Multilocus sequence typing and genomic characterization of the novel Streptomyces strain SCPE-10, that resists 2,4-D toxicity and has bioremediation potential

Nildo Alfredo Nhampossa; João Victor Castro de Almeida Araújo; Vicente Almeida Serafim da Silva; João Ricardo Vidal Amaral; Cinara Souza da Conceição; Carlos Alberto Xavier Gonçalves; Eamim Daidrê Squizani; Sheila da Silva; Marcia Soares Vidal; Yinglong Chen; Andrew Macrae; Rodrigo Pires do Nascimento

doi:10.1007/s42770-026-01875-2

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Multilocus sequence typing and genomic characterization of the novel Streptomyces strain SCPE-10, that resists 2,4-D toxicity and has bioremediation potential

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Multilocus sequence typing and genomic characterization of the novel Streptomyces strain SCPE-10, that resists 2,4-D toxicity and has bioremediation potential

Nildo Alfredo Nhampossa, João Victor Castro de Almeida Araújo, Vicente Almeida Serafim da Silva, João Ricardo Vidal Amaral, Cinara Souza da Conceição, Carlos Alberto Xavier Gonçalves, Eamim Daidrê Squizani, Sheila da Silva, Marcia Soares Vidal, Yinglong Chen, …

Brazilian journal of microbiology, Vol.57(1), 61

2026

DOI: https://doi.org/10.1007/s42770-026-01875-2

PMID: 41733838

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Abstract

Streptomyces SCPE-10

2,4-D degradation

Aromatic compounds

Xenobiotic biodegradation

Bioremediation

The widespread use of aromatic herbicides such as 2,4-dichlorophenoxyacetic acid (2,4-D) has led to persistent environmental contamination, requiring efficient and sustainable biodegradation strategies. In this study, we isolated and characterized a novel actinobacterial strain, Streptomyces sp. SCPE-10, from contaminated coastal soil, capable of using 2,4-D as its sole carbon source. Phenotypic assays revealed robust growth on aromatic substrates, while whole-genome sequencing (Submission no. SUB15461668) followed by multilocus sequence analysis (16 S rRNA, recA, rpoB, atpD, gyrB, and trpB) revealed that SCPE-10 is closely related to Streptomyces phaeoluteichromatogenes. Functional genome annotation revealed a high abundance of genes involved in aromatic compound degradation, including cytochrome P450 monooxygenases, ring-cleaving dioxygenases, and dehalogenases. KEGG and antiSMASH analyses identified multiple metabolic pathways and 28 biosynthetic gene clusters (BGCs), including clusters for polyketides, nonribosomal peptides, terpenes, siderophores, and ectoine. Notably, SCPE-10 harbors key genes related to the degradation of benzoate, naphthalene, toluene, xylene, and 2,4-D, indicating broad-spectrum catabolic potential. These findings suggest that Streptomyces sp. SCPE-10 is a promising candidate for the bioremediation of herbicide-contaminated environments and the exploration of novel secondary metabolites.

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Title: Multilocus sequence typing and genomic characterization of the novel Streptomyces strain SCPE-10, that resists 2,4-D toxicity and has bioremediation potential
Authors/Creators: Nildo Alfredo Nhampossa - Programa de Pós-Graduação de Biotecnologia Vegetal e Bioprocessos da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco K, 2° Andar-Sala 032, Rio de Janeiro, 21941-902, Brazil
João Victor Castro de Almeida Araújo - Laboratorio de Ecologia e Processos Microbianos-LEPM 108, Escola de Química, Centro de Tecnologia, Universidade Federal do Rio de Janeiro, Av. Athos da Silveira Ramos, 149 - Cidade Universitária, Rio de Janeiro, RJ, 21941-909, Brazil
Vicente Almeida Serafim da Silva - Laboratório de Biotecnologia Sustentável e Bioinformática Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, 21941-902, Brazil
João Ricardo Vidal Amaral - Laboratório de Biotecnologia Sustentável e Bioinformática Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, 21941-902, Brazil
Cinara Souza da Conceição - Instituto SENAI de Inovação em Biossintéticos e Fibras, Cidade Universitária, Rio de Janeiro, 21941-857, Brazil
Carlos Alberto Xavier Gonçalves - Instituto SENAI de Inovação em Biossintéticos e Fibras, Cidade Universitária, Rio de Janeiro, 21941-857, Brazil
Eamim Daidrê Squizani - Instituto SENAI de Inovação em Biossintéticos e Fibras, Cidade Universitária, Rio de Janeiro, 21941-857, Brazil
Sheila da Silva - Laboratório de Biotecnologia Sustentável e Bioinformática Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, 21941-902, Brazil
Marcia Soares Vidal - Embrapa Agrobiologia, Rodovia BR 465, km 07, Seropédica, RJ, 23891-000, Brazil
Yinglong Chen - School of Agriculture and Environmental Science, University of Western Australia, Perth, Australia
Andrew Macrae - Laboratório de Biotecnologia Sustentável e Bioinformática Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, 21941-902, Brazil
Rodrigo Pires do Nascimento - Programa de Pós-Graduação de Biotecnologia Vegetal e Bioprocessos da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco K, 2° Andar-Sala 032, Rio de Janeiro, 21941-902, Brazil. rodrigopires@eq.ufrj.br
Publication Details: Brazilian journal of microbiology, Vol.57(1), 61
Identifiers: 991005894367107891
Murdoch Affiliation: Food Futures Institute
Language: English
Resource Type: Journal article

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