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Microorganisms are employed to mine economically important elements from rocks, including the rare earth elements (REEs), used in electronic industries and alloy production. We carried out a mining experiment on the International Space Station to test hypotheses on the bioleaching of REEs from basaltic rock in microgravity and simulated Mars and Earth gravities using three microorganisms and a purposely designed biomining reactor. Sphingomonas desiccabilis enhanced mean leached concentrations of REEs compared to non-biological controls in all gravity conditions. No significant difference in final yields was observed between gravity conditions, showing the efficacy of the process under different gravity regimens. Bacillus subtilis exhibited a reduction in bioleaching efficacy and Cupriavidus metallidurans showed no difference compared to non-biological controls, showing the microbial specificity of the process, as on Earth. These data demonstrate the potential for space biomining and the principles of a reactor to advance human industry and mining beyond Earth.

The detection and identification of biosignatures on planetary bodies such as Mars in situ is extremely challenging. Current knowledge from space exploration missions suggests that a suite of complementary instruments is required in situ for a successful identification of past or present life. For future exploration missions, new and innovative instrumentation capable of high spatial resolution chemical (elemental and isotope) analysis of solids with improved measurement capabilities is of considerable interest because a multitude of potential signatures of extinct or extant life have dimensions on the micrometer scale. The aim of this study is to extend the current measurement capabilities of a miniature laser ablation ionization mass spectrometer (LIMS) designed for space exploration missions to detect signatures of microbial life. In total, 14 martian mudstone analogue samples were investigated regarding their elemental composition. Half the samples were artificially inoculated with a low number density of microbes, and half were used as abiotic controls. The samples were treated in a number of ways. Some were cultured anaerobically and some aerobically; some abiotic samples were incubated with water, and some remained dry. Some of the samples were exposed to a large dose of γ radiation, and some were left un-irradiated. While no significant elemental differences were observed between the applied sample treatments, the instrument showed the capability to detect biogenic element signatures of the inoculated microbes by monitoring biologically relevant elements, such as hydrogen, carbon, sulfur, iron, and so on. When an enrichment in carbon was measured in the samples but no simultaneous increase in other biologically relevant elements was detected, it suggests, for example, a carbon-containing inclusion; when the enrichment was in carbon and in bio-relevant elements, it suggests the presences of microbes. This study presents first results on the detection of biogenic element patterns of microbial life using a miniature LIMS system designed for space exploration missions.

Motivated by an interest in understanding the habitability of aqueous environments on Earth and in extraterrestrial settings, this study investigated the influence of ions in an artificial sodium-magnesium-sulfate-chloride ion system on the growth parameters (lag phase, growth rate, and final cell concentration) of bacteria. These four ions, in different combinations, are key components of many aqueous environments on Earth and elsewhere. We investigated non-halophilic bacteria deliberately to remove the bias of prior adaptations to high concentrations of selected ions so that we could compare the effects of different ions. We tested the hypothesis that water activity determined the growth parameters independent of the ion types. Neither water activity or ionic strength alone could predict growth. However, when ionic strengths were matched, many differences in growth parameters could be explained by the water activity. We suggest that species-specific effects (caused by differences in biochemical and physiological influences), the role of individual ions in cellular processes, and potentially the chaotropicity and kosmotropicity of solutions influenced the growth. Our data show that although extreme combinations of these ions allow for general predictions on the habitability of extraterrestrial aqueous environments, a complex interplay of ionic effects influences the growth and thus the adaptations required for given ion combinations. The data also show that an accurate quantification of the habitability of ocean worlds, such as Europa and Enceladus, can only be made when samples are obtained from these water bodies and the ion combinations are determined.

Asteroid and comet impacts are known to have caused profound disruption to multicellular life, yet their influence on habitats for microorganisms, which comprise the majority of Earth's biomass, is less well understood. Of particular interest are geological changes in the target lithology at and near the point of impact that can persist for billions of years. Deep subsurface and surface-dwelling microorganisms are shown to gain advantages from impact-induced fracturing of rocks. Deleterious changes are associated with impact-induced closure of pore spaces in rocks. Superimposed on these long-term geological changes are post-impact alterations such as changes in the hydrological system in and around a crater. The close coupling between geological changes and the conditions for microorganisms yields a synthesis of the fields of microbiology and impact cratering. We use these data to discuss how craters can be used in the search for life beyond Earth.

Discovery of a remnant habitable environment by the Mars Science Laboratory in the sedimentary record of Gale Crater has reinvigorated the search for evidence of martian life. In this study, we used a simulated martian mudstone material, based on data from Gale Crater, that was inoculated and cultured over several months and then dried and pressed. The simulated mudstone was analysed with a range of techniques to investigate the detectability of biosignatures. Cell counting and DNA extraction showed a diverse but low biomass microbial community that was highly dispersed. Pellets were analysed with bulk Elemental Analysis - Isotope Ratio Mass Spectrometry (EA-IRMS), high-resolution Laser-ablation Ionisation Mass Spectrometry (LIMS), Raman spectroscopy and Fourier Transform InfraRed (FTIR) spectroscopy, which are all techniques of relevance to current and future space missions. Bulk analytical techniques were unable to differentiate between inoculated samples and abiotic controls, despite total levels of organic carbon comparable with that of the martian surface. Raman spectroscopy, FTIR spectroscopy and LIMS, which are high sensitivity techniques that provide chemical information at high spatial resolution, retrieved presumptive biosignatures but these remained ambiguous and the sedimentary matrix presented challenges for all techniques. This suggests challenges for detecting definitive evidence for life, both in the simulated lacustrine environment via standard microbiological techniques and in the simulated mudstone via analytical techniques with relevance to robotic missions. Our study suggests that multiple co-incident high-sensitivity techniques that can scan the same micrometre-scale spots are required to unambiguously detect biosignatures, but the spatial coverage of these techniques needs to be high enough not to miss individual cellular-scale structures in the matrix.

Biological processes on the Earth operate within a parameter space that is constrained by physical and chemical extremes. Aerobic respiration can result in adenosine triphosphate yields up to over an order of magnitude higher than those attained anaerobically and, under certain conditions, may enable microbial multiplication over a broader range of extremes than other modes of catabolism. We employed growth data published for 241 prokaryotic strains to compare temperature, pH and salinity values for cell division between aerobically and anaerobically metabolizing taxa. Isolates employing oxygen as the terminal electron acceptor exhibited a considerably more extensive three-dimensional phase space for cell division (90% of the total volume) than taxa using other inorganic substrates or organic compounds as the electron acceptor (15% and 28% of the total volume, respectively), with all groups differing in their growth characteristics. Understanding the mechanistic basis of these differences will require integration of research into microbial ecology, physiology and energetics, with a focus on global-scale processes. Critical knowledge gaps include the combined impacts of diverse stress parameters on Gibbs energy yields and rates of microbial activity, interactions between cellular energetics and adaptations to extremes, and relating laboratory-based data to in situ limits for cell division., (© 2015 The Author(s).)

Bacteria inhabiting crystalline rocks from two terrestrial Icelandic volcanic lava flows of similar age and from the same geographical region, but differing in porosity and mineralogy, were characterised. Microarray (PhyloChip) and clone library analysis of 16S rRNA genes revealed the presence of a diverse assemblage of bacteria in each lava flow. Both methods suggested a more diverse community at the Dómadalshraun site (rhyolitic/andesitic lava flow) than that present at the Hnausahraun site (basaltic lava flow). Proteobacteria dominated the clone library at the Dómadalshraun site, while Acidobacteria was the most abundant phylum in the Hnausahraun site. Although analysis of similarities of denaturing gradient gel electrophoresis profiles suggested a strong correlation of community structure with mineralogy, rock porosity may also play an important role in shaping the bacterial community in crystalline volcanic rocks. Clone sequences were most similar to uncultured microorganisms, mainly from soil environments. Of these, Antarctic soils and temperate rhizosphere soils were prominent, as were clones retrieved from Hawaiian and Andean volcanic soils. The novel diversity of these Icelandic microbial communities was supported by the finding that up to 46% of clones displayed <85% sequence identities to sequences currently deposited in the RDP database.

Shales play an important role in many earth system processes including coastal erosion, and they form the foundations of many engineering structures. The geobiology of the interior of pyrite-containing receding shale cliffs on the coast of northeast England was examined. The surface of the weathered shales was characterised by a thin layer of disordered authigenic iron oxyhydroxides and localised acicular, platy and aggregated gypsum, which was characterised by Raman spectroscopy, XAS and SEM. These chemical changes are likely to play an important role in causing rock weakening along fractures at the micron scale, which ultimately lead to coastal retreat at the larger scale. The surface of the shale hosts a novel, low-diversity microbial community. The bacterial community was dominated by Proteobacteria, with phylotypes closely associating with Methylocella and other members of the γ-subdivision. The second largest phylogenetic group corresponded to Nitrospira. The archaeal 16S rRNA phylotypes were dominated by a single group of sequences that matched phylotypes reported from South African gold mines and possessed ammonia monooxygenase (amoA) genes. Both the phylogenetic and the mineral data show that acidic microenvironments play an important role in shale weathering, but the shale has a higher microbial diversity than previously described pyritic acid mine drainage sites. The presence of a potentially biogeochemically active microbial population on the rock surface suggests that microorganisms may contribute to early events of shale degradation and coastal erosion.

The diversity of microbial communities inhabiting two terrestrial volcanic glasses of contrasting mineralogy and age was characterised. Basaltic glass from a <0.8 Ma hyaloclastite deposit (Valafell) harboured a more diverse Bacteria community than the younger rhyolitic glass from ∼150-300 AD (Dόmadalshraun lava flow). Actinobacteria dominated 16S rRNA gene clone libraries from both sites, however, Proteobacteria, Acidobacteria and Cyanobacteria were also numerically abundant in each. A significant proportion (15-34%) of the sequenced clones displayed <85% sequence similarities with current database sequences, thus suggesting the presence of novel microbial diversity in each volcanic glass. The majority of clone sequences shared the greatest similarity to uncultured organisms, mainly from soil environments, among these clones from Antarctic environments and Hawaiian and Andean volcanic deposits. Additionally, a large number of clones within the Cyanobacteria and Proteobacteria were more similar to sequences from other lithic environments, included among these Icelandic clones from crystalline basalt and rhyolite, however, no similarities to sequences reported from marine volcanic glasses were observed. PhyloChip analysis detected substantially greater numbers of phylotypes at both sites than the corresponding clone libraries, but nonetheless also identified the basaltic glass community as the richer, containing approximately 29% unique phylotypes compared to rhyolitic glass.

Geomicrobiology investigates the interactions of microorganisms with geological substrates, and this branch of microbiology has enormous potential in the exploration and settlement of space. Microorganisms can be used to extract useful elements from extraterrestrial materials for industrial processes or for use as nutrients in life support systems. In addition, microorganisms could be used to create soil from lunar and Martian rocks. Furthermore, understanding the interactions of microorganisms with rocks is essential for identifying mineral biomarkers to be used in the search for life on other planetary bodies. Increasing space exploration activities make geomicrobiology an important applied science beyond Earth., (Copyright 2010 Elsevier Ltd. All rights reserved.)

Microorganisms from diverse environments actively bore into rocks, contributing significantly to rock weathering. Carbonates are the most common substrate into which they bore, although there are also reports of microbial borings into volcanic glass. One of the most intriguing questions in microbial evolutionary biology is why some microorganisms bore. A variety of possible selection pressures, including nutrient acquisition, protection from UV radiation and predatory grazing could promote boring. None of these pressures is mutually exclusive and many of them could have acted in concert with varying strengths in different environments to favour the development of microorganisms that bore. We suggest that microbial boring might have begun in some environments as a mechanism against entombment by mineralization.

The last decade has been marked by a large number of studies focused on understanding the distribution of microorganisms in volcanic environments. These studies are motivated by the desire to elucidate how the geochemically extreme conditions of such environments can influence microbial diversity both on the surface and in the subsurface of the Earth. The exploration of microbial community diversity has generally not relied on culture-dependent methods, but has been carried out using environmental DNA extraction. Because of the large diversity of chemically and physically complex samples, extracting DNA from volcanic environments is technically challenging. In view of the emerging literature, and our own experience in the optimisation of methods for DNA extraction from volcanic materials, it is timely to provide a methodological comparison. This review highlights and discusses new insights and methods published on DNA extraction methods from volcanic samples, considering the different volcanic environments. A description of a recent method for DNA extraction from basalt and obsidian glass rock samples from Iceland is included. Finally, we discuss these approaches in the wider context of modern work to understand the microbial diversity of volcanic environments.

Previous work on possible surface reflectance biosignatures for Earth-like planets has typically focused on analogues to spectral features produced by photosynthetic organisms on Earth, such as the vegetation red edge. Although oxygenic photosynthesis, facilitated by pigments evolved to capture photons, is the dominant metabolism on our planet, pigmentation has evolved for multiple purposes to adapt organisms to their environment. We present an interdisciplinary study of the diversity and detectability of nonphotosynthetic pigments as biosignatures, which includes a description of environments that host nonphotosynthetic biologically pigmented surfaces, and a lab-based experimental analysis of the spectral and broadband color diversity of pigmented organisms on Earth. We test the utility of broadband color to distinguish between Earth-like planets with significant coverage of nonphotosynthetic pigments and those with photosynthetic or nonbiological surfaces, using both 1-D and 3-D spectral models. We demonstrate that, given sufficient surface coverage, nonphotosynthetic pigments could significantly impact the disk-averaged spectrum of a planet. However, we find that due to the possible diversity of organisms and environments, and the confounding effects of the atmosphere and clouds, determination of substantial coverage by biologically produced pigments would be difficult with broadband colors alone and would likely require spectrally resolved data.

A major objective in the exploration of Mars is to test the hypothesis that the planet hosted life. Even in the absence of life, the mapping of habitable and uninhabitable environments is an essential task in developing a complete understanding of the geological and aqueous history of Mars and, as a consequence, understanding what factors caused Earth to take a different trajectory of biological potential. We carried out the aseptic collection of samples and comparison of the bacterial and archaeal communities associated with basaltic fumaroles and rocks of varying weathering states in Hawai'i to test four hypotheses concerning the diversity of life in these environments. Using high-throughput sequencing, we found that all these materials are inhabited by a low-diversity biota. Multivariate analyses of bacterial community data showed a clear separation between sites that have active fumaroles and other sites that comprised relict fumaroles, unaltered, and syn-emplacement basalts. Contrary to our hypothesis that high water flow environments, such as fumaroles with active mineral leaching, would be sites of high biological diversity, alpha diversity was lower in active fumaroles compared to relict or nonfumarolic sites, potentially due to high-temperature constraints on microbial diversity in fumarolic sites. A comparison of these data with communities inhabiting unaltered and weathered basaltic rocks in Idaho suggests that bacterial taxon composition of basaltic materials varies between sites, although the archaeal communities were similar in Hawai'i and Idaho. The taxa present in both sites suggest that most of them obtain organic carbon compounds from the atmosphere and from phototrophs and that some of them, including archaeal taxa, cycle fixed nitrogen. The low diversity shows that, on Earth, extreme basaltic terrains are environments on the edge of sustaining life with implications for the biological potential of similar environments on Mars and their exploration by robots and humans. [ABSTRACT FROM AUTHOR]

The limits of life of aerobic microorganisms are well understood, but the responses of anaerobic microorganisms to individual and combined extreme stressors are less well known. Motivated by an interest in understanding the survivability of anaerobic microorganisms under Martian conditions, we investigated the responses of a new isolate, Yersinia intermedia MASE-LG-1 to individual and combined stresses associated with the Martian surface. This organism belongs to an adaptable and persistent genus of anaerobic microorganisms found in many environments worldwide. The effects of desiccation, low pressure, ionizing radiation, varying temperature, osmotic pressure, and oxidizing chemical compounds were investigated. The strain showed a high tolerance to desiccation, with a decline of survivability by four orders of magnitude during a storage time of 85 days. Exposure to X-rays resulted in dose-dependent inactivation for exposure up to 600 Gy while applied doses above 750 Gy led to complete inactivation. The effects of the combination of desiccation and irradiation were additive and the survivability was influenced by the order in which they were imposed. Ionizing irradiation and subsequent desiccation was more deleterious than vice versa. By contrast, the presence of perchlorates was not found to significantly affect the survival of the Yersinia strain after ionizing radiation. These data show that the organism has the capacity to survive and grow in physical and chemical stresses, imposed individually or in combination that are associated with Martian environment. Eventually it lost its viability showing that many of the most adaptable anaerobic organisms on Earth would be killed on Mars today. [ABSTRACT FROM AUTHOR]

Evaporative silicification can drive microbial fossilization within diverse natural habitats. Research into this process is pivotal to understanding the terrestrial fossil record and the preservation of biomarkers within extreme environments. We employed laboratory experiments to silicify the polyextremotolerant bacteriumHalomonas hydrothermaliscultured at low, intermediate and high salinities (1, 3.5 or 11.8% w/v of NaCl) under iron-rich or iron-deprived conditions. Silicification was achieved by adding sodium silicate solution (30 or 150 ppm of Si) onto cultures, followed by evaporation. Scanning electron microscopy demonstrated the presence of mineralized bacteria with intact morphology across all culture conditions. However, multivariate analysis of the attenuated total reflectance Fourier-transform infrared (ATR-FT-IR) spectra of silicified cultures showed significant differences between the examined salinities, most notably between cultures silicified after incubation at high salinity and those at lower salinities. Although the spectra of mineralized low- and intermediate-salinity cultures appeared distinct from their nonsilicified counterparts, these differences were less pronounced at high salinity. By showing that differences in salinity can influence microbial responses to mineralization at the molecular level, these data indicate that the potential for evaporative silicification to contribute to microbial fossilization may differ between freshwater and hypersaline environments. [ABSTRACT FROM PUBLISHER]

The weathering of silicate in the world's critical-zone (rock-soil interface) is a natural mechanism providing a feedback on atmospheric CO2concentrations through the carbonate-silicate cycle. We examined culturable bacterial communities from a critical-zone in western Iceland to determine the optimum growth temperature and their ability to solubilize phosphate-containing minerals, which are abundant within the critical-zone area examined here. The majority of isolated bacteria were able to solubilize mineral-state phosphate. Almost all bacterial isolates were mesophilic (growth optima of 20–45°C), despite critical-zone temperatures that were continuously below 15°C, although all isolates could grow at temperatures associated with the critical-zone (−2.8–13.1°C). Only three isolates were shown to have thermal optima for growth that were within temperatures experienced at the critical-zone. These findings show that the bacteria that inhabit the western Icelandic critical-zone have temperature growth optima suboptimally adapted to their environment, implying that other adaptations may be more important for their long-term persistance in this environment. Moreover, our study showed that the cold basaltic critical-zone is a region of active phosphate mineral-weathering. [ABSTRACT FROM PUBLISHER]

Silicate weathering improves soils by releasing bioessential nutrients from the bedrock to the soil ecosystem. However, whether bacteria are capable of inhabiting subsurface critical zones (zone of active rock weathering), and their role therein, are unknown. Next-generation sequencing and community fingerprinting permitted us to characterize communities from an Icelandic critical zone environment. Communities were compared with respect to physico-chemical properties of the environment to determine the factors influencing bacterial diversity. We showed that land coverage influenced critical zone communities. Analysis of tree-covered site ( TCS) soils exhibited high cell densities ( TCS = 2.25 × 107 g−1), whereas lichen- and moss-covered sites ( LMS) had lower cell densities ( LMS = 1.06 × 107 cells g−1), thought to be a result of the organic carbon produced by the trees. Differences in the bacterial community were observed from the abundance of 16S rRNA gene sequences affiliated with Acidobacteria and Proteobacteria, with TCS possessing higher abundances of Proteobacteria [no of sequences: LMS = 1526 (±497); TCS = 2214 (±531)], specifically Alpha- and Betaproteobacteria, and lower Acidobacteria numbers [no of sequences: LMS = 1244 (±338); TCS = 598 (±140)]. Diversity indices and 16S rRNA gene rarefaction showed that communities from TCS soils had lower α-diversity than sites without, indicative of specialized communities at sites with root-forming plants. [ABSTRACT FROM AUTHOR]

Since the first descriptions of Antarctic subglacial lakes, there has been a growing interest and awareness of the possibility that life will exist and potentially thrive in these unique and little known environments. The unusual combination of selection pressures, and isolation from the rest of the biosphere, might have led to novel adaptations and physiology not seen before, or indeed to the potential discovery of relic populations that may have become extinct elsewhere. Here we report the first microbiological analysis of a sample taken from a former subglacial lake sediment in Antarctica (Lake Hodgson, on the Antarctic Peninsula). This is one of a number of subglacial lakes just emerging at the margins of the Antarctic ice sheet due to the renewed onset of deglaciation. Microbial diversity was divided into 23.8% Actinobacteria, 21.6% Proteobacteria, 20.2% Planctomycetes and 11.6% Chloroflexi, characteristic of a range of habitat types ( Overall, common sequences were neither distinctly polar, low temperature, freshwater nor marine). Twenty three percent of this diversity could only be identified to "unidentified bacterium". Clearly these are diverse ecosystems with enormous potential. [ABSTRACT FROM AUTHOR]

The majority of the biomass and biodiversity of life on the Earth is accounted for by microbes. They play pivotal roles in biogeochemical cycles and harbour novel metabolites that have industrial uses. For these reasons the conservation of microbial ecosystems, communities and even specific taxa should be a high priority. We review the reasons for including microorganisms in conservation agenda. We discuss some of the complications in this endeavour, including the unresolved argument about whether microorganisms have intrinsic value, which influences some of the non instrumental motivations for their conservation and, from a more pragmatic perspective, exactly what it is that we seek to conserve (microorganisms, their habitats or their gene pools). Despite complications, priorities can be defined for microbial conservation and we provide practical examples of such priorities. [ABSTRACT FROM AUTHOR]

As a result of the recent application of DNA based technology to the investigation of maritime Antarctic freshwater lakes, patterns have begun to emerge in the bacterioplankton communities that dominate these systems. In this study, the bacterioplankton communities of five Antarctic and five Arctic freshwater lakes were assessed and compared with existing data in the literature, to determine whether emerging patterns in Antarctic lakes also applied to Arctic systems. Such a bipolar comparison is particularly timely, given the current interest in biogeography, the global distribution of microorganisms and the controversy over the global ubiquity hypothesis. In addition, it has recently been discovered that commonly encountered bacterial sequences, often originating from uncultivated bacteria obtained on different continents, form coherent phylogenetic freshwater clusters. In this study we encountered both identical sequences and sequences with a high degree of similarity among the bacterioplankton in lake water from both poles. In addition, Arctic freshwater lakes appeared to be dominated by some of the same groups of bacterioplankton thought to be dominant in Antarctic lakes, the vast majority of which represented uncultivated groups. [ABSTRACT FROM AUTHOR]

Abstract: In the space experiments Lithopanspermia, experimental support was provided to the likelihood of the lithopanspermia concept that considers a viable transport of microorganisms between the terrestrial planets by means of meteorites. The rock colonising lichens Rhizocarpon geographicum and Xanthoria elegans, the vagrant lichen Aspicilia fruticulosa, and endolithic and endoevaporitic communities of cyanobacteria and bacteria with their natural rock substrate were exposed to space for 10days onboard the Biopan facility of the European Space Agency (ESA). Biopan was closed during launch and re-entry. In addition, in the Stone facility, one sample of R. geographicum on its natural granitic substrate was attached at the outer surface of the re-entry capsule close to the stagnation point, only protected by a thin cover of glass textolite. Post-flight analysis, which included determination of the photosynthetic activity, LIVE/DEAD staining, and germination capacity of the ascospores, demonstrated that all three lichen were quite resistant to outer space conditions, which include the full spectrum of solar extraterrestrial electromagnetic radiation or selected wavelength ranges. This high resistance of the lichens to space appears to be due to their symbiotic nature and protection by their upper pigmented layer, the cortex. In contrast, the rock- or halite-inhabiting bacteria were severely damaged by the same exposure. After atmospheric re-entry, the granite of the Stone sample was transformed into a glassy, nearly homogenous material, with several friction striae. None of the lichen cells survived this re-entry process. The data suggest that lichens are suitable candidates for testing the concept of lithopanspermia, because they are extremely resistant to the harsh environment of outer space. The more critical event is the atmospheric re-entry after being captured by a planet. Experiments simulating the re-entry process of a microbe-carrying meteoroid did not show any survivors. [Copyright &y& Elsevier]