Microorganism response to stressed terrestrial environments: a Raman spectroscopic perspective of extremophilic life strategies

Trichocoleus desertorum isolated from Negev desert petroglyphs: Characterization, adaptation and bioerosion potential

The Negev petroglyphs are considered valuable cultural heritage sites, but unfortunately, they are exposed to deterioration processes caused by anthropogenic and natural forces. Despite the many studies that have already pointed to the role of cyanobacteria in biogenic rock weathering, the knowledge involved in the process is still lacking. In this study, a cyanobacterial strain was isolated from the Negev Desert petroglyphs aiming to reveal its involvement in geochemical cycles and in the weathering processes of the rock substrate. The strain was characterized using morphological, molecular, and microscopic studies. The morphological research revealed a green-bluish, bundle-forming filamentous strain characterized by trichomes embedded in a common sheath. A combination of Nanopore and Illumina sequencing technologies facilitated the assembly of a near-complete genome containing 5,458,034 base pairs. A total of 5027 coding sequences were revealed by implementing PROKKA software. Annotation of five replicas of the 16S ribosomal RNA genes revealed that the Negev cyanobacteria isolate is closely (99.73 %) related to Trichocoleus desertorum LSB90_MW403957 isolated from the Sahara Desert, Algeria. The local strain was thus named Trichocoleus desertorum NBK24 CP116619. Several gene sequences that code for possible environmental adaptation mechanisms were found. Our study also identified genes for membrane transporters involved in the exchange of chemical elements, suggesting a possible interaction with rock minerals. Microscopic observations of T. desertorum NBK24 CP116619 infected onto calcareous stone slabs under laboratory conditions demonstrated the effect of the isolated cyanobacteria on stone surface degradation. In conclusion, the findings of this study further our understanding of terrestrial cyanobacterial genomes and functions and highlight the role of T. desertorum NBK24 CP116619 in stone weathering processes. This information may contribute to the creation of efficient restoration strategies for stone monuments affected by cyanobacteria.

Biological soil crust development affects bacterial communities in the Caragana microphylla community in alpine sandy areas

Introduction

Biological soil crusts (BSCs) constitute a substantial portion of primary production in dryland ecosystems. They successionally mature to deliver a series of ecosystem services. Bacteria, as an important community in BSCs, play critical roles in maintaining the structure and functions of BSCs. However, the process by which bacterial diversity and community are altered with BSC development is not fully understood.

Methods

In this study, amplicons sequencing was used to investigate bacterial diversity and community compositions across five developmental stages of BSCs (bare sand, microbial crusts, algae crusts, lichen crusts, and moss crusts) and their relationship with environmental variables in the Gonghe basin sandy land in Qinghai-Tibet Plateau, northwestern China.

Results

The results showed that Proteobacteria, Actinobacteria, Cyanobacteria, Acidobacteria, Bacteroidetes, and Firmicutes were predominant in different developmental stages of BSCs, accounting for more than 77% of the total relative abundance. The phyla of Acidobacteria and Bacteroidetes were abundant in this region. With BSC development, bacterial diversity significantly increased, and the taxonomic community composition significantly altered. The relative abundance of copiotrophic bacteria, such as Actinobacteria, Acidobacteria, Bacteroidetes, Verrucomicrobia, Planctomycetes, and Gemmatimonadetes significantly increased, whereas the relative abundance of oligotrophic bacteria, such as Proteobacteria and Firmicutes significantly decreased. The relative abundance of Cyanobacteria in the algae crusts was significantly higher than that in the other developmental stages (p < 0.05).

Conclusion

Variations in bacterial composition suggested that the potential ecological functions of the bacterial community were altered with BSC development. The functions varied from enhancing soil surface stability by promoting soil particle cementation in the early stages to promoting material circulation of the ecosystem by fixing carbon and nitrogen and decomposing litter in the later stages of BSC development. Bacterial community is a sensitive index of water and nutrient alterations during BSC development. SWC, pH value, TC, TOC, TN, NO3−, TP and soil texture were the primary environmental variables that promoted changes in the bacterial community composition of BSCs.

Detecting Kerogen as a Biosignature Using Colocated UV Time-Gated Raman and Fluorescence Spectroscopy

The Mars 2020 mission will analyze samples in situ and identify any that could have preserved biosignatures in ancient habitable environments for later return to Earth. Highest priority targeted samples include aqueously formed sedimentary lithologies. On Earth, such lithologies can contain fossil biosignatures as aromatic carbon (kerogen). In this study, we analyzed nonextracted kerogen in a diverse suite of natural, complex samples using colocated UV excitation (266 nm) time-gated (UV-TG) Raman and laser-induced fluorescence spectroscopies. We interrogated kerogen and its host matrix in samples to (1) explore the capabilities of UV-TG Raman and fluorescence spectroscopies for detecting kerogen in high-priority targets in the search for possible biosignatures on Mars; (2) assess the effectiveness of time gating and UV laser wavelength in reducing fluorescence in Raman spectra; and (3) identify sample-specific issues that could challenge rover-based identifications of kerogen using UV-TG Raman spectroscopy. We found that ungated UV Raman spectroscopy is suited to identify diagnostic kerogen Raman bands without interfering fluorescence and that UV fluorescence spectroscopy is suited to identify kerogen. These results highlight the value of combining colocated Raman and fluorescence spectroscopies, similar to those obtainable by SHERLOC on Mars 2020, to strengthen the confidence of kerogen detection as a potential biosignature in complex natural samples. Key Words: Raman spectroscopy-Laser-induced fluorescence spectroscopy-Mars Sample Return-Mars 2020 mission-Kerogen-Biosignatures. Astrobiology 18, 431-453.

Alteration of rocks by endolithic organisms is one of the pathways for the beginning of soils on Earth

Subaerial endolithic systems of the current extreme environments on Earth provide exclusive insight into emergence and development of soils in the Precambrian when due to various stresses on the surfaces of hard rocks the cryptic niches inside them were much more plausible habitats for organisms than epilithic ones. Using an actualistic approach we demonstrate that transformation of silicate rocks by endolithic organisms is one of the possible pathways for the beginning of soils on Earth. This process led to the formation of soil-like bodies on rocks in situ and contributed to the raise of complexity in subaerial geosystems. Endolithic systems of East Antarctica lack the noise from vascular plants and are among the best available natural models to explore organo-mineral interactions of a very old “phylogenetic age” (cyanobacteria-to-mineral, fungi-to-mineral, lichen-to-mineral). On the basis of our case study from East Antarctica we demonstrate that relatively simple endolithic systems of microbial and/or cryptogamic origin that exist and replicate on Earth over geological time scales employ the principles of organic matter stabilization strikingly similar to those known for modern full-scale soils of various climates.

The Hybrid Strategy of Thermoactinospora rubra YIM 77501T for Utilizing Cellulose as a Carbon Source at Different Temperatures

Thermoactinospora rubra YIM 77501^T is an aerobic, Gram-positive, spore-forming and cellulose degrading thermophilic actinomycete isolated from a sandy soil sample of a volcano. Its growth temperature range is 28–60°C. The genomic sequence of this strain revealed that there are 27 cellulase genes belonging to six glycoside hydrolase families. To understand the strategy that this strain uses to utilize carbon sources such as cellulose at different temperatures, comparative transcriptomics analysis of T. rubra YIM 77501^T was performed by growing it with cellulose (CMC) and without cellulose (replaced with glucose) at 30, 40, and 50°C, respectively. Transcriptomic analyses showed four cellulase genes (TrBG2, TrBG3, TrBG4, and ThrCel6B) were up-regulated at 30, 40, and 50°C. The rate of gene expression of TrBG2, TrBG3, TrBG4, and ThrCel6B were 50°C > 30°C > 40°C. One cellulase gene (TrBG1) and two cellulase genes (TrBG5 and ThrCel6A) were up-regulated only at 30 and 50°C, respectively. These up-regulated cellulase genes were cloned and expressed in Escherichia coli. The enzymatic properties of up-regulated cellulases showed a variety of responses to temperature. Special up-regulated cellulases TrBG1 and ThrCel6A displayed temperature acclimation for each growth condition. These expression patterns revealed that a hybrid strategy was used by T. rubra to utilize carbon sources at different temperatures. This study provides genomic, transcriptomics, and experimental data useful for understanding how microorganisms respond to environmental changes and their application in enhancing cellulose hydrolysis for animal feed and bioenergy production.

Preservation of Biomarkers from Cyanobacteria Mixed with Mars-Like Regolith Under Simulated Martian Atmosphere and UV Flux

The space mission EXPOSE-R2 launched on the 24th of July 2014 to the International Space Station is carrying the BIOMEX (BIOlogy and Mars EXperiment) experiment aimed at investigating the endurance of extremophiles and stability of biomolecules under space and Mars-like conditions. In order to prepare the analyses of the returned samples, ground-based simulations were carried out in Planetary and Space Simulation facilities. During the ground-based simulations, Chroococcidiopsis cells mixed with two Martian mineral analogues (phyllosilicatic and sulfatic Mars regolith simulants) were exposed to a Martian simulated atmosphere combined or not with UV irradiation corresponding to the dose received during a 1-year-exposure in low Earth orbit (or half a Martian year on Mars). Cell survival and preservation of potential biomarkers such as photosynthetic and photoprotective pigments or DNA were assessed by colony forming ability assays, confocal laser scanning microscopy, Raman spectroscopy and PCR-based assays. DNA and photoprotective pigments (carotenoids) were detectable after simulations of the space mission (570 MJ/m(2) of UV 200-400 nm irradiation and Martian simulated atmosphere), even though signals were attenuated by the treatment. The fluorescence signal from photosynthetic pigments was differently preserved after UV irradiation, depending on the thickness of the samples. UV irradiation caused a high background fluorescence of the Martian mineral analogues, as revealed by Raman spectroscopy. Further investigation will be needed to ensure unambiguous identification and operations of future Mars missions. However, a 3-month exposure to a Martian simulated atmosphere showed no significant damaging effect on the tested cyanobacterial biosignatures, pointing out the relevance of the latter for future investigations after the EXPOSE-R2 mission. Data gathered during the ground-based simulations will contribute to interpret results from space experiments and guide our search for life on Mars.

Raman Characterization of the UV-Protective Pigment Gloeocapsin and Its Role in the Survival of Cyanobacteria

Extracellular UV-screening pigments gloeocapsin and scytonemin present in the exopolysaccharide (EPS) envelopes of extremophilic cyanobacteria of freshwater and marine environments were studied by Raman spectroscopy and compared to their intracellular photosynthetic pigments. This Raman spectral analysis of the extracellular pigment gloeocapsin showed that it shared Raman spectral signatures with parietin, a radiation-protective pigment known in lichens. The UV-light spectra also show similarities. Gloeocapsin occurs in some cyanobacterial species, mostly with exclusion of scytonemin, indicating that these pigments have evolved in cyanobacteria as separate protective strategies. Both gloeocapsin and scytonemin are widely and species-specifically distributed in different cyanobacterial genera and families. The widespread occurrence of these pigments may suggest an early origin, while their detection by Raman spectroscopy makes them potential biosignatures for cyanobacteria in the fossil record and demonstrates the usefulness of nondestructive Raman spectroscopy analyses for the search for complex organics, including possible photosynthetic pigments, if preservable in early Earth and extraterrestrial samples.

Raman spectroscopic identification of scytonemin and its derivatives as key biomarkers in stressed environments

Raman spectroscopy has been identified as an important first-pass analytical technique for deployment on planetary surfaces as part of a suite of instrumentation in projected remote space exploration missions to detect extant or extinct extraterrestrial life signatures. Aside from the demonstrable advantages of a non-destructive sampling procedure and an ability to record simultaneously the molecular signatures of biological, geobiological and geological components in admixture in the geological record, the interrogation and subsequent interpretation of spectroscopic data from these experiments will be critically dependent upon the recognition of key biomolecular markers indicative of life existing or having once existed in extreme habitats. A comparison made with the characteristic Raman spectral wavenumbers obtained from standards is not acceptable because of shifts that can occur in the presence of other biomolecules and their host mineral matrices. In this paper, we identify the major sources of difficulty experienced in the interpretation of spectroscopic data centring on a key family of biomarker molecules, namely scytonemin and its derivatives; the parent scytonemin has been characterized spectroscopically in cyanobacterial colonies inhabiting some of the most extreme terrestrial environments and, with the support of theoretical calculations, spectra have been predicted for the characterization of several of its derivatives which could occur in novel extraterrestrial environments. This work will form the foundation for the identification of novel biomarkers and for their Raman spectroscopic discrimination, an essential step in the interpretation of potentially complex and hitherto unknown biological radiation protectants based on the scytoneman and scytonin molecular skeletons which may exist in niche geological scenarios in the surface and subsurface of planets and their satellites in our Solar System.