Diversity of Lysis-Resistant Bacteria and Archaea in the Polyextreme Environment of Salar de Huasco

Abstract

The production of specialized resting cells is a remarkable strategy developed by several organisms to survive unfavorable environmental conditions. Spores are specialized resting cells that are characterized by low to absent metabolic activity and higher resistance. Spore-like cells are known from multiple groups of bacteria, which can form spores under suboptimal growth conditions (e.g., starvation). In contrast, little is known about the production of specialized resting cells in archaea. In this study, we applied a culture-independent method that uses physical and chemical lysis, to assess the diversity of lysis-resistant bacteria and archaea and compare it to the overall prokaryotic diversity (direct DNA extraction). The diversity of lysis-resistant cells was studied in the polyextreme environment of the Salar de Huasco. The Salar de Huasco is a high-altitude athalassohaline wetland in the Chilean Altiplano. Previous studies have shown a high diversity of bacteria and archaea in the Salar de Huasco, but the diversity of lysis-resistant microorganisms has never been investigated. The underlying hypothesis was that the combination of extreme abiotic conditions might favor the production of specialized resting cells. Samples were collected from sediment cores along a saline gradient and microbial mats were collected in small surrounding ponds. A significantly different diversity and composition were found in the sediment cores or microbial mats. Furthermore, our results show a high diversity of lysis-resistant cells not only in bacteria but also in archaea. The bacterial lysis-resistant fraction was distinct in comparison to the overall community. Also, the ability to survive the lysis-resistant treatment was restricted to a few groups, including known spore-forming phyla such as Firmicutes and Actinobacteria. In contrast to bacteria, lysis resistance was widely spread in archaea, hinting at a generalized resistance to lysis, which is at least comparable to the resistance of dormant cells in bacteria. The enrichment of Natrinema and Halarchaeum in the lysis-resistant fraction could hint at the production of cyst-like cells or other resistant cells. These results can guide future studies aiming to isolate and broaden the characterization of lysis-resistant archaea.

Planktonic archaea reveal stronger dispersal limitation and more network connectivity than planktonic bacteria in the Jinsha River of southwestern China

“…At large spatial scales, microorganisms are influenced more by dispersal limitation than environmental selection, presumably because microorganisms are not well adapted to disperse over large areas (Chen et al, 2020). In addition to geographical scales, the one‐way flow of rivers limits the dispersal of microorganisms, which is mainly reflected in difficulty moving from downstream to upstream (Chen et al, 2019; Ramírez et al, 2022).…”

“…Archaea have more in common with eukaryotic microbes than bacteria, because bacteria lack certain characteristics such as the presence of histones, complex RNA polymerases and methionine translation initiation (Baker et al, 2020). Accordingly, archaea and bacteria have major differences in their membrane structures, metabolic capacities, dormancy abilities, environmental sensitivities and substrate‐use modes (Baker et al, 2010; Bang & Schmitz, 2018; Ramírez et al, 2022; Santonja et al, 2018; Wei et al, 2020). Thanks to advances in sequencing technology, it is now feasible to conduct highly detailed surveys of microbial communities and explore geographical distributions of microorganisms (Trouche et al, 2021).…”

Assessment of fungal spores and spore-like diversity in environmental samples by targeted lysis

“…Nonetheless, by calculating a lysis-resistant enrichment index of each ASV (including those unclassified), the existence of a fungal seed bank distinct from the lysis prone fraction (considered to be active vegetative cells) was evaluated. The enrichment index showed that, as in the case of Bacteria [32], most ASVs were either enriched in the lysis-resistant fraction or in the total community, with only a small proportion of them showing equal abundance in both fractions.…”

“…A similar enrichment of intracellular bacteria was found after the application of the lysis-resistant enrichment method. The phyla Tenericutes and Chlamydiae, which are composed of intracellular pathogens [68,69], were enriched in the lysis-resistant fraction [32].…”

“…The use of the method for enriching lysis-resistant cells has been recently extended to study lysis-resistant communities in archaea. While in bacteria, lysis-resistance was shown to be restricted to a few groups, in archaea, resistance to lysis was widely spread [32]. This is likely due to specific cellular adaptations (i.e., lipid composition, diversity of cell envelope composition) within this domain [33][34][35][36].…”