Distinct ecotypes within a natural haloarchaeal population enable adaptation to changing environmental conditions without causing population sweeps

Abstract

Microbial communities thriving in hypersaline brines of solar salterns are highly resistant and resilient to environmental changes, and salinity is a major factor that deterministically influences community structure. Here, we demonstrate that this resilience occurs even after rapid osmotic shocks caused by a threefold change in salinity (a reduction from 34 to 12% salts) leading to massive amounts of archaeal cell lysis. Specifically, our temporal metagenomic datasets identified two co-occurring ecotypes within the most dominant archaeal population of the brines Haloquadratum walsbyi that exhibited different salt concentration preferences. The dominant ecotype was generally more abundant and occurred in high-salt conditions (34%); the low abundance ecotype always co-occurred but was enriched at salinities around 20% or lower and carried unique gene content related to solute transport and gene regulation. Despite their apparent distinct ecological preferences, the ecotypes did not outcompete each other presumably due to weak functional differentiation between them. Further, the osmotic shock selected for a temporal increase in taxonomic and functional diversity at both the Hqr. walsbyi population and whole-community levels supporting the specialization-disturbance hypothesis, that is, the expectation that disturbance favors generalists. Altogether, our results provide new insights into how intraspecies diversity is maintained in light of substantial gene-content differences and major environmental perturbations.

Fig. 1. The experimental setup of the study.

A Control pond E1 (left) is salt-saturated and therefore salt crystals are observed at the sediment interface; dilution pond E6 (right) have brines below the salt-saturation threshold, and therefore no salt precipitates form. B Salinity shifts throughout the experiment. Ponds were sampled at time zero (T0h), 1 day (T1), 2 days (T2), 1 week (T7), and 1 month (T31). After dilution, the E6 pond was not refilled during the experimental period.

Fig. 2. Taxonomic shifts during the dilution experiment.

A Shifts in abundance of the C-MAGs. B Dynamics of the archaeal vs. bacterial fraction of the communities based on OPUs (bars; primary y axis), and alpha diversity based on Nonpareil (red line; secondary y axis).

Fig. 3. Similarity among the metagenomes determined in this study.

Clustering of all metagenomes based on: A whole metagenome MASH distance, B Jaccard distance based on OPUs, C the abundance of SEED subsystems. Metagenomes of the control pond E1 are labeled in black and those of the dilution pond E6 in blue.

Fig. 4. Shifts in the abundances of the control and dilution MAGs during the sampling period.

A D-MAGs and B C-MAGs. MAGs that decreased in abundance after the osmotic shock are shown in red while those that increased in abundance after osmotic shock but decreased after 1 week of dilution are shown in green. MAGs that increased in abundance in the intermediate salinities (i.e., T1, T2, and T7 time points) are shown in blue for comparison.

Fig. 5. Dynamics of the two Haloquadratum walsbyi ecotypes.

Metagenomic relative abundance of reads from control (left column) and dilution pond (right column) mapping to (i) core MAG genes with identity >98%, (ii) relative abundance based on competitive blast of reads mapping to core genes, and (iii) to MAG-specific genes.

Fig. 6. Hqr. walsbyi D2T0 and D2T7 gene-content variability depending on normalized gene coverage (geneTAD80/avg. genome TAD80) and comparison of functional gene content between whole MAG genes and variable MAG genes.

A Metagenome clustering based on normalized TAD80 values using the variable genes of the MAG D2T0. Gene clusters (vertical clustering) in red indicate genes with high coverage in sample T7 and in blue, genes with lower coverage in the sample T7. Red and blue boxes indicate the gene function of the marked clusters. B Same representation as A but using variable genes of the MAG D2T7 as a reference. C Comparison of the functional gene content of MAG D2T0 and D2T7 and the functions encoded for the variable genes represented in A and B. Genes were annotated against TrEMBL databases. The numbers of genes were normalized to 100% to compare functional categories.