Prokaryotic diversity and biogeochemical characteristics of field living and laboratory cultured stromatolites from the hypersaline Laguna Interna, Salar de Atacama (Chile)

Key energy metabolisms in modern living microbialites from hypersaline Andean lagoons of the Salar de Atacama, Chile

Microbialites are organosedimentary structures formed mainly due to the precipitation of carbonate minerals, although they can also incorporate siliceous, phosphate, ferric, and sulfate minerals. The minerals' precipitation occurs because of local chemical changes triggered by changes in pH and redox transformations catalyzed by the microbial energy metabolisms. Here, geochemistry, metagenomics, and bioinformatics tools reveal the key energy metabolisms of microbial mats, stromatolites and an endoevaporite distributed across four hypersaline lagoons from the Salar de Atacama. Chemoautotrophic and chemoheterotrophic microorganisms seem to coexist and influence microbialite formation. The microbialite types of each lagoon host unique microbial communities and metabolisms that influence their geochemistry. Among them, photosynthetic, carbon- and nitrogen- fixing and sulfate-reducing microorganisms appear to control the main biogeochemical cycles. Genes associated with non-conventional energy pathways identified in MAGs, such as hydrogen production/consumption, arsenic oxidation/reduction, manganese oxidation and selenium reduction, also contribute to support life in microbialites. The presence of genes encoding for enzymes associated with ureolytic processes in the Cyanobacteria phylum and Gammaproteobacteria class might induce carbonate precipitation in hypersaline environments, contributing to the microbialites formation. To the best of our knowledge, this is the first study characterizing metagenomically microbialites enriched in manganese and identifying metabolic pathways associated with manganese oxidation, selenium reduction, and ureolysis in this ecosystem, which suggests that the geochemistry and bioavailability of energy sources (As, Mn and Se) shapes the microbial metabolisms in the microbialites.

Asgard archaea in saline environments

Members of candidate Asgardarchaeota superphylum appear to share numerous eukaryotic-like attributes thus being broadly explored for their relevance to eukaryogenesis. On the contrast, the ecological roles of Asgard archaea remains understudied. Asgard archaea have been frequently associated to low-oxygen aquatic sedimentary environments worldwide spanning a broad but not extreme salinity range. To date, the available information on diversity and potential biogeochemical roles of Asgardarchaeota mostly sourced from marine habitats and to a much lesser extend from true saline environments (i.e., > 3% w/v total salinity). Here, we provide an overview on diversity and ecological implications of Asgard archaea distributed across saline environments and briefly explore their metagenome-resolved potential for osmoadaptation. Loki-, Thor- and Heimdallarchaeota are the dominant Asgard clades in saline habitats where they might employ anaerobic/microaerophilic organic matter degradation and autotrophic carbon fixation. Homologs of primary solute uptake ABC transporters seemingly prevail in Thorarchaeota, whereas those putatively involved in trehalose and ectoine biosynthesis were mostly inferred in Lokiarchaeota. We speculate that Asgardarchaeota might adopt compatible solute-accumulating ('salt-out') strategy as response to salt stress. Our current understanding on the distribution, ecology and salt-adaptive strategies of Asgardarchaeota in saline environments are, however, limited by insufficient sampling and incompleteness of the available metagenome-assembled genomes. Extensive sampling combined with 'omics'- and cultivation-based approaches seem, therefore, crucial to gain deeper knowledge on this particularly intriguing archaeal lineage.

Mineral Paragenesis Precipitating in Salt Flat Pools of Continental Environments Replicated in Microbial Mat Microcosms without Evaporation

Mineral precipitation can be observed in natural environments, such as lagoons, rivers, springs, and soils. The primary precipitation process has long been believed to be abiotic due to evaporation, leading to phase supersaturation. However, biotic interactions of microbial metabolism, organic compounds, and dissolved ions leading to mineral precipitation has been shown in laboratory studies using single-organism culture. The increase in pH inducing calcium carbonate precipitation due to oxygenic photosynthesis by Cyanobacteria and the release of ions due to organic matter decomposition by Firmicutes-inducing magnesium carbonate precipitation are recognized examples. As microbes do not live as pure cultures in natural environments but form complex communities, such pure culture lab studies do not reflect natural conditions. In this study, we grew natural complex microbial communities in microcosm conditions using filtered brine as water column and two types of natural gypsum substrates, and we replenished incubations to avoid evaporation. We monitored microbial communities through optical microscopy and analyzed mineral paragenesis in association with and without microbes, using different analytical techniques, such X-ray diffraction, and optical and field emission scanning electron microscopies. To detect changes throughout the experiment, small amounts of water column brine were extracted for physicochemial determinations. We were able to detect mineral paragenesis, avoiding evaporation, including major phases of chemical sedimentary rocks, such as gypsum, calcium carbonate, and some silicates in association to microbes. In addition, we evidenced that the use of natural substrates positively impacts growth of microbial communities, promoting the development of more biomass. This study can be seen as the first attempt and proof of concept of differentiating biotic and abiotic participation in evaporitic deposits, as they can form mineral paragenesis without evaporation. Future studies with microcosm experiments using microbial mats will be needed to establish mineral precipitation induced by micro-organisms and their extracellular polymeric substances (EPS), specifically to replicate mineral paragenesis sedimented from natural brines.

Geobiology of Andean Microbial Ecosystems Discovered in Salar de Atacama, Chile

The Salar de Atacama in the Chilean Central Andes harbors unique microbial ecosystems due to extreme environmental conditions, such as high altitude, low oxygen pressure, high solar radiation, and high salinity. Combining X-ray diffraction analyses, scanning electron microscopy and molecular diversity studies, we have characterized twenty previously unexplored Andean microbial ecosystems in eight different lakes and wetlands from the middle-east and south-east regions of this salt flat. The mats and microbialites studied are mainly formed by calcium carbonate (aragonite and calcite) and halite, whereas the endoevaporites are composed predominantly of gypsum and halite. The carbonate-rich mats and microbialites are dominated by Bacteroidetes and Proteobacteria phyla. Within the phylum Proteobacteria, the most abundant classes are Alphaproteobacteria, Gammaproteobacteria and Deltaproteobacteria. While in the phylum Bacteroidetes, the most abundant classes are Bacteroidia and Rhodothermia. Cyanobacteria, Chloroflexi, Planctomycetes, and Verrucomicrobia phyla are also well-represented in the majority of these systems. Gypsum endoevaporites, on the contrary, are dominated by Proteobacteria, Bacteroidetes, and Euryarchaeota phyla. The Cyanobacteria phylum is also abundant in these systems, but it is less represented in comparison to mats and microbialites. Regarding the eukaryotic taxa, diatoms are key structural components in most of the microbial ecosystems studied. The genera of diatoms identified were Achnanthes, Fallacia, Halamphora, Mastogloia, Navicula, Nitzschia, and Surirella. Normally, in the mats and microbialites, diatoms form nano-globular carbonate aggregates with filamentous cyanobacteria and other prokaryotic cells, suggesting their participation in the mineral precipitation process. This work expands our knowledge of the microbial ecosystems inhabiting the extreme environments from the Central Andes region, which is important to ensure their protection and conservation.