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 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.
Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Floor 4, C1113AAD CABA, Argentina.
José L
JL
López
Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría 'Juan P. Garrahan', Combate de los Pozos 1881, C1245AAM CABA, Argentina.
Marcelo
M
Golemba
Instituto Antártico Argentino, UNSAM Campus Miguelete, 25 de Mayo y Francia, B1650HMJ San Martín, Buenos Aires, Argentina.|Facultad de Farmacia y Bioquímica, Cátedra de Biotecnología e Instituto de Nanobiotecnología UBA-CONICET, Universidad de Buenos Aires, Junin 956 Floor 6, C1113AAD CABA, Argentina.
Edgardo
E
Hernández
Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Puerto Madryn, U9120ACD, Chubut, Argentina.
Mariana
M
Lozada
Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Puerto Madryn, U9120ACD, Chubut, Argentina.
Hebe
H
Dionisi
Pacific Northwest National Laboratory, MSIN: J4-18, Richland, WA 99352, USA.
Janet K
JK
Jansson
CAGE-Centre for Arctic Gas Hydrate, Environment and Climate, UiT The Arctic University of Norway, N-9037, Tromsø, Norway.|Akvaplan-niva, Fram-High North Research Centre for Climate and the Environment, NO-9296, Tromsø, Norway.
Jolynn
J
Carroll
Department of Systems Ecology, Stockholm University, SE-10691, Sweden.
Leif
L
Lundgren
School of Natural Sciences, Technology and Environmental Studies, Sodertorn University, 14189 Huddinge, Sweden.
Sara
S
Sjöling
Instituto Antártico Argentino, UNSAM Campus Miguelete, 25 de Mayo y Francia, B1650HMJ San Martín, Buenos Aires, Argentina.|Facultad de Farmacia y Bioquímica, Cátedra de Biotecnología e Instituto de Nanobiotecnología UBA-CONICET, Universidad de Buenos Aires, Junin 956 Floor 6, C1113AAD CABA, Argentina.
Walter P
WP
Mac Cormack
D000864:Antarctic Regions; D001118:Argentina; D001419:Bacteria / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D005658:Fungi / Q000145:classification / Q000235:genetics*; D019015:Geologic Sediments / Q000382:microbiology* / Q000821:virology; D054892:Metagenome; D009664:Norway; D017862:Phycodnaviridae / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D012243:Rhodopsin / Q000235:genetics; D012623:Seawater / Q000382:microbiology* / Q000821:virology; D013548:Sweden; D014764:Viral Proteins / Q000235:genetics*
D014764:Viral Proteins; D012243:Rhodopsin
marine sediment; metagenomes; microbial rhodopsin; phylogeography; polar/subpolar; viral rhodopsin