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Methane is the second most important greenhouse gas after carbon dioxide and approximately 11% of the global anthropogenic methane emissions originate from rice fields. Sulfate amendment is a mitigation strategy to reduce methane emissions from rice fields because sulfate reducers and methanogens compete for the same substrates. Cable bacteria are filamentous bacteria known to increase sulfate levels via electrogenic sulfide oxidation. Here we show that one-time inoculation of rice-vegetated soil pots with cable bacteria increases the sulfate inventory 5-fold, which leads to the reduction of methane emissions by 93%, compared to control pots lacking cable bacteria. Promoting cable bacteria in rice fields by enrichment or sensible management may thus become a strategy to reduce anthropogenic methane emissions. Rice paddies are a major source of the Earth’s atmospheric methane, making these important food crops potent contributors to greenhouse gas emissions. Here the authors show that inoculation of paddies with a particular bacterium could significantly curb methane production.

Spirochaetes are frequently detected in anoxic hydrocarbon- and organohalide-polluted groundwater, but their role in such ecosystems has remained unclear. To address this, we studied a sulfate-reducing, naphthalene-degrading enrichment culture, mainly comprising the sulfate reducer Desulfobacterium N47 and the rod-shaped Spirochete Rectinema cohabitans HM. Genome sequencing and proteome analysis suggested that the Spirochete is an obligate fermenter that catabolizes proteins and carbohydrates, resulting in acetate, ethanol, and molecular hydrogen (H 2 ) production. Physiological experiments inferred that hydrogen is an important link between the two bacteria in the enrichment culture, with H 2 derived from fermentation by R. cohabitans used as reductant for sulfate reduction by Desulfobacterium N47. Differential proteomics and physiological experiments showed that R. cohabitans utilizes biomass (proteins and carbohydrates) released from dead cells of Desulfobacterium N47. Further comparative and community genome analyses indicated that other Rectinema phylotypes are widespread in contaminated environments and may perform a hydrogenogenic fermentative lifestyle similar to R. cohabitans . Together, these findings indicate that environmental Spirochaetes scavenge detrital biomass and in turn drive necromass recycling at anoxic hydrocarbon-contaminated sites and potentially other habitats.

Anaerobic microbial degradation of hydrocarbons, typically occurring at the oil-water transition zone, influences the quality of oil reservoirs. In Pitch Lake, Trinidad and Tobago—the world's largest asphalt lake—we found that microorganisms are metabolically active in minuscule water droplets (1 to 3 microliters) entrapped in oil. Pyrotag sequencing of individual droplet microbiomes revealed complex methanogenic microbial communities actively degrading the oil into a diverse range of metabolites, as shown by nuclear magnetic resonance and Fourier transform ion cyclotron resonance mass spectrometry. High salinity and water-stable isotopes of the droplets indicate a deep subsurface origin. The 13.5% water content and the large surface area of the droplets represent an underestimated potential for biodegradation of oil away from the oil-water transition zone.

Here, we present a detailed functional and phylogenetic characterization of an iron-reducing enrichment culture maintained in our lab with benzene as sole carbon and energy source. We used DNA-stable isotope probing to identify microbes within the enrichment most active in the assimilation of 13C-label. When 12C6- and 13C6-benzene were added as comparative substrates, marked differences in the quantitative buoyant density distribution became apparent especially for uncultured microbes within the Gram-positive Peptococcaceae, closely related to environmental clones retrieved from contaminated aquifers world wide and only distantly related to cultured representatives of the genus Thermincola. Prominent among the other constituents of the enrichment were uncultured Deltaproteobacteria, as well as members of the Actinobacteria. Although their presence within the enrichment seems to be stable they did not assimilate 13C-label as significantly as the Clostridia within the time course of our experiment. We hypothesize that benzene degradation in our enrichment involves an unusual syntrophy, where members of the Clostridia primarily oxidize benzene. Electrons from the contaminant are both directly transferred to ferric iron by the primary oxidizers, but also partially shared with the Desulfobulbaceae as syntrophic partners. Alternatively, electrons may also be quantitatively transferred to the partners, which then reduce the ferric iron. Thus our results provide evidence for the importance of a novel clade of Gram-positive iron-reducers in anaerobic benzene degradation, and a role of syntrophic interactions in this process. These findings shed a totally new light on the factors controlling benzene degradation in anaerobic contaminated environments.

Humic acid-coated goethite nanoparticles (HA-GoeNPs) have been recently proposed as an effective reagent for the in situ nanoremediation of contaminated aquifers. However, the effective dosage of these particles has been studied only at laboratory scale to date. This study investigates the possibility of using HA-GoeNPs in remediation of real field sites by mimicking the injection and transport of HA-GoeNPs under realistic conditions. To this purpose, a three-dimensional (3D) transport experiment was conducted in a large-scale container representing a heterogeneous unconfined aquifer. Monitoring data, including particle size distribution, total iron (Fetot) content and turbidity measurements, revealed a good subsurface mobility of the HA-GoeNP suspension, especially within the higher permeability zones. A radius of influence of 2 m was achieved, proving that HA-GoeNPs delivery is feasible for aquifer restoration. A flow and transport model of the container was built using the numerical code Micro and Nanoparticle transport Model in 3D geometries (MNM3D) to predict the particle behavior during the experiment. The agreement between modeling and experimental results validated the capability of the model to reproduce the HA-GoeNP transport in a 3D heterogeneous aquifer. Such result confirms MNM3D as a valuable tool to support the design of field-scale applications of goethite-based nanoremediation.

Cable bacteria of the family Desulfobulbaceae couple spatially separated sulfur oxidation and oxygen or nitrate reduction by long-distance electron transfer, which can constitute the dominant sulfur oxidation process in shallow sediments. However, it remains unknown how cells in the anoxic part of the centimeter-long filaments conserve energy. We found 16S rRNA gene sequences similar to groundwater cable bacteria in a 1-methylnaphthalene-degrading culture (1MN). Cultivation with elemental sulfur and thiosulfate with ferrihydrite or nitrate as electron acceptors resulted in a first cable bacteria enrichment culture dominated >90% by 16S rRNA sequences belonging to the Desulfobulbaceae . Desulfobulbaceae -specific fluorescence in situ hybridization (FISH) unveiled single cells and filaments of up to several hundred micrometers length to belong to the same species. The Desulfobulbaceae filaments also showed the distinctive cable bacteria morphology with their continuous ridge pattern as revealed by atomic force microscopy. The cable bacteria grew with nitrate as electron acceptor and elemental sulfur and thiosulfate as electron donor, but also by sulfur disproportionation when Fe(Cl) 2 or Fe(OH) 3 were present as sulfide scavengers. Metabolic reconstruction based on the first nearly complete genome of groundwater cable bacteria revealed the potential for sulfur disproportionation and a chemo-litho-autotrophic metabolism. The presence of different types of hydrogenases in the genome suggests that they can utilize hydrogen as alternative electron donor. Our results imply that cable bacteria not only use sulfide oxidation coupled to oxygen or nitrate reduction by LDET for energy conservation, but sulfur disproportionation might constitute the energy metabolism for cells in large parts of the cable bacterial filaments.

Compound-specific stable isotope analysis (CSIA) using gas chromatography-isotope ratio mass spectrometry (GC/IRMS) has developed into a mature analytical method in many application areas over the last decade. This is in particular true for carbon isotope analysis, whereas measurements of the other elements amenable to CSIA (hydrogen, nitrogen, oxygen) are much less routine. In environmental sciences, successful applications to date include (i) the allocation of contaminant sources on a local, regional, and global scale, (ii) the identification and quantification of (bio)transformation reactions on scales ranging from batch experiments to contaminated field sites, and (iii) the characterization of elementary reaction mechanisms that govern product formation. These three application areas are discussed in detail. The investigated spectrum of compounds comprises mainly n-alkanes, monoaromatics such as benzene and toluene, methyl tert-butyl ether (MTBE), polycyclic aromatic hydrocarbons (PAHs), and chlorinated hydrocarbons such as tetrachloromethane, trichloroethylene, and polychlorinated biphenyls (PCBs). Future research directions are primarily set by the state of the art in analytical instrumentation and method development. Approaches to utilize HPLC separation in CSIA, the enhancement of sensitivity of CSIA to allow field investigations in the microg L(-1) range, and the development of methods for CSIA of other elements are reviewed. Furthermore, an alternative scheme to evaluate isotope data is outlined that would enable estimates of position-specific kinetic isotope effects and, thus, allow one to extract mechanistic chemical and biochemical information.

In almost all respiratory organisms, organic substrates are degraded via catabolic processes to the central metabolite acetyl-CoA which is then oxidized to CO 2 for energy metabolism or used as a building block for anabolism. Most microorganisms have either the closed tricarboxylic acid cycle or the complete Wood-Ljungdahl-pathway for acetyl-CoA oxidation, but the sulfate-reducing, naphthalene-degrading culture N47 possesses both completely. Combining 13 C- labeled substrates and mass-specific GC-MS analysis of amino acids and fatty acids with enzyme activity assays suggests that N47 has a chemoorganoautotrophic metabolism degrading complex organic substrates such as naphthalene. Surprisingly, however, the biomass is mainly produced from acetyl-CoA generated de novo via CO 2 -fixation. This metabolism probably requires both a complete Wood-Ljungdahl pathway for acetyl-CoA oxidation and a reverse tricarboxylic acid cycle for CO 2 fixation. Based on genome analysis, this chemoorganoautotrophic metabolism seems to also occur in other sulfate-reducers and anaerobic ammonium-oxidizers.

Arsenic contamination of groundwater occurs due to both geogenic and anthropogenic processes. Conventional arsenic remediation techniques require extraction of groundwater into pump-and-treat systems, which are expensive and require long operational times. Hence, there is a need for cost-effective remediation. In this study, we assessed and validated the in situ remediation of arsenic contamination in groundwater resources using permeable reactive barriers (PRBs) made of injectable, colloidal iron oxide nanoparticles in the laboratory and in field-scale pilot tests. Sand-packed, flow-through column studies were used in order to assess the sorption behavior of the iron oxide nanoparticles using field materials (sand, groundwater) in the laboratory. The breakthrough curves were analyzed using a reactive transport model considering linear and nonlinear adsorption isotherms and were fitted best with a chemical nonequilibrium consideration. The results were used to design a pilot-scale field test. The injected 28 m3 of nanoparticles (ca. 280 kg dry weight of iron oxide) were successfully delivered to the aquifer via an injection well. No mobile iron was detected downstream, confirming that a stable in situ barrier was formed that did not move with the groundwater flow. Arsenic concentrations in groundwater were reduced to the aimed 50% of the background value, despite the relatively short contact time between arsenic and the iron oxide in the barrier, due to the high flow velocity of 1.21 m/day. We compared the results of the laboratory and field tests and concluded that the single-parameter models based on retardation factor and/or adsorption capacity fail to predict the longevity of the barrier and the evolution of arsenic breakthrough with time, most likely because they do not consider the chemical nonequilibrium effects. Therefore, we propose that upscaling the laboratory findings to field design must be carried out with care and be coupled with detailed reactive transport models.