Genome sequence of Desulfurella amilsii strain TR1 and comparative genomics of Desulfurellaceae family

Detalhes bibliográficos
Autor(a) principal: Florentino, Anna
Data de Publicação: 2017
Outros Autores: Stams, Alfons Johannes Maria, Sánchez-Andrea, Irene
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/1822/46348
Resumo: The acidotolerant sulfur reducer Desulfurella amilsii was isolated from sediments of Tinto river, an extremely acidic environment. Its ability to grow in a broad range of pH and to tolerate certain heavy metals offers potential for metal recovery processes. Here we report its high-quality draft genome sequence and compare it to the available genome sequences of other members of Desulfurellaceae family: D. acetivorans, D. multipotens, Hippea maritima, H. alviniae, H. medeae and H. jasoniae. For most species, pairwise comparisons for average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) revealed ANI values from 67.5 to 80% and DDH values from 12.9 to 24.2%. D. acetivorans and D. multipotens, however, surpassed the estimated thresholds of species definition for both DDH (98.6%) and ANI (88.1%). Therefore, they should be merged to a single species. Comparative analysis of Desulfurellaceae genomes revealed different gene content for sulfur respiration between Desulfurella and Hippea species. Sulfur reductase is only encoded in D. amilsii, in which it is suggested to play a role in sulfur respiration, especially at low pH. Polysulfide reductase is only encoded in Hippea species; it is likely that this genus uses polysulfide as electron acceptor. Genes encoding thiosulfate reductase are present in all the genomes, but dissimilatory sulfite reductase is only present in Desulfurella species. Thus, thiosulfate respiration via sulfite is only likely in this genus. Although sulfur disproportionation occurs in Desulfurella species, the molecular mechanism behind this process is not yet understood, hampering a genome prediction. The metabolism of acetate in Desulfurella species can occur via the acetyl-CoA synthetase or via acetate kinase in combination with phosphate acetyltransferase, while in Hippea species, it might occur via the acetate kinase. Large differences in gene sets involved in resistance to acidic conditions were not detected among the genomes. Therefore, the regulation of those genes, or a mechanism not yet known, might be responsible for the unique ability of D. amilsii. This is the first report on comparative genomics of sulfur-reducing bacteria, which is valuable to give insight into this poorly understood metabolism, but of great potential for biotechnological purposes and of environmental significance.
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spelling Genome sequence of Desulfurella amilsii strain TR1 and comparative genomics of Desulfurellaceae familycomparative genomicsDesulfurellaceaesulfur reducersacidophilesmetabolismScience & TechnologyThe acidotolerant sulfur reducer Desulfurella amilsii was isolated from sediments of Tinto river, an extremely acidic environment. Its ability to grow in a broad range of pH and to tolerate certain heavy metals offers potential for metal recovery processes. Here we report its high-quality draft genome sequence and compare it to the available genome sequences of other members of Desulfurellaceae family: D. acetivorans, D. multipotens, Hippea maritima, H. alviniae, H. medeae and H. jasoniae. For most species, pairwise comparisons for average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) revealed ANI values from 67.5 to 80% and DDH values from 12.9 to 24.2%. D. acetivorans and D. multipotens, however, surpassed the estimated thresholds of species definition for both DDH (98.6%) and ANI (88.1%). Therefore, they should be merged to a single species. Comparative analysis of Desulfurellaceae genomes revealed different gene content for sulfur respiration between Desulfurella and Hippea species. Sulfur reductase is only encoded in D. amilsii, in which it is suggested to play a role in sulfur respiration, especially at low pH. Polysulfide reductase is only encoded in Hippea species; it is likely that this genus uses polysulfide as electron acceptor. Genes encoding thiosulfate reductase are present in all the genomes, but dissimilatory sulfite reductase is only present in Desulfurella species. Thus, thiosulfate respiration via sulfite is only likely in this genus. Although sulfur disproportionation occurs in Desulfurella species, the molecular mechanism behind this process is not yet understood, hampering a genome prediction. The metabolism of acetate in Desulfurella species can occur via the acetyl-CoA synthetase or via acetate kinase in combination with phosphate acetyltransferase, while in Hippea species, it might occur via the acetate kinase. Large differences in gene sets involved in resistance to acidic conditions were not detected among the genomes. Therefore, the regulation of those genes, or a mechanism not yet known, might be responsible for the unique ability of D. amilsii. This is the first report on comparative genomics of sulfur-reducing bacteria, which is valuable to give insight into this poorly understood metabolism, but of great potential for biotechnological purposes and of environmental significance.The authors thank CNPq (Conselho Nacional de Desenvolvimento Cientifiìco e Tecnoloìgico),organization of the Brazilian Government for supporting the doctoral study program for the development of Science and Technology. Research of IS-A and AM Stams is financed by ERC grant project 323009, and Gravitation grant project 024.002.002 fromTheNetherlands Ministry of Education, Culture and Science. Thanks to Bastian Hornung for the bioinformatics support and to Robert Smith for the English revision.info:eu-repo/semantics/publishedVersionFrontiers MediaUniversidade do MinhoFlorentino, AnnaStams, Alfons Johannes MariaSánchez-Andrea, Irene2017-01-312017-01-31T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/46348engFlorentino, Anna; Stams, A. J. M.; Sánchez-Andrea, Irene, Genome sequence of Desulfurella amilsii strain TR1 and comparative genomics of Desulfurellaceae family. Frontiers in Microbiology, 8(222), 20171664-302X1664-302X10.3389/fmicb.2017.00222http://journal.frontiersin.org/journal/microbiologyinfo: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:RCAAP2023-07-21T12:26:18Zoai:repositorium.sdum.uminho.pt:1822/46348Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:20:41.795455Repositório 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 Genome sequence of Desulfurella amilsii strain TR1 and comparative genomics of Desulfurellaceae family
title Genome sequence of Desulfurella amilsii strain TR1 and comparative genomics of Desulfurellaceae family
spellingShingle Genome sequence of Desulfurella amilsii strain TR1 and comparative genomics of Desulfurellaceae family
Florentino, Anna
comparative genomics
Desulfurellaceae
sulfur reducers
acidophiles
metabolism
Science & Technology
title_short Genome sequence of Desulfurella amilsii strain TR1 and comparative genomics of Desulfurellaceae family
title_full Genome sequence of Desulfurella amilsii strain TR1 and comparative genomics of Desulfurellaceae family
title_fullStr Genome sequence of Desulfurella amilsii strain TR1 and comparative genomics of Desulfurellaceae family
title_full_unstemmed Genome sequence of Desulfurella amilsii strain TR1 and comparative genomics of Desulfurellaceae family
title_sort Genome sequence of Desulfurella amilsii strain TR1 and comparative genomics of Desulfurellaceae family
author Florentino, Anna
author_facet Florentino, Anna
Stams, Alfons Johannes Maria
Sánchez-Andrea, Irene
author_role author
author2 Stams, Alfons Johannes Maria
Sánchez-Andrea, Irene
author2_role author
author
dc.contributor.none.fl_str_mv Universidade do Minho
dc.contributor.author.fl_str_mv Florentino, Anna
Stams, Alfons Johannes Maria
Sánchez-Andrea, Irene
dc.subject.por.fl_str_mv comparative genomics
Desulfurellaceae
sulfur reducers
acidophiles
metabolism
Science & Technology
topic comparative genomics
Desulfurellaceae
sulfur reducers
acidophiles
metabolism
Science & Technology
description The acidotolerant sulfur reducer Desulfurella amilsii was isolated from sediments of Tinto river, an extremely acidic environment. Its ability to grow in a broad range of pH and to tolerate certain heavy metals offers potential for metal recovery processes. Here we report its high-quality draft genome sequence and compare it to the available genome sequences of other members of Desulfurellaceae family: D. acetivorans, D. multipotens, Hippea maritima, H. alviniae, H. medeae and H. jasoniae. For most species, pairwise comparisons for average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) revealed ANI values from 67.5 to 80% and DDH values from 12.9 to 24.2%. D. acetivorans and D. multipotens, however, surpassed the estimated thresholds of species definition for both DDH (98.6%) and ANI (88.1%). Therefore, they should be merged to a single species. Comparative analysis of Desulfurellaceae genomes revealed different gene content for sulfur respiration between Desulfurella and Hippea species. Sulfur reductase is only encoded in D. amilsii, in which it is suggested to play a role in sulfur respiration, especially at low pH. Polysulfide reductase is only encoded in Hippea species; it is likely that this genus uses polysulfide as electron acceptor. Genes encoding thiosulfate reductase are present in all the genomes, but dissimilatory sulfite reductase is only present in Desulfurella species. Thus, thiosulfate respiration via sulfite is only likely in this genus. Although sulfur disproportionation occurs in Desulfurella species, the molecular mechanism behind this process is not yet understood, hampering a genome prediction. The metabolism of acetate in Desulfurella species can occur via the acetyl-CoA synthetase or via acetate kinase in combination with phosphate acetyltransferase, while in Hippea species, it might occur via the acetate kinase. Large differences in gene sets involved in resistance to acidic conditions were not detected among the genomes. Therefore, the regulation of those genes, or a mechanism not yet known, might be responsible for the unique ability of D. amilsii. This is the first report on comparative genomics of sulfur-reducing bacteria, which is valuable to give insight into this poorly understood metabolism, but of great potential for biotechnological purposes and of environmental significance.
publishDate 2017
dc.date.none.fl_str_mv 2017-01-31
2017-01-31T00:00:00Z
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 http://hdl.handle.net/1822/46348
url http://hdl.handle.net/1822/46348
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Florentino, Anna; Stams, A. J. M.; Sánchez-Andrea, Irene, Genome sequence of Desulfurella amilsii strain TR1 and comparative genomics of Desulfurellaceae family. Frontiers in Microbiology, 8(222), 2017
1664-302X
1664-302X
10.3389/fmicb.2017.00222
http://journal.frontiersin.org/journal/microbiology
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 Frontiers Media
publisher.none.fl_str_mv Frontiers Media
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
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instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
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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
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