues, L. R. |
| author2_role |
author author author author author author author author |
| dc.contributor.none.fl_str_mv |
Universidade do Minho |
| dc.contributor.author.fl_str_mv |
Pereira, Cátia Sofia Santos Sousa, Joana Costa, Ângela Maria Araújo Santos, A. O. Rito, Teresa Soares, Pedro Franco-Duarte, Ricardo Silvério, Sara Isabel Cruz Rodrigues, L. R. |
| dc.subject.por.fl_str_mv |
CAZymes Composting Glycoside hydrolases Lignocellulose Metagenomics |
| topic |
CAZymes Composting Glycoside hydrolases Lignocellulose Metagenomics |
| description |
The online version contains supplementary material available at: https://doi.org/10.1007/s00253-023-12627-9. |
| publishDate |
2023 |
| dc.date.none.fl_str_mv |
2023-07-07 2023-07-07T00:00:00Z |
| dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
| dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
| format |
article |
| status_str |
publishedVersion |
| dc.identifier.uri.fl_str_mv |
https://hdl.handle.net/1822/86538 |
| url |
https://hdl.handle.net/1822/86538 |
| dc.language.iso.fl_str_mv |
eng |
| language |
eng |
| dc.relation.none.fl_str_mv |
Cátia S. Pereira; Sousa, Joana; Costa, Ângela; Santos, A. O.; Rito, Teresa; Soares, Pedro; Franco-Duarte, Ricardo; Silvério, Sara C.; Rodrigues, Lígia R., Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples. Applied Microbiology and Biotechnology, 107, 5379-5401, 2023 01757598 10.1007/s00253-023-12627-9 37417976 http://www.springer.com/chemistry/biotechnology/journal/253 |
| dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
| eu_rights_str_mv |
openAccess |
| dc.format.none.fl_str_mv |
application/pdf |
| dc.publisher.none.fl_str_mv |
Springer Nature |
| publisher.none.fl_str_mv |
Springer Nature |
| dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
| instname_str |
Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
| instacron_str |
RCAAP |
| institution |
RCAAP |
| reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
| collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
| repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
| repository.mail.fl_str_mv |
|
| _version_ |
1799133575373651968 |