Metagenomic Insights of the Microbial Community from a Polluted River in Brazil 2020
Resumo
The water in the Metropolitan Region of Rio de Janeiro and in some municipalities in the Baixada Fluminense comes from the hydrological basin of the Guandu River (GR) and its potability is guaranteed by the Water Treatment Station of the Companhia Estadual de Águas e Esgotos. Along its route to the CEDAE dams, the GR suffers urban influences, being heavily impacted by receiving in natura effluents. To check the quality of the water in the GR, daily monitoring is carried out throughout its distribution network, including bacteriology. However, so far there is no metagenomics work to know what are the other microorganisms that exist in the GR that can cause diseases. This work aims to perform a metagenomic analysis of the GR to assess its diversity. Samples distributed in the catchment area of CEDAE and drinking water were collected, submitted to DNA sequencing using Illumina. Quality control of Qpherd >30 sequences and joining of paired-end sequences forward and reverse with the Prinseq program. 203,951,644 sequences were obtained. The bacterial diversity index analysis did not show significant differences among the samples. The most abundant class was Betaproteobacteria. The cluster analysis showed to be significant for the drinking water sample to be grouped together with the raw water sample. The PCA-Biplot showed three clusters and which variables differentiate the samples, some genera having great contributions such as: Staphylococcus, Chthoniobacter and Riemerella.
Palavras-chave:
Metagenomic, Diversity indexes, River
Referências
CEDAE.COMPANHIA ESTADUAL DE ÁGUAS E ESGOTOS. Estações de Tratamento do Guandu e Laranjal. [link]. (2008). Accessed 20 Feb 2021
ANACIONAL DE ÁGUAS-ANA/MINIST. MEIO AMBIENTE. Plano Estratégico de Recursos Hídricos da Bacia Hidrográfica dos Rios do Guandu, da Guarda e Guandu-Mirim (2006)
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Tringe, S.G., et al.: Comparative metagenomics of microbial communities. Science 308(5721), 554–557 (2005)
Huson, D.H., et al.: Methods for comparative metagenomics. BMC Bioinform. 10(1), 1–10 (2009)
Walter, J.M., et al.: Taxonomic and functional metagenomic signature of turfs in the Abrolhos reef system (Brazil). PLoS One 11(8), e0161168 (2016)
Schmieder, R., Edwards, R.: Quality control and preprocessing of metagenomic datasets. Bioinformatics 27(6), 863–864 (2011)
Coil, D., Jospin, G., Darling, A.E.: A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 31(4), 587–589 (2015)
Altschul, S.F., et al.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17), 3389–3402 (1997)
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Oksanen, J., et al.: Package ‘vegan’. Community Ecol. Package, Version 2(9), 1–295 (2013)
Glöckner, F.O., Fuchs, B.M., Rudolf, A.: Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl. Environ. Microbiol. 65(8), 3721–3726 (1999)
Lindström, E.S., Kamst-Van Agterveld, M.P., Zwart, G.: Distribution of typical freshwater bacterial groups is associated with pH, temperature, and lake water retention time. Appl. Environ. Microbiol. 71(12), 8201–8206 (2005)
Wei, J., et al.: Simultaneous Microcystis algicidal and microcystin synthesis inhibition by a red pigment prodigiosin. Environ. Poll. 256, 113444 (2020)
Jang, J., et al.: Environmental Escherichia coli: ecology and public health implications—a review. J. Appl. Microbiol. 123(3), 570–581 (2017)
Daniel, D.S., et al.: Public health risks of multiple-drug-resistant Enterococcus spp. in Southeast Asia. Appl. Environ. Microbiol. 81(18), 6090–6097 (2015)
Iljazovic, A., et al.: Modulation of inflammatory responses by gastrointestinal Prevotella spp.–from associations to functional studies. Int. J. Med. Microbiol. 151472 (2021)
Moller, A.G., Lindsay, J.A., Read, T.D.: Determinants of phage host range in Staphylococcus species. Appl. Environ. Microbiol. 85(11), e00209–19 (2019)
Jiang, C., et al.: Diverse and abundant antibiotic resistance genes in mangrove area and their relationship with bacterial communities-a study in Hainan Island, China. Environ. Poll. 276, 116704 (2021)
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ANACIONAL DE ÁGUAS-ANA/MINIST. MEIO AMBIENTE. Plano Estratégico de Recursos Hídricos da Bacia Hidrográfica dos Rios do Guandu, da Guarda e Guandu-Mirim (2006)
IBGE. INSTITUTO BRASILEIRO DE GEOGRAFIA E ESTATÍSTICA. Rio de Janeiro. https://cidades.ibge.gov.br/brasil/rj/rio-de-janeiro/panorama. Accessed 25 May 2021
CEDAE.COMPANHIA ESTADUAL DE ÁGUAS E ESGOTOS. Qualidade da Água; Relatórios Guandu.2021. Available in: https://cedae.com.br/relatoriosguandu. Access in 02/20/2021.
Simon, C., Daniel, R.: Metagenomic analyses: past and future trends. Appl. Environ. Microbiol. 77(4), 1153–1161 (2011)
Tringe, S.G., et al.: Comparative metagenomics of microbial communities. Science 308(5721), 554–557 (2005)
Huson, D.H., et al.: Methods for comparative metagenomics. BMC Bioinform. 10(1), 1–10 (2009)
Walter, J.M., et al.: Taxonomic and functional metagenomic signature of turfs in the Abrolhos reef system (Brazil). PLoS One 11(8), e0161168 (2016)
Schmieder, R., Edwards, R.: Quality control and preprocessing of metagenomic datasets. Bioinformatics 27(6), 863–864 (2011)
Coil, D., Jospin, G., Darling, A.E.: A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 31(4), 587–589 (2015)
Altschul, S.F., et al.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17), 3389–3402 (1997)
Buchfink, B., Xie, C., Huson, D.H.: Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12(1), 59–60 (2015)
Huson, D.H., et al.: Integrative analysis of environmental sequences using MEGAN4. Genome Res. 21(9), 1552–1560 (2011)
Scolforo, J.R., et al.: Diversidade, equabilidade e similaridade no domínio da caatinga. Inventário Florestal de Minas Gerais: Floresta Estacional Decidual-Florística, Estrutura,Similaridade, Distribuição Diamétrica e de Altura, Volumetria, Tendências de Crescimento e Manejo Florestal, 118–133 (2008)
Oksanen, J., et al.: Package ‘vegan’. Community Ecol. Package, Version 2(9), 1–295 (2013)
Glöckner, F.O., Fuchs, B.M., Rudolf, A.: Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl. Environ. Microbiol. 65(8), 3721–3726 (1999)
Lindström, E.S., Kamst-Van Agterveld, M.P., Zwart, G.: Distribution of typical freshwater bacterial groups is associated with pH, temperature, and lake water retention time. Appl. Environ. Microbiol. 71(12), 8201–8206 (2005)
Wei, J., et al.: Simultaneous Microcystis algicidal and microcystin synthesis inhibition by a red pigment prodigiosin. Environ. Poll. 256, 113444 (2020)
Jang, J., et al.: Environmental Escherichia coli: ecology and public health implications—a review. J. Appl. Microbiol. 123(3), 570–581 (2017)
Daniel, D.S., et al.: Public health risks of multiple-drug-resistant Enterococcus spp. in Southeast Asia. Appl. Environ. Microbiol. 81(18), 6090–6097 (2015)
Iljazovic, A., et al.: Modulation of inflammatory responses by gastrointestinal Prevotella spp.–from associations to functional studies. Int. J. Med. Microbiol. 151472 (2021)
Moller, A.G., Lindsay, J.A., Read, T.D.: Determinants of phage host range in Staphylococcus species. Appl. Environ. Microbiol. 85(11), e00209–19 (2019)
Jiang, C., et al.: Diverse and abundant antibiotic resistance genes in mangrove area and their relationship with bacterial communities-a study in Hainan Island, China. Environ. Poll. 276, 116704 (2021)
Omaleki, L., et al.: Molecular and serological characterization of Riemerella isolates associated with poultry in Australia. Avian Pathol. 50, 1–10 (2020)
Publicado
22/11/2021
Como Citar
GIL, Carolina O. P.; PINTO, Larissa Macedo; NOBRE, Flavio F.; THOMPSON, Cristiane; THOMPSON, Fabiano; TSCHOKE, Diogo Antonio.
Metagenomic Insights of the Microbial Community from a Polluted River in Brazil 2020. In: SIMPÓSIO BRASILEIRO DE BIOINFORMÁTICA (BSB), 14. , 2021, Online.
Anais [...].
Porto Alegre: Sociedade Brasileira de Computação,
2021
.
p. 137-144.
ISSN 2316-1248.
