Diversity and distribution of marine heterotrophic bacteria from a large culture collection

Abstract Background Isolation of marine microorganisms is fundamental to gather information about their physiology, ecology and genomic content. To date, most of the bacterial isolation efforts have focused on the photic ocean leaving the deep ocean less explored. We have created a marine culture collection of heterotrophic bacteria (MARINHET) using a standard marine medium comprising a total of 1561 bacterial strains, and covering a variety of oceanographic regions from different seasons and years, from 2009 to 2015. Specifically, our marine collection includes isolates from both photic (817) and aphotic layers (744), including the oxygen minimum zone (OMZ, 362) and the bathypelagic (382), from the North Western Mediterranean Sea, the North and South Atlantic Ocean, the Indian, the Pacific, and the Arctic Oceans. With this study, we describe the taxonomy, the phylogenetic diversity and the biogeography of a fraction of the marine culturable microorganisms to enhance our knowledge about which heterotrophic marine isolates are recurrently retrieved across oceans and along all the water column. Results The partial sequencing of the 16S rRNA gene of all isolates revealed that they mainly affiliate with the classes Alphaproteobacteria (35.9%), Gammaproteobacteria (38.6%), and phylum Bacteroidetes (16.5%). In addition, Alteromonas and Erythrobacter genera were found the most common heterotrophic bacteria in the ocean growing in solid agar medium. When comparing photic, OMZ, and bathypelagic isolates sequences, a 37% of them were 100% identical. This percentage increased up to 59% when the comparison was restricted between photic and aphotic sequences (OMZ and bathypelagic together) indicating the ubiquity of some bacterial isolates along the water column. Finally, we isolated three strains related with the genus Mesonia sp. that may represent new species since their whole 16S rRNA gene shared less than 95% sequence similarity with any other culture representative. Conclusions Overall, this study highlights the relevance of culture dependent studies, with focus on marine isolated bacteria from different oceanographic regions and depths, to provide a more comprehensive view of marine microbial diversity.