Bacillus endospores isolated from granite: close molecular relationships to globally distributed Bacillus spp. from endolithic and extreme environments

A 3D-Printed Portable Sterilizer to Be Used During Surgical Procedures in Spaceflight

INTRODUCTION: During spaceflight, it is important to consider the mechanisms by which surgeries and medical procedures can be safely and efficiently conducted. Instruments used to carry out these processes need to be sterilized. Thus, we have designed and tested a three-dimensional-printed (3D-printed) portable sterilizer that implements far ultraviolet-C (Far UV-C) light radiation to disinfect bacteria and microorganisms from surgical instruments.METHODS: The sterilizer was 3D-printed with polylactic acid filament. Effectiveness was assessed through three trials at differing times of sterilization and compared against a control group of no sterilization and against Clorox wipes. Cultures were incubated on agar dishes and counted with ImageJ.RESULTS: Increasing time under Far UV-C light radiation increased the percentage of sterilization up to 100% at 10 min. The 3D-printed sterilizer was significantly better than Clorox wipes and control.DISCUSSION: As sterilization will be necessary for surgical procedures in microgravity and upmass is a significant concern, we have successfully demonstrated a 3D-printable portable sterilizer for surgical instruments that achieves 100% success in using Far UV-C light to disinfect its surface of bacteria with a 10-min sterilizing time. Further research is necessary to test this design in microgravity and with differently sized and shaped instruments.Kovalski E, Salazar L, Levin D, Kamine TH. A 3D-printed portable sterilizer to be used during surgical procedures in spaceflight. Aerosp Med Hum Perform. 2023; 94(11):857-860.

Post-dispersal astrobiological events: modelling macroevolutionary dynamics for lithopanspermia

Lithopanspermia is defined as dispersal of living extremophiles from one planetary body to another, through life-bearing rocks ejected by meteor impacts. If lithopanspermia proves concrete, it should be viewed as an eco-evolutionary phenomenon. Biogeographic/microevolutionary models have been proposed as analogues for lithopanspermia dynamics; however, extremophile arrival on a planetary body is not the end of story. Here, we suggest that eco-evolutionary (environment + organismal microevolution) dynamics can lead to distinct macroevolutionary scenarios after extremophile arrival on a planetary body. Speciation would be the most important factor in interplanetary dynamics due to the possibly long time and distance between dispersive events, similar to long-distance dispersal dynamics on Earth. In previously uninhabited planets, persistence of extremophiles and descendants depends almost only on evolvability of extremophiles against abiotic filters. Considering a previously inhabited planet, ecological interactions at local or global scales could drive persistence (speciation/extinction) of extremophiles in the new habitat. Thus, we might expect high extinction rates if negative interactions are dominant, or, high speciation, if positive interactions occur, with extremophile lineages overpower (or not) the native biota. If interplanetary dispersal is possible, theories about the evolution of life may be universal, leading to a general eco-evolutionary model for life in the Universe.

Bacteriobiota of the Cave Church of Sts. Peter and Paul in Serbia-Culturable and Non-Culturable Communities' Assessment in the Bioconservation Potential of a Peculiar Fresco Painting

The principal aim of this study was to determine bacterial diversity within the Cave Church of Sts. Peter and Paul, via culturable and non-culturable approaches, and elucidate the antifungal potential of autochthonous antagonistic bacterial isolates against biodeteriogenic fungi. Furthermore, whole-genome sequencing of selected bacterial antagonists and the analysis of genes included in the synthesis of secondary metabolites were performed. With the highest RA values, determined in metabarcoding analysis, phyla Actinobacteriota (12.08-54.00%) and Proteobacteria (25.34-44.97%) dominated most of the samples. A total of 44 different species, out of 96 obtained isolates, were determined as part of the culturable bacteriobiota, with the predominance of species from the genus Bacillus. Bacillus simplex was the only isolated species simultaneously present in all investigated substrata within the church. The best antagonistic activity against 10 biodeteriogenic fungi was documented for Streptomyces anulatus, followed by Bacillus altitudinis, Chryseobacterium viscerum, and Streptomyces sp. with their highest PGI% values ranging of from 55.9% to 80.9%. These promising results indicate that characterized bacteria are excellent candidates for developing biocontrol strategies for suppressing deteriogenic fungi responsible for the deterioration of investigated fresco painting. Finally, isolate 11-11MM, characterized as Streptomyces sp., represents a new species for science prompting the need for further study.

Bacillus spp.-Mediated Growth Promotion of Rice Seedlings and Suppression of Bacterial Blight Disease under Greenhouse Conditions

Rice (Oryza sativa L.) is a major cereal and staple food crop worldwide, and its growth and production are affected by several fungal and bacterial phytopathogens. Bacterial blight (BB) is one of the world's most devastating rice diseases, caused by Xanthomonas oryzae pv. oryzae (Xoo). In the current study, Bacillus atrophaeus FA12 and B. cabrialesii FA26 were isolated from the rice rhizosphere and characterized as having broad-range antifungal and antibacterial activities against various phytopathogens, including Xoo. In addition, the selected strains were further evaluated for their potent rice growth promotion and suppression efficacy against BB under greenhouse conditions. The result shows that FA12 and FA26, applied as seed inoculants, significantly enhanced the vigor index of rice seedlings by 78.89% and 108.70%, respectively. Suppression efficacy against BB disease by FA12 and FA26 reached up to 59.74% and 54.70%, respectively, in pot experiments. Furthermore, MALDI-TOF MS analysis of selected strains revealed the masses ranged from m/z 1040 to 1540, representing that iturins and fengycin are the major antimicrobial compounds in the crude extracts, which might have beneficial roles in rice defence responses against BB. In conclusion, FA12 and FA26 possess broad-range antagonistic activity and have the capability to promote plant growth traits. More importantly, applying these strains has a high potential for implementing eco-friendly, cost-effective, and sustainable management practices for BB disease.

A Seed-Endophytic Bacillus safensis Strain With Antimicrobial Activity Has Genes for Novel Bacteriocin-Like Antimicrobial Peptides

Bacteriocins are a highly diverse group of antimicrobial peptides that have been identified in a wide range of commensal and probiotic organisms, especially those resident in host microbiomes. Rising antibiotic resistance have fueled renewed research into new drug scaffolds such as antimicrobial peptides for use in therapeutics. In this investigation, we examined mung bean seeds for endophytes possessing activity against human and plant pathogens. We isolated a novel strain of Bacillus safensis, from the contents of surface-sterilized mung bean seed, which we termed B. safensis C3. Genome sequencing of C3 identified three distinct biosynthetic systems that produce bacteriocin-based peptides. C3 exhibited antibacterial activity against Escherichia coli, Xanthomonas axonopodis, and Pseudomonas syringae. Robust antimicrobial activity of B. safensis C3 was observed when C3 was co-cultured with Bacillus subtilis. Using the cell-free supernatant of C3 and cation exchange chromatography, we enriched a product that retained antimicrobial activity against B. subtilis. The peptide was found to be approximately 3.3 kDa in size by mass spectrometry, and resistant to proteolysis by Carboxypeptidase Y and Endoproteinase GluC, suggesting that it is a modified variant of an AS-48 like bacteriocin. Our findings open new avenues into further development of novel bacteriocin-based scaffolds for therapeutic development, as well as further investigations into how our discoveries of bacteriocin-producing plant commensal microorganisms may have the potential for an immediate impact on the safety of food supplies.

Microbial Involvement in Carbon Transformation via CH4 and CO2 in Saline Sedimentary Pool

Simple Summary

Methane and carbon dioxide are commonly found in the environment and are considered the most important greenhouse gases. Transformation of these gases is in large carried by microorganisms, which occur even in extreme environments. This study presents methane-related biological processes in saline sediments of the Miocene Wieliczka Formation, Poland. Biological activity (carbon dioxide and methane production or methane oxidation), confirmed by stable isotope indices, occurred in all of the studied Wieliczka rocks. CH₄-utilizing microbes constituted 0.7–3.6% while methanogens (represented by Methanobacterium) only 0.01–0.5% of taxa present in the Wieliczka Salt Mine rocks. Water activity was the key factor regulating microbial activity in saline subsurface sediments. Generally, CO₂ respiration was higher in anaerobic conditions while methanogenic and methanotrophic activities were dependent on the type of rock.

Abstract

Methane and carbon dioxide are one of the most important greenhouse gases and significant components of the carbon cycle. Biogeochemical methane transformation may occur even in the extreme conditions of deep subsurface ecosystems. This study presents methane-related biological processes in saline sediments of the Miocene Wieliczka Formation, Poland. Rock samples (W2, W3, and W4) differed in lithology (clayey salt with veins of fibrous salt and lenses of gypsum and anhydrite; siltstone and sandstone; siltstone with veins of fibrous salt and lenses of anhydrite) and the accompanying salt type (spiza salts or green salt). Microbial communities present in the Miocene strata were studied using activity measurements and high throughput sequencing. Biological activity (i.e., carbon dioxide and methane production or methane oxidation) occurred in all of the studied clayey salt and siltstone samples but mainly under water-saturated conditions. Microcosm studies performed at elevated moisture created more convenient conditions for the activity of both methanogenic and methanotrophic microorganisms than the intact sediments. This points to the fact that water activity is an important factor regulating microbial activity in saline subsurface sediments. Generally, respiration was higher in anaerobic conditions and ranged from 36 ± 2 (W2_200%t.w.c) to 48 ± 4 (W3_200%t.w.c) nmol CO₂ gdw⁻¹ day⁻¹. Methanogenic activity was the highest in siltstone and sandstone (W3, 0.025 ± 0.018 nmol CH₄ gdw⁻¹ day⁻¹), while aerobic methanotrophic activity was the highest in siltstone with salt and anhydrite (W4, 220 ± 66 nmol CH₄ gdw⁻¹ day⁻¹). The relative abundance of CH₄-utilizing microorganisms (Methylomicrobium, Methylomonas, Methylocystis) constituted 0.7–3.6% of all taxa. Methanogens were represented by Methanobacterium (0.01–0.5%). The methane-related microbes were accompanied by a significant number of unclassified microorganisms (3–64%) and those of the Bacillus genus (4.5–91%). The stable isotope composition of the CO₂ and CH₄ trapped in the sediments suggests that methane oxidation could have influenced δ¹³C_CH4, especially in W3 and W4.

Eukaryotic Colonization of Micrometer-Scale Cracks in Rocks: A "Microfluidics" Experiment Using Naturally Weathered Meteorites from the Nullarbor Plain, Australia

The advent of microfluidics has revolutionized the way we understand how microorganisms propagate through microporous spaces. Here, we apply this understanding to the study of how endolithic environmental microorganisms colonize the interiors of sterile rock. The substrates used for our study are stony meteorites from the Nullarbor Plain, Australia; a semiarid limestone karst that provides an ideal setting for preserving meteorites. Periodic flooding of the Nullarbor provides a mechanism by which microorganisms and exogenous nutrients may infiltrate meteorites. Our laboratory experiments show that environmental microorganisms reach depths greater than 400 μm by propagating through existing brecciation, passing through cracks no wider than the diameter of a resident cell (i.e., ∼5 μm). Our observations are consistent with the propagation of these eukaryotic cells via growth and cell division rather than motility. The morphology of the microorganisms changed as a result of propagation through micrometer-scale cracks, as has been observed previously for bacteria on microfluidic chips. It has been suggested that meteorites could have served as preferred habitats for microorganisms on ancient Mars. Based on our results, the depths reached by terrestrial microorganisms within meteorites would be sufficient to mitigate against the harmful effects of ionizing radiation, such as UV light, in Earth's deserts and potentially on Mars, if similar processes of microbial colonization had once been active there. Thus, meteorites landing in ancient lakes on Mars, that later dried out, could have been some of the last inhabited locations on the surface, serving as refugia before the planet's surface became inhospitable. Finally, our observations suggest that terrestrial microorganisms can colonize very fine cracks within meteorites (and potentially spaceships and rovers) on unexpectedly short timescales, with important implications for both recognition of extraterrestrial life in returned geological samples and planetary protection.

Altitude and fungal diversity influence the structure of Antarctic cryptoendolithic Bacteria communities

Endolithic growth within rocks is a critical adaptation of microbes living in harsh environments where exposure to extreme temperature, radiation, and desiccation limits the predominant life forms, such as in the ice-free regions of Continental Antarctica. The microbial diversity of the endolithic communities in these areas has been sparsely examined. In this work, diversity and composition of bacterial assemblages in the cryptoendolithic lichen-dominated communities of Victoria Land (Continental Antarctica) were explored using a high-throughput metabarcoding approach, targeting the V4 region of 16S rDNA. Rocks were collected in 12 different localities (from 14 different sites), along a gradient ranging from 1000 to 3300 m a.s.l. and at a sea distance ranging from 29 to 96 km. The results indicate Actinobacteria and Proteobacteria are the dominant taxa in all samples and defined a 'core' group of bacterial taxa across all sites. The structure of bacteria communities is correlated with the fungal counterpart and among the environmental parameters considered, altitude was found to influence bacterial biodiversity, while distance from sea had no evident influence.

Comparing Spore Resistance of Bacillus Strains Isolated from Hydrothermal Vents and Spacecraft Assembly Facilities to Environmental Stressors and Decontamination Treatments

Submarine hydrothermal vents are inhabited by a variety of microorganisms capable of tolerating environmental extremes, making them ideal candidates to further expand our knowledge of the limitations for terrestrial life, including their ability to survive the exposure of spaceflight-relevant conditions. The spore resistance of two Bacillus spp. strains, APA and SBP3, isolated from two shallow vents off Panarea Island (Aeolian Islands, Italy), to artificial and environmental stressors (i.e., UVC radiation, X-rays, heat, space vacuum, hydrogen peroxide [H₂O₂], and low-pressure plasma), was compared with that of two close phylogenetic relatives (Bacillus horneckiae and Bacillus oceanisediminis). Additional comparisons were made with Bacillus sp. isolated from spacecraft assembly facilities (B. horneckiae, Bacillus pumilus SAFR-032, and Bacillus nealsonii) and the biodosimetry strain and space microbiology model organism Bacillus subtilis. Overall, a high degree of spore resistance to stressors was observed for the strains isolated from spacecraft assembly facilities, with an exceptional level of resistance seen by B. pumilus SAFR-032. The environmental isolate SBP3 showed a more robust spore resistance to UVC, X-rays, H₂O₂, dry heat, and space vacuum than the closely related B. horneckiae. Both strains (SBP3 and APA) were more thermotolerant than their relatives, B. horneckiae and B. oceanisediminis, respectively. SBP3 may have a novel use as a bacterial model organism for future interrogations into the potential of forward contamination in extraterrestrial environments (e.g., icy moons of Jupiter or Saturn), spacecraft sterilization and, broadly, microbial responses to spaceflight-relevant environmental stressors.

Precursor-directed combinatorial biosynthesis of cephalosporin analogue by endolithic actinobacterium Streptomyces sp. AL51 by utilizing thiophene derivative

Natural products or their derivatives provide a reliable resource for new drugs. The multi-step chemical reaction to produce new drug is not only expensive but also release pollutants. The precursor-based combinatorial biosynthesis (PCB) is, however, a better option to produce novel natural products with potential pharmaceutical applications. The present work is an attempt to synthesize an antibacterial compound by transforming thiophene precursor using endolithic Streptomyces sp. AL51. The Streptomyces sp. AL51 was isolated from a granite rock sample collected from Mylliem, Meghalaya, India. The isolate was identified as Streptomyces sp. based on its cultural, morphological, biochemical and molecular characteristics. The bioactive compound CAx1 was extracted from the fermentation broth. The compound was characterized by bioactivity-guided fractionation and identified by infrared, UV-visible, nuclear magnetic resonance and mass spectrometry data and identified as 7-[1-(thiophene-5-yl)-1-formamido]-3-propylenyl-3-cephem-4-carboxylic acid with molecular formula C₁₅H₁₄N₂O₄S₂. The purified compound showed considerable in vitro antibacterial activity against both Gram-positive and Gram-negative bacteria showing its broad spectrum property. The obtained results provide promising baseline information for the potential use of endolithic actinobacterium for semisynthetic drug discovery. This is the first report on PCB of broad range antibacterial compound by endolithic Streptomyces strain.

Tales from the tomb: the microbial ecology of exposed rock surfaces

Although a broad diversity of eukaryotic and bacterial taxa reside on rock surfaces where they can influence the weathering of rocks and minerals, these communities and their contributions to mineral weathering remain poorly resolved. To build a more comprehensive understanding of the diversity, ecology and potential functional attributes of microbial communities living on rock, we sampled 149 tombstones across three continents and analysed their bacterial and eukaryotic communities via marker gene and shotgun metagenomic sequencing. We found that geographic location and climate were important factors structuring the composition of these communities. Moreover, the tombstone-associated microbial communities varied as a function of rock type, with granite and limestone tombstones from the same cemeteries harbouring taxonomically distinct microbial communities. The granite and limestone-associated communities also had distinct functional attributes, with granite-associated bacteria having more genes linked to acid tolerance and chemotaxis, while bacteria on limestone were more likely to be lichen associated and have genes involved in photosynthesis and radiation resistance. Together these results indicate that rock-dwelling microbes exhibit adaptations to survive the stresses of the rock surface, differ based on location, climate and rock type, and seem pre-disposed to different ecological strategies (symbiotic versus free-living lifestyles) depending on the rock type.

A Combination of Extreme Environmental Conditions Favor the Prevalence of Endospore-Forming Firmicutes

Environmental conditions unsuitable for microbial growth are the rule rather than the exception in most habitats. In response to this, microorganisms have developed various strategies to withstand environmental conditions that limit active growth. Endospore-forming Firmicutes (EFF) deploy a myriad of survival strategies in order to resist adverse conditions. Like many bacterial groups, they can form biofilms and detect nutrient scarcity through chemotaxis. Moreover, within this paraphyletic group of Firmicutes, ecophysiological optima are diverse. Nonetheless, a response to adversity that delimits this group is the formation of wet-heat resistant spores. These strategies are energetically demanding and therefore might affect the biological success of EFF. Therefore, we hypothesize that abundance and diversity of EFF should be maximized in those environments in which the benefits of these survival strategies offsets the energetic cost. In order to address this hypothesis, geothermal and mineral springs and drillings were selected because in these environments of steep physicochemical gradients, diversified survival strategies may become a successful strategy.We collected 71 samples from geothermal and mineral environments characterized by none (null), single or multiple limiting environmental factors (temperature, pH, UV radiation, and specific mineral composition). To measure success, we quantified EFF gene copy numbers (GCN; spo0A gene) in relation to total bacterial GCN (16S rRNA gene), as well as the contribution of EFF to community composition. The quantification showed that relative GCN for EFF reached up to 20% at sites characterized by multiple limiting environmental factors, whereas it corresponded to less than 1% at sites with one or no limiting environmental factor. Pyrosequencing of the 16S rRNA gene supports a higher contribution of EFF at sites with multiple limiting factors. Community composition suggested a combination of phylotypes for which active growth could be expected, and phylotypes that are most likely in the state of endospores, in all the sites. In summary, our results suggest that diversified survival strategies, including sporulation and metabolic adaptations, explain the biological success of EFF in geothermal and natural springs, and that multiple extreme environmental factors favor the prevalence of EFF.

A selective medium for recovery and enumeration of endolithic bacteria

The study of lithic microbial communities, inhabiting rock substrates has been gathering momentum due to a growing attention of their wide importance as model systems in ecological studies and for their community structure. It is generally accepted that the success of cultivation-based technique is primarily based on suitable culture medium for isolation. The media available for enumeration and recovery of endolithic bacteria are mainly specific to particular type of rock which may not be suitable to isolate endolithic bacterial community from diverse lithobiontic niches. In this study, a new unoptimized medium was formulated, designated LM10 (unoptimized) for enumeration and recovery of endolithic bacteria by addition and/or omission of media components to the basal medium R2G, which was selected after experimental evaluation of five different existing media. The endolithic bacterial count in LM10 medium (unoptimized) was significantly higher than the R2G medium (t=-12.57, p<0.0001). The culture and nutritional parameters associated with unoptimized LM10 medium were optimized using statistical approach to maximize the recovery and enumeration of endolithic bacteria. The first phase of the study comprised of a Plackett-Burman (PB) design experiment conducted to screen thirteen medium components and two culture parameters as variables with effect on bacterial enumeration and recovery. Out of these, Yeast extract, Casein hydrolysate, Glucose, Starch and Sodium thiosulphate were found to be significantly affecting the bacterial count (p<0.05) based on PB design. On keeping rest of the media components and culture conditions at fixed value as per the PB design analyses (p>0.05 and coefficients), further optimization was carried out for significant factors using Box-Behnken design (BBD) of response surface methodology (RSM). Optimized media components obtained by BBD were Yeast extract, Casein hydrolysate, Glucose and Starch in 0.05g/l each and Sodium thiosulphate in 0.047g/l concentrations. The composition of optimized LM10 medium formulated (per litre) is 0.05g Yeast extract, 0.05g Casein hydrolysate, 0.05g Glucose, 0.05g Starch, 0.01g K2HPO4, 0.02g Sodium pyruvate, 0.2g MgSO4, 0.001g FeSO4·7H2O, 0.285g NH4Cl, 0.039g CaCl2·2H2O, 0.047g Na2S2O3·5H2O, 0.002g NaHCO3 and 11g Gellan gum (pH=7.4). Validation of optimized LM10 medium using nine different rock samples from Meghalaya clearly indicated that optimized LM10 medium was better suited for higher recovery and enumeration of endolithic bacteria under both aerobic and anaerobic conditions.

Predominant populations of indigenous soybean-nodulating Bradyrhizobium japonicum strains obtained from organic farming systems in Minnesota

AIMS

Bradyrhizobium from organic fields in Minnesota were isolated and genotyped to assess diversity of soybean-bradyrhizobia in organic farming systems that can be used to improve soybean productivity.

METHODS AND RESULTS

Soil samples were collected from 25 organic fields in Minnesota during May to July 2012. Soybean (cv. Lambert) was used as a host to trap indigenous bradyrhizobia in each sample. Genetic diversity of Bradyrhizobium strains (n=733) was determined using the horizontal, fluorophore-enhanced, repetitive extragenic palindromic-PCR (HFERP) DNA fingerprinting technique and the soybean-bradyrhizobia were classified into 79 different genotypes. Of these, 15 dominant genotypes were found and were highly similar (>92% fingerprint similarity) to serotypes USDA 127 (40.4%), USDA 4 (31.8%) and USDA 123 (15.5%), which were the three main populations of soybean-bradyrhizobia in organic fields.

CONCLUSIONS

Bradyrhizobium japonicum serogroup USDA 4 strains were found to make up a previously unrecognized, predominant rhizobial population in the organic farming soils examined. The relative abundance of strain USDA 4 was negatively correlated with that of USDA 127 and this relationship may be influenced by the levels of NO3 -N and other soil edaphic factors.

SIGNIFICANCE AND IMPACT OF THE STUDY

The local community of bradyrhizobia can be affected by applying inoculant bacteria to organic fields. Based on these results, soybean production in organic farms may be improved by displacing strains similar to USDA 4 with those better at nitrogen fixation and competitive ability than indigenous strains.

Genetically-enriched microbe-facilitated self-healing concrete – a sustainable material for a new generation of construction technology

Genetically modified spore formingB. subtilisbacterial cells for eco-friendly sustainable self-healing bio-concrete.

Antibacterial activity of silver nanoparticles grafted on stone surface

Microbial colonization has a relevant impact on the deterioration of stone materials with consequences ranging from esthetic to physical and chemical changes. Avoiding microbial growth on cultural stones therefore represents a crucial aspect for their long-term conservation. The antimicrobial properties of silver nanoparticles (AgNPs) have been extensively investigated in recent years, showing that they could be successfully applied as bactericidal coatings on surfaces of different materials. In this work, we investigated the ability of AgNPs grafted to Serena stone surfaces to inhibit bacterial viability. A silane derivative, which is commonly used for stone consolidation, and Bacillus subtilis were chosen as the grafting agent and the target bacterium, respectively. Results show that functionalized AgNPs bind to stone surface exhibiting a cluster disposition that is not affected by washing treatments. The antibacterial tests on stone samples revealed a 50 to 80 % reduction in cell viability, with the most effective AgNP concentration of 6.7 μg/cm(2). To our knowledge, this is the first report on antimicrobial activity of AgNPs applied to a stone surface. The results suggest that AgNPs could be successfully used in the inhibition of microbial colonization of stone artworks.

Utilisation of Rep-PCR to track microbes in aerosols collected adjacent to their source, a saline lake in Victoria, Australia

Dust storms are a major source of aerosolized bacteria, especially in the drought conditions experienced in Australia in the decade to 2009. The major aims of this project were to identify the culturable bacteria in environmental samples and to genetically fingerprint all isolates using repetitive element PCR (Rep-PCR) to investigate the possibility of tracking isolates from their source into the atmosphere. Four field trips were conducted to a dry lake in western Victoria, Australia to sample aerosols and sediments. Aerosols were collected at heights up to 150 m using vacuum pumps with filters attached to a tethered helium balloon, while corresponding sediments were collected in sterile polypropylene tubes. Isolates were cultivated on Tryptic Soy Agar, R2 Agar and Marine Agar, and grown in dark conditions at ambient temperature. By sequencing the 16S rRNA gene of 270 isolates, fifteen different bacterial families were identified, with both the aerosols and sediments dominated by the Bacillaceae family. Four sets of Rep-PCR primers were tested, with the ERIC and (GTG)5 primers proving to be the most suitable for fingerprinting the cultured taxa. Rep-PCR revealed very high strain diversity in the samples collected, however some strains were still able to be tracked from sediments up to 150 m in height. This shows the potential of Rep-PCR, however very large reference databases would be required for the technique to be more useful.

Growth of Carnobacterium spp. from permafrost under low pressure, temperature, and anoxic atmosphere has implications for Earth microbes on Mars

The ability of terrestrial microorganisms to grow in the near-surface environment of Mars is of importance to the search for life and protection of that planet from forward contamination by human and robotic exploration. Because most water on present-day Mars is frozen in the regolith, permafrosts are considered to be terrestrial analogs of the martian subsurface environment. Six bacterial isolates were obtained from a permafrost borehole in northeastern Siberia capable of growth under conditions of low temperature (0 °C), low pressure (7 mbar), and a CO(2)-enriched anoxic atmosphere. By 16S ribosomal DNA analysis, all six permafrost isolates were identified as species of the genus Carnobacterium, most closely related to C. inhibens (five isolates) and C. viridans (one isolate). Quantitative growth assays demonstrated that the six permafrost isolates, as well as nine type species of Carnobacterium (C. alterfunditum, C. divergens, C. funditum, C. gallinarum, C. inhibens, C. maltaromaticum, C. mobile, C. pleistocenium, and C. viridans) were all capable of growth under cold, low-pressure, anoxic conditions, thus extending the low-pressure extreme at which life can function.

Microbial diversity in Calamita ferromagnetic sand

Calamita is a black ferromagnetic sand from a marine iron ore on Elba Island (Italy). Its total iron content is approximately 80% and a major fraction (63% w/w) has magnetic properties. Desiccation, ultraviolet irradiation and the high temperature induced by the thermal conductivity of iron make Calamita sand an extreme biotope. We report, for the first time, the geomicrobiological characterization of Calamita sand, which showed a low bacterial biodiversity as determined by denaturing gradient gel electrophoresis and 16S rRNA gene clone library analysis. We retrieved sequences closely affiliated with uncultured bacteria inhabiting the harshest deserts on Earth. Radiation- and desiccation-tolerant bacteria from the phyla Proteobacteria, Actinobacteria and Deinococcus-Thermus dominated the community. Heavy metal-resistant organisms, for example Variovorax sp. were also abundant. Sequences of organisms with an inferred metabolism based on lithotrophic iron oxidation were detected. The sands also contained thermophilic bacilli, which were cultivated at 60°C. These data provided important insights also into the biogeographical distribution of these organisms in the Mediterranean region. In summary, this study on Calamita helps to expand our knowledge of the biodiversity in extreme, iron-rich, environments.

Bioconservation of deteriorated monumental calcarenite stone and identification of bacteria with carbonatogenic activity

The deterioration of the stone built and sculptural heritage has prompted the search and development of novel consolidation/protection treatments that can overcome the limitations of traditional ones. Attention has been drawn to bioconservation, particularly bacterial carbonatogenesis (i.e. bacterially induced calcium carbonate precipitation), as a new environmentally friendly effective conservation strategy, especially suitable for carbonate stones. Here, we study the effects of an in situ bacterial bioconsolidation treatment applied on porous limestone (calcarenite) in the sixteenth century San Jeronimo Monastery in Granada, Spain. The treatment consisted in the application of a nutritional solution (with and without Myxococcus xanthus inoculation) on decayed calcarenite stone blocks. The treatment promoted the development of heterotrophic bacteria able to induce carbonatogenesis. Both the consolidation effect of the treatment and the response of the culturable bacterial community present in the decayed stone were evaluated. A significant surface strengthening (consolidation) of the stone, without altering its surface appearance or inducing any detrimental side effect, was achieved upon application of the nutritional solution. The treatment efficacy was independent of the presence of M. xanthus (which is known as an effective carbonatogenic bacterium). The genetic diversity of 116 bacterial strains isolated from the stone, of which 113 strains showed carbonatogenic activity, was analysed by repetitive extragenic palindromic-polymerase chain reaction (REP-PCR) and 16S rRNA gene sequencing. The strains were distributed into 31 groups on the basis of their REP-PCR patterns, and a representative strain of each group was subjected to 16S rRNA gene sequencing. Analysis of these sequences showed that isolates belong to a wide variety of phylogenetic groups being closely related to species of 15 genera within the Proteobacteria, Firmicutes and the Actinobacteria. This study shows that the abundant carbonatogenic bacteria present in the decayed stone are able to effectively consolidate the degraded stone by producing new calcite (and vaterite) cement if an adequate nutritional solution is used. The implications of these results for the conservation of cultural heritage are discussed.

Adaptation of Bacillus subtilis cells to Archean-like UV climate: relevant hints of microbial evolution to remarkably increased radiation resistance

In a precursory study for the space experiment ADAPT ("Molecular adaptation strategies of microorganisms to different space and planetary UV climate conditions"), cells of Bacillus subtilis 168 were continuously cultured for 700 generations under periodic polychromatic UV irradiation (200-400 nm) to model the suggested UV radiation environment on early Earth at the origin of the first microbial ecosystem during the Archean eon when Earth lacked a significant ozone layer. Populations that evolved under UV stress were about 3-fold more resistant than the ancestral and non-UV-evolved populations. UV-evolved cells were 7-fold more resistant to ionizing radiation than their non-UV-exposed evolved relatives and ancestor. In addition to the acquired increased UV resistance, further changes in microbial stress response to hydrogen peroxide, increased salinity, and desiccation were observed in UV-evolved cells. This indicates that UV-sensitive ancestral cells are capable of adapting to periodically applied UV stress via the evolution of cells with an increased UV resistance level and further enhanced responses to other environmental stressors, which thereby allows them to survive and reproduce under extreme UV radiation as a selection pressure.

Space microbiology

The responses of microorganisms (viruses, bacterial cells, bacterial and fungal spores, and lichens) to selected factors of space (microgravity, galactic cosmic radiation, solar UV radiation, and space vacuum) were determined in space and laboratory simulation experiments. In general, microorganisms tend to thrive in the space flight environment in terms of enhanced growth parameters and a demonstrated ability to proliferate in the presence of normally inhibitory levels of antibiotics. The mechanisms responsible for the observed biological responses, however, are not yet fully understood. A hypothesized interaction of microgravity with radiation-induced DNA repair processes was experimentally refuted. The survival of microorganisms in outer space was investigated to tackle questions on the upper boundary of the biosphere and on the likelihood of interplanetary transport of microorganisms. It was found that extraterrestrial solar UV radiation was the most deleterious factor of space. Among all organisms tested, only lichens (Rhizocarpon geographicum and Xanthoria elegans) maintained full viability after 2 weeks in outer space, whereas all other test systems were inactivated by orders of magnitude. Using optical filters and spores of Bacillus subtilis as a biological UV dosimeter, it was found that the current ozone layer reduces the biological effectiveness of solar UV by 3 orders of magnitude. If shielded against solar UV, spores of B. subtilis were capable of surviving in space for up to 6 years, especially if embedded in clay or meteorite powder (artificial meteorites). The data support the likelihood of interplanetary transfer of microorganisms within meteorites, the so-called lithopanspermia hypothesis.

Exposure of DNA and Bacillus subtilis spores to simulated martian environments: use of quantitative PCR (qPCR) to measure inactivation rates of DNA to function as a template molecule

Several NASA and ESA missions are planned for the next decade to investigate the possibility of present or past life on Mars. Evidence of extraterrestrial life will likely rely on the detection of biomolecules, which highlights the importance of preventing forward contamination not only with viable microorganisms but also with biomolecules that could compromise the validity of life-detection experiments. The designation of DNA as a high-priority biosignature makes it necessary to evaluate its persistence in extraterrestrial environments and the effects of those conditions on its biological activity. We exposed DNA deposited on spacecraft-qualified aluminum coupons to a simulated martian environment for periods ranging from 1 minute to 1 hour and measured its ability to function as a template for replication in a quantitative polymerase chain reaction (qPCR) assay. We found that inactivation of naked DNA or DNA extracted from exposed spores of Bacillus subtilis followed a multiphasic UV-dose response and that a fraction of DNA molecules retained functionality after 60 minutes of exposure to simulated full-spectrum solar radiation in martian atmospheric conditions. The results indicate that forward-contaminant DNA could persist for considerable periods of time at the martian surface.

Biodiversity of streptomycetes isolated from a succession sequence at a post-mining site and their evidence in Miocene lacustrine sediment

The genetic diversity of streptomycetes in colliery spoil heaps (Sokolov, Czech Republic) was investigated by restriction pattern analysis of 16S-internal transcribed spacer rDNA and 16S sequences. We sampled freshly excavated Miocene sediment (17-19-million-year-old) and four sites of primary succession (initial, early, middle, and late stages; aged 1-44 years) on the same sediment. Active bacteria were present even in fresh Miocene sediment, and the relative proportion of actinomycetes among total bacterial and their genetic diversity increased significantly with the age of the sampling site. The replacement of pioneer species by late succession species during succession was observed. Plate assays of Streptomyces strains revealed 27% antibiotic-producing strains. Screening for nonribosomal peptide synthases and type I polyketide synthases systems suggested that 90% and 55% streptomycetes, respectively, are putative producers of biologically active compounds. The frequencies of tetracycline-, amoxicillin-, and chloramphenicol-resistant streptomycetes were 6%, 9%, and 15%, respectively. These findings document the occurrence of genetic elements encoding antibiotic resistance genes and the production of antibiotics by streptomycetes located in pristine environments. Our results indicate key roles for ancient streptomycetes related to S. microflavus, S. spororaveus, and S. flavofuscus in pioneering community development in freshly excavated substrates.

Microbiology of the atmosphere-rock interface: how biological interactions and physical stresses modulate a sophisticated microbial ecosystem

Life at the atmosphere-lithosphere boundary is an ancient terrestrial niche that is sparsely covered by thin subaerial biofilms. The microbial inhabitants of these biofilms (a) have adapted to all types of terrestrial/subaerial stresses (e.g., desiccation, extreme temperatures, low nutrient availability, intense solar radiation), (b) interact with minerals that serve as both a dwelling and a source of mineral nutrients, and (c) provoke weathering of rocks and soil formation. Subaerial communities comprise heterotrophic and phototrophic microorganisms that support each other's lifestyle. Major lineages of eubacteria associated with the early colonization of land (e.g., Actinobacteria, Cyanobacteria) are present in these habitats along with eukaryotes such as microscopic green algae and ascomycetous fungi. The subaerial biofilm inhabitants have adapted to desiccation, solar radiation, and other environmental challenges by developing protective, melanized cell walls, assuming microcolonial architectures and symbiotic lifestyles. How these changes occurred, their significance in soil formation, and their potential as markers of climate change are discussed below.

Bacterial spores in granite survive hypervelocity launch by spallation: implications for lithopanspermia

Bacterial spores are considered good candidates for endolithic life-forms that could survive interplanetary transport by natural impact processes, i.e., lithopanspermia. Organisms within rock can only embark on an interplanetary journey if they survive ejection from the surface of the donor planet and the associated extremes of compressional shock, heating, and acceleration. Previous simulation experiments have measured each of these three stresses more or less in isolation of one another, and results to date indicate that spores of the model organism Bacillus subtilis can survive each stress applied singly. Few simulations, however, have combined all three stresses simultaneously. Because considerable experimental and theoretical evidence supports a spallation mechanism for launch, we devised an experimental simulation of launch by spallation using the Ames Vertical Gun Range (AVGR). B. subtilis spores were applied to the surface of a granite target that was impacted from above by an aluminum projectile fired at 5.4 km/s. Granite spall fragments were captured in a foam recovery fixture and then recovered and assayed for shock damage by transmission electron microscopy and for spore survival by viability assays. Peak shock pressure at the impact site was calculated to be 57.1 GPa, though recovered spall fragments were only very lightly shocked at pressures of 5-7 GPa. Spore survival was calculated to be on the order of 10(-5), which is in agreement with results of previous static compressional shock experiments. These results demonstrate that endolithic spores can survive launch by spallation from a hypervelocity impact, which lends further evidence in favor of lithopanspermia theory.

Ancient micronauts: interplanetary transport of microbes by cosmic impacts

Recent developments in microbiology, geophysics and planetary sciences raise the possibility that the planets in our solar system might not be biologically isolated. Hence, the possibility of lithopanspermia (the interplanetary transport of microbial passengers inside rocks) is presently being re-evaluated, with implications for the origin and evolution of life on Earth and within our solar system. Here, I summarize our current understanding of the physics of impacts, space transport of meteorites, and the potentiality of microorganisms to undergo and survive interplanetary transfer.

Fluorescent-BOX-PCR for resolving bacterial genetic diversity, endemism and biogeography

Background

BOX-A1R-based repetitive extragenic palindromic-PCR (BOX-PCR) is one of the most used techniques in biogeography studies of microbial isolates. However the traditional separation of BOX-PCR patterns by agarose gel electrophoresis suffers many limitations. The aim of this research was to set up a fluorescent BOX-PCR (F-BOX-PCR) assay in which separation of PCR products is automated in a capillary electrophoresis system. F-BOX-PCR was compared with the traditional BOX-PCR using bacterial strains with different G+C content (Bacillus cereus; Escherichia coli; isolates of the family Geodermatophilaceae). Resolution, discriminatory power and reproducibility were evaluated by assaying different electrophoretic runs, PCR reactions and independent DNA extractions. BOX-PCR and F-BOX-PCR were compared for the analysis of 29 strains of Modestobacter multiseptatus isolated from three different microsites in an altered carbonatic wall from Cagliari, Italy, and 45 strains of Streptococcus thermophilus isolated from 34 samples of the hand-made, yogurt-like product Matsoni, collected in different locations in Georgia.

Results

Fluorophore 6-FAM proved more informative than HEX and BOX-PCR both in agarose gel electrophoresis (p < 0.004 and p < 0.00003) and in capillary electrophoresis (compared only with HEX, p < 2 × 10^-7). 6-FAM- and HEX-based F-BOX-PCR respectively detected up to 12.0 and 11.3 times more fragments than BOX-PCR. Replicate separations of F-BOX-PCR showed an accuracy of the size calling of ± 0.5 bp until 500 bp, constantly decreasing to ± 10 bp at 2000 bp. Cluster analysis of F-BOX-PCR profiles grouped M. multiseptatus strains according to the microsite of isolation and S. thermophilus strains according to the geographical origin of Matsoni, but resulted intermixed when a BOX-PCR dataset was used.

Conclusion

F-BOX-PCR represents an improved method for addressing bacterial biogeography studies both in term of sensitivity, reproducibility and data analysis.

Isolation of rpoB mutations causing rifampicin resistance in Bacillus subtilis spores exposed to simulated Martian surface conditions

ABSTRACT Bacterial spores are considered prime candidates for Earth-to-Mars transport by natural processes and human spaceflight activities. Previous studies have shown that exposure of Bacillus subtilis spores to ultrahigh vacuum (UHV) characteristic of space both increased the spontaneous mutation rate and altered the spectrum of mutation in various marker genes; but, to date, mutagenesis studies have not been performed on spores exposed to milder low pressures encountered in the martian environment. Mutations to rifampicin-resistance (Rif(R)) were isolated in B. subtilis spores exposed to simulated martian atmosphere (99.9% CO(2), 710 Pa) for 21 days in a Mars Simulation Chamber (MSC) and compared to parallel Earth controls. Exposure in the MSC reduced spore viability by approximately 67% compared to Earth controls, but this decrease was not statistically significant (P = 0.3321). The frequency of mutation to Rif(R) was also not significantly increased in the MSC compared to Earth-exposed spores (P = 0.479). Forty-two and 51 Rif(R) mutant spores were isolated from the MSC- and Earth-exposed controls, respectively. Nucleotide sequencing located the Rif(R) mutations in the rpoB gene encoding the beta subunit of RNA polymerase at residue V135F of the N-cluster and at residues Q469K/L, H482D/P/R/Y, and S487L in Cluster I. No mutations were found in rpoB Clusters II or III. Two new alleles, Q469L and H482D, previously unreported in B. subtilis rpoB, were isolated from spores exposed in the MSC; otherwise, only slight differences were observed in the spectra of spontaneous Rif(R) mutations from spores exposed to Earth vs. the MSC. However, both spectra are distinctly different from Rif(R) mutations previously reported arising from B. subtilis spores exposed to simulated space vacuum.

Predicting Salmonella enterica serotypes by repetitive sequence-based PCR

Repetitive extragenic palindromic sequence-based PCR (rep-PCR) utilizing a semi-automated system, was evaluated as a method to determine Salmonella serotypes. A group of 216 Salmonella isolates belonging to 13 frequently isolated serotypes and one rarer serotype from poultry were used to create a DNA fingerprint library with the DiversiLab System software. Subsequently, a blinded set of 44 poultry isolates were fingerprinted and queried against the library in an attempt to putatively assign a serotype designation to each Salmonella isolate. The query isolates were previously typed employing standard serological techniques. Utilizing pair-wise similarity percentages as calculated by the Pearson correlation coefficient, the predicted serotype of 28 isolates matched the serological typing result. For eight isolates, rep-PCR results were interpreted as one of two very closely-related serotypes, Hadar and the rarer Istanbul. Traditional serological assays have difficulty distinguishing between these groups, and sequencing interspacer regions of the rrfH gene was unable to differentiate among isolates of these two serovars. Six of the remaining isolates resulted in no match to the database (similarity values <95%) and these indeed proved to be serotypes not included in the original library. The two remaining samples proved discrepant at the 95% similarity threshold, however examination of electropherograms clearly indicated fingerprint variability between query and library samples, suggesting an expanded rep-PCR library will be necessary for increased utility. Since serological assays can take several days to weeks to provide information, the DiversiLab System holds promise for more rapid serotype classification for members of this group.

Role of DNA protection and repair in resistance of Bacillus subtilis spores to ultrahigh shock pressures simulating hypervelocity impacts

Impact-induced ejections of rocks from planetary surfaces are frequent events in the early history of the terrestrial planets and have been considered as a possible first step in the potential interplanetary transfer of microorganisms. Spores of Bacillus subtilis were used as a model system to study the effects of a simulated impact-caused ejection on rock-colonizing microorganisms using a high-explosive plane wave setup. Embedded in different types of rock material, spores were subjected to extremely high shock pressures (5 to 50 GPa) lasting for fractions of microseconds to seconds. Nearly exponential pressure response curves were obtained for spore survival and linear dependency for the induction of sporulation-defective mutants. Spores of strains defective in major small, acid-soluble spore proteins (SASP) (alpha/beta-type SASP) that largely protect the spore DNA and spores of strains deficient in nonhomologous-end-joining DNA repair were significantly more sensitive to the applied shock pressure than were wild-type spores. These results indicate that DNA may be the sensitive target of spores exposed to ultrahigh shock pressures. To assess the nature of the critical physical parameter responsible for spore inactivation by ultrahigh shock pressures, the resulting peak temperature was varied by lowering the preshock temperature, changing the rock composition and porosity, or increasing the water content of the samples. Increased peak temperatures led to increased spore inactivation and reduced mutation rates. The data suggested that besides the potential mechanical stress exerted by the shock pressure, the accompanying high peak temperatures were a critical stress parameter that spores had to cope with.

Use of the DiversiLab repetitive sequence-based PCR system for genotyping and identification of Archaea

Repetitive elements are short stretches of DNA that are randomly distributed throughout the chromosomes of prokaryotes. The use of PCR primers to amplify intervening sequences of DNA between specific repetitive elements in Bacteria has become a standard method for rapidly genotyping bacterial strains and providing good resolution between multiple strains within a single species. Rapid, standardized methods for high resolution genotyping of Archaea are not widely available. We evaluated the DiversiLab system from Bacterial Barcodes that utilizes a kit-based repetitive sequence-based (rep-PCR) method that has been optimized for genotyping DNA was extracted from the source organisms using either a standard chemical DNA extraction kit or Whatman FTA paper. Rep-PCR was performed using an archaeal primer set and, the products were run on an Agilent, Lab-on-a-Chip DNA analyzer. Results were analyzed and compared using DiversiLab web-based software from Bacterial Barcodes. Seventy-nine strains representing 27 genera of Crenarchaeota and Euryarchaeota were analyzed. All the organisms could be successfully genotyped and the results were reproducible. We could not detect differences in rep-PCR profiles between DNA extracted using the chemical extraction kit and FTA paper. Thus far, 14 genera and 32 species of methanogens have been analyzed, and all yielded unique genotypes. For halophiles, 11 genera and 28 different species were analyzed, and all yielded unique genotypes. A comparison of 7 different strains of Halobacterium salinarium demonstrated that 6 of the 7 strains had a unique genotype. A comparison of 4 strains of Methanosarcina mazei indicated that each strain produced a unique genotype. There was little systematic inference that could be made from dendrograms comparing different strains, species, and genera of Archaea based on UPGMA cluster analysis. Based on these results, rep-PCR was a useful tool for the genotyping and strain identification of Archaea.

Endolithic Microbial Ecosystems

The endolithic environment, the pore space in rocks, is a ubiquitous microbial habitat and an interface between biology and geology. Photosynthesis-based endolithic communities inhabit the outer centimeters of rocks exposed to the surface, and offer model systems for microbial ecology, geobiology, and astrobiology. Endolithic ecosystems are among the simplest microbial ecosystems known and as such provide tractable models for testing ecological hypotheses. Such hypotheses have been difficult to test because microbial ecosystems are extraordinarily diverse. We review here recent culture-independent, ribosomal RNA-based studies that evaluate hypotheses about endolithic ecosystems, and provide insight for understanding general principles in microbial ecology. Comparison of endolithic communities supports the principle that patterns of microbial diversity are governed by similar principles observed in macroecological systems. Recent results also explore geobiological processes that shape the current biosphere and potentially provide clues to life's history on Earth and where to seek life elsewhere in the Solar System.

Survival and germinability of Bacillus subtilis spores exposed to simulated Mars solar radiation: implications for life detection and planetary protection

Bacterial spores have been considered as microbial life that could survive interplanetary transport by natural impact processes or human spaceflight activity. Deposition of terrestrial microbes or their biosignature molecules onto the surface of Mars could negatively impact life detection experiments and planetary protection measures. Simulated Mars solar radiation, particularly the ultraviolet component, has been shown to reduce spore viability, but its effect on spore germination and resulting production of biosignature molecules has not been explored. We examined the survival and germinability of Bacillus subtilis spores exposed to simulated martian conditions that include solar radiation. Spores of B. subtilis that contain luciferase resulting from expression of an sspB-luxAB gene fusion were deposited on aluminum coupons to simulate deposition on spacecraft surfaces and exposed to simulated Mars atmosphere and solar radiation. The equivalent of 42 min of simulated Mars solar radiation exposure reduced spore viability by nearly 3 logs, while germination-induced bioluminescence, a measure of germination metabolism, was reduced by less than 1 log. The data indicate that spores can retain the potential to initiate germination-associated metabolic processes and produce biological signature molecules after being rendered nonviable by exposure to Mars solar radiation.