Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions
Rhodopsins are broadly distributed. In this work, we analyzed 23 metagenomes corresponding to marine sediment samples from four regions that share cold climate conditions (Norway; Sweden; Argentina and Antarctica). In order to investigate the genes evolution of viral rhodopsins, an initial set of 62...
Published in: | FEMS Microbiology Ecology |
---|---|
Main Authors: | , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Wiley Blackwell Publishing, Inc
|
Subjects: | |
Online Access: | http://hdl.handle.net/11336/39117 |
id |
ftconicet:oai:ri.conicet.gov.ar:11336/39117 |
---|---|
record_format |
openpolar |
spelling |
ftconicet:oai:ri.conicet.gov.ar:11336/39117 2023-10-09T21:47:13+02:00 Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions Lopez, Jose Luis Golemba, Marcelo Darío Hernández, Edgardo Lozada, Mariana Dionisi, Hebe Monica Jansson, Janet K. Carroll, Jolynn Lundgren, Leif Sjöling, Sara Mac Cormack, Walter Patricio application/pdf http://hdl.handle.net/11336/39117 eng eng Wiley Blackwell Publishing, Inc info:eu-repo/semantics/altIdentifier/doi/10.1093/femsec/fiw216 info:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/femsec/article/93/1/fiw216/2666416 http://hdl.handle.net/11336/39117 Lopez, Jose Luis; Golemba, Marcelo Darío; Hernández, Edgardo; Lozada, Mariana; Dionisi, Hebe Monica; et al.; Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions; Wiley Blackwell Publishing, Inc; Fems Microbiology Ecology; 93; 1; 1-2017; 1-9 0168-6496 1574-6941 CONICET Digital CONICET info:eu-repo/semantics/restrictedAccess https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ MARINE SEDIMENT METAGENOMES MICROBIAL RHODOPSIN PHYLOGEOGRAPHY POLAR/SUBPOLAR VIRAL RHODOPSIN https://purl.org/becyt/ford/1.6 https://purl.org/becyt/ford/1 info:eu-repo/semantics/article info:ar-repo/semantics/artículo info:eu-repo/semantics/publishedVersion ftconicet https://doi.org/10.1093/femsec/fiw216 2023-09-24T19:47:06Z Rhodopsins are broadly distributed. In this work, we analyzed 23 metagenomes corresponding to marine sediment samples from four regions that share cold climate conditions (Norway; Sweden; Argentina and Antarctica). In order to investigate the genes evolution of viral rhodopsins, an initial set of 6224 bacterial rhodopsin sequences according to COG5524 were retrieved from the 23 metagenomes. After selection by the presence of transmembrane domains and alignment, 123 viral (51) and non-viral (72) sequences (>50 amino acids) were finally included in further analysis. Viral rhodopsin genes were homologs of Phaeocystis globosa virus and Organic lake Phycodnavirus. Non-viral microbial rhodopsin genes were ascribed to Bacteroidetes, Planctomycetes, Firmicutes, Actinobacteria, Cyanobacteria, Proteobacteria, Deinococcus-Thermus and Cryptophyta and Fungi. A rescreening using Blastp, using as queries the viral sequences previously described, retrieved 30 sequences (>100 amino acids). Phylogeographic analysis revealed a geographical clustering of the sequences affiliated to the viral group. This clustering was not observed for the microbial non-viral sequences. The phylogenetic reconstruction allowed us to propose the existence of a putative ancestor of viral rhodopsin genes related to Actinobacteria and Chloroflexi. This is the first report about the existence of a phylogeographic association of the viral rhodopsin sequences from marine sediments. Fil: Lopez, Jose Luis. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; Argentina Fil: Golemba, Marcelo Darío. Gobierno de la Ciudad de Buenos Aires. Hospital de Pediatría Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Hernández, Edgardo. Ministerio de Relaciones Exteriores, Comercio Interno y Culto. Dirección Nacional del Antártico. Instituto Antártico Argentino; Argentina. Universidad de Buenos Aires; Argentina Fil: Lozada, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico ... Article in Journal/Newspaper Antarc* Antarctica Dirección Nacional del Antártico Instituto Antártico Argentino CONICET Digital (Consejo Nacional de Investigaciones Científicas y Técnicas) Argentina Argentino Edgardo ENVELOPE(-64.517,-64.517,-64.833,-64.833) Lopez ENVELOPE(-63.567,-63.567,-64.850,-64.850) Norway Organic Lake ENVELOPE(78.190,78.190,-68.457,-68.457) FEMS Microbiology Ecology 93 1 fiw216 |
institution |
Open Polar |
collection |
CONICET Digital (Consejo Nacional de Investigaciones Científicas y Técnicas) |
op_collection_id |
ftconicet |
language |
English |
topic |
MARINE SEDIMENT METAGENOMES MICROBIAL RHODOPSIN PHYLOGEOGRAPHY POLAR/SUBPOLAR VIRAL RHODOPSIN https://purl.org/becyt/ford/1.6 https://purl.org/becyt/ford/1 |
spellingShingle |
MARINE SEDIMENT METAGENOMES MICROBIAL RHODOPSIN PHYLOGEOGRAPHY POLAR/SUBPOLAR VIRAL RHODOPSIN https://purl.org/becyt/ford/1.6 https://purl.org/becyt/ford/1 Lopez, Jose Luis Golemba, Marcelo Darío Hernández, Edgardo Lozada, Mariana Dionisi, Hebe Monica Jansson, Janet K. Carroll, Jolynn Lundgren, Leif Sjöling, Sara Mac Cormack, Walter Patricio Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions |
topic_facet |
MARINE SEDIMENT METAGENOMES MICROBIAL RHODOPSIN PHYLOGEOGRAPHY POLAR/SUBPOLAR VIRAL RHODOPSIN https://purl.org/becyt/ford/1.6 https://purl.org/becyt/ford/1 |
description |
Rhodopsins are broadly distributed. In this work, we analyzed 23 metagenomes corresponding to marine sediment samples from four regions that share cold climate conditions (Norway; Sweden; Argentina and Antarctica). In order to investigate the genes evolution of viral rhodopsins, an initial set of 6224 bacterial rhodopsin sequences according to COG5524 were retrieved from the 23 metagenomes. After selection by the presence of transmembrane domains and alignment, 123 viral (51) and non-viral (72) sequences (>50 amino acids) were finally included in further analysis. Viral rhodopsin genes were homologs of Phaeocystis globosa virus and Organic lake Phycodnavirus. Non-viral microbial rhodopsin genes were ascribed to Bacteroidetes, Planctomycetes, Firmicutes, Actinobacteria, Cyanobacteria, Proteobacteria, Deinococcus-Thermus and Cryptophyta and Fungi. A rescreening using Blastp, using as queries the viral sequences previously described, retrieved 30 sequences (>100 amino acids). Phylogeographic analysis revealed a geographical clustering of the sequences affiliated to the viral group. This clustering was not observed for the microbial non-viral sequences. The phylogenetic reconstruction allowed us to propose the existence of a putative ancestor of viral rhodopsin genes related to Actinobacteria and Chloroflexi. This is the first report about the existence of a phylogeographic association of the viral rhodopsin sequences from marine sediments. Fil: Lopez, Jose Luis. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; Argentina Fil: Golemba, Marcelo Darío. Gobierno de la Ciudad de Buenos Aires. Hospital de Pediatría Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Hernández, Edgardo. Ministerio de Relaciones Exteriores, Comercio Interno y Culto. Dirección Nacional del Antártico. Instituto Antártico Argentino; Argentina. Universidad de Buenos Aires; Argentina Fil: Lozada, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico ... |
format |
Article in Journal/Newspaper |
author |
Lopez, Jose Luis Golemba, Marcelo Darío Hernández, Edgardo Lozada, Mariana Dionisi, Hebe Monica Jansson, Janet K. Carroll, Jolynn Lundgren, Leif Sjöling, Sara Mac Cormack, Walter Patricio |
author_facet |
Lopez, Jose Luis Golemba, Marcelo Darío Hernández, Edgardo Lozada, Mariana Dionisi, Hebe Monica Jansson, Janet K. Carroll, Jolynn Lundgren, Leif Sjöling, Sara Mac Cormack, Walter Patricio |
author_sort |
Lopez, Jose Luis |
title |
Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions |
title_short |
Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions |
title_full |
Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions |
title_fullStr |
Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions |
title_full_unstemmed |
Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions |
title_sort |
microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions |
publisher |
Wiley Blackwell Publishing, Inc |
url |
http://hdl.handle.net/11336/39117 |
long_lat |
ENVELOPE(-64.517,-64.517,-64.833,-64.833) ENVELOPE(-63.567,-63.567,-64.850,-64.850) ENVELOPE(78.190,78.190,-68.457,-68.457) |
geographic |
Argentina Argentino Edgardo Lopez Norway Organic Lake |
geographic_facet |
Argentina Argentino Edgardo Lopez Norway Organic Lake |
genre |
Antarc* Antarctica Dirección Nacional del Antártico Instituto Antártico Argentino |
genre_facet |
Antarc* Antarctica Dirección Nacional del Antártico Instituto Antártico Argentino |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1093/femsec/fiw216 info:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/femsec/article/93/1/fiw216/2666416 http://hdl.handle.net/11336/39117 Lopez, Jose Luis; Golemba, Marcelo Darío; Hernández, Edgardo; Lozada, Mariana; Dionisi, Hebe Monica; et al.; Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions; Wiley Blackwell Publishing, Inc; Fems Microbiology Ecology; 93; 1; 1-2017; 1-9 0168-6496 1574-6941 CONICET Digital CONICET |
op_rights |
info:eu-repo/semantics/restrictedAccess https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
op_doi |
https://doi.org/10.1093/femsec/fiw216 |
container_title |
FEMS Microbiology Ecology |
container_volume |
93 |
container_issue |
1 |
container_start_page |
fiw216 |
_version_ |
1779310166871638016 |