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Living with Salt: Genetics and Ecology of Halophiles

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Natural hypersaline habitats exist across our planet, usually prevailing in coastal regions characterized by warm and dry climate, but also present in inland water bodies, deep-sea locations or geological strata, or even associated with surfaces of animals, plants and food. Such sites can be chemically ...

Natural hypersaline habitats exist across our planet, usually prevailing in coastal regions characterized by warm and dry climate, but also present in inland water bodies, deep-sea locations or geological strata, or even associated with surfaces of animals, plants and food. Such sites can be chemically diverse and commonly reach salinity levels almost ten times greater than that in normal seawater, excluding most lifeforms on Earth.
High-salinities are particularly challenging because cells need to effectively counterbalance the increase in osmotic pressure in the environment to prevent water loss and the corresponding disturbances in cellular activities and/or viability. Some halophiles increase internal ion concentrations (“salt in” strategy) to combat the high salinity, but this usually also requires permanent structural changes in their intrinsic enzymes and cellular machinery, which in the long term, prevents normal enzymatic functions at lower salinities. While the “salt-in” strategy is chiseled in textbooks as a hallmark trait of extreme halophiles, recent genomic data suggests that some lineages likely adopted the salt-in strategy for osmoregulation without imposing dramatic shifts in the structural properties of their proteins.

Several other halophiles rely on an alternative strategy, leading to the production of compatible solutes (osmolytes), which allows cells to cope with multiple salinity regimes without also changing their proteomic properties. However, the osmolyte strategy is energetically costly. As a rule of thumb, metabolic diversity is constrained by energetics at high salinities, which explains also the often-low taxonomic diversity in hypersaline environments. Other confounding factors such as the high density of viruses and distinct chemical profiles of hypersaline environments likely also contribute to the low diversity. Despite such adversities, halophiles thrive and are found in all three domains of life.

Notwithstanding primary research efforts in the last decades, many fundamental facets in the microbial ecology of dominant groups, particularly their biochemistry and roles remain uncharacterized, highlighting key research directions for further exploration. Moreover, hypersaline habitats contain an unprecedented array of uncultivated novel groups decorating the prokaryotic tree of life; most cultivated species currently serve as treasure troves for enzymes in food and medical biotechnologies.

Although significant strides in sequencing technologies have opened a path for large-scale exploration of structure-function relationships in hypersaline environments, the metabolic traits underpinning the roles of a vast majority of signature groups remain untapped due to the paucity of genomic data. Thus, details regarding the ecology of many of these microbes remain obscure. Against this backdrop, is the recent evidence indicating that some of these lineages harbor metabolic traits presumptively constrained by bioenergetics, which also offered clues to the evolutionary history of methanogenesis. Also, a challenge currently remains on how to study the metabolic activity and transcriptional landscape of these microorganisms that are located in relatively inaccessible deep-sea settings or present at centimeter-scale environmental gradients.

The present Research Topic on “Living with Salt: Genetics and Ecology of Halophiles” aims to assemble contributions from scientists working on the genetics and microbial ecology of hypersaline habitats and environments with steep salinity gradients. Here, we would like to encourage authors to contribute research articles that are interdisciplinary, including original research, techniques, reviews, and synthesis articles.
Broadly, we would like contributions covering the following areas of research:
1). General physiology and biochemistry of novel candidate divisions or lineages
2). Adaptations to life under high salinity
3). Evolutionary history of halophiles
4). Microbial life in salinity gradients
5). Extracellular DNA: roles in nutritional ecology and epigenetics of halophiles
6). Phylogeny, taxonomy and biodiversity of halophiles
7). Halophiles as models for astrobiology
8). Future directions in the microbial ecology of hypersaline environments


Keywords: Halophiles, Ecogenomics, salinity gradients, Epigenetics, Evolution, Taxonomy, Diversity


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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