Genomic insight of sulfate reducing bacterial genus Desulfofaba reveals their metabolic versatility in biogeochemical cycling.

BACKGROUND: Sulfate-reducing bacteria (SRB) drive the ocean sulfur and carbon cycling. They constitute a diverse phylogenetic and physiological group and are widely distributed in anoxic marine environments. From a physiological viewpoint, SRB's can be categorized as complete or incomplete oxidizers, meaning that they either oxidize their carbon substrate completely to CO2 or to a stoichiometric mix of CO2 and acetate. Members of Desulfofabaceae family are incomplete oxidizers, and within that family, Desulfofaba is the only genus with three isolates that are classified into three species. Previous physiological experiments revealed their capability of respiring oxygen. RESULTS: Here, we sequenced the genomes of three isolates in Desulfofaba genus and reported on a genomic comparison of the three species to reveal their metabolic potentials. Based on their genomic contents, they all could oxidize propionate to acetate and CO2. We confirmed their phylogenetic position as incomplete oxidizers based on dissimilatory sulfate reductase (DsrAB) phylogeny. We found the complete pathway for dissimilatory sulfate reduction, but also different key genes for nitrogen cycling, including nitrogen fixation, assimilatory nitrate/nitrite reduction, and hydroxylamine reduction to nitrous oxide. Their genomes also contain genes that allow them to cope with oxygen and oxidative stress. They have genes that encode for diverse central metabolisms for utilizing different substrates with the potential for more strains to be isolated in the future, yet their distribution is limited. CONCLUSIONS: Results based on marker gene search and curated metagenome assembled genomes search suggest a limited environmental distribution of this genus. Our results reveal a large metabolic versatility within the Desulfofaba genus which establishes their importance in biogeochemical cycling of carbon in their respective habitats, as well as in the support of the entire microbial community through releasing easily degraded organic matters.

Indoor Airborne Microbiome and Endotoxin: Meteorological Events and Occupant Characteristics Are Important Determinants.

Airborne bacteria and endotoxin may affect asthma and allergies. However, there is limited understanding of the environmental determinants that influence them. This study investigated the airborne microbiomes in the homes of 1038 participants from five cities in Northern Europe: Aarhus, Bergen, Reykjavik, Tartu, and Uppsala. Airborne dust particles were sampled with electrostatic dust fall collectors (EDCs) from the participants' bedrooms. The dust washed from the EDCs' clothes was used to extract DNA and endotoxin. The DNA extracts were used for quantitative polymerase chain (qPCR) measurement and 16S rRNA gene sequencing, while endotoxin was measured using the kinetic chromogenic limulus amoebocyte lysate (LAL) assay. The results showed that households in Tartu and Aarhus had a higher bacterial load and diversity than those in Bergen and Reykjavik, possibly due to elevated concentrations of outdoor bacterial taxa associated with low precipitation and high wind speeds. Bergen-Tartu had the highest difference (ANOSIM R = 0.203) in ß diversity. Multivariate regression models showed that α diversity indices and bacterial and endotoxin loads were positively associated with the occupants' age, number of occupants, cleaning frequency, presence of dogs, and age of the house. Further studies are needed to understand how meteorological factors influence the indoor bacterial community in light of climate change.

Identity and hydrocarbon degradation activity of enriched microorganisms from natural oil and asphalt seeps in the Kurdistan Region of Iraq (KRI).

A previous cultivation-independent investigation of the microbial community structure of natural oil and asphalt seeps in the Kurdistan Region of Iraq (KRI) revealed the dominance of uncultured bacterial taxa belonging to the phyla Deferribacterota and Coprothermobacterota and the orders Thermodesulfobacteriales, Thermales, and Burkholderiales. Here we report on a cultivation-dependent approach to identify members of these groups involved in hydrocarbon degradation in the KRI oil and asphalt seeps. For this purpose, we set up anoxic crude oil-degrading enrichment cultures based on cultivation media known to support the growth of members of the above-mentioned taxonomic groups. During 100-200 days incubation periods, nitrate-reducing and fermentative enrichments showed up to 90% degradation of C8-C17 alkanes and up to 28% degradation of C18-C33 alkanes along with aromatic hydrocarbons. Community profiling of the enrichment cultures showed that they were dominated by diverse bacterial taxa, which were rare in situ community members in the investigated seeps. Groups initially targeted by our approach were not enriched, possibly because their members are slow-growing and involved in the degradation of recalcitrant hydrocarbons. Nevertheless, the enriched taxa were taxonomically related to phylotypes recovered from hydrocarbon-impacted environments as well as to characterized bacterial isolates not previously known to be involved in hydrocarbon degradation. Marker genes (assA and bssA), diagnostic for fumarate addition-based anaerobic hydrocarbon degradation, were not detectable in the enrichment cultures by PCR. We conclude that hydrocarbon biodegradation in our enrichments occurred via unknown pathways and synergistic interactions among the enriched taxa. We suggest, that although not representing abundant populations in situ, studies of the cultured close relatives of these taxa will reveal an unrecognized potential for anaerobic hydrocarbon degradation, possibly involving poorly characterized mechanisms.

A method for studying the metabolic activity of individual tardigrades by measuring oxygen uptake using microrespirometry.

Studies of tardigrade biology have been severely limited by the sparsity of appropriate quantitative techniques, informative on a single-organism level. Therefore, many studies rely on motility-based survival scoring and quantifying reproductive success. Measurements of O2 respiration rates, as an integrating expression of the metabolic activity of single tardigrades, would provide a more comprehensive insight into how an individual tardigrade is responding to specific environmental factors or changes in life stages. Here, we present and validate a new method for determining the O2 respiration rate (nmol O2 mg-1 h-1) of single tardigrades under steady state, using O2 microsensors. As an example, we show that the O2 respiration rate determined in MilliQ water for individuals of Richtersius coronifer and of Macrobiotus macrocalix at 22°C was 10.8±1.84 and 13.1±2.19 nmol O2 mg-1 h-1, respectively.

High-Flow-Rate Impinger for the Study of Concentration, Viability, Metabolic Activity, and Ice-Nucleation Activity of Airborne Bacteria.

The study of airborne bacteria relies on a sampling strategy that preserves their integrity and in situ physiological state, e.g. viability, cultivability, metabolic activity, and ice-nucleation activity. Because ambient air harbors low concentrations of bacteria, an effective bioaerosol sampler should have a high sampling efficiency and a high airflow. We characterize a high-flow-rate impinger with respect to particle collection and retention efficiencies in the range 0.5-3.0 µm, and we investigated its ability to preserve the physiological state of selected bacterial species and seawater bacterial community in comparison with four commercial bioaerosol samplers. The collection efficiency increased with particle size and the cutoff diameter was between 0.5 and 1 µm. During sampling periods of 120-300 min, the impinger retained the cultivability, metabolic activity, viability, and ice-nucleation activity of investigated bacteria. Field studies in semiurban, high-altitude, and polar environments included periods of low bacterial air concentrations, thus demonstrating the benefits of the impinger's high flow rate. In conclusion, the impinger described here has many advantages compared with other bioaerosol samplers currently on the market: a potential for long sampling time, a high flow rate, a high sampling and retention efficiency, low costs, and applicability for diverse downstream microbiological and molecular analyses.

Assessment of the Forward Contamination Risk of Mars by Clean Room Isolates from Space-Craft Assembly Facilities through Aeolian Transport - a Model Study.

The increasing number of missions to Mars also increases the risk of forward contamination. Consequently there is a need for effective protocols to ensure efficient protection of the Martian environment against terrestrial microbiota. Despite the fact of constructing sophisticated clean rooms for spacecraft assembly a 100 % avoidance of contamination appears to be impossible. Recent surveys of these facilities have identified a significant number of microbes belonging to a variety of taxonomic groups that survive the harsh conditions of clean rooms. These microbes may have a strong contamination potential, which needs to be investigate to apply efficient decontamination treatments. In this study we propose a series of tests to evaluate the potential of clean room contaminants to survive the different steps involved in forward contamination. We used Staphylococcus xylosus as model organism to illustrate the different types of stress that potential contaminants will be subjected to on their way from the spacecraft onto the surface of Mars. Staphylococcus xylosus is associated with human skin and commonly found in clean rooms and could therefore contaminate the spacecraft as a result of human activity during the assembling process. The path the cell will take from the surface of the spacecraft onto the surface of Mars was split into steps representing different stresses that include desiccation, freezing, aeolian transport in a Martian-like atmosphere at Martian atmospheric pressure, and UV radiation climate. We assessed the surviving fraction of the cellular population after each step by determining the integrated metabolic activity of the survivor population by measuring their oxygen consumption rate. The largest fraction of the starting culture (around 70 %) was killed during desiccation, while freezing, Martian vacuum and short-term UV radiation only had a minor additional effect on the survivability of Staphylococcus xylosus. The study also included a simulation of atmospheric transport on Martian dust, which did not significantly alter the metabolic potential of the cells. The high survival potential of skin microbes, which are not among the most robust isolates, clearly underlines the necessity for efficient decontamination protocols and of adequate planetary protection measures. Thus we propose a series of tests to be included into the description of isolates from spacecraft assembly clean rooms in order to assess the forward contamination potential of the specific isolate and to categorize the risk level according to the organisms survival potential. We are aware that the tests that we propose do not exhaust the types of challenges that the microbes would meet on their way and therefore the series of tests is open to being extended.

The Tubular Sheaths Encasing Methanosaeta thermophila Filaments Are Functional Amyloids.

Archaea are renowned for their ability to thrive in extreme environments, although they can be found in virtually all habitats. Their adaptive success is linked to their unique cell envelopes that are extremely resistant to chemical and thermal denaturation and that resist proteolysis by common proteases. Here we employ amyloid-specific conformation antibodies and biophysical techniques to show that the extracellular cell wall sheaths encasing the methanogenic archaea Methanosaeta thermophila PT are functional amyloids. Depolymerization of sheaths and subsequent MS/MS analyses revealed that the sheaths are composed of a single major sheath protein (MspA). The amyloidogenic nature of MspA was confirmed by in vitro amyloid formation of recombinant MspA under a wide range of environmental conditions. This is the first report of a functional amyloid from the archaeal domain of life. The amyloid nature explains the extreme resistance of the sheath, the elastic properties that allow diffusible substrates to penetrate through expandable hoop boundaries, and how the sheaths are able to split and elongate outside the cell. The archaeal sheath amyloids do not share homology with any of the currently known functional amyloids and clearly represent a new function of the amyloid protein fold.

Disproportionation of elemental sulfur by haloalkaliphilic bacteria from soda lakes.

Microbial disproportionation of elemental sulfur to sulfide and sulfate is a poorly characterized part of the anoxic sulfur cycle. So far, only a few bacterial strains have been described that can couple this reaction to cell growth. Continuous removal of the produced sulfide, for instance by oxidation and/or precipitation with metal ions such as iron, is essential to keep the reaction exergonic. Hitherto, the process has exclusively been reported for neutrophilic anaerobic bacteria. Here, we report for the first time disproportionation of elemental sulfur by three pure cultures of haloalkaliphilic bacteria isolated from soda lakes: the Deltaproteobacteria Desulfurivibrio alkaliphilus and Desulfurivibrio sp. AMeS2, and a member of the Clostridia, Dethiobacter alkaliphilus. All cultures grew in saline media at pH 10 by sulfur disproportionation in the absence of metals as sulfide scavengers. Our data indicate that polysulfides are the dominant sulfur species under highly alkaline conditions and that they might be disproportionated. Furthermore, we report the first organism (Dt. alkaliphilus) from the class Clostridia that is able to grow by sulfur disproportionation.

Investigation of the Cytotoxicity of Mars-Relevant Minerals upon Abrasion.

Since the Viking Labeled Release experiments were carried out on Mars in the 1970s, it has been evident that the martian surface regolith has a strong oxidizing capacity that can convert organic compounds into CO2 and probably water. While H2O2 was suggested originally for being the oxidizing agent responsible for the outcome of the Viking experiments, recent analyses of the martian regolith by the Phoenix lander and by consecutive missions point toward radiation-mediated decomposition products of perchlorate salts as the primary oxidant. In a series of experiments, we have shown that abrasion and triboelectric charging of basalt by simulated saltation could be an additional way of activating regolith. We have also shown that abraded basalt with a chemical composition close to that of martian regolith is toxic to several bacterial species and thus may affect the habitability of the martian surface. In the present study, we investigated the effect of the quantitatively most important minerals (olivine, augite, and plagioclase) and iron oxides (hematite, magnetite, and maghemite) on the survival of bacterial cells to elucidate whether a specific mineral that constitutes basalt is responsible for our observations. We observed that suspensions of iron-containing minerals olivine and augite in phosphate-buffered saline (1 × PBS) significantly reduce the number of surviving cells of our model organism Pseudomonas putida after 24 h of incubation. In contrast, the iron-free mineral plagioclase showed no effect. We also observed that suspending abraded olivine and augite in 1 × PBS led to a dramatic increase in pH compared to the pH of 1 × PBS alone. The sudden increase in pH caused by the presence of these minerals may partly explain the observed cytotoxicity. The cytotoxic effect of augite could be relieved when a strong buffer (20 × PBS) was used. In contrast, olivine, despite the stronger buffer, maintained its cytotoxicity. Iron oxides per se have no negative effect on the survival of our test organism. Overall, our experiments confirm the cytotoxicity of basalt and show that no single constituent mineral of the basalt can account for its toxicity. We could show that abraded iron-containing minerals (olivine and augite) change the pH of water when brought into suspension and thereby could affect the habitability of martian regolith.

Non-enzymatic palladium recovery on microbial and synthetic surfaces.

The use of microorganisms as support for reduction of dissolved Pd(II) to immobilized Pd(0) nanoparticles is an environmentally friendly approach for Pd recovery from waste. To better understand and engineer Pd(0) nanoparticle synthesis, one has to consider the mechanisms by which Pd(II) is reduced on microbial surfaces. Escherichia coli, Shewanella oneidensis, and Pseudomonas putida were used as model organisms in order to elucidate the role of microbial cells in Pd(II) reduction under acidic conditions. Pd(II) was reduced by formate under acidic conditions, and the process occurred substantially faster in the presence of cells as compared to cell-free controls. We found no difference between native (untreated) and autoclaved cells, and could demonstrate that even a non-enzymatic protein (bovine serum albumin) stimulated Pd(II) reduction as efficiently as bacterial cells. Amine groups readily interact with Pd(II), and to specifically test their role in surface-assisted Pd(II) reduction by formate, we replaced bacterial cells with polystyrene microparticles functionalized with amine or carboxyl groups. Amine-functionalized microparticles had the same effect on Pd(II) reduction as bacterial cells, and the effect could be hampered if the amine groups were blocked by acetylation. The interaction with amine groups was confirmed by infrared spectroscopy on whole cells and amine-functionalized microparticles. In conclusion, bio-supported Pd(II) reduction on microbial surfaces is possibly mediated by a non-enzymatic mechanism. We therefore suggest the use of amine-rich biomaterials rather than intact cells for Pd bio-recovery from waste.

Seasonal Variation of the Atmospheric Bacterial Community in the Greenlandic High Arctic Is Influenced by Weather Events and Local and Distant Sources.

The Arctic is a hot spot for climate change with potentially large consequences on a global scale. Aerosols, including bioaerosols, are important players in regulating the heat balance through direct interaction with sunlight and indirectly, through inducing cloud formation. Airborne bacteria are the major bioaerosols with some species producing the most potent ice nucleating compounds known, which are implicated in the formation of ice in clouds. Little is known about the numbers and dynamics of airborne bacteria in the Arctic and even less about their seasonal variability. We collected aerosol samples and wet deposition samples in spring 2015 and summer 2016, at the Villum Research Station in Northeast Greenland. We used amplicon sequencing and qPCR targeting the 16S rRNA genes to assess the quantities and composition of the DNA and cDNA-level bacterial community. We found a clear seasonal variation in the atmospheric bacterial community, which is likely due to variable sources and meteorology. In early spring, the atmospheric bacterial community was dominated by taxa originating from temperate and Subarctic regions and arriving at the sampling site through long-range transport. We observed an efficient washout of the aerosolized bacterial cells during a snowstorm, which was followed by very low concentrations of bacteria in the atmosphere during the consecutive 4 weeks. We suggest that this is because in late spring, the long-range transport ceased, and the local sources which comprised only of ice and snow surfaces were weak resulting in low bacterial concentrations. This was supported by observed changes in the chemical composition of aerosols. In summer, the air bacterial community was confined to local sources such as soil, plant material and melting sea-ice. Aerosolized and deposited Cyanobacteria in spring had a high activity potential, implying their activity in the atmosphere or in surface snow. Overall, we show how the composition of bacterial aerosols in the high Arctic varies on a seasonal scale, identify their potential sources, demonstrate how their community sizes varies in time, investigate their diversity and determine their activity potential during and post Arctic haze.

Cow Farmers' Homes Host More Diverse Airborne Bacterial Communities Than Pig Farmers' Homes and Suburban Homes.

Living on a farm has been linked to a lower risk of immunoregulatory disorders, such as asthma, allergy, and inflammatory bowel disease. It is hypothesized that a decrease in the diversity and composition of indoor microbial communities is a sensible explanation for the upsurge in immunoregulatory diseases, with airborne bacteria contributing to this protective effect. However, the composition of this potentially beneficial microbial community in various farm and suburban indoor environments is still to be characterized. We collected settled airborne dust from stables and the associated farmers' homes and from suburban homes using electrostatic dust collectors (EDCs) over a period of 14 days. Then, quantitative PCR (qPCR) was used to assess bacterial abundance. The V3-V4 region of the bacterial 16S rRNA gene was amplified and sequenced using Ilumina MiSeq in order to assess microbial diversity. The Divisive Amplicon Denoising Algorithm (DADA2) algorithm was used for the inference of amplicon sequence variants from amplicon data. Airborne bacteria were significantly more abundant in farmers' indoor environments than in suburban homes (p < 0.001). Cow farmers' homes had significantly higher bacterial diversity than pig farmers' and suburban homes (p < 0.001). Bacterial taxa, such as Firmicutes, Prevotellaceae, Lachnospiraceae, and Lactobacillus were significantly more abundant in farmers' homes than suburban homes, and the same was true for beneficial intestinal bacterial species, such as Lactobacillus amylovorus, Eubacterium hallii, and Faecalibacterium prausnitzii. Furthermore, we found a higher similarity between bacterial communities in individual farmers' homes and their associated cow stables than for pig stables. Our findings contribute with important knowledge on bacterial composition, abundance, and diversity in different environments, which is highly valuable in the discussion on how microbial exposure may contribute to the development of immune-mediated diseases in both children and adults.

Structure and Protein-Protein Interactions of Ice Nucleation Proteins Drive Their Activity.

Microbially-produced ice nucleating proteins (INpro) are unique molecular structures with the highest known catalytic efficiency for ice formation. Airborne microorganisms utilize these proteins to enhance their survival by reducing their atmospheric residence times. INpro also have critical environmental effects including impacts on the atmospheric water cycle, through their role in cloud and precipitation formation, as well as frost damage on crops. INpro are ubiquitously present in the atmosphere where they are emitted from diverse terrestrial and marine environments. Even though bacterial genes encoding INpro have been discovered and sequenced decades ago, the details of how the INpro molecular structure and oligomerization foster their unique ice-nucleation activity remain elusive. Using machine-learning based software AlphaFold 2 and trRosetta, we obtained and analysed the first ab initio structural models of full length and truncated versions of bacterial INpro. The modeling revealed a novel beta-helix structure of the INpro central repeat domain responsible for ice nucleation activity. This domain consists of repeated stacks of two beta strands connected by two sharp turns. One beta-strand is decorated with a TxT amino acid sequence motif and the other strand has an SxL[T/I] motif. The core formed between the stacked beta helix-pairs is unusually polar and very distinct from previous INpro models. Using synchrotron radiation circular dichroism, we validated the ß-strand content of the central repeat domain in the model. Combining the structural model with functional studies of purified recombinant INpro, electron microscopy and modeling, we further demonstrate that the formation of dimers and higher-order oligomers is key to INpro activity. Using computational docking of the new INpro model based on rigid-body algorithms we could reproduce a previously proposed homodimer structure of the INpro CRD with an interface along a highly conserved tyrosine ladder and show that the dimer model agrees with our functional data. The parallel dimer structure creates a surface where the TxT motif of one monomer aligns with the SxL[T/I] motif of the other monomer widening the surface that interacts with water molecules and therefore enhancing the ice nucleation activity. This work presents a major advance in understanding the molecular foundation for bacterial ice-nucleation activity.

Respiration Measurements of Individual Tardigrades of the Species Richtersius cf coronifer as a Function of Temperature and Salinity and Termination of Anhydrobiosis.

Numerous studies have demonstrated that tardigrades in a resting state (tun state) are very resistant to exceptional stress levels in comparison with the resistance observed in multicellular organisms in general. The types of stress include desiccation and radiation, which are also relevant in astrobiological research, and therefore, tardigrades are used as multicellular model organisms. For example, tardigrades have been investigated in the TARSE, TARDIS, RoTaRad, and TARDIKISS projects; their survival has been evaluated according to stressful conditions that prevail in low earth orbit, including the effects of cosmic radiation and microgravity. Despite this interest, the study of tardigrade biology has been severely hampered by the sparsity of appropriate quantitative techniques that inform at the single-organism level. In this study, we present results on mass-specific respiration rates as a function of termination of anhydrobiosis and variations in temperature and salinity, including Mars-analog perchlorate solutions, by using microsensor technology to measure respiration. Based on our results for Richtersius cf coronifer, we estimated the activation energy (50.8 kJ/mole O2) for its metabolism as well as Q10 for selected temperature intervals. Q10 was constant-∼1.5-between 2°C and 33°C, except for the interval 11-16°C, where Q10 was 5.5. The steady-state mass-specific respiration rate of individuals of Richtersius cf coronifer increased with increasing salinity below the lethal limit, likely representing the energy requirements of its osmoregulatory response. We report the first quantitative data of a tardigrade's metabolic dynamics during the termination of anhydrobiosis, revealing significant variation between individuals. However, we observed a general trend, that is, a high initial metabolic rate after exposure to water. Our approach would allow us to carry out quantitative physiological studies of tardigrades on board of the International Space Station, and thus significantly extend the possibility of studying the response of multicellular organisms in space. Summary statement This article reports on first measurements of mass-specific respiration rates of individual tardigrades of the species Richtersius cf coronifer during termination of anhydrobiosis as well as measurements of the impact of temperature and salinity on oxygen uptake rates.

Ice-nucleating proteins are activated by low temperatures to control the structure of interfacial water.

Ice-nucleation active (INA) bacteria can promote the growth of ice more effectively than any other known material. Using specialized ice-nucleating proteins (INPs), they obtain nutrients from plants by inducing frost damage and, when airborne in the atmosphere, they drive ice nucleation within clouds, which may affect global precipitation patterns. Despite their evident environmental importance, the molecular mechanisms behind INP-induced freezing have remained largely elusive. We investigate the structural basis for the interactions between water and the ice-nucleating protein InaZ from the INA bacterium Pseudomonas syringae. Using vibrational sum-frequency generation (SFG) and two-dimensional infrared spectroscopy, we demonstrate that the ice-active repeats of InaZ adopt a ß-helical structure in solution and at water surfaces. In this configuration, interaction between INPs and water molecules imposes structural ordering on the adjacent water network. The observed order of water increases as the interface is cooled to temperatures close to the melting point of water. Experimental SFG data combined with molecular-dynamics simulations and spectral calculations show that InaZ reorients at lower temperatures. This reorientation can enhance water interactions, and thereby the effectiveness of ice nucleation.

Microbially-Enhanced Vanadium Mining and Bioremediation Under Micro- and Mars Gravity on the International Space Station.

As humans explore and settle in space, they will need to mine elements to support industries such as manufacturing and construction. In preparation for the establishment of permanent human settlements across the Solar System, we conducted the ESA BioRock experiment on board the International Space Station to investigate whether biological mining could be accomplished under extraterrestrial gravity conditions. We tested the hypothesis that the gravity (g) level influenced the efficacy with which biomining could be achieved from basalt, an abundant material on the Moon and Mars, by quantifying bioleaching by three different microorganisms under microgravity, simulated Mars and Earth gravitational conditions. One element of interest in mining is vanadium (V), which is added to steel to fabricate high strength, corrosion-resistant structural materials for buildings, transportation, tools and other applications. The results showed that Sphingomonas desiccabilis and Bacillus subtilis enhanced the leaching of vanadium under the three gravity conditions compared to sterile controls by 184.92 to 283.22%, respectively. Gravity did not have a significant effect on mean leaching, thus showing the potential for biomining on Solar System objects with diverse gravitational conditions. Our results demonstrate the potential to use microorganisms to conduct elemental mining and other bioindustrial processes in space locations with non-1 × g gravity. These same principles apply to extraterrestrial bioremediation and elemental recycling beyond Earth.

Microbial links between sulfate reduction and metal retention in uranium- and heavy metal-contaminated soil.

Sulfate-reducing bacteria (SRB) can affect metal mobility either directly by reductive transformation of metal ions, e.g., uranium, into their insoluble forms or indirectly by formation of metal sulfides. This study evaluated in situ and biostimulated activity of SRB in groundwater-influenced soils from a creek bank contaminated with heavy metals and radionuclides within the former uranium mining district of Ronneburg, Germany. In situ activity of SRB, measured by the (35)SO(4)(2-) radiotracer method, was restricted to reduced soil horizons with rates of < or =142 +/- 20 nmol cm(-3) day(-1). Concentrations of heavy metals were enriched in the solid phase of the reduced horizons, whereas pore water concentrations were low. X-ray absorption near-edge structure (XANES) measurements demonstrated that approximately 80% of uranium was present as reduced uranium but appeared to occur as a sorbed complex. Soil-based dsrAB clone libraries were dominated by sequences affiliated with members of the Desulfobacterales but also the Desulfovibrionales, Syntrophobacteraceae, and Clostridiales. [(13)C]acetate- and [(13)C]lactate-biostimulated soil microcosms were dominated by sulfate and Fe(III) reduction. These processes were associated with enrichment of SRB and Geobacteraceae; enriched SRB were closely related to organisms detected in soils by using the dsrAB marker. Concentrations of soluble nickel, cobalt, and occasionally zinc declined < or =100% during anoxic soil incubations. In contrast to results in other studies, soluble uranium increased in carbon-amended treatments, reaching < or =1,407 nM in solution. Our results suggest that (i) ongoing sulfate reduction in contaminated soil resulted in in situ metal attenuation and (ii) the fate of uranium mobility is not predictable and may lead to downstream contamination of adjacent ecosystems.

Formation of palladium(0) nanoparticles at microbial surfaces.

The increasing demand and limited natural resources for industrially important platinum-group metal (PGM) catalysts render the recovery from secondary sources such as industrial waste economically interesting. In the process of palladium (Pd) recovery, microorganisms have revealed a strong potential. Hitherto, bacteria with the property of dissimilatory metal reduction have been in focus, although the biochemical reactions linking enzymatic Pd(II) reduction and Pd(0) deposition have not yet been identified. In this study we investigated Pd(II) reduction with formate as the electron donor in the presence of Gram-negative bacteria with no documented capacity for reducing metals for energy production: Cupriavidus necator, Pseudomonas putida, and Paracoccus denitrificans. Only large and close-packed Pd(0) aggregates were formed in cell-free buffer solutions. Pd(II) reduction in the presence of bacteria resulted in smaller, well-suspended Pd(0) particles that were associated with the cells (called "bioPd(0)" in the following). Nanosize Pd(0) particles (3-30 nm) were only observed in the presence of bacteria, and particles in this size range were located in the periplasmic space. Pd(0) nanoparticles were still deposited on autoclaved cells of C. necator that had no hydrogenase activity, suggesting a hydrogenase-independent formation mechanism. The catalytic properties of Pd(0) and bioPd(0) were determined by the amount of hydrogen released in a reaction with hypophosphite. Generally, bioPd(0) demonstrated a lower level of activity than the Pd(0) control, possibly due to the inaccessibility of the Pd(0) fraction embedded in the cell envelope. Our results demonstrate the suitability of bacterial cells for the recovery of Pd(0), and formation and immobilization of Pd(0) nanoparticles inside the cell envelope. However, procedures to make periplasmic Pd(0) catalytically accessible need to be developed for future nanobiotechnological applications.

Desulfovibrio oceani subsp. oceani sp. nov., subsp. nov. and Desulfovibrio oceani subsp. galateae subsp. nov., novel sulfate-reducing bacteria isolated from the oxygen minimum zone off the coast of Peru.

Two deltaproteobacterial sulfate reducers, designated strain I.8.1(T) and I.9.1(T), were isolated from the oxygen minimum zone water column off the coast of Peru at 400 and 500 m water depth. The strains were Gram-negative, vibrio-shaped and motile. Both strains were psychrotolerant, grew optimally at 20 degrees C at pH 7.0-8.0 and at 2.5-3.5% NaCl (w/v). The strains grew by utilizing hydrogen/acetate, C(3-4) fatty acids, amino acids and glycerol as electron acceptors for sulfate reduction. Fumarate, lactate and pyruvate supported fermentative growth. Sulfate, sulfite, thiosulfate and taurin supported growth as electron acceptors. Both strains were catalase-positive and highly oxygen-tolerant, surviving 24 days of exposure to atmospheric concentrations. MK6 was the only respiratory quinone. The most prominent cellular fatty acid was iso-17:1-omega9c (18%) for strain I.8.1(T) and iso-17:0-omega9c (14%) for strain I.9.1(T). The G+C contents of their genomic DNA were 45-46 mol%. Phylogenetic analysis of 16S rRNA and dsrAB gene sequences showed that both strains belong to the genus Desulfovibrio. Desulfovibrio acrylicus DSM 10141(T) and Desulfovibrio marinisediminis JCM 14577(T) represented their closest validly described relatives with pairwise 16S rRNA gene sequence identities of 98-99%. The level of DNA-DNA hybridization between strains I.8.1(T) and I.9.1(T) was 30-38%. The two strains shared 10-26% DNA-DNA relatedness with D. acrylicus. Based on a polyphasic investigation it is proposed that strains I.8.1(T) and I.9.1(T) represent a novel species for which the name Desulfovibrio oceani sp. nov. is proposed with the two subspecies D. oceani subsp. oceani (type strain, I.8.1(T) = DSM 21390(T) = JCM 15970(T)) and D. oceani subsp. galateae (type strain, I.9.1(T) = DSM 21391(T) = JCM 15971(T)).

Space station biomining experiment demonstrates rare earth element extraction in microgravity and Mars gravity.

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.