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 contains isolates from both photic (817) and aphotic layers (744), including the mesopelagic (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. We described 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 different depths. 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 all photic, mesopelagic, and bathypelagic isolates sequences retrieved from different stations, 37% of them were 100% identical. This percentage increased up to 59% when mesopelagic and bathypelagic strains were grouped as the aphotic dataset and compared to the photic dataset of isolates, indicating the ubiquity of some bacterial isolates along different ocean depths. Finally, we isolated three strains that represent a new species, and the genome comparison and phenotypic characterization of two of these strains (ISS653 and ISS1889) concluded that they belong to a new species within the genus Mesonia. 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 the culturable marine bacteria as part of the total marine microbial diversity.

A Simple Culture Method Enhances the Recovery of Culturable Actinobacteria From Coastal Sediments

“…The Defluviimonas recovered from S. alterniflora sediment possibly has been enriched due to the sewage effluent into this S. alterniflora sediment (Supplementary Figure 1). Another group of Alphaprotebacteria is Erythrobacter (Figure 2), which is also found as a most cultivated group in open ocean water (Sanz-Sáez et al, 2020). Our data supported that Erythrobacter are generalists in the marine environment from coastal sediment to the open ocean.…”

Depth Profile of Nitrifying Archaeal and Bacterial Communities in the Remote Oligotrophic Waters of the North Pacific

“…The highest degree of correlations was found for unclassified ASVs belonging to Chloroflexi, Marinimicrobia (formerly known as Marine Group A and SAR406), α- and γ-Proteobacteria ( Supplementary Table 2 ). Both α- and γ-Proteobacteria are dominant classes of heterotrophic bacteria in the marine environment ( Sanz-Sáez et al, 2020 ), while Chloroflexi organisms represent a diverse range of metabolisms, such as aerobic/anaerobic heterotrophy or anoxygenic photosynthesis, and are present in multiple habitats around the planet, from the human oral cavity to sponges or the deep sea ( Bayer et al, 2018 ). Marinimicrobia, with no cultured representatives so far, is globally distributed in the oceans and appears to have a wide diversity of metabolic properties and syntrophic interactions ( Hawley et al, 2017 ).…”

Aerobic Denitrification and Heterotrophic Sulfur Oxidation in the Genus Halomonas Revealed by Six Novel Species Characterizations and Genome-Based Analysis

“…At present, more than 100 species in the genus Halomonas have been described 1 . As a cosmopolitan taxon, members of the genus Halomonas widely inhabit diverse saline environments, such as salt and soda lakes, saline soil, solar salterns, sea ice, seafood, marine invertebrates, effluents, seawater, sea basins, hadal, and hydrothermal vent environments ( Kaye and Baross, 2000 ; Kaye et al, 2004 , 2011 ; Biddle et al, 2005 ; Inagaki et al, 2006 ; Arahal et al, 2007 ; Kim et al, 2013 ; Nunoura et al, 2015 ; Salazar et al, 2016 ; Sanz-Sáez et al, 2020 ).…”