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Dissimilatory nitrate reduction to ammonium (DNRA), driven by nitrate-ammonifying bacteria, is an increasingly appreciated nitrogen-cycling pathway in terrestrial ecosystems. This process reportedly generates nitrous oxide (N2O), a strong greenhouse gas with ozone-depleting effects. However, it remains poorly understood how N2O is produced by environmental nitrate-ammonifiers and how to identify DNRA-derived N2O. In this study, we characterize two novel enzymatic pathways responsible for N2O production in Geobacteraceae strains, which are predominant nitrate-ammonifying bacteria in paddy soils. The first pathway involves a membrane-bound nitrate reductase (Nar) and a hybrid cluster protein complex (Hcp–Hcr) that catalyzes the conversion of NO2− to NO and subsequently to N2O. The second pathway is observed in Nar-deficient bacteria, where the nitrite reductase (NrfA) generates NO, which is then reduced to N2O by Hcp–Hcr. These enzyme combinations are prevalent across the domain Bacteria. Moreover, we observe distinctive isotopocule signatures of DNRA-derived N2O from other established N2O production pathways, especially through the highest 15N-site preference (SP) values (43.0‰–49.9‰) reported so far, indicating a robust means for N2O source partitioning. Our findings demonstrate two novel N2O production pathways in DNRA that can be isotopically distinguished from other pathways.IMPORTANCEStimulation of DNRA is a promising strategy to improve fertilizer efficiency and reduce N2O emission in agriculture soils. This process converts water-leachable NO3− and NO2− into soil-adsorbable NH4+, thereby alleviating nitrogen loss and N2O emission resulting from denitrification. However, several studies have noted that DNRA can also be a source of N2O, contributing to global warming. This contribution is often masked by other N2O generation processes, leading to a limited understanding of DNRA as an N2O source. Our study reveals two widespread yet overlooked N2O production pathways in Geobacteraceae, the predominant DNRA bacteria in paddy soils, along with their distinctive isotopocule signatures. These findings offer novel insights into the role of the DNRA bacteria in N2O production and underscore the significance of N2O isotopocule signatures in microbial N2O source tracking.

The in situ stimulation of Fe(III) oxide reduction by Geobacter bacteria leads to the concomitant precipitation of hexavalent uranium [U(VI)] from groundwater. Despite its promise for the bioremediation of uranium contaminants, the biological mechanism behind this reaction remains elusive. Because Fe(III) oxide reduction requires the expression of Geobacter's conductive pili, we evaluated their contribution to uranium reduction in Geobacter sulfurreducens grown under pili-inducing or noninducing conditions. A pilin-deficient mutant and a genetically complemented strain with reduced outer membrane c-cytochrome content were used as controls. Pili expression significantly enhanced the rate and extent of uranium immobilization per cell and prevented periplasmic mineralization. As a result, pili expression also preserved the vital respiratory activities of the cell envelope and the cell's viability. Uranium preferentially precipitated along the pili and, to a lesser extent, on outer membrane redox-active foci. In contrast, the pilus-defective strains had different degrees of periplasmic mineralization matching well with their outer membrane c-cytochrome content. X-ray absorption spectroscopy analyses demonstrated the extracellular reduction of U(VI) by the pili to mononuclear tetravalent uranium U(IV) complexed by carbon-containing ligands, consistent with a biological reduction. In contrast, the U(IV) in the pilin-deficient mutant cells also required an additional phosphorous ligand, in agreement with the predominantly periplasmic mineralization of uranium observed in this strain. These findings demonstrate a previously unrecognized role for Geobacter conductive pili in the extracellular reduction of uranium, and highlight its essential function as a catalytic and protective cellular mechanism that is of interest for the bioremediation of uranium-contaminated groundwater.

The large leakage accidents of heavy metals from industrial facilities pose a serious environmental problem; however, not enough studies have been conducted to assess the long-term ecological risk associated with such accidents. This study evaluated changes in the bacterial communities within river sediment and identified the key functional microorganisms responding to the 2012 cadmium contamination incident in the Long River, Guangxi Province, China. Results revealed that after a prolonged period of pollution accidents, cadmium pollution still had a discernible effect on the bacterial communities of the river sediment. In comparison to the control site (S1), the bacterial α-diversity in sediments from the accident area (S3) and its downstream (S5) showed a significant increase following the incident. In the control site, Burkholderiaceae was dominant, while in S3 and S5, Pedosphaeraceae, Nitrosomonadaceae, Nitrospiraceae and Geobacteraceae were significantly increased. Sulfur bacteria were found to be more responsive to this cadmium contamination than other bacteria. At site S3, the abundances of Sulfuricurvum, Sulfurifustis, Thioalkalispira, Desulfobacteraceae and Desulfarculaceae were hundreds of times higher than at site S1, indicating an intensification of sulfur cycling processes. The functional prediction implied that cadmium pollution may promote methane oxidation coupled with sulfate reduction reactions and altered the processes of nitrification and denitrification. Environmental factors influencing the microbial community included the levels of metals (cadmium, arsenic, iron) in sediment, as well as other sediment characteristics like temperature and electrical conductivity. These findings contribute to our understanding of the long-term ecological consequences of environmental pollution in river ecosystems.

Anaerobic ammonium oxidation coupled to ferric iron reduction (Feammox) has been assumed to play an important role in nitrogen removal from ecosystems. This study assessed the potential role of Feammox in nitrogen transformation in eutrophic lake sediment using an isotope tracing technique in sediment slurry incubation experiments. Feammox was discovered in eutrophic lake sediment. A significant correlation was found between Feammox rates and iron-reducing rates. Furthermore, the positive correlations between the abundance of iron-reducing bacteria (FeRB), such as Geobacteraceae spp. and Shewanella spp., and Feammox rates indicate that Feammox was mediated by FeRB. The potential rate of Feammox in the isotopic tracer incubation treatment was 0.23–0.43 mg N kg −1 day −1 . The estimated nitrogen loss caused by Feammox accounts for 5.0–9.2% of the human-induced N input annually into the eutrophic lake. Feammox alone or coupled with anaerobic ammonium oxidation (anammox) and/or denitrification may have an essential role in the nitrogen cycle within eutrophic lake sediment.

PurposeSoil erosion and deposition are natural occurrences that can greatly affect the functions of soil. Currently, soil erosion has become an important cause of soil degradation in the northeast China, which severely limits the sustainable development of agriculture. Therefore, understanding the effects of soil erosion and deposition on multiple soil ecosystem functions and soil microbial communities can facilitate a comprehensive assessment of their influence on soil quality and fertility of this region.Materials and methodsThis study investigated the effects of soil erosion and deposition on microbial diversity and community in agroecosystems with Mollisols (black soil) at different sites of a slope in northeastern China. The study involves comparison of four slope sites with different erosion intensities and a deposition site. Firstly, a multifunctionality index was generated after determination of a number of soil physicochemical and microbiological parameters. Then, the soil bacteria were determined by 16 s rRNA gene sequencing technology. Finally, the above data were analyzed to investigate the relationship among microbial community characteristics, soil multifunctionality, and soil erosion and deposition.Results and discussionErosion reduces while deposition enhances soil multifunctionality and microbial diversity. Soil multifunctionality decreased from 0.52 (TS) to –0.83 (LS) and increased to 0.85 (FS). Erosion and deposition significantly changed the abundance of Desulfobacterota, Geobacteraceae, Methylomirabilota, and others, which may be related to soil physicochemical properties and hydrothermal conditions. Erosion reduced the complexity and stability of the co-occurrence network of bacteria, whose node and robustness respectively decreased from 540 and 0.1936 (TS) to 488 and 0.1881 (LS), and the vulnerability increased from 0.0006 (TS) to 0.0013 (LS). Moreover, the complexity and stability showed positive correlations with soil multifunctionality and microbial diversity. Overall, our results indicated that erosion and deposition can significantly affect soil multifunctionality and microbial diversity, which will further alter soil microbial communities and their functions.ConclusionsSoil degradation caused by soil erosion may be reflected not only by the reduction of soil nutrients and destruction of soil structure, but also by decreases in soil microbial diversity, network complexity, and stability. Soil degradation caused by erosion includes a decline in soil multifunctionality and microbial characteristics, both of which should be taken into account when treating and rehabilitating degraded soils caused by erosion.

Anode potential can affect the degradation pathway of complex substrates in bioelectrochemical systems (BESs), thereby influencing current production and coulombic efficiency. However, the intricacies behind this interplay are poorly understood. This study used glucose as a model substrate to comprehensively investigate the effect of different anode potentials (− 150 mV, 0 mV and + 200 mV) on the relationship between current production, the electrogenic pathway and the abundance of the electrogenic microorganisms involved in batch mode fed BESs. Current production in glucose-acclimatized reactors was a function of the abundance of Geobacteraceae and of the availability of acetate and formate produced by glucose degradation. Current production was increased by high anode potentials during acclimation (0 mV and + 200 mV), likely due to more Geobacteraceae developing. However, this effect was much weaker than a stimulus from an artificial high acetate supply: acetate was the rate-limiting intermediate in these systems. The supply of acetate could not be influenced by anode potential; altering the flow regime, batch time and management of the upstream fermentation processes may be a greater engineering tool in BES. However, these findings suggest that if high current production is the focus, it will be extremely difficult to achieve success with complex waste streams such as domestic wastewater.

In this work, we analyzed the community structure and metabolic potential of sediment microbial communities in high-latitude coastal environments subjected to low to moderate levels of chronic pollution. Subtidal sediments from four low-energy inlets located in polar and subpolar regions from both Hemispheres were analyzed using large-scale 16S rRNA gene and metagenomic sequencing. Communities showed high diversity (Shannon’s index 6.8 to 10.2), with distinct phylogenetic structures (< 40% shared taxa at the Phylum level among regions) but similar metabolic potential in terms of sequences assigned to KOs. Environmental factors (mainly salinity, temperature, and in less extent organic pollution) were drivers of both phylogenetic and functional traits. Bacterial taxa correlating with hydrocarbon pollution included families of anaerobic or facultative anaerobic lifestyle, such as Desulfuromonadaceae, Geobacteraceae, and Rhodocyclaceae. In accordance, biomarker genes for anaerobic hydrocarbon degradation (bamA, ebdA, bcrA, and bssA) were prevalent, only outnumbered by alkB, and their sequences were taxonomically binned to the same bacterial groups. BssA-assigned metagenomic sequences showed an extremely wide diversity distributed all along the phylogeny known for this gene, including bssA sensu stricto, nmsA, assA, and other clusters from poorly or not yet described variants. This work increases our understanding of microbial community patterns in cold coastal sediments, and highlights the relevance of anaerobic hydrocarbon degradation processes in subtidal environments.

Energy in the form of electricity can be harvested from marine sediments by placing a graphite electrode (the anode) in the anoxic zone and connecting it to a graphite cathode in the overlying aerobic water. We report a specific enrichment of microorganisms of the family Geobacteraceae on energy-harvesting anodes, and we show that these microorganisms can conserve energy to support their growth by oxidizing organic compounds with an electrode serving as the sole electron acceptor. This finding not only provides a method for extracting energy from organic matter, but also suggests a strategy for promoting the bioremediation of organic contaminants in subsurface environments.

A possible approach to enhance the performance of microbial electrochemical system such as microbial fuel cells is to increase the conductivity of catalytic biofilms and thereby the direct extracellular electron transfer within the biofilms and from the electrode. In the present study, we evaluated the impact of static low-intensity magnetic field on the anodic biofilms in microbial fuel cells (MFCs). Results demonstrated that the application of a low-intensity magnetic field (105 and 150 mT) can significantly shorten the startup time and enhance the overall performance of single-chamber MFCs in terms of current density (300%) and power density (150%). In situ conductance evaluation indicated that short-term application of magnetic field can increase biofilm conductivity, although the long-term enhancements were likely results of increased conductivity of the anodic biofilms associated with enriched population of Geobacteraceae. The peak-manner response of conductivity over gate potentials and the positive response of mature biofilm conductance to low intensity of magnetic field support the redox conduction model of the conductive exoelectrogenic biofilms.

Soils are rich in organics, particularly those that support the growth of plants. These organics are possible sources of sustainable energy, and a microbial fuel cell (MFC) system can potentially be used for this purpose. In this, the soil organic content expelled from plant root was possibly converted into electrical energy through the microbial metabolic process. The integration of MFC systems with living plant root system is a novel approach, which will facilitate sustainable resource for energy production. Therefore, the objective of this study is to electrochemically evaluate the paddy field MFCs (PF-MFCs) performance and methane emission under organic and conventional fertilization systems in paddy fields, and its impact on bacterial communities involved in bioelectricity production. Graphite (anode) and carbon (cathode) electrode MFC systems were configured and assembled in organic and conventionally fertilized paddy fields. The anode and bulk soil-associated bacterial communities were examined using high-throughput Illumina MiSeq sequencing platform. Our results revealed that the maximum electricity production and power density were observed in CFPF-MFC with less methane emission compared to OFPF-MFC. The next-generation sequencing (NGS) libraries showed that the bacterial population was significantly increased in the organic-fertilized field and the enhanced occurrence of the Geobacteraceae family in CFPF-MFC anode. By enhancing Geobacteraceae occurrence on the anode, the conventional fertilization improved the bioelectricity production with less methane emission. Further extension in the establishment of plant MFCs in various sedimentary environments will solve the global energy crisis.