Identification of microbial and viral-like rhodopsin sequences in sediments from four cold coastal environments

LÓPEZ, J. L.; HERNANDEZ, E.; DIONISI, H. M.; LOZADA, M. ; JANSSON, J.; LUNDGREN, L.; SJOLING, SARA; MAC CORMACK, W. P.

Auckland

Conferencia; XXXIII SCAR Biennial Meetings and Open Science Conference; 2014

Scientific Committee on Antarctic Research (SCAR)

Bioprospecting of genes encoding microbial rhodopsins have a biotechnological interest for its future applications as solar energy transductors and fluorescence voltage-indicators probes..Here, we describe a diverse group of microbial rhodopsin sequences found in the marine sediment from four subpolar geographic regions of the world: a) Adventfjord (Svalbard Archipelago, Norway; 78º 14.2´ N-15º 40.6´ E and 78º 14.6´ N-15º 39.4´ E), b) Värtahamnen (Baltic Sea, Sweden; 59.21.48 N-18.06.69 E and 59.21,667 N 018.06,291 E), c) Ushuaia Bay (Tierra del Fuego, Argentina, 54º 48.656´ S 68º 17.731´ W and 54º 48.256´ S 68º 17.296´ W) and d) Potter Cove (King George Island, Antarctic Peninsula; 62º 13´ 50´´ S 58º 39´ 22´´ W and 62º 13´ 55´´ S 58º 39´ 18´´ W). Sediment samplings were performed on August-December in all those geographic regions, at a 9.5-50 meters depth range. Total DNA was extracted from approximately 0.5 g of dry sediment. A total of 23 metagenomes were obtained by 454 pyrosequencing from the total microbial community present in the marine sediment samples. Screening of thr metagenome sequences was performed by using automatic assignment COG categories (COG5524) and depurated using BlastClust. Transmembrane helices in proteins were predicted using the TMHMM program. Further alignment of 128 putative rhodopsin sequences from this work together with a set of reference sequences from data banks was performed by using Muscle program. phylogenetic analysis was made using online PhyML.Rhodopsin genes were not found in all sediment samples. Bacterial, archaeal, eukaryotic and viral-like rhodopsins sequences were detected at the DNA level in 18 out of 23 metagenomes. A great diversity of rhodopsin sequences was observed when these sequences were compared with those previously reported.To our knowledge, this is the first report about microbial rhodopsins from costal marine sediments. A selection of the more divergent kind of rhodopsin sequences for further cloning and functional characterization would be necessary to evaluate its biothecnological applications.