Primer design for an accurate view of picocyanobacterial community structure by using high-throughput sequencing

Autores
Huber, Maria Paula; Cornejo Castillo, Francisco M.; Ferrera, Isabel; Sánchez, Pablo; Logares, Ramiro; Metz, Sebastián Darío; Balagué, Vanessa; Acinas, Silvia G.; Gasol, Josep M.; Unrein, Fernando
Año de publicación
2019
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
High-throughput sequencing (HTS) of the 16S rRNA gene has been used successfully to describe the structure and dynamics of microbial communities. Picocyanobacteria are important members of bacterioplankton communities, and, so far, they have predominantly been targeted using universal bacterial primers, providing a limited resolution of the picocyanobacterial community structure and dynamics. To increase such resolution, the study of a particular target group is best approached with the use of specific primers. Here, we aimed to design and evaluate specific primers for aquatic picocyanobacterial genera to be used with high-throughput sequencing. Since the various regions of the 16S rRNA gene have different degrees of conservation in different bacterial groups, we therefore first determined which hypervariable region of the 16S rRNA gene provides the highest taxonomic and phylogenetic resolution for the genera Synechococcus, Prochlorococcus, and Cyanobium. An in silico analysis showed that the V5, V6, and V7 hypervariable regions appear to be the most informative for this group. We then designed primers flanking these hypervariable regions and tested them in natural marine and freshwater communities. We successfully detected that most (97%) of the obtained reads could be assigned to picocyanobacterial genera. We defined operational taxonomic units as exact sequence variants (zero-radius operational taxonomic units [zOTUs]), which allowed us to detect higher genetic diversity and infer ecologically relevant information about picocyanobacterial community composition and dynamics in different aquatic systems. Our results open the door to future studies investigating picocyanobacterial diversity in aquatic systems.
Fil: Huber, Maria Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina
Fil: Cornejo Castillo, Francisco M.. Consejo Superior de Investigaciones Científicas. Instituto de Ciencias del Mar; España. University Of California At Santa Cruz.; Estados Unidos
Fil: Ferrera, Isabel. Consejo Superior de Investigaciones Científicas. Instituto de Ciencias del Mar; España. Instituto Español de Oceanografía. Centro Oceanográfico de Málaga; España
Fil: Sánchez, Pablo. Consejo Superior de Investigaciones Científicas. Instituto de Ciencias del Mar; España
Fil: Logares, Ramiro. Consejo Superior de Investigaciones Científicas. Instituto de Ciencias del Mar; España
Fil: Metz, Sebastián Darío. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina
Fil: Balagué, Vanessa. Consejo Superior de Investigaciones Científicas. Instituto de Ciencias del Mar; España
Fil: Acinas, Silvia G.. Consejo Superior de Investigaciones Científicas. Instituto de Ciencias del Mar; España
Fil: Gasol, Josep M.. Consejo Superior de Investigaciones Científicas. Instituto de Ciencias del Mar; España
Fil: Unrein, Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina
Materia
16S RRNA GENE
CYANOBIUM
HTS
PRIMER DESIGN
PROCHLOROCOCCUS
SYNECHOCOCCUS
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/117273
Acceder
id CONICETDig_e08011fffd2ff253fa6371e2406e98ce
oai_identifier_str oai:ri.conicet.gov.ar:11336/117273
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Primer design for an accurate view of picocyanobacterial community structure by using high-throughput sequencingHuber, Maria PaulaCornejo Castillo, Francisco M.Ferrera, IsabelSánchez, PabloLogares, RamiroMetz, Sebastián DaríoBalagué, VanessaAcinas, Silvia G.Gasol, Josep M.Unrein, Fernando16S RRNA GENECYANOBIUMHTSPRIMER DESIGNPROCHLOROCOCCUSSYNECHOCOCCUShttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1High-throughput sequencing (HTS) of the 16S rRNA gene has been used successfully to describe the structure and dynamics of microbial communities. Picocyanobacteria are important members of bacterioplankton communities, and, so far, they have predominantly been targeted using universal bacterial primers, providing a limited resolution of the picocyanobacterial community structure and dynamics. To increase such resolution, the study of a particular target group is best approached with the use of specific primers. Here, we aimed to design and evaluate specific primers for aquatic picocyanobacterial genera to be used with high-throughput sequencing. Since the various regions of the 16S rRNA gene have different degrees of conservation in different bacterial groups, we therefore first determined which hypervariable region of the 16S rRNA gene provides the highest taxonomic and phylogenetic resolution for the genera Synechococcus, Prochlorococcus, and Cyanobium. An in silico analysis showed that the V5, V6, and V7 hypervariable regions appear to be the most informative for this group. We then designed primers flanking these hypervariable regions and tested them in natural marine and freshwater communities. We successfully detected that most (97%) of the obtained reads could be assigned to picocyanobacterial genera. We defined operational taxonomic units as exact sequence variants (zero-radius operational taxonomic units [zOTUs]), which allowed us to detect higher genetic diversity and infer ecologically relevant information about picocyanobacterial community composition and dynamics in different aquatic systems. Our results open the door to future studies investigating picocyanobacterial diversity in aquatic systems.Fil: Huber, Maria Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); ArgentinaFil: Cornejo Castillo, Francisco M.. Consejo Superior de Investigaciones Científicas. Instituto de Ciencias del Mar; España. University Of California At Santa Cruz.; Estados UnidosFil: Ferrera, Isabel. Consejo Superior de Investigaciones Científicas. Instituto de Ciencias del Mar; España. Instituto Español de Oceanografía. Centro Oceanográfico de Málaga; EspañaFil: Sánchez, Pablo. Consejo Superior de Investigaciones Científicas. Instituto de Ciencias del Mar; EspañaFil: Logares, Ramiro. Consejo Superior de Investigaciones Científicas. Instituto de Ciencias del Mar; EspañaFil: Metz, Sebastián Darío. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); ArgentinaFil: Balagué, Vanessa. Consejo Superior de Investigaciones Científicas. Instituto de Ciencias del Mar; EspañaFil: Acinas, Silvia G.. Consejo Superior de Investigaciones Científicas. Instituto de Ciencias del Mar; EspañaFil: Gasol, Josep M.. Consejo Superior de Investigaciones Científicas. Instituto de Ciencias del Mar; EspañaFil: Unrein, Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); ArgentinaAmerican Society for Microbiology2019-04info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/117273Huber, Maria Paula; Cornejo Castillo, Francisco M.; Ferrera, Isabel; Sánchez, Pablo; Logares, Ramiro; et al.; Primer design for an accurate view of picocyanobacterial community structure by using high-throughput sequencing; American Society for Microbiology; Applied and Environmental Microbiology; 85; 7; 4-2019; 1-170099-2240CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1128/AEM.02659-18info:eu-repo/semantics/altIdentifier/url/https://aem.asm.org/content/85/7/e02659-18info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:19:59Zoai:ri.conicet.gov.ar:11336/117273instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:19:59.808CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Primer design for an accurate view of picocyanobacterial community structure by using high-throughput sequencing
title Primer design for an accurate view of picocyanobacterial community structure by using high-throughput sequencing
spellingShingle Primer design for an accurate view of picocyanobacterial community structure by using high-throughput sequencing
Huber, Maria Paula
16S RRNA GENE
CYANOBIUM
HTS
PRIMER DESIGN
PROCHLOROCOCCUS
SYNECHOCOCCUS
title_short Primer design for an accurate view of picocyanobacterial community structure by using high-throughput sequencing
title_full Primer design for an accurate view of picocyanobacterial community structure by using high-throughput sequencing
title_fullStr Primer design for an accurate view of picocyanobacterial community structure by using high-throughput sequencing
title_full_unstemmed Primer design for an accurate view of picocyanobacterial community structure by using high-throughput sequencing
title_sort Primer design for an accurate view of picocyanobacterial community structure by using high-throughput sequencing
dc.creator.none.fl_str_mv Huber, Maria Paula
Cornejo Castillo, Francisco M.
Ferrera, Isabel
Sánchez, Pablo
Logares, Ramiro
Metz, Sebastián Darío
Balagué, Vanessa
Acinas, Silvia G.
Gasol, Josep M.
Unrein, Fernando
author Huber, Maria Paula
author_facet Huber, Maria Paula
Cornejo Castillo, Francisco M.
Ferrera, Isabel
Sánchez, Pablo
Logares, Ramiro
Metz, Sebastián Darío
Balagué, Vanessa
Acinas, Silvia G.
Gasol, Josep M.
Unrein, Fernando
author_role author
author2 Cornejo Castillo, Francisco M.
Ferrera, Isabel
Sánchez, Pablo
Logares, Ramiro
Metz, Sebastián Darío
Balagué, Vanessa
Acinas, Silvia G.
Gasol, Josep M.
Unrein, Fernando
author2_role author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv 16S RRNA GENE
CYANOBIUM
HTS
PRIMER DESIGN
PROCHLOROCOCCUS
SYNECHOCOCCUS
topic 16S RRNA GENE
CYANOBIUM
HTS
PRIMER DESIGN
PROCHLOROCOCCUS
SYNECHOCOCCUS
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv High-throughput sequencing (HTS) of the 16S rRNA gene has been used successfully to describe the structure and dynamics of microbial communities. Picocyanobacteria are important members of bacterioplankton communities, and, so far, they have predominantly been targeted using universal bacterial primers, providing a limited resolution of the picocyanobacterial community structure and dynamics. To increase such resolution, the study of a particular target group is best approached with the use of specific primers. Here, we aimed to design and evaluate specific primers for aquatic picocyanobacterial genera to be used with high-throughput sequencing. Since the various regions of the 16S rRNA gene have different degrees of conservation in different bacterial groups, we therefore first determined which hypervariable region of the 16S rRNA gene provides the highest taxonomic and phylogenetic resolution for the genera Synechococcus, Prochlorococcus, and Cyanobium. An in silico analysis showed that the V5, V6, and V7 hypervariable regions appear to be the most informative for this group. We then designed primers flanking these hypervariable regions and tested them in natural marine and freshwater communities. We successfully detected that most (97%) of the obtained reads could be assigned to picocyanobacterial genera. We defined operational taxonomic units as exact sequence variants (zero-radius operational taxonomic units [zOTUs]), which allowed us to detect higher genetic diversity and infer ecologically relevant information about picocyanobacterial community composition and dynamics in different aquatic systems. Our results open the door to future studies investigating picocyanobacterial diversity in aquatic systems.
Fil: Huber, Maria Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina
Fil: Cornejo Castillo, Francisco M.. Consejo Superior de Investigaciones Científicas. Instituto de Ciencias del Mar; España. University Of California At Santa Cruz.; Estados Unidos
Fil: Ferrera, Isabel. Consejo Superior de Investigaciones Científicas. Instituto de Ciencias del Mar; España. Instituto Español de Oceanografía. Centro Oceanográfico de Málaga; España
Fil: Sánchez, Pablo. Consejo Superior de Investigaciones Científicas. Instituto de Ciencias del Mar; España
Fil: Logares, Ramiro. Consejo Superior de Investigaciones Científicas. Instituto de Ciencias del Mar; España
Fil: Metz, Sebastián Darío. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina
Fil: Balagué, Vanessa. Consejo Superior de Investigaciones Científicas. Instituto de Ciencias del Mar; España
Fil: Acinas, Silvia G.. Consejo Superior de Investigaciones Científicas. Instituto de Ciencias del Mar; España
Fil: Gasol, Josep M.. Consejo Superior de Investigaciones Científicas. Instituto de Ciencias del Mar; España
Fil: Unrein, Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina
description High-throughput sequencing (HTS) of the 16S rRNA gene has been used successfully to describe the structure and dynamics of microbial communities. Picocyanobacteria are important members of bacterioplankton communities, and, so far, they have predominantly been targeted using universal bacterial primers, providing a limited resolution of the picocyanobacterial community structure and dynamics. To increase such resolution, the study of a particular target group is best approached with the use of specific primers. Here, we aimed to design and evaluate specific primers for aquatic picocyanobacterial genera to be used with high-throughput sequencing. Since the various regions of the 16S rRNA gene have different degrees of conservation in different bacterial groups, we therefore first determined which hypervariable region of the 16S rRNA gene provides the highest taxonomic and phylogenetic resolution for the genera Synechococcus, Prochlorococcus, and Cyanobium. An in silico analysis showed that the V5, V6, and V7 hypervariable regions appear to be the most informative for this group. We then designed primers flanking these hypervariable regions and tested them in natural marine and freshwater communities. We successfully detected that most (97%) of the obtained reads could be assigned to picocyanobacterial genera. We defined operational taxonomic units as exact sequence variants (zero-radius operational taxonomic units [zOTUs]), which allowed us to detect higher genetic diversity and infer ecologically relevant information about picocyanobacterial community composition and dynamics in different aquatic systems. Our results open the door to future studies investigating picocyanobacterial diversity in aquatic systems.
publishDate 2019
dc.date.none.fl_str_mv 2019-04
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/117273
Huber, Maria Paula; Cornejo Castillo, Francisco M.; Ferrera, Isabel; Sánchez, Pablo; Logares, Ramiro; et al.; Primer design for an accurate view of picocyanobacterial community structure by using high-throughput sequencing; American Society for Microbiology; Applied and Environmental Microbiology; 85; 7; 4-2019; 1-17
0099-2240
CONICET Digital
CONICET
url http://hdl.handle.net/11336/117273
identifier_str_mv Huber, Maria Paula; Cornejo Castillo, Francisco M.; Ferrera, Isabel; Sánchez, Pablo; Logares, Ramiro; et al.; Primer design for an accurate view of picocyanobacterial community structure by using high-throughput sequencing; American Society for Microbiology; Applied and Environmental Microbiology; 85; 7; 4-2019; 1-17
0099-2240
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1128/AEM.02659-18
info:eu-repo/semantics/altIdentifier/url/https://aem.asm.org/content/85/7/e02659-18
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv American Society for Microbiology
publisher.none.fl_str_mv American Society for Microbiology
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.070432

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