MutS and MutL Are Dispensable for Maintenance of the Genomic Mutation Rate in the Halophilic Archaeon Halobacterium salinarum NRC-1

BACKGROUND: The genome of the halophilic archaeon Halobacterium salinarum NRC-1 encodes for homologs of MutS and MutL, which are key proteins of a DNA mismatch repair pathway conserved in Bacteria and Eukarya. Mismatch repair is essential for retaining the fidelity of genetic information and defects in this pathway result in the deleterious accumulation of mutations and in hereditary diseases in humans. METHODOLOGY/PRINCIPAL FINDINGS: We calculated the spontaneous genomic mutation rate of H. salinarum NRC-1 using fluctuation tests targeting genes of the uracil monophosphate biosynthesis pathway. We found that H. salinarum NRC-1 has a low incidence of mutation suggesting the presence of active mechanisms to control spontaneous mutations during replication. The spectrum of mutational changes found in H. salinarum NRC-1, and in other archaea, appears to be unique to this domain of life and might be a consequence of their adaption to extreme environmental conditions. In-frame targeted gene deletions of H. salinarum NRC-1 mismatch repair genes and phenotypic characterization of the mutants demonstrated that the mutS and mutL genes are not required for maintenance of the observed mutation rate. CONCLUSIONS/SIGNIFICANCE: We established that H. salinarum NRC-1 mutS and mutL genes are redundant to an alternative system that limits spontaneous mutation in this organism. This finding leads to the puzzling question of what mechanism is responsible for maintenance of the low genomic mutation rates observed in the Archaea, which for the most part do not have MutS and MutL homologs

Colonization patterns of soil microbial communities in the Atacama Desert

BACKGROUND: The Atacama Desert is one of the driest deserts in the world and its soil, with extremely low moisture, organic carbon content, and oxidizing conditions, is considered to be at the dry limit for life. RESULTS: Analyses of high throughput DNA sequence data revealed that bacterial communities from six geographic locations in the hyper-arid core and along a North-South moisture gradient were structurally and phylogenetically distinct (ANOVA test for observed operating taxonomic units at 97% similarity (OTU(0.03)), P <0.001) and that communities from locations in the hyper-arid zone displayed the lowest levels of diversity. We found bacterial taxa similar to those found in other arid soil communities with an abundance of Rubrobacterales, Actinomycetales, Acidimicrobiales, and a number of families from the Thermoleophilia. The extremely low abundance of Firmicutes indicated that most bacteria in the soil were in the form of vegetative cells. Integrating molecular data with climate and soil geochemistry, we found that air relative humidity (RH) and soil conductivity significantly correlated with microbial communities’ diversity metrics (least squares linear regression for observed OTU(0.03) and air RH and soil conductivity, P <0.001; UniFrac PCoA Spearman’s correlation for air RH and soil conductivity, P <0.0001), indicating that water availability and salt content are key factors in shaping the Atacama soil microbiome. Mineralization studies showed communities actively metabolizing in all soil samples, with increased rates in soils from the southern locations. CONCLUSIONS: Our results suggest that microorganisms in the driest soils of the Atacama Desert are in a state of stasis for most of the time, but can potentially metabolize if presented with liquid water for a sufficient duration. Over geological time, rare rain events and physicochemical factors potentially played a major role in selecting micro-organisms that are most adapted to extreme desiccating conditions

An integrated systems approach for understanding cellular responses to gamma radiation

Cellular response to stress entails complex mRNA and protein abundance changes, which translate into physiological adjustments to maintain homeostasis as well as to repair and minimize damage to cellular components. We have characterized the response of the halophilic archaeon Halobacterium salinarum NRC-1 to (60)Co ionizing gamma radiation in an effort to understand the correlation between genetic information processing and physiological change. The physiological response model we have constructed is based on integrated analysis of temporal changes in global mRNA and protein abundance along with protein–DNA interactions and evolutionarily conserved functional associations. This systems view reveals cooperation among several cellular processes including DNA repair, increased protein turnover, apparent shifts in metabolism to favor nucleotide biosynthesis and an overall effort to repair oxidative damage. Further, we demonstrate the importance of time dimension while correlating mRNA and protein levels and suggest that steady-state comparisons may be misleading while assessing dynamics of genetic information processing across transcription and translation

In situ metabolism in halite endolithic microbial communities of the hyperarid Atacama Desert

The Atacama Desert of northern Chile is one of the driest regions on Earth, with areas that exclude plants and where soils have extremely low microbial biomass. However, in the driest parts of the desert there are microorganisms that colonize the interior of halite nodules in fossil continental evaporites, where they are sustained by condensation of atmospheric water triggered by the salt substrate. Using a combination of in situ observations of variable chlorophyll fluorescence and controlled laboratory experiments, we show that this endolithic community is capable of carbon fixation both through oxygenic photosynthesis and potentially ammonia oxidation. We also present evidence that photosynthetic activity is finely tuned to moisture availability and solar insolation and can be sustained for days, and perhaps longer, after a wetting event. This is the first demonstration of in situ active metabolism in the hyperarid core of the Atacama Desert, and it provides the basis for proposing a self-contained, endolithic community that relies exclusively on non-rainfall sources of water. Our results contribute to an increasing body of evidence that even in hyperarid environments active metabolism, adaptation and growth can occur in highly specialized microhabitats

Astrophysical and Astrobiological Implications of Gamma-Ray Burst Properties

Combining results for the local cosmic rate and mean peak luminosity of GRBs with the cosmic history of the star formation rate, we provide estimates for the local GRB rate per unit blue luminosity in galaxies. We find a typical GRB rate per unit B luminosity of 2.4x10^-17 h_{70}^2/Lsun/yr. The corresponding mean rate in the Milky Way is 5.5x10^-7 h_{70}^2/yr. We conclude: 1) the ratio of supernova rate to isotropic equivalent GRB rate is large: more than 6000 SNIbc per GRB or 30,000 SNII per GRB. GRBs could arise in a large fraction of black hole-forming events only with collimation in the range 0.01 - 0.001 and a steep enough slope of the IMF; 2) GRBs cannot account for the majority of large HI holes observed in galaxies; 3) the probability that the solar system was exposed to a fluence large enough to melt the chondrules during the first 10^7 yr of solar system history is negligibly small; 4) Even for very opaque atmospheres, a significant fraction of the GRB energy is transmitted as UV lines due to excitation by secondary electrons. For eukaryotic-like organisms in thin atmospheres (e.g. contemporary Mars), or for UV line exposure in thick atmospheres (e.g. Earth), biologically significant events occur at a rate of about 100--500 /Gyr. The direct contribution of these "jolts" to mutational evolution may, however, be negligible because of the short duration of the GRBs. Evolutionary effects due to partial sterilizations and to longer-lived disruptions of atmospheric chemistry should be more important. (Abridged)Comment: 36 pages, no figures Accepted by Astrophysical Journal Oct. 2001. First submitted December,1999. Substantially rewritten discussion of burst source count distributions and of biological implication

Solar X-ray Flare Hazards on the Surface of Mars

Putative organisms on the Martian surface would be exposed to potentially high doses of ionizing radiation during strong solar X-ray flares. We extrapolate the observed flare frequency-energy release scaling relation to releases much larger than seen so far for the sun, an assumption supported by observations of flares on other solar- and subsolar-mass main sequence stars. We calculate the surficial reprocessed X-ray spectra using a Monte Carlo code we have developed. Biological doses from indirect genome damage are calculated for each parameterized flare spectrum by integration over the X-ray opacity of water. We estimate the mean waiting time for solar flares producing a given biological dose of ionizing radiation on Mars and compare with lethal dose data for a wide range of terrestrial organisms. These timescales range from decades for significant human health risk to 0.5 Myr for D. radiodurans lethality. Such doses require total flare energies of 10^33--10^38 erg, the lower range of which has been observed for other stars. Flares are intermittent bursts, so acute lethality will only occur on the sunward hemisphere during a sufficiently energetic flare, unlike low-dose-rate, extended damage by cosmic rays. We estimate the soil and CO_2 ice columns required to provide 1/e shielding as 4--9 g cm^-2, depending on flare mean energy and atmospheric column density. Topographic altitude variations give a factor of two variation in dose for a given flare. Life in ice layers that may exist ~ 100 g cm^-2 below the surface would be well protected.Comment: To be published in Planetary and Space Science; 33 pages, 3 figure

Coordination of frontline defense mechanisms under severe oxidative stress

Inference of an environmental and gene regulatory influence network (EGRINOS) by integrating transcriptional responses to H2O2 and paraquat (PQ) has revealed a multi-tiered oxidative stress (OS)-management program to transcriptionally coordinate three peroxidase/catalase enzymes, two superoxide dismutases, production of rhodopsins, carotenoids and gas vesicles, metal trafficking, and various other aspects of metabolism.ChIP-chip, microarray, and survival assays have validated important architectural aspects of this network, identified novel defense mechanisms (including two evolutionarily distant peroxidase enxymes), and showed that general transcription factors of the transcription factor B family have an important function in coordinating the OS response (OSR) despite their inability to directly sense ROS.A comparison of transcriptional responses to sub-lethal doses of H2O2 and PQ with predictions of these responses made by an EGRIN model generated earlier from responses to other environmental factors has confirmed that a significant fraction of the OSR is made up of a generalized component that is also observed in response to other stressors.Analysis of active regulons within environment and gene regulatory influence network for OS (EGRINOS) across diverse environmental conditions has identified the specialized component of oxidative stress response (OSR) that is triggered by sub-lethal OS, but not by other stressors, including sub-inhibitory levels of redox-active metals, extreme changes in oxygen tension, and a sub-lethal dose of γ rays

‘Follow the Water’: Microbial Water Acquisition in Desert Soils

Water availability is the dominant driver of microbial community structure and function in desert soils. However, these habitats typically only receive very infrequent large-scale water inputs (e.g., from precipitation and/or run-off). In light of recent studies, the paradigm that desert soil microorganisms are largely dormant under xeric conditions is questionable. Gene expression profiling of microbial communities in desert soils suggests that many microbial taxa retain some metabolic functionality, even under severely xeric conditions. It, therefore, follows that other, less obvious sources of water may sustain the microbial cellular and community functionality in desert soil niches. Such sources include a range of precipitation and condensation processes, including rainfall, snow, dew, fog, and nocturnal distillation, all of which may vary quantitatively depending on the location and geomorphological characteristics of the desert ecosystem. Other more obscure sources of bioavailable water may include groundwater-derived water vapour, hydrated minerals, and metabolic hydro-genesis. Here, we explore the possible sources of bioavailable water in the context of microbial survival and function in xeric desert soils. With global climate change projected to have profound effects on both hot and cold deserts, we also explore the potential impacts of climate-induced changes in water availability on soil microbiomes in these extreme environments