Hypersaline sapropels act as hotspots for microbial dark matter

Abstract

Present-day terrestrial analogue sites are crucial ground truth proxies for studying life in geochemical conditions close to those assumed to be present on early Earth or inferred to exist on other celestial bodies (e.g. Mars, Europa). Although hypersaline sapropels are border-of-life habitats with moderate occurrence, their microbiological and physicochemical characterization lags behind. Here, we study the diversity of life under low water activity by describing the prokaryotic communities from two disparate hypersaline sapropels (Transylvanian Basin, Romania) in relation to geochemical milieu and pore water chemistry, while inferring their role in carbon cycling by matching taxa to known taxon-specific biogeochemical functions. The polyphasic approach combined deep coverage SSU rRNA gene amplicon sequencing and bioinformatics with RT-qPCR and physicochemical investigations. We found that sapropels developed an analogous elemental milieu and harbored prokaryotes affiliated with fifty-nine phyla, among which the most abundant were Proteobacteria, Bacteroidetes and Chloroflexi. Containing thirty-two candidate divisions and possibly undocumented prokaryotic lineages, the hypersaline sapropels were found to accommodate one of the most diverse and novel ecosystems reported to date and may contribute to completing the phylogenetic branching of the tree of life.

Figure 1

PCoA analyses of prokaryotic communities found in the water columns (triangles) and sapropels (circles) of Ursu and Fara Fund lakes, generated by using both unweighted (A) and weighted (B) UniFrac distance matrices. The water column sequences were recovered from SRA (accession numbers: SRS691458, SRS691457, SRS691436 and SRS691388). Abbreviations: Us3m – Ursu Lake sapropel sample from 3 m depth; FFs2m – Fara Fund Lake sapropel sample from 2 m depth; Uw0.5 m and Uw2.5 m – Ursu Lake water samples from 0.5 m and 2.5 m depths; FFw0.5 m and FFw2m – Fara Fund Lake water samples from 0.5 and 2 m depths.

Figure 2

Phylogenetic diversity (Faith’s PD) estimates of Ursu (ULS) and Fara Fund (FFLS) sapropels in relation to other (hyper)saline sediments. The terrestrial (TS), aquatic (AS) and exposed lakebed (ELS) sediments are from La Sal del Rey hypersaline lake (sequences recovered from the following archives: SRS004880, SRS004879, SRS004878, SRS004877, SRS004876, SRS004875, SRS004874, SRS004873). The pooled (PMS) and subsampled marsh (SMS) sediments are from Rowley River salt marsh complex (sequences recovered from the following archives: SRS118669, SRS118662, SRS118663, SRS118664, SRS118665, SRS118666, SRS118667, SRS118668).

Figure 3

Phylum-level taxonomic profiles of sapropels prokaryotic communities using 16 S rRNA gene sequences.

Figure 4

Sapropels’ taxonomic-to-phenotipic cladogram showing the putative metabolic profiles of sapropels’ microbial communities (based on 16 S rRNA gene). The cladogram does not reflect the functional status of the microbial communities, but rather their metabolic potential. The red internal ring is a circular heatmap; the colour intensity is proportional with the number of sequences affiliated with a metabolic profile. The emerald triangles (▴) correspond to the metabolic profiles of Ursu sapropels, while the inverted (▾) green ones correspond to Fara Fund sapropels.