Phylogenetic and Functional Substrate Specificity for Endolithic Microbial Communities in Hyper-Arid Environments

Under extreme water deficit, endolithic (inside rock) microbial ecosystems are considered environmental refuges for life in cold and hot deserts, yet their diversity and functional adaptations remain vastly unexplored. The metagenomic analyses of the communities from two rock substrates, calcite and ignimbrite, revealed that they were dominated by Cyanobacteria, Actinobacteria, and Chloroflexi. The relative distribution of major phyla was significantly different between the two substrates and biodiversity estimates, from 16S rRNA gene sequences and from the metagenomic data, all pointed to a higher taxonomic diversity in the calcite community. While both endolithic communities showed adaptations to extreme aridity and to the rock habitat, their functional capabilities revealed significant differences. ABC transporters and pathways for osmoregulation were more diverse in the calcite chasmoendolithic community. In contrast, the ignimbrite cryptoendolithic community was enriched in pathways for secondary metabolites, such as non-ribosomal peptides (NRP) and polyketides (PK). Assemblies of the metagenome data produced population genomes for the major phyla found in both communities and revealed a greater diversity of Cyanobacteria population genomes for the calcite substrate. Draft genomes of the dominant Cyanobacteria in each community were constructed with more than 93% estimated completeness. The two annotated proteomes shared 64% amino acid identity and a significantly higher number of genes involved in iron update, and NRPS gene clusters, were found in the draft genomes from the ignimbrite. Both the community-wide and genome-specific differences may be related to higher water availability and the colonization of large fissures and cracks in the calcite in contrast to a harsh competition for colonization space and nutrient resources in the narrow pores of the ignimbrite. Together, these results indicated that the habitable architecture of both lithic substrates- chasmoendolithic versus cryptoendolithic - might be an essential element in determining the colonization and the diversity of the microbial communities in endolithic substrates at the dry limit for life.

Endolithic microbial habitats as refuges for life in polyextreme environment of the Atacama Desert

The extremely harsh conditions of hyperarid deserts are a true challenge for microbial life. Microorganisms thriving in such polyextreme environments are fascinating as they can tell us more about life, its strategies and its boundaries than other groups of organisms. The Atacama Desert (North Chile) holds two world records of extreme environmental characteristics: the lowest rainfall and greatest surface ultraviolet radiation and total solar irradiance ever measured on Earth. Despite these limiting conditions for life, we recently identified several remarkable examples of endolithic habitats colonized by phototrophic and heterotrophic microorganisms in the hyperarid core of the Atacama Desert.

Raman imaging of microbial colonization in rock-some analytical aspects

Raman imaging allows one to obtain spatially resolved chemical information in a nondestructive manner. Herein, we present analytical aspects of effective in situ and in vivo Raman imaging of algae and cyanobacteria from within their native rock habitats. Specifically, gypsum and halite inhabited by endolithic communities from the hyperarid Atacama Desert were analyzed. Raman imaging of these phototrophic colonization reveals a pigment composition within the aggregates that helps in understanding some of their adaptation strategies to survive in this harsh polyextreme environment. The study is focused on methodical aspects of Raman imaging acquisition and subsequent data processing. Point imaging is compared with line imaging in terms of their image quality, spatial resolution, spectral signal-to-noise ratio, time requirements, and risk of laser-induced sample alteration. The roles of excitation wavelength, exposure time, and step size of the imaging grid on successful Raman imaging results are also discussed. Graphical abstract.

Characterization of a functional serum response element in the Actin403 gene promoter from the crustacean Artemia franciscana

The serum response factor (SRF) activates expression of several genes in response to growth factors present in serum. SRF also regulates the expression of tissue-specific genes, including those in vertebrate muscles. An SRF-binding site (CArG box) present in the Artemia franciscana Actin403 promoter was shown to be necessary for transcriptional activity in cultured cells from Drosophila melanogaster and mammals. This DNA region bound mammalian and Drosophila SRFs in vitro and mediated transcriptional activation of the Actin403 promoter in response to serum, phorbol esters and lysophosphatidic acid in transfected cultured mammalian cells. Mutations in the CArG box greatly reduced promoter activity and stimulation by extracellular compounds.

A serum response factor homologue is expressed in ectodermal tissues during development of the crustacean Artemia franciscana

Complementary DNA clones have been isolated from the crustacean Artemia franciscana coding for a serum response factor (SRF)-homologue that is more than 96% identical to human and Drosophila melanogaster SRFs in their MADS boxes. The SRF homologue is expressed in ectodermal tissues, as determined by in situ hybridization experiments. A SRF-binding site has been identified in the promoter region of the Actin403 gene that is also expressed in ectodermal tissues, in accordance with its transcriptional regulation by the SRF homologue. The mRNA coding for A. franciscana SRF is present at similar levels in cryptobiotic encysted embryos and in developing nauplii. However, there is a significant increase in CArG-binding activity at the later developmental stage, indicating a postranscriptional regulation of SRF during A. franciscana embryonic development.