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Anaerobic microbial manganese oxidation (AMMO) has been considered an ancient biological metabolism for Mn element cycling on Archaean Earth before the presence of oxygen. A light-dependent AMMO was recently observed under strictly anoxic conditions, providing a new proxy for the interpretation of the evolution of oxygenic photosynthesis. However, the feasibility of biotic Mn(II) oxidation in dark geological habitats that must have been abundant remains unknown. Therefore, we discovered that it would be possible to achieve AMMO in a light-independent electrosyntrophic coculture between Rhodopseudomonas palustris and Geobacter metallireducens. Transmission electron microscopy analysis revealed insoluble particle formation in the coculture with Mn(II) addition. X-ray diffraction and X-ray photoelectron spectroscopy analysis verified that these particles were a mixture of MnO

Microbial iron cycling influences the flux of major nutrients in the environment (e.g., through the adsorptive capacity of iron oxides) and includes biotically induced iron oxidation and reduction processes. The ecological extent of microbial iron cycling is not well understood, even with increased sequencing efforts, in part due to limitations in gene annotation pipelines and limitations in experimental studies linking phenotype to genotype. This is particularly true for the marine subseafloor, which remains undersampled, but represents the largest contiguous habitat on Earth. To address this limitation, we used FeGenie, a database and bioinformatics tool that identifies microbial iron cycling genes and enables the development of testable hypotheses on the biogeochemical cycling of iron. Herein, we survey the microbial iron cycle in diverse subseafloor habitats, including sediment-buried crustal aquifers, as well as surficial and deep sediments. We inferred the genetic potential for iron redox cycling in 32 of the 46 metagenomes included in our analysis, demonstrating the prevalence of these activities across underexplored subseafloor ecosystems. We show that while some processes (e.g., iron uptake and storage, siderophore transport potential, and iron gene regulation) are near-universal, others (e.g., iron reduction/oxidation, siderophore synthesis, and magnetosome formation) are dependent on local redox and nutrient status. Additionally, we detected niche-specific differences in strategies used for dissimilatory iron reduction, suggesting that geochemical constraints likely play an important role in dictating the dominant mechanisms for iron cycling. Overall, our survey advances the known distribution, magnitude, and potential ecological impact of microbe-mediated iron cycling and utilization in sub-benthic ecosystems.

Three highly alkaliphilic bacterial strains designated as A1T, H1T and B1T were isolated from two highly alkaline springs at The Cedars, a terrestrial serpentinizing site. Cells from all strains were motile, Gram-negative and rod-shaped. Strains A1T, H1T and B1T were mesophilic (optimum, 30 °C), highly alkaliphilic (optimum, pH 11) and facultatively autotrophic. Major cellular fatty acids were saturated and monounsaturated hexadecenoic and octadecanoic acids. The genome size of strains A1T, H1T and B1T was 2 574 013, 2 475 906 and 2 623 236 bp, and the G+C content was 66.0, 66.2 and 66.1 mol%, respectively. Analysis of the 16S rRNA genes showed the highest similarity to the genera Malikia (95.1–96.4 %), Macromonas (93.0–93.6 %) and Hydrogenophaga (93.0–96.6 %) in the family Comamonadaceae . Phylogenetic analysis based on 16S rRNA gene and phylogenomic analysis based on core gene sequences revealed that the isolated strains diverged from the related species, forming a distinct branch. Average amino acid identity values of strains A1T, H1T and B1T against the genomes of related members in this family were below 67 %, which is below the suggested threshold for genera boundaries. Average nucleotide identity by blast values and digital DNA–DNA hybridization among the three strains were below 92.0 and 46.6 % respectively, which are below the suggested thresholds for species boundaries. Based on phylogenetic, genomic and phenotypic characterization, we propose Serpentinimonas gen. nov., Serpentinimonas raichei sp. nov. (type strain A1T=NBRC 111848T=DSM 103917T), Serpentinimonas barnesii sp. nov. (type strain H1T= NBRC 111849T=DSM 103920T) and Serpentinimonas maccroryi sp. nov. (type strain B1T=NBRC 111850T=DSM 103919T) belonging to the family Comamonadaceae . We have designated Serpentinimonas raichei the type species for the genus because it is the dominant species in The Cedars springs.

The direct conversion of CO(2) to value-added chemical commodities, thereby storing solar energy, offers a promising option for alleviating both the current energy crisis and global warming. Semiconductor-biological hybrid systems are novel approaches. However, the inherent defects of photocorrosion, photodegradation, and the toxicity of the semiconductor limit the application of these biohybrid systems. We report here that Rhodopseudomonas palustris was able to directly act as a living photosensitizer to drive CO(2) to CH(4) conversion by Methanosarcina barkeri under illumination after coculturing. Specifically, R. palustris formed a direct electric syntrophic coculture with M. barkeri. Here, R. palustris harvested solar energy, performed anoxygenic photosynthesis using sodium thiosulfate as an electron donor, and transferred electrons extracellularly to M. barkeri to drive methane generation. The methanogenesis of M. barkeri in coculture was a light-dependent process with a production rate of 4.73 ± 0.23 μM/h under light, which is slightly higher than that of typical semiconductor-biohybrid systems (approximately 4.36 μM/h). Mechanistic and transcriptomic analyses showed that electrons were transferred either directly or indirectly (via electron shuttles), subsequently driving CH(4) production. Our study suggests that R. palustris acts as a natural photosensitizer that, in coculture with M. barkeri, results in a new way to harvest solar energy that could potentially replace semiconductors in biohybrid systems.

In natural anoxic environments, anoxygenic photosynthetic bacteria fix CO2 by photoheterotrophy, photoautotrophy, or syntrophic anaerobic photosynthesis. Here, we describe electroautotrophy, a previously unidentified dark CO2 fixation mode enabled by the electrosyntrophic interaction between Geobacter metallireducens and Rhodopseudomonas palustris. After an electrosyntrophic coculture is formed, electrons are transferred either directly or indirectly (via electron shuttles) from G. metallireducens to R. palustris, thereby providing reducing power and energy for the dark CO2 fixation. Transcriptomic analyses demonstrated the high expression of genes encoding for the extracellular electron transfer pathway in G. metallireducens and the Calvin-Benson-Bassham carbon fixation cycle in R. palustris Given that sediments constitute one of the most ubiquitous and abundant niches on Earth and that, at depth, most of the sedimentary niche is both anoxic and dark, dark carbon fixation provides a metabolic window for the survival of anoxygenic phototrophs, as well as an as-yet unappreciated contribution to the global carbon cycle.

Silicate minerals represent an important reservoir of nutrients at Earth's surface and a source of alkalinity that modulates long-term geochemical cycles. Due to the slow kinetics of primary silicate mineral dissolution and the potential for nutrient immobilization by secondary mineral precipitation, the bioavailability of many silicate-bound nutrients may be limited by the ability of micro-organisms to actively scavenge these nutrients via redox alteration and/or organic ligand production. In this study, we use targeted laboratory experiments with olivine and the siderophore deferoxamine B to explore how microbial ligands affect nutrient (Fe) release and the overall rate of mineral dissolution. Our results show that olivine dissolution rates are accelerated in the presence of micromolar concentrations of deferoxamine B. Based on the non-linear decrease in rates with time and formation of a Fe3+ -ligand complex, we attribute this acceleration in dissolution rates to the removal of an oxidized surface coating that forms during the dissolution of olivine at circum-neutral pH in the presence of O2 and the absence of organic ligands. While increases in dissolution rates are observed with micromolar concentrations of siderophores, it remains unclear whether such conditions could be realized in natural environments due to the strong physiological control on microbial siderophore production. So, to contextualize our experimental results, we also developed a feedback model, which considers how microbial physiology and ligand-promoted mineral dissolution kinetics interact to control the extent of biotic enhancement of dissolution rates expected for different environments. The model predicts that physiological feedbacks severely limit the extent to which dissolution rates may be enhanced by microbial activity, though the rate of physical transport modulates this limitation.

The Scanning Habitable Environments with Raman and Luminescence for Organics and Chemicals (SHERLOC) is a robotic arm-mounted instrument on NASA’s Perseverance rover. SHERLOC has two primary boresights. The Spectroscopy boresight generates spatially resolved chemical maps using fluorescence and Raman spectroscopy coupled to microscopic images (10.1 μm/pixel). The second boresight is a Wide Angle Topographic Sensor for Operations and eNgineering (WATSON); a copy of the Mars Science Laboratory (MSL) Mars Hand Lens Imager (MAHLI) that obtains color images from microscopic scales (∼13 μm/pixel) to infinity. SHERLOC Spectroscopy focuses a 40 μs pulsed deep UV neon-copper laser (248.6 nm), to a ∼100 μm spot on a target at a working distance of ∼48 mm. Fluorescence emissions from organics, and Raman scattered photons from organics and minerals, are spectrally resolved with a single diffractive grating spectrograph with a spectral range of 250 to ∼370 nm. Because the fluorescence and Raman regions are naturally separated with deep UV excitation (−1 (250 to 273 nm) and the fluorescence region (274 to ∼370 nm) are acquired simultaneously without time gating or additional mechanisms. SHERLOC science begins by using an Autofocus Context Imager (ACI) to obtain target focus and acquire 10.1 μm/pixel greyscale images. Chemical maps of organic and mineral signatures are acquired by the orchestration of an internal scanning mirror that moves the focused laser spot across discrete points on the target surface where spectra are captured on the spectrometer detector. ACI images and chemical maps (< 100 μm/mapping pixel) will enable the first Mars in situ view of the spatial distribution and interaction between organics, minerals, and chemicals important to the assessment of potential biogenicity (containing CHNOPS). Single robotic arm placement chemical maps can cover areas up to 7x7 mm in area and, with the < 10 min acquisition time per map, larger mosaics are possible with arm movements. This microscopic view of the organic geochemistry of a target at the Perseverance field site, when combined with the other instruments, such as Mastcam-Z, PIXL, and SuperCam, will enable unprecedented analysis of geological materials for both scientific research and determination of which samples to collect and cache for Mars sample return.

In natural anoxic environments, anoxygenic photosynthetic bacteria fix CO

Serpentinite-hosted systems represent modern-day analogs of early Earth environments. In these systems, water-rock interactions generate highly alkaline and reducing fluids that can contain hydrogen, methane, and low-molecular-weight hydrocarbons-potent reductants capable of fueling microbial metabolism. In this study, we investigated the microbiota of Hakuba Happo hot springs (∼50°C; pH∼10.5-11), located in Nagano (Japan), which are impacted by the serpentinization process. Analysis of the 16S rRNA gene amplicon sequences revealed that the bacterial community comprises Nitrospirae (47%), "Parcubacteria" (19%), Deinococcus-Thermus (16%), and Actinobacteria (9%), among others. Notably, only 57 amplicon sequence variants (ASV) were detected, and fifteen of these accounted for 90% of the amplicons. Among the abundant ASVs, an early-branching, uncultivated actinobacterial clade identified as RBG-16-55-12 in the SILVA database was detected. Ten single-cell genomes (average pairwise nucleotide identity: 0.98-1.00; estimated completeness: 33-93%; estimated genome size: ∼2.3 Mb) that affiliated with this clade were obtained. Taxonomic classification using single copy genes indicates that the genomes belong to the actinobacterial class-level clade UBA1414 in the Genome Taxonomy Database. Based on metabolic pathway predictions, these actinobacteria are anaerobes, capable of glycolysis, dissimilatory nitrate reduction and CO2 fixation via the Wood-Ljungdahl (WL) pathway. Several other genomes within UBA1414 and two related class-level clades also encode the WL pathway, which has not yet been reported for the Actinobacteria phylum. For the Hakuba actinobacterium, the energy metabolism related to the WL pathway is likely supported by a combination of the Rnf complex, group 3b and 3d [NiFe]-hydrogenases, [FeFe]-hydrogenases, and V-type (H+/Na+ pump) ATPase. The genomes also harbor a form IV ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) complex, also known as a RubisCO-like protein, and contain signatures of interactions with viruses, including clustered regularly interspaced short palindromic repeat (CRISPR) regions and several phage integrases. This is the first report and detailed genome analysis of a bacterium within the Actinobacteria phylum capable of utilizing the WL pathway. The Hakuba actinobacterium is a member of the clade UBA1414/RBG-16-55-12, formerly within the group "OPB41." We propose to name this bacterium 'Candidatus Hakubanella thermoalkaliphilus.'

Some microbes can capture energy through redox reactions with electron flow to solid-phase electron acceptors, such as metal-oxides or poised electrodes, via extracellular electron transfer (EET). While diverse oxide minerals, exhibiting different surface redox potentials, are widely distributed on Earth, little is known about how microbes sense and use the minerals. Here we show electrochemical, metabolic, and transcriptional responses of EET-active microbial communities established on poised electrodes to changes in the surface redox potentials (as electron acceptors) and surrounding substrates (as electron donors). Combination of genome-centric stimulus-induced metatranscriptomics and metabolic pathway investigation revealed that nine Geobacter/Pelobacter microbes performed EET activity differently according to their preferable surface potentials and substrates. While the Geobacter/Pelobacter microbes coded numerous numbers of multi-heme c-type cytochromes and conductive e-pili, wide variations in gene expression were seen in response to altering surrounding substrates and surface potentials, accelerating EET via poised electrode or limiting EET via an open circuit system. These flexible responses suggest that a wide variety of EET-active microbes utilizing diverse EET mechanisms may work together to provide such EET-active communities with an impressive ability to handle major changes in surface potential and carbon source availability.

Sulfur Cave (Puturosu Mountain, Romania) is an extreme environment, unique for displaying life in a gas chemocline. The lower part of the cave is filled with CO2, CH4, and H2S of mofettic origin, while the upper part contains air that floats above the heavier volcanic gasses. S° and H2SO4 (from sulfur-oxidation) cover the cave wall at and below the CO2-H2S:O2 gas/gas interface. On the cave wall, near the interface the pH is, SCOPUS: ar.j, info:eu-repo/semantics/published

Summary Electromicrobiology is the domain of those prokaryotes able to interact with charged electrodes, using them as electron donors and/or electron acceptors. This is performed via a process called extracellular electron transport, in which outer membrane cytochromes are used to oxidize and/or reduce otherwise unavailable insoluble electron acceptors. EET‐capable bacteria can thus be used for a variety of purposes, ranging from small power sources, water reclamation, to pollution remediation and electrosynthesis. Because the study of EET‐capable bacteria is in its nascent phase, the applications are mostly in developmental stages, but the potential for significant contributions to environmental quality is high and moving forward.

Serpentinization is a geologic process that produces highly reduced, hydrogen-rich fluids that support microbial communities under high pH conditions. We investigated the activity of microbes capable of extracellular electron transfer in a terrestrial serpentinizing system known as 'The Cedars'. Measuring current generation with an on-site two-electrode system, we observed daily oscillations in current with the current maxima and minima occurring during daylight hours. Distinct members of the microbial community were enriched. Current generation in lab-scale electrochemical reactors did not oscillate, but was correlated with carbohydrate amendment in Cedars-specific minimal media. Gammaproteobacteria and Firmicutes were consistently enriched from lab electrochemical systems on δ-MnO2 and amorphous Fe(OH)3 at pH 11. However, isolation of an electrogenic strain proved difficult as transfer cultures failed to grow after multiple rounds of media transfer. Lowering the bulk pH in the media allowed us to isolate a Firmicutes strain (Paenibacillus sp.). This strain was capable of electrode and mineral reduction (including magnetite) at pH 9. This report provides evidence of the in situ activity of microbes using extracellular substrates as sinks for electrons at The Cedars, but also highlights the potential importance of community dynamics for supporting microbial life through either carbon fixation, and/or moderating pH stress.

Mariprofundus sp. strain EBB-1 was isolated from a pyrrhotite biofilm incubated in seawater from East Boothbay (ME, USA). Strain EBB-1 is an autotrophic member of the class Zetaproteobacteria with the ability to form iron oxide biominerals. Here, we present the 2.88-Mb genome sequence of EBB-1, which contains 2,656 putative protein-coding sequences.

Extracellular electron transport (EET) occurs in environmental iron-reducing bacteria and is mediated by an outer membrane multi-heme cytochrome complex (Cyts). It has critical implications for global mineral cycling and electrochemical microbial catalysis. The rate of EET mediated by multiple heme redox centers significantly increases in the presence of flavins and quinones. Their electron free energy does not entirely account for the fact that differential effects on EET rate enhancement vary significantly by factors ≥100. Here, we report on whole-cell electrochemical analysis ofShewanella oneidensisMR-1 using six flavin analogs and four quinones. We demonstrated that protonation of the nitrogen atom at position 5 (N5) of the isoalloxazine ring is essential for electron outflow acceleration as a bound non-covalent cofactor of Cyts. EET mediated by Cyts was accelerated at a rate dependent on pKa(N5). The EET rate largely decreased in response to the addition of deuterated water (D2O), while low concentration of D2O (4 %) had little impact on electron free energy difference of the heme and non-covalent bound cofactors, strongly suggesting that the protonation of N5 limits the rate of EET. Our findings directly link EET kinetics to proton transport reaction via N5 and provide a basis for the development of novel strategies for controlling EET-associated biological reactions.Significance statementThe potential of various small molecules such as flavins and quinones to enhance the rate of extracellular electron transport (EET) has been exploited to develop environmental energy conversion systems. Flavins and quinones have similar molecular structures but their abilities to enhance EET vary by >100× inShewanella oneidensisMR-1. These large differences are inconsistent with conventional models, which rely on redox potentials or diffusion constant of shuttling electron mediators. In this study, we demonstrated that the basicity of the nitrogen atom of the isoalloxazine ring (N5) enhances the rate of electron outflow when a flavin or quinone is a non-covalent cofactor ofS. oneidensisMR-1 outer membranec-type cytochromes.

Summary Electromicrobiology is a subdiscipline of microbiology that involves extracellular electron transfer (EET) to (or from) insoluble electron active redox compounds located outside the outer membrane of the cell. These interactions can often be studied using electrochemical techniques which have provided novel insights into microbial physiology in recent years. The mechanisms (and variations) of outward EET are well understood for two model systems, Shewanella and Geobacter, both of which employ multihaem cytochromes to provide an electron conduit to the cell exterior. In contrast, little is known of the intricacies of inward EET, even in these model systems. Given the number of labs now working on EET, it seems likely that most of the mechanistic details will be understood in a few years for the model systems, and the many applications of electromicrobiology will continue to move forward. But emerging work, using electrodes as electron acceptors and donors is providing an abundance of new types of microbes capable of EET inward and/or outward: microbes that are clearly different from our known systems. The extent of this very diverse, and perhaps widely distributed and biogeochemically important ability needs to be determined to understand the mechanisms, importance, and raison d'etre of EET for microbial biology.

Manganese oxides are often highly reactive and easily reduced, both abiotically, by a variety of inorganic chemical species, and biologically during anaerobic respiration by microbes. To evaluate the reaction mechanisms of these different reduction routes and their potential lasting products, we measured the sequence progression of microbial manganese(IV) oxide reduction mediated by chemical species (sulfide and ferrous iron) and the common metal-reducing microbe Shewanella oneidensis MR-1 under several endmember conditions, using synchrotron X-ray spectroscopic measurements complemented by X-ray diffraction and Raman spectroscopy on precipitates collected throughout the reaction. Crystalline or potentially long-lived phases produced in these experiments included manganese(II)-phosphate, manganese(II)-carbonate, and manganese(III)-oxyhydroxides. Major controls on the formation of these discrete phases were alkalinity production and solution conditions such as inorganic carbon and phosphate availability. The formation of a long-lived Mn(III) oxide appears to depend on aqueous Mn(2+) production and the relative proportion of electron donors and electron acceptors in the system. These real-time measurements identify mineralogical products during Mn(IV) oxide reduction, contribute to understanding the mechanism of various Mn(IV) oxide reduction pathways, and assist in interpreting the processes occurring actively in manganese-rich environments and recorded in the geologic record of manganese-rich strata.

Hexavalent chromium (CrVI) is a carcinogenic heavy metal that is a product of many industrial processes and an important contaminant in aquifers. The study investigates alternative remediation options for CrVI through the integration of effective contaminant transport and microbial biofilms. Bioactive sand reactor studies were conducted using columns charged with Shewanella oneidensis MR-1 biofilm growth in sand media. A biofilm reactor dynamics model was employed to predict CrVI reduction in bioactive sand columns from the standpoint of aquifer remediation and water treatment. The model utilized biokinetic parameters determined from independent microbial batch reactor studies using the Monod model. The biokinetic and reactor dynamics models further demonstrated that humic acid acted as electron shuttle and electron acceptor with lactate as electron donor, enhancing biological activity and CrVI reduction. The reactor model accurately forecast process dynamics for both scenarios with and without humic acid. Model sensitivity studies provided additional insight into the influence of various parameters on system dynamics and the means for improving process efficiencies.

Serpentinization is a process whereby water interacts with reduced mantle rock called peridotite to produce a new suite of minerals (e.g., serpentine), a highly alkaline fluid, and hydrogen. In previous reports, we identified abundance of microbes of the candidate phylum NPL-UPA2 in a serpentinization site called The Cedars. Here, we report the first metagenome assembled genome (MAG) of the candidate phylum as well as the in-situ gene expression. The MAG of the phylum NPL-UPA2, named Unc8, is only about 1 Mbp and its biosynthetic properties suggest it should be capable of independent growth. In keeping with the highly reducing niche of Unc8, its genome encodes none of the known oxidative stress response genes including superoxide dismutases. With regard to energy metabolism, the MAG of Unc8 encodes all enzymes for Wood-Ljungdahl acetogenesis pathway, a ferredoxin:NAD+ oxidoreductase (Rnf) and electron carriers for flavin-based electron bifurcation (Etf, Hdr). Furthermore, the transcriptome of Unc8 in the waters of The Cedars showed enhanced levels of gene expression in the key enzymes of the Wood-Ljungdahl pathway [e.g., Carbon monoxide dehydrogenase /Acetyl-CoA synthase complex (CODH/ACS), Rnf, Acetyl-CoA synthetase (Acd)], which indicated that the Unc8 is an acetogen. However, the MAG of Unc8 encoded no well-known hydrogenase genes, suggesting that the energy metabolism of Unc8 might be focused on CO as the carbon and energy sources for the acetate formation. Given that CO could be supplied via abiotic reaction associated with deep subsurface serpentinization, while available CO2 would be at extremely low concentrations in this high pH environment, CO-associated metabolism could provide advantageous approach. The CODH/ACS in Unc8 is a Bacteria/Archaea hybrid type of six-subunit complex and the electron carriers, Etf and Hdr, showed the highest similarity to those in Archaea, suggesting that archaeal methanogenic energy metabolism was incorporated into the bacterial acetogenesis in NPL-UPA2. Given that serpentinization systems are viewed as potential habitats for early life, and that acetogenesis via the Wood-Ljungdahl pathway is proposed as an energy metabolism of Last Universal Common Ancestor, a phylogenetically distinct acetogen from an early earth analog site may provide important insights in primordial lithotrophs and their habitat.

Anaerobic respiration coupled with electron transport to insoluble minerals (referred to as extracellular electron transport [EET]) is thought to be critical for microbial energy production and persistence in many subsurface environments, especially those lacking soluble terminal electron acceptors. While EET-capable microbes have been successfully isolated from various environments, the diversity of bacteria capable of EET is still poorly understood, especially in difficult-to-sample, low energy or extreme environments, such as many subsurface ecosystems. Here, we describe an on-site electrochemical system to enrich EET-capable bacteria using an anode as a respiratory terminal electron acceptor. This anode is connected to a cathode capable of catalyzing abiotic oxygen reduction. Comparing this approach with electrocultivation methods that use a potentiostat for poising the electrode potential, the two-electrode system does not require an external power source. We present an example of our on-site enrichment utilized in an alkaline pond at the Cedars, a terrestrial serpentinization site in Northern California. Prior attempts to cultivate mineral reducing bacteria were unsuccessful, which is likely due to the low-biomass nature of this site and/or the low relative abundance of metal reducing microbes. Prior to implementing our two-electrode enrichment, we measured the vertical profile of dissolved oxygen concentration. This allowed us to place the carbon felt anode and platinum-electroplated carbon felt cathode at depths that would support anaerobic and aerobic processes, respectively. Following on-site incubation, we further enriched the anodic electrode in the laboratory and confirmed a distinct microbial community compared to the surface-attached or biofilm communities normally observed at the Cedars. This enrichment subsequently led to the isolation of the first electrogenic microbe from the Cedars. This method of on-site microbial enrichment has the potential to greatly enhance the isolation of EET-capable bacteria from low biomass or difficult to sample habitats.

A taxonomic and physiologic characterization was carried out on Thioclava strain ElOx9T, which was isolated from a bacterial consortium enriched on electrodes poised at electron donating potentials. The isolate is Gram-negative, catalase-positive and oxidase-positive; the cells are motile short rods. The bacterium is facultatively anaerobic with the ability to utilize nitrate as an electron acceptor. Autotrophic growth with H2 and S0 (oxidized to sulfate) was observed. The isolate also grows heterotrophically with organic acids and sugars. Growth was observed at salinities from 0 to 10% NaCl and at temperatures from 15 to 41 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belongs in the genus Thioclava ; it had the highest sequence similarity of 98.8 % to Thioclava atlantica 13D2W-2T, followed by Thioclava dalianensis DLFJ1-1T with 98.5 % similarity, Thioclava pacifica TL 2T with 97.7 % similarity, and then Thioclava indica DT23-4T with 96.9 %. All other sequence similarities were below 97 % to characterized strains. The digital DNA–DNA hybridization estimated when compared to T. atlantica 13D2W-2T, T. dalianensis DLFJ1-1T, T. pacifica TL 2T and T. indica DT23-4T were 15.8±2.1, 16.7+2.1, 14.3±1.9 and 18.3±2.1 %. The corresponding average nucleotide identity values between these strains were determined to be 65.1, 67.8, 68.4 and 64.4 %, respectively. The G+C content of the chromosomal DNA is 63.4 mol%. Based on these results, a novel species Thioclava electrotropha sp. nov. is proposed, with the type strain ElOx9T (=DSM 103712T=ATCC TSD-100T).

Hydrogenovibrio sp. strain SC-1 was isolated from pyrrhotite incubated in situ in the marine surface sediment of Catalina Island, CA. Strain SC-1 has demonstrated autotrophic growth through the oxidation of thiosulfate and iron. Here, we present the 2.45-Mb genome sequence of SC-1, which contains 2,262 protein-coding genes.

Hydrogenovibrio sp. strain SC-1 was isolated from pyrrhotite incubated in situ in the marine surface sediment of Catalina Island, CA. Strain SC-1 has demonstrated autotrophic growth through the oxidation of thiosulfate and iron. Here, we present the 2.45-Mb genome sequence of SC-1, which contains 2,262 protein-coding genes.

International audience; Recent measurements of methane (CH4) by the Mars Science Laboratory (MSL) now confront us with robust data that demand interpretation. Thus far, the MSL data have revealed a baseline level of CH4 (*0.4 parts per billion by volume [ppbv]), with seasonal variations, as well as greatly enhanced spikes of CH4 with peak abundances of *7 ppbv. What do these CH4 revelations with drastically different abundances and temporal signatures represent in terms of interior geochemical processes, or is martian CH4 a biosignature? Discerning how CH4 generation occurs on Mars may shed light on the potential habitability of Mars. There is no evidence of life on the surface of Mars today, but microbes might reside beneath the surface. In this case, the carbon flux represented by CH4 would serve as a link between a putative subterranean biosphere on Mars and what we can measure above the surface. Alternatively, CH4 records modern geochemical activity. Here we ask the fundamental question: how active is Mars, geochemically and/or biologically? In this article, we examine geological, geochemical, and biogeo- chemical processes related to our overarching question. The martian atmosphere and surface are an over- whelmingly oxidizing environment, and life requires pairing of electron donors and electron acceptors, that is, redox gradients, as an essential source of energy. Therefore, a fundamental and critical question regarding the possibility of life on Mars is, ‘‘Where can we find redox gradients as energy sources for life on Mars?’’ Hence, regardless of the pathway that generates CH4 on Mars, the presence of CH4, a reduced species in an oxidant-rich environment, suggests the possibility of redox gradients supporting life and habitability on Mars. Recent missions such as ExoMars Trace Gas Orbiter may provide mapping of the global distribution of CH4. To discriminate between abiotic and biotic sources of CH4 on Mars, future studies should use a series of diagnostic geochemical analyses, preferably performed below the ground or at the ground/atmosphere interface, including measurements of CH4 isotopes, methane/ethane ratios, H2 gas concentration, and species such as acetic acid. Advances in the fields of Mars exploration and instrumentation will be driven, augmented, and supported by an improved un- derstanding of atmospheric chemistry and dynamics, deep subsurface biogeochemistry, astrobiology, planetary geology, and geophysics. Future Mars exploration programs will have to expand the integration of complementary areas of expertise to generate synergistic and innovative ideas to realize breakthroughs in advancing our under- standing of the potential of life and habitable conditions having existed on Mars. In this spirit, we conducted a set of interdisciplinary workshops. From this series has emerged a vision of technological, theoretical, and meth- odological innovations to explore the martian subsurface and to enhance spatial tracking of key volatiles, such as CH4.

Accurately detecting and counting sparse bacterial samples has many applications in the food, beverage, and pharmaceutical processing industries, in medical diagnostics, and for life detection by robotic missions to other planets and moons of the solar system. Currently, sparse bacterial samples are counted by culture plating or epifluorescence microscopy. Culture plates require long incubation times (days to weeks), and epifluorescence microscopy requires extensive staining and concentration of the sample. Here, we demonstrate how to use off-axis digital holographic microscopy (DHM) to enumerate bacteria in very dilute cultures (100-10(4) cells/mL). First, the construction of the custom DHM is discussed, along with detailed instructions on building a low-cost instrument. The principles of holography are discussed, and a statistical model is used to estimate how long videos should be to detect cells, based on the optical performance characteristics of the instrument and the concentration of the bacterial solution (Table 2). Video detection of cells at 10(5), 10(4), 10(3), and 100 cells/mL is demonstrated in real time using un-reconstructed holograms. Reconstruction of amplitude and phase images is demonstrated using an open-source software package.

Widely distributed outer-membrane cytochromes enable sulfur-reducing bacteria to obtain energy from solid electron donors., Bacterial reduction of oxidized sulfur species (OSS) is critical for energy production in anaerobic marine subsurfaces. In organic-poor sediments, H2 has been considered as a major energy source for bacterial respiration. We identified outer-membrane cytochromes (OMCs) that are broadly conserved in sediment OSS-respiring bacteria and enable cells to directly use electrons from insoluble minerals via extracellular electron transport. Biochemical, transcriptomic, and microscopic analyses revealed that the identified OMCs were highly expressed on the surface of cells and nanofilaments in response to electron donor limitation. This electron uptake mechanism provides sufficient but minimum energy to drive the reduction of sulfate and other OSS. These results suggest a widespread mechanism for survival of OSS-respiring bacteria via electron uptake from solid minerals in energy-poor marine sediments.

While typically investigated as a microorganism capable of extracellular electron transfer to minerals or anodes,Shewanella oneidensisMR-1 can also facilitate electron flow from a cathode to terminal electron acceptors such as fumarate or oxygen, thereby providing a model systems for a process that has significant environmental and technological implications. This work demonstrates that cathodic electrons enter the electron transport chain of S.oneidensiswhen oxygen is used as the terminal electron acceptor. The effect of electron transport chain inhibitors suggested that a proton gradient is generated during cathode-oxidation, consistent with the higher cellular ATP levels measured in cathode-respiring cells relative to controls. Cathode oxidation also correlated with an increase in the cellular redox (NADH/FMNH2) pool using a bioluminescent assay. Using a proton uncoupler, generation of NADH/FMNH2under cathodic conditions was linked to reverse electron flow mediated by the proton pumping NADH oxidase Complex I. A decrease in cathodic electron uptake was observed in various mutant strains including those lacking the extracellular electron transfer components necessary for anodic current generation. While no cell growth was observed under these conditions, here we show that cathode oxidation is linked to cellular energy conservation, resulting in a quantifiable reduction in cellular decay rate. This work highlights a potential mechanism for cell survival and/or persistence in environments where growth and division are severely limited.

Geobacter species are among the most efficient current-producing bacterial species, yet their electron-transfer mechanisms have been scarcely investigated at the molecular level. Here, we provide evidence that Geobacter cells secrete and utilize riboflavin as a bound-cofactor in outer-membrane c-type cytochromes. This finding highlights the potential roles of riboflavin as a major electron carrier in current production.