Anaerobic oxidation of propane coupled to nitrate reduction by a lineage within the class Symbiobacteriia

Nitrifying niche in estuaries is expanded by the plastisphere

The estuarine plastisphere, a novel ecological habitat in the Anthropocene, has garnered global concerns. Recent geochemical evidence has pointed out its potential role in influencing nitrogen biogeochemistry. However, the biogeochemical significance of the plastisphere and its mechanisms regulating nitrogen cycling remain elusive. Using 15N- and 13C-labelling coupled with metagenomics and metatranscriptomics, here we unveil that the plastisphere likely acts as an underappreciated nitrifying niche in estuarine ecosystems, exhibiting a 0.9 ~ 12-fold higher activity of bacteria-mediated nitrification compared to surrounding seawater and other biofilms (stone, wood and glass biofilms). The shift of active nitrifiers from O2-sensitive nitrifiers in the seawater to nitrifiers with versatile metabolisms in the plastisphere, combined with the potential interspecific cooperation of nitrifying substrate exchange observed among the plastisphere nitrifiers, collectively results in the unique nitrifying niche. Our findings highlight the plastisphere as an emerging nitrifying niche in estuarine environment, and deepen the mechanistic understanding of its contribution to marine biogeochemistry.

Coupling Nitrate-Dependent Anaerobic Ethane Degradation with Anaerobic Ammonium Oxidation

The microbial oxidation of short-chain gaseous alkanes (SCGAs, consisting of ethane, propane, and butane) serves as an efficient sink to mitigate these gases' emission to the atmosphere, thus reducing their negative impacts on air quality and climate. "Candidatus Alkanivorans nitratireducens" are recently found to mediate nitrate-dependent anaerobic ethane oxidation (n-DAEO). In natural ecosystems, anaerobic ammonium-oxidizing (anammox) bacteria may consume nitrite generated from nitrate reduction by "Ca. A. nitratireducens", thereby alleviating the inhibition caused by nitrite accumulation on the metabolism of "Ca. A. nitratireducens". Here, we demonstrate the coupling of n-DAEO with anammox in a laboratory-scale model system to prevent nitrite accumulation. Our results suggest that a high concentration of ethane (6.9-7.9%) has acute inhibition on anammox activities, thus making the coupling process a significant challenge. By maintaining ethane concentrations within the range of 1.7-5.5%, stable ethane and ammonium oxidation, nitrate reduction, and dinitrogen gas generation without nitrite accumulation were finally achieved. After the accomplished coupling of n-DAEO with anammox, nitrate reduction rates increased by 8.1 times compared to the rate observed with n-DAEO alone. Microbial community profiling via 16S rRNA gene amplicon sequencing showed "Ca. A. nitratireducens" (6.6-12.9%) and anammox bacteria "Candidatus Kuenenia" (3.4-5.6%) were both dominant in the system, indicating they potentially form a syntrophic partnership to jointly contribute to nitrogen removal. Our findings offer insights into the cross-feeding interaction between "Ca. A. nitratireducens" and anammox bacteria in anoxic environments.

Selective Nitrate Electroreduction to Ammonia on CNT Electrodes with Controllable Interfacial Wettability

The development of electrocatalysts that can efficiently reduce nitrate (NO3-) to ammonia (NH3) has garnered increasing attention due to their potential to reduce carbon emissions and promote environmental protection. Intensive efforts have focused on catalyst development, but a thorough understanding of the effect of the microenvironment around the reactive sites of the catalyst is also crucial to maximize the performance of the electrocatalysts. This study explored an electrocatalytic system that utilized quaternary ammonium surfactants with a range of alkyl chain lengths to modify an electrode made of carbon nanotubes (CNT), with the goal of regulating interfacial wettability toward NO3- reduction. Trimethyltetradecylammonium bromide with a moderate alkyl chain length created a very hydrophobic interface, which led to a high selectivity in the production of NH3 (∼87%). Detailed mechanistic investigations that used operando Fourier-transform infrared (FTIR) spectroscopy and online differential electrochemical mass spectrometry (DEMS) revealed that the construction of a hydrophobic modified CNT played a synergistic role in suppressing a side reaction involving the generation of hydrogen, which would compete with the reduction of NO3-. This electrocatalytic system led to a favorable process for the reduction of NO3- to NH3 through a direct electron transfer pathway. Our findings underscore the significance of controlling the hydrophobic surface of electrocatalysts as an effective means to enhance electrochemical performance in aqueous media.

Methane-dependent complete denitrification by a single Methylomirabilis bacterium

Methane-dependent nitrate and nitrite removal in anoxic environments is thought to rely on syntrophy between ANME-2d archaea and bacteria in the genus 'Candidatus Methylomirabilis'. Here we enriched and purified a single Methylomirabilis from paddy soil fed with nitrate and methane, which is capable of coupling methane oxidation to nitrate reduction via nitrite to dinitrogen independently. Isotope labelling showed that this bacterium we name 'Ca. Methylomirabilis sinica' stoichiometrically performed methane-dependent complete nitrate reduction to dinitrogen gas. Multi-omics analyses collectively demonstrated that 'M. sinica' actively expressed a well-established pathway for this process, especially including nitrate reductase Nap. Furthermore, 'M. sinica' exhibited a higher nitrate affinity than most denitrifiers, implying its competitive fitness under oligotrophic nitrogen-limited conditions. Our findings revise the paradigm of methane-dependent denitrification performed by two organisms, and the widespread presence of 'M. sinica' in public databases suggests that the coupling of methane oxidation and complete denitrification in single cells substantially contributes to global methane and nitrogen budgets.

Anaerobic oxidation of ammonium and short-chain gaseous alkanes coupled to nitrate reduction by a bacterial consortium

The bacterial species "Candidatus Alkanivorans nitratireducens" was recently demonstrated to mediate nitrate-dependent anaerobic oxidation of short-chain gaseous alkanes (SCGAs). In previous bioreactor enrichment studies, the species appeared to reduce nitrate in two phases, switching from denitrification to dissimilatory nitrate reduction to ammonium (DNRA) in response to nitrite accumulation. The regulation of this switch or the nature of potential syntrophic partnerships with other microorganisms remains unclear. Here, we describe anaerobic multispecies cultures of bacteria that couple the oxidation of propane and butane to nitrate reduction and the oxidation of ammonium (anammox). Batch tests with 15N-isotope labelling and multi-omic analyses collectively supported a syntrophic partnership between "Ca. A. nitratireducens" and anammox bacteria, with the former species mediating nitrate-driven oxidation of SCGAs, supplying the latter with nitrite for the oxidation of ammonium. The elimination of nitrite accumulation by the anammox substantially increased SCGA and nitrate consumption rates, whereas it suppressed DNRA. Removing ammonium supply led to its eventual production, the accumulation of nitrite, and the upregulation of DNRA gene expression for the abundant "Ca. A. nitratireducens". Increasing the supply of SCGA had a similar effect in promoting DNRA. Our results suggest that "Ca. A. nitratireducens" switches to DNRA to alleviate oxidative stress caused by nitrite accumulation, giving further insight into adaptability and ecology of this microorganism. Our findings also have important implications for the understanding of the fate of nitrogen and SCGAs in anaerobic environments.

Nitrate-driven anaerobic oxidation of ethane and butane by bacteria

The short-chain gaseous alkanes (ethane, propane, and butane; SCGAs) are important components of natural gas, yet their fate in environmental systems is poorly understood. Microbially mediated anaerobic oxidation of SCGAs coupled to nitrate reduction has been demonstrated for propane, but is yet to be shown for ethane or butane-despite being energetically feasible. Here we report two independent bacterial enrichments performing anaerobic ethane and butane oxidation, respectively, coupled to nitrate reduction to dinitrogen gas and ammonium. Isotopic 13C- and 15N-labelling experiments, mass and electron balance tests, and metabolite and meta-omics analyses collectively reveal that the recently described propane-oxidizing "Candidatus Alkanivorans nitratireducens" was also responsible for nitrate-dependent anaerobic oxidation of the SCGAs in both these enrichments. The complete genome of this species encodes alkylsuccinate synthase genes for the activation of ethane/butane via fumarate addition. Further substrate range tests confirm that "Ca. A. nitratireducens" is metabolically versatile, being able to degrade ethane, propane, and butane under anoxic conditions. Moreover, our study proves nitrate as an additional electron sink for ethane and butane in anaerobic environments, and for the first time demonstrates the use of the fumarate addition pathway in anaerobic ethane oxidation. These findings contribute to our understanding of microbial metabolism of SCGAs in anaerobic environments.

Elucidating Multiple Electron-Transfer Pathways for Metavanadate Bioreduction by Actinomycetic Streptomyces microflavus

While microbial reduction has gained widespread recognition for efficiently remediating environments polluted by toxic metavanadate [V(V)], the pool of identified V(V)-reducing strains remains rather limited, with the vast majority belonging to bacteria and fungi. This study is among the first to confirm the V(V) reduction capability of Streptomyces microflavus, a representative member of ubiquitous actinomycetes in environment. A V(V) removal efficiency of 91.0 ± 4.35% was achieved during 12 days of operation, with a maximum specific growth rate of 0.073 d-1. V(V) was bioreduced to insoluble V(IV) precipitates. V(V) reduction took place both intracellularly and extracellularly. Electron transfer was enhanced during V(V) bioreduction with increased electron transporters. The electron-transfer pathways were revealed through transcriptomic, proteomic, and metabolomic analyses. Electrons might flow either through the respiratory chain to reduce intracellular V(V) or to cytochrome c on the outer membrane for extracellular V(V) reduction. Soluble riboflavin and quinone also possibly mediated extracellular V(V) reduction. Glutathione might deliver electrons for intracellular V(V) reduction. Bioaugmentation of the aquifer sediment with S. microflavus accelerated V(V) reduction. The strain could successfully colonize the sediment and foster positive correlations with indigenous microorganisms. This study offers new microbial resources for V(V) bioremediation and improve the understanding of the involved molecular mechanisms.

Modulating the Active Hydrogen Adsorption on Fe─N Interface for Boosted Electrocatalytic Nitrate Reduction with Ultra-Long Stability

The electrocatalytic reduction of nitrate (NO3 - ) to nitrogen (N2 ) is an environmentally friendly approach for efficient N-cycle management (toward a nitrogen-neutral cycle). However, poor catalyst durability and the competitive hydrogen evolution reaction significantly impede its practical application. Interface-chemistry engineering, utilizing the close relationship between the catalyst surface/interface microenvironment and electron/proton transfer process, has facilitated the development of catalysts with high intrinsic activity and physicochemical durability. This study reports the synthesis of a nitrogen-doped carbon-coated rice-like iron nitride (RL-Fe2 N@NC) electrocatalyst with excellent electrocatalytic nitrate-reduction reaction activity (high N2 selectivity (≈96%) and NO3 - conversion (≈86%)). According to detailed mechanistic investigations by in situ tests and theoretical calculations, the strong hydrogenation ability of iron nitride and enhanced nitrate enrichment of the system synergistically contribute to the rapid hydrogenation of nitrogen-containing species, increasing the intrinsic activity of the catalyst and reducing the occurrence of the competing hydrogen-evolution side reaction. Moreover, RL-Fe2 N@NC shows excellent stability, retaining good NO3 - -to-N2 electrocatalysis activity for more than 40 cycles (one cycle per day). This paper could guide the interfacial design of Fe-based composite nanostructures for electrocatalytic nitrate reduction, facilitating a shift toward nitrogen neutrality.

Carbon and hydrogen stable isotope fractionation due to monooxygenation of short-chain alkanes by butane monooxygenase of Thauera butanivorans Bu-B1211

Multi element compound-specific stable isotope analysis (ME-CSIA) is a tool to assess (bio)chemical reactions of molecules in the environment based on their isotopic fingerprints. To that effect, ME-CSIA concepts are initially developed with laboratory model experiments to determine the isotope fractionation factors specific for distinct (bio)chemical reactions. Here, we determined for the first time the carbon and hydrogen isotope fractionation factors for the monooxygenation of the short-chain alkanes ethane, propane, and butane. As model organism we used Thauera butanivorans strain Bu-B1211 which employs a non-haem iron monooxygenase (butane monooxygenase) to activate alkanes. Monooxygenation of alkanes was associated with strong carbon and hydrogen isotope effects: εbulkC = -2.95 ± 0.5 ‰ for ethane, -2.68 ± 0.1 ‰ for propane, -1.19 ± 0.18 ‰ for butane; εbulkH = -56.3 ± 15 ‰ for ethane, -40.5 ± 2.3 ‰ for propane, -14.6 ± 3.6 ‰ for butane. This resulted in lambda (Λ ≈ εHbulk/εCbulk) values of 16.2 ± 3.7 for ethane, 13.2 ± 0.7 for propane, and 11.4 ± 2.8 for butane. The results show that ME-CSIA can be used to track the occurrence and impact of monooxygenase-dependent aerobic processes converting short-chain alkanes in natural settings like marine and terrestrial seeps, gas reservoirs, and other geological formations impacted by natural gas.