Abstract
Marine Euryarchaeota remain among the least understood major components of marine microbial communities. Marine group II Euryarchaeota (MG-II) are more abundant in surface waters (4–20% of the total prokaryotic community), whereas marine group III Euryarchaeota (MG-III) are generally considered low-abundance members of deep mesopelagic and bathypelagic communities. Using genome assembly from direct metagenome reads and metagenomic fosmid clones, we have identified six novel MG-III genome sequence bins from the photic zone (Epi1–6) and two novel bins from deep-sea samples (Bathy1–2). Genome completeness in those genome bins varies from 44% to 85%. Photic-zone MG-III bins corresponded to novel groups with no similarity, and significantly lower GC content, when compared with previously described deep-MG-III genome bins. As found in many other epipelagic microorganisms, photic-zone MG-III bins contained numerous photolyase and rhodopsin genes, as well as genes for peptide and lipid uptake and degradation, suggesting a photoheterotrophic lifestyle. Phylogenetic analysis of these photolyases and rhodopsins as well as their genomic context suggests that these genes are of bacterial origin, supporting the hypothesis of an MG-III ancestor that lived in the dark ocean. Epipelagic MG-III occur sporadically and in relatively small proportions in marine plankton, representing only up to 0.6% of the total microbial community reads in metagenomes. None of the reconstructed epipelagic MG-III genomes were present in metagenomes from aphotic zone depths or from high latitude regions. Most low-GC bins were highly enriched at the deep chlorophyll maximum zones, with the exception of Epi1, which appeared evenly distributed throughout the photic zone worldwide.
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Acknowledgements
We are thankful to José de la Torre for editing the manuscript. We are thankful to L Gasperini and G Bortoluzzi of the Instituto di Geologia Marina (ISMAR), CNR, Bologna (Italy) for allowing PLG to participate in the Marmara2010 R/V Urania cruise during which part of the samples analyzed in this study were collected. This work was supported by projects MEDIMAX BFPU2013–48007-P from the Spanish Ministerio de Economía y Competitividad, MaCuMBA Project 311975 of the European Commission FP7, project AQUAMET II/2014/012 from the Generalitat Valenciana and by the French Agence Nationale de la Recherche (ANR-08-GENM-024–001,EVOLDEEP). JHM was supported with a PhD fellowship from the Spanish Ministerio de Economía y Competitividad.
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Haro-Moreno, J., Rodriguez-Valera, F., López-García, P. et al. New insights into marine group III Euryarchaeota, from dark to light. ISME J 11, 1102–1117 (2017). https://doi.org/10.1038/ismej.2016.188
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DOI: https://doi.org/10.1038/ismej.2016.188
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