Distinctive gene and protein characteristics of extremely piezophilic Colwellia

Abstract

Background: The deep ocean is characterized by low temperatures, high hydrostatic pressures, and low concentrations of organic matter. While these conditions likely select for distinct genomic characteristics within prokaryotes, the attributes facilitating adaptation to the deep ocean are relatively unexplored. In this study, we compared the genomes of seven strains within the genus Colwellia, including some of the most piezophilic microbes known, to identify genomic features that enable life in the deep sea.

Results: Significant differences were found to exist between piezophilic and non-piezophilic strains of Colwellia. Piezophilic Colwellia have a more basic and hydrophobic proteome. The piezophilic abyssal and hadal isolates have more genes involved in replication/recombination/repair, cell wall/membrane biogenesis, and cell motility. The characteristics of respiration, pilus generation, and membrane fluidity adjustment vary between the strains, with operons for a nuo dehydrogenase and a tad pilus only present in the piezophiles. In contrast, the piezosensitive members are unique in having the capacity for dissimilatory nitrite and TMAO reduction. A number of genes exist only within deep-sea adapted species, such as those encoding d-alanine-d-alanine ligase for peptidoglycan formation, alanine dehydrogenase for NADH/NAD⁺ homeostasis, and a SAM methyltransferase for tRNA modification. Many of these piezophile-specific genes are in variable regions of the genome near genomic islands, transposases, and toxin-antitoxin systems.

Conclusions: We identified a number of adaptations that may facilitate deep-sea radiation in members of the genus Colwellia, as well as in other piezophilic bacteria. An enrichment in more basic and hydrophobic amino acids could help piezophiles stabilize and limit water intrusion into proteins as a result of high pressure. Variations in genes associated with the membrane, including those involved in unsaturated fatty acid production and respiration, indicate that membrane-based adaptations are critical for coping with high pressure. The presence of many piezophile-specific genes near genomic islands highlights that adaptation to the deep ocean may be facilitated by horizontal gene transfer through transposases or other mobile elements. Some of these genes are amenable to further study in genetically tractable piezophilic and piezotolerant deep-sea microorganisms.

Keywords: Colwellia; Deep sea; Genomic island; Hadal; Hydrostatic pressure; Piezophile; Trench.

Fig. 1

a Approximate sample collection locations for the Colwellia strains compared in this study. The map was created using the R package marmap [104]. b Whole genome phylogenetic tree and shared average nucleotide identities among the seven strains of interest

Fig. 2

a; Isoelectric point distribution of proteins within piezophilic (blue points) or piezosensitive (black) strains, with an average line of fit within each group. b; Isoelectric point protein bias within each strain as a function of their growth pressure. c; Asymmetry index values indicating preference of amino acids in the piezophiles or C. psychrerythraea 34H within orthologous proteins present in all strains. d; Specific amino acid substitutions from C. psychrerythraea 34H to the piezophiles within orthologous proteins. The substitutions shown were also identified within comparisons between piezophilic and piezosensitive Shewanella

Fig. 3

a; Distribution of genes within the seven comparative strains using Roary [103]. Core genes were found in all seven genomes, shell genes in 2–6 genomes, and cloud genes in only one genome. b; Differentially abundant COG categories within piezophilic or piezosensitive Colwellia. c Specific genomic attributes that were differentially present in piezophilic or piezosensitive strains. Present, grey; absent, white

Fig. 4

The location of a d-ala-d-ala ligase (a) and alanine dehydrogenase (c) in strains MT41 and TT2012, with surrounding genes labeled. Protein trees of the d-ala-d-ala ligase (b) and alanine dehydrogenase (d) with sequences approximately > 50% similar shown

Fig. 5

A cell schematic highlighting adaptations within piezophilic Colwellia identified in this study. The figure was created using Biorender.com