Global dominance of Haloquadratum walsbyi by a single genomovar with distinct gene content and viral cohorts from close relatives

Abstract

Haloquadratum walsbyi is generally the dominant species in hypersaline ecosystems at salt saturation conditions. Here, we followed the dynamics of its genomovars and associated viruses during recurrent evaporation-dilution disturbances of varying intensities at the mesocosm scale over 813 days. The diversity observed within a single mesocosm was also compared with that in a global-scale inventory of hypersaline environments of thalassohaline origin. The 140 binned metagenome assembled genomes (MAGs) together with the genomes of the (only) two available of H. walsbyi isolates grouped into four highly related (98.25% > Average Nucleotide Identity [ANI] > 99.5%) dominant genomovars (intra-genomovar ANI > 99.5%). In mesocosm experiments, moderate disturbances (i.e. recurrent dilution from saturation to 20% salts) enhanced the abundance of the already-dominant genomovar Hqrw1, resulting in reduced intraspecific diversity. This genomovar also dominated in almost all sites sampled around the globe. In contrast, more intense disturbance (i.e. recurrent dilution from saturation to 13% salts) decreased the abundance of Hqrw1 to lower levels than genomovar Hqrw2 by the end of the incubation, which seems to resist better osmotic changes. Further, our results showed that genomovars were followed by their viral cohorts, who play a significant role in the global dominance of the four H. walsbyi genomovars and their replacement under unfavorable conditions. We propose that the global dominance of H. walsbyi in thalassohaline hypersaline sites is enabled by both the success of Hqrw1 in high but stable salinities and the larger resistance of Hqrw2 to extreme osmotic stress, safeguarding the presence of the species in the system.

Keywords: Haloquadratum walsbyi; genomovar; halovirus; intraspecies diversity; metagenomics; osmotic disturbances; time-series.

Figure 1

Influence of recurrent disturbances on Hqr. walsbyi abundance and intraspecies diversity. Oscillations in (A) temperature (°C) and (B) salinity (%) over the 813 days of mesocosm operation (modified from [38]). Temporal dynamics of Hqr. walsbyi are shown for (C) relative abundance, (D) genomic similarity (ANI), and (E) intraspecies diversity (ANIr), including trend lines over time with 95% confidence intervals (CIs), for the D13 (36% to 13% salts) and D20 (36% to 20% salts) mesocosms.

Figure 2

Location of the hypersaline sites sampled by the HSP. A map showing the HSP sampling sites used to estimate the global diversity of Hqr. walsbyi. Gradient indicates either which genomovar dominate each HSP sample or where Hqr. walsbyi did not bin.

Figure 3

Genomic diversity of Hqr. walsbyi genomes. Heatmap showing the 142 x 142 ANI comparisons among D13 (36% to 13% salts), D20 (36% to 20% salts), and HSP (global study) Hqr. walsbyi genomes. Hierarchical clustering was conducted using the “average” algorithm with Euclidean distances. Genomovars were identified based on ANI values (see figure key for details).

Figure 4

Genomovar and viral cohort abundances of Hqr. walsbyi at global scale. Barplot representing the cumulative abundance of (A) each genomovar and (B) their assigned viral cohorts across HSP (global study) metagenomes.

Figure 5

Genomovar and viral cohort dynamics of Hqr. walsbyi at mesocosm scale. Lineplots representing the relative abundance of each genomovar in (A) D13 (36% to 13% salts) and (B) D20 (36% to 20% salts) mesocosms. Lineplots representing the relative abundance of their assigned viral cohorts in (C) D13 (36% to 13% salts) and (D) D20 (36% to 20% salts) mesocosms.

Figure 6

High heterogeneity of viral abundances at both mesocosm and global scales. Heatmap representing the relative abundance at logaritmic scale of each vOTU, grouped by viral cohorts, along the 813 days of experimentation in D13 (36% to 13% salts) and D20 (36% to 20% salts) metagenomes, and across HSP (global study) samples. Note that HSP samples were ordered by distance (km) from Spain to New Zealand hypersaline environments.