Phenomics and Genomics Reveal Adaptation of Virgibacillus dokdonensis Strain 21D to Its Origin of Isolation, the Seawater-Brine Interface of the Mediterranean Sea Deep Hypersaline Anoxic Basin Discovery

Abstract

The adaptation of sporeformers to extreme environmental conditions is frequently questioned due to their capacity to produce highly resistant endospores that are considered as resting contaminants, not representing populations adapted to the system. In this work, in order to gain a better understanding of bacterial adaptation to extreme habitats, we investigated the phenotypic and genomic characteristics of the halophile Virgibacillus sp. 21D isolated from the seawater-brine interface (SBI) of the MgCl 2 -saturated deep hypersaline anoxic basin Discovery located in the Eastern Mediterranean Sea. Vegetative cells of strain 21D showed the ability to grow in the presence of high concentrations of MgCl 2, such as 14.28% corresponding to 1.5 M. Biolog phenotype MicroArray (PM) was adopted to investigate the strain phenotype, with reference to carbon energy utilization and osmotic tolerance. The strain was able to metabolize only 8.4% of 190 carbon sources provided in the PM1 and PM2 plates, mainly carbohydrates, in accordance with the low availability of nutrients in its habitat of origin. By using in silico DNA-DNA hybridization the analysis of strain 21D genome, assembled in one circular contig, revealed that the strain belongs to the species Virgibacillus dokdonensis . The genome presented compatible solute-based osmoadaptation traits, including genes encoding for osmotically activated glycine-betaine/carnitine/choline ABC transporters, as well as ectoine synthase enzymes. Osmoadaptation of the strain was then confirmed with phenotypic assays by using the osmolyte PM9 Biolog plate and growth experiments. Furthermore, the neutral isoelectric point of the reconstructed proteome suggested that the strain osmoadaptation was mainly mediated by compatible solutes. The presence of genes involved in iron acquisition and metabolism indicated that osmoadaptation was tailored to the iron-depleted saline waters of the Discovery SBI. Overall, both phenomics and genomics highlighted the potential capability of V. dokdonensis 21D vegetative cells to adapt to the environmental conditions in Discovery SBI.

Current state of athalassohaline deep‐sea hypersaline anoxic basin research—recommendations for future work and relevance to astrobiology

“…Although few athalassohaline DHAB isolates exist, relevant well‐characterized taxa, such as Methanohalophilus species, are available in public culture collections: these species, however, are largely isolated from surficial hypersaline environments such as solar salterns, bitterns and soda lakes and may be evolutionarily distant and physiologically distinct. Recent isolation and whole‐genome sequencing of a Virgibacillus dokdonensis strain from the Discovery interface layer revealed significant MgCl 2 tolerance (1.8 M) and proteome adaptation to DHAB conditions, such as osmoregulation, and the ability to use diverse carbon sources (Zeaiter et al ., 2019). It should be noted that fungal species are also relevant to athalassohaline DHABs as some can grow at extremely low water activities and high concentrations of magnesium chloride and should be targeted for future DHAB culture work (Zajc et al ., 2014).…”

A deep‐sea bacterium related to coastal marine pathogens

“…Additionally, betaine‐choline‐carnitine transporter genes family were detected. Many halophilic bacteria adjust their cell turgor pressure through the acquisition of different osmoprotectants from the surroundings, such as ectoine, betaine, carnitine or choline, or by the synthesis from their precursors (Oren, 2008 ; Zeaiter et al ., 2019 ). The presence of these transporters may contribute to the accumulation of these osmoprotectants inside the bacterial cell favouring the adaptation to high hydrostatic pressure.…”

What lies on macroalgal surface: diversity of polysaccharide degraders in culturable epiphytic bacteria

“…Marine environments, characterized by specific physicochemical parameters as well as by the presence of unusual carbon sources (Rao et al 2017 ; Zeaiter et al 2019 ), host organisms constituting a reservoir of biotechnologically relevant functions that could be exploited in medical, pharmaceutical and industrial applications (Iwamoto et al 2001 ; Wang et al 2020 ; Rodrigues et al 2017 ).…”