Availability Of Electron Acceptors Research Articles

Transcriptional response of Methanosarcina acetivorans to repression of the energy-conserving methanophenazine: CoM-CoB heterodisulfide reductase enzyme HdrED

ABSTRACT Methane-producing archaea are key organisms in the anaerobic carbon cycle. These organisms, also called methanogens, grow by converting substrate to methane gas in a process called methanogenesis. Previous research showed that the reduction of the terminal electron acceptor is the rate-limiting step in methanogenesis by Methanosarcina acetivorans . In order to gain insight into how the cells sense and respond to the availability of the terminal electron acceptor, we designed an experiment to deplete cells of the essential terminal oxidase enzyme, HdrED. We found that the depletion of HdrED in vivo results in a higher abundance of transcripts for methyltransferases ( mtaC2, mtaB3, mtaC3 ), coenzyme B biosynthesis, C1 metabolism, and pyrimidine compounds. In most cases, these changes were distinct from transcript abundance changes observed during the transition from exponential growth to stationary phase cultures. These data implicate the methylotrophic methanogenesis regulator MsrC (MA4383) in CoM-S-S-CoB heterodisulfide sensing and indicate cells have a specific mechanism to sense intracellular ratio of CoM-S-S-CoB, coenzyme M, and coenzyme B thiols and further suggest transcripts encoding translation and methanogenesis functions are controlled by feed-forward regulation depending on substrate availability. IMPORTANCE Methanosarcina is an emerging model archaeon and synthetic biology platform for the production of renewable energy and sustainable chemicals to reduce dependence on petroleum. Research into metabolic networks and gene regulation in this organism and other methanogens will inform genome-scale metabolic modeling and microbial function prediction in uncultured or non-model anaerobes and archaea. This study suggests methanogens use unknown mechanisms to efficiently couple methanogenesis to gene regulation via CoM-S-S-CoB and ATP availability.

The human gut microbiome in health and disease: time for a new chapter?

The gut microbiome, composed of the colonic microbiota and their host environment, is important for many aspects of human health. A gut microbiome imbalance (gut dysbiosis) is associated with major causes of human morbidity and mortality. Despite the central part our gut microbiome plays in health and disease, mechanisms that maintain homeostasis and properties that demarcate dysbiosis remain largely undefined. Here we discuss that sorting taxa into meaningful ecological units reveals that the availability of respiratory electron acceptors, such as oxygen, in the host environment has a dominant influence on gut microbiome health. During homeostasis, host functions that limit the diffusion of oxygen into the colonic lumen shelter a microbial community dominated by primary fermenters from atmospheric oxygen. In turn, primary fermenters break down unabsorbed nutrients into fermentation products that support host nutrition. This symbiotic relationship is disrupted when host functions that limit the luminal availability of host-derived electron acceptors become weakened. The resulting changes in the host environment drive alterations in the microbiota composition, which feature an elevated abundance of facultatively anaerobic microbes. Thus, the part of the gut microbiome that becomes imbalanced during dysbiosis is the host environment, whereas changes in the microbiota composition are secondary to this underlying cause. This shift in our understanding of dysbiosis provides a novel starting point for therapeutic strategies to restore microbiome health. Such strategies can either target the microbes through metabolism-based editing or strengthen the host functions that control their environment.

Experimental simulation of H2 coinjection via a high-pressure reactor with natural gas in a low-salinity deep aquifer used for current underground gas storage.

If dihydrogen (H2) becomes a major part of the energy mix, massive storage in underground gas storage (UGS), such as in deep aquifers, will be needed. The development of H2 requires a growing share of H2 in natural gas (and its current infrastructure), which is expected to reach approximately 2% in Europe. The impact of H2 in aquifers is uncertain, mainly because its behavior is site dependent. The main concern is the consequences of its consumption by autochthonous microorganisms, which, in addition to energy loss, could lead to reservoir souring and alter the petrological properties of the aquifer. In this work, the coinjection of 2% H2 in a natural gas blend in a low-salinity deep aquifer was simulated in a three-phase (aquifer rock, formation water, and natural gas/H2 mix) high-pressure reactor for 3 months with autochthonous microorganisms using a protocol described in a previous study. This protocol was improved by the addition of protocol coupling experimental measures and modeling to calculate the pH and redox potential of the reactor. Modeling was performed to better analyze the experimental data. As in previous experiments, sulfate reduction was the first reaction to occur, and sulfate was quickly consumed. Then, formate production, acetogenesis, and methanogenesis occurred. Overall, H2 consumption was mainly caused by methanogenesis. Contrary to previous experiments simulating H2 injection in aquifers of higher salinity using the same protocol, microbial H2 consumption remained limited, probably because of nutrient depletion. Although calcite dissolution and iron sulfide mineral precipitation likely occurred, no notable evolution of the rock phase was observed after the experiment. Overall, our results suggested that H2 can be stable in this aquifer after an initial loss. More generally, aquifers with low salinity and especially low electron acceptor availability should be favored for H2 costorage with natural gas.

Salmonella Typhimurium expansion in the inflamed murine gut is dependent on aspartate derived from ROS-mediated microbiota lysis

Inflammation boosts the availability of electron acceptors in the intestinal lumen, creating a favorable niche for pathogenic Enterobacteriaceae. However, the mechanisms linking intestinal inflammation-mediated changes in luminal metabolites and pathogen expansion remain unclear. Here, we show that mucosal inflammation induced by Salmonella enterica serovar Typhimurium (S. Tm) infection increases intestinal levels of the amino acid aspartate. S. Tm used aspartate-ammonia lyase (aspA)-dependent fumarate respiration for growth in the murine gut only during inflammation. AspA-dependent growth advantage was abolished in the gut of germ-free mice and restored in gnotobiotic mice colonized with members of the classes Bacteroidia and Clostridia. Reactive oxygen species (ROS) produced during the host response caused lysis of commensal microbes, resulting in the release of microbiota-derived aspartate that was used by S. Tm, in concert with nitrate-dependent anaerobic respiration, to outcompete commensal Enterobacteriaceae. Our findings demonstrate the role of microbiota-derived amino acids in driving respiration-dependent S. Tm expansion during colitis.

Trace gas oxidation sustains energy needs of a thermophilic archaeon at suboptimal temperatures

Diverse aerobic bacteria use atmospheric hydrogen (H2) and carbon monoxide (CO) as energy sources to support growth and survival. Such trace gas oxidation is recognised as a globally significant process that serves as the main sink in the biogeochemical H2 cycle and sustains microbial biodiversity in oligotrophic ecosystems. However, it is unclear whether archaea can also use atmospheric H2. Here we show that a thermoacidophilic archaeon, Acidianus brierleyi (Thermoproteota), constitutively consumes H2 and CO to sub-atmospheric levels. Oxidation occurs across a wide range of temperatures (10 to 70 °C) and enhances ATP production during starvation-induced persistence under temperate conditions. The genome of A. brierleyi encodes a canonical CO dehydrogenase and four distinct [NiFe]-hydrogenases, which are differentially produced in response to electron donor and acceptor availability. Another archaeon, Metallosphaera sedula, can also oxidize atmospheric H2. Our results suggest that trace gas oxidation is a common trait of Sulfolobales archaea and may play a role in their survival and niche expansion, including during dispersal through temperate environments.

Biostimulation with oxygen and electron donors supports micropollutant biodegradation in an experimentally simulated nitrate-reducing aquifer

The availability of suitable electron donors and acceptors limits micropollutant natural attenuation in oligotrophic groundwater. This study investigated how electron donors with different biodegradability (humics, dextran, acetate, and ammonium), and different oxygen concentrations affect the biodegradation of 15 micropollutants (initial concentration of each micropollutant = 50 μg/L) in simulated nitrate reducing aquifers. Tests mimicking nitrate reducing field conditions showed no micropollutant biodegradation, even with electron donor amendment. However, 2,4-dichlorophenoxyacetic acid and mecoprop were biodegraded under (micro)aerobic conditions with and without electron donor addition. The highest 2,4-dichlorophenoxyacetic acid and mecoprop biodegradation rates and removal efficiencies were obtained under fully aerobic conditions with amendment of an easily biodegradable electron donor. Under microaerobic conditions, however, amendment with easily biodegradable dissolved organic carbon (DOC) inhibited micropollutant biodegradation due to competition between micropollutants and DOC for the limited oxygen available. Microbial community composition was dictated by electron acceptor availability and electron donor amendment, not by micropollutant biodegradation. Low microbial community richness and diversity led to the absence of biodegradation of the other 13 micropollutants (such as bentazon, chloridazon, and carbamazepine). Finally, adaptation and potential growth of biofilms interactively determined the location of the micropollutant removal zone relative to the point of amendment. This study provides new insight on how to stimulate in situ micropollutant biodegradation to remediate oligotrophic groundwaters as well as possible limitations of this process.

Uncovering the role of oxygen on organic carbon cycling: insights from a continuous culture study with a facultative anaerobic bacterioplankton species (Shewanella baltica)

Deoxygenation is tied to organic carbon (Corg) supply and utilization in marine systems. Under oxygen-depletion, bacteria maintain Corg respiration using alternative electron acceptors such as nitrate. Since anaerobic respiration’s energy yield is lower, Corg remineralization may be reduced and its residence time increased. We investigated the influence of oxygen and alternative electron acceptors’ availability on Corg cycling by heterotrophic bacteria during a continuous culture experiment with Shewanella baltica, a facultative anaerobic γ-Proteobacteria in the Baltic Sea. We tested six different oxygen levels, from suboxic (<5 µmol L-1) to fully oxic conditions, using a brackish (salinity=14 g L-1) media supplied with high (HighN) or low (LowN) inorganic nitrogen concentrations relative to glucose as labile Corg source. Our results show that suboxia limited DOC (glucose) uptake and cell growth only under LowN, while higher availability of alternative electron acceptors seemingly compensated oxygen limitation under HighN. N-loss was observed under suboxia in both nitrogen treatments. Under HighN, N-loss was highest and a C:N loss ratio of ~2.0 indicated that Corg was remineralized via denitrification. Under LowN, the C:N loss ratio under suboxia was higher (~5.5), suggesting the dominance of other anaerobic respiration pathways, such as dissimilatory nitrate reduction to ammonium (DNRA). Bacterial growth efficiency was independent of oxygen concentration but higher under LowN (34 ± 3.0%) than HighN (26 ± 1.6%). Oxygen concentration also affected dissolved organic matter (DOM) cycling. Under oxic conditions, the release of dissolved combined carbohydrates was enhanced, and the amino acid-based degradation index (DI) pointed to more diagenetically altered DOM. Our results suggest bacterial Corg uptake in low-oxygen systems dominated by S. baltica can be limited by oxygen but compensated by high nitrate availability. Hence, suboxia diminishes Corg remineralisation only when alternative electron acceptors are lacking. Under high nitrate:Corg supply, denitrification leads to a higher N:C loss ratio, potentially counteracting eutrophication in the long run. Low nitrate:Corg supply may favour other anaerobic respiration pathways like DNRA, which sustains labile nitrogen in the system, potentially intensifying the cycle of eutrophication. Going forward, it will be crucial to establish the validity of our findings for S. baltica in natural systems with diverse organic substrates and microbial consortia.

Unravelling substrate availability and redox interactions on methane production in peat soils of China

AbstractThe availability of electron acceptors (EAs) in peatlands determines the potential of methane (CH4) formation under waterlogged conditions. Previous studies suggested that EAs can suppress CH4 production based on Gibbs free energy under the Redox Ladder Theory. However, growing evidence challenges this theory, raising the question of how the coupling of soil substrates with EAs influences CH4 emissions. To answer this key question, peat soils were collected across different climatic zones with different degrees of soil degradation. Anoxic incubation experiments were set up, and continuous addition of SO42−, Fe3+ and humic acid (HA) at different concentrations was followed by characterization of dissolved organic matter using fluorescence spectroscopy. Results suggest that low concentrations of SO42− (1000 μmol L−1), Fe3+ (100 μmol L−1) and HA (30 mgC L−1) promoted CH4 production in most of the peat soils. With the addition of SO42− and HA, increased CH4 emissions were attributed to the facilitation of dissolved organic carbon and increased quinone‐like component C1, which increased the substrate availability for methanogenesis. Furthermore, strengthened microbial activity as indicated by fluorescence component C2 led to higher CH4 production under Fe3+ treatments. On the other hand, at high concentrations of SO42− (5000 μmol L−1), Fe3+ (500 μmol L−1) and HA (50 mgC L−1), CH4 emissions rapidly decreased by 70.65 ± 1.57% to 96.25 ± 0.45% compared to control group without EAs addition, accompanied by increased δ13C‐CH4 signatures indicating the outweighed CH4 production under anaerobic oxidation of methane (AOM) when coupling with reduced EAs. The effect of EAs on CH4 emissions in peat soils could also be related to lability and characteristics of natural organic matter. Our results suggest that the CH4 production in waterlogged peatlands could be facilitated by regulating organic substrates at low EAs concentrations, but excessive EAs will reduce net CH4 emissions through AOM. The valuable discovery of CH4 production and oxidation processes provides insights for mitigating methane emissions from peatlands and regulating global climate change.

Gut dysbiosis: Ecological causes and causative effects on human disease.

The gut microbiota plays a role in many human diseases, but high-throughput sequence analysis does not provide a straightforward path for defining healthy microbial communities. Therefore, understanding mechanisms that drive compositional changes during disease (gut dysbiosis) continues to be a central goal in microbiome research. Insights from the microbial pathogenesis field show that an ecological cause for gut dysbiosis is an increased availability of host-derived respiratory electron acceptors, which are dominant drivers of microbial community composition. Similar changes in the host environment also drive gut dysbiosis in several chronic human illnesses, and a better understanding of the underlying mechanisms informs approaches to causatively link compositional changes in the gut microbiota to an exacerbation of symptoms. The emerging picture suggests that homeostasis is maintained by host functions that control the availability of resources governing microbial growth. Defining dysbiosis as a weakening of these host functions directs attention to the underlying cause and identifies potential targets for therapeutic intervention.

Microalgal cycling in the cathode of microbial fuel cells (MFCs) induced oxygen reduction reaction (ORR) and electricity: A biocatalytic process for clean energy

Development in electricity generation technologies is necessary to ensure a safe and sustainable future. Catalytic activity of oxygen reduction reaction (ORR) is still the key challenge in microbial fuel cells (MFCs) which has not improved significantly even upon the application of catalysts. In this study, microalgae as biocatalysts (i.e., availability of electron acceptors and maintain ORR) were applied for spontaneous bioelectricity generation. Microalgal cycling was performed at various concentrations (5, 10, 15, and 20 % vv−1) in the cathode whereas, 2 % fat, oil, and grease (FOG) were added in the anode. Electrochemical and next-generation sequencing (NGS) analyses along with biological parameters were studied to fully understand the anodic and cathodic behavior towards electrogenesis. Continuous microalgal cycling resulted in the highest power density (21.0 mW m−2) and current density (245 mA m−2) in the reactor loaded with 2 % FOG + 15 % vv−1 microalgae. Electrochemical analysis showed the potential of 2 % FOG + 15 % vv−1 microalgae via exhibiting Ohmic resistance of 34. 9 Ω and charge transfer resistance of 100 Ω with improved ORR activity. NGS revealed that Clostridium (7–16.5 %), Bacteroidetes (4.54–12.87 %), and Geobacter (6.5–22.7 %) were the dominant species involved in the electron transport mechanism. CoA ligase, acetyl-CoA C-acetyltransferase, and acetate kinase were the major enzymes involved in β-oxidation and electrogenesis. This study demonstrated the baseline for the use of microalgae as biocatalyst in cathode of MFCs to improve the catalytic efficiency of ORR.

Comparative genomics sheds light on transcription factor-mediated regulation in the extreme acidophilic Acidithiobacillia representatives

Extreme acidophiles thrive in acidic environments, confront a multitude of challenges, and demonstrate remarkable adaptability in their metabolism to cope with the ever-changing environmental fluctuations, which encompass variations in temperature, pH levels, and the availability of electron acceptors and donors. The survival and proliferation of members within the Acidithiobacillia class rely on the deployment of transcriptional regulatory systems linked to essential physiological traits. The study of these transcriptional regulatory systems provides valuable insights into critical processes, such as energy metabolism and nutrient assimilation, and how they integrate into major genetic-metabolic circuits. In this study, we examined the transcriptional regulatory repertoires and potential interactions of forty-three Acidithiobacillia complete and draft genomes, encompassing nine species. To investigate the function and diversity of Transcription Factors (TFs) and their DNA Binding Sites (DBSs), we conducted a genome-wide comparative analysis, which allowed us to identify these regulatory elements in representatives of Acidithiobacillia. We classified TFs into gene families and compared their occurrence among all representatives, revealing conservation patterns across the class. The results identified conserved regulators for several pathways, including iron and sulfur oxidation, the main pathways for energy acquisition, providing new evidence for viable regulatory interactions and branch-specific conservation in Acidithiobacillia. The identification of TFs and DBSs not only corroborates existing experimental information for selected species, but also introduces novel candidates for experimental validation. Moreover, these promising candidates have the potential for further extension to new representatives within the class.

Soil greenhouse gas emissions from drained and rewetted agricultural bare peat mesocosms are linked to geochemistry

In view of climate considerations regarding the management of peatlands, there is a need to assess whether rewetting can mitigate greenhouse gas (GHG) emissions, and notably how site-specific soil-geochemistry will influence differences in emission magnitudes. However, there are inconsistent results regarding the correlation of soil properties with heterotrophic respiration (Rh) of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) from bare peat. In this study, we determined 1) soil-, and site-specific geochemical components as drivers for emissions from Rh on five Danish fens and bogs, and 2) emission magnitudes under drained and rewetted conditions. For this, a mesocosm experiment was performed under equal exposure to climatic conditions and water table depths controlled to either -40 cm, or -5 cm. For the drained soils, we found that annual cumulative emissions, accounting for all three gases, were dominated by CO2, contributing with, on average, 99 % to a varying global warming potential (GWP) of 12.2–16.9 t CO2eq ha−1 yr−1. Rewetting lowered annual cumulative emissions from Rh by 3.2–5.1 t CO2eq ha−1 yr−1 for fens and bogs, respectively, despite a high variability of site-specific CH4 emissions, contributing with 0.3–3.4 t CO2 ha−1 yr−1 to the GWP. Overall, analyses using generalized additive models (GAM) showed that emission magnitudes were well explained by geochemical variables. Under drained conditions, significant soil-specific predictor variables for CO2 flux magnitudes were pH, phosphorus (P), and the soil substrate's relative water holding capacity (WHC). When rewetted, CO2 and CH4 emissions from Rh were affected by pH, WHC, as well as contents of P, total carbon and nitrogen. In conclusion, our results found the highest GHG reduction on fen peatlands, further highlighting that peat nutrient status and acidity, and the potential availability of alternative electron acceptors, might be used as proxies for prioritising peatland areas for GHG mitigation efforts by rewetting.

Simultaneous dissolved methane and nitrogen removal from low-strength wastewater using anaerobic granule-based sequencing batch reactor

Anaerobic treatment of mainstream wastewater has been proposed as a promising solution to enhance bioenergy recovery for wastewater treatment plants (WWTPs). However, the limited organics for downstream nitrogen removal and emissions of dissolved methane into the atmosphere are two major barriers to the broad application of anaerobic wastewater treatment. This study aims to develop a novel technology to overcome these two challenges by achieving simultaneous removal of dissolved methane and nitrogen, and unravel the microbial competitions underpinning the process from the microbial and kinetic perspectives. To this end, a laboratory granule-based sequencing batch reactor (GSBR) coupling anammox and nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) microorganisms was developed to treat wastewater mimicking effluent from mainstream anaerobic treatment. The GSBR achieved high-level nitrogen and dissolved methane removal rates (> 250 mg N/L/d and > 65 mg CH4/L/d) and efficiencies (> 99% total nitrogen removal and > 90% total methane removal) during the long-term demonstration. The availability of different electron acceptors (nitrite or nitrate) imposed significant effects on the removal of ammonium and dissolved methane, as well as on the microbial communities, and the abundance and expression of functional genes. The analysis of apparent microbial kinetics showed that anammox bacteria had a higher nitrite affinity than n-DAMO bacteria, while n-DAMO bacteria had a higher methane affinity than n-DAMO archaea. These kinetics underpin the observation that nitrite is a preferred electron acceptor for removing ammonium and dissolved methane than nitrate. The findings not only extend the applications of novel n-DAMO microorganisms in nitrogen and dissolved methane removal, but also provide insights into microbial cooperation and competition in granular systems.

In vivo noninvasive mitochondrial redox assessment of the optic nerve head to predict disease.

Eye diseases are diagnosed by visualizing often irreversible structural changes occurring late in disease progression, such as retinal ganglion cell loss in glaucoma. The retina and optic nerve head have high mitochondrial energy need. Early mitochondrial/energetics dysfunction may predict vulnerability to permanent structural changes. In the in vivo murine eye, we used light-based resonance Raman spectroscopy (RRS) to assess noninvasively the redox states of mitochondria and hemoglobin which reflect availability of electron donors (fuel) and acceptors (oxygen). As proof of principle, we demonstrated that the mitochondrial redox state at the optic nerve head correlates with later retinal ganglion loss after acute intraocular pressure (IOP) elevation. This technology can potentially map the metabolic health of eye tissue in vivo complementary to optical coherence tomography, defining structural changes. Early detection (and normalization) of mitochondrial dysfunction before irreversible damage could lead to prevention of permanent neural loss.

Restricting electron flow at cytochrome b6f when downstream electron acceptors are severely limited.

Photosynthetic organisms frequently experience abiotic stress that restricts their growth and development. Under such circumstances, most absorbed solar energy cannot be used for CO2 fixation and can cause the photoproduction of reactive oxygen species (ROS) that can damage the photosynthetic reaction centers of PSI and PSII, resulting in a decline in primary productivity. This work describes a biological "switch" in the green alga Chlamydomonas reinhardtii that reversibly restricts photosynthetic electron transport (PET) at the cytochrome b6f (Cyt b6f) complex when the capacity for accepting electrons downstream of PSI is severely limited. We specifically show this restriction in STARCHLESS6 (sta6) mutant cells, which cannot synthesize starch when they are limited for nitrogen (growth inhibition) and subjected to a dark-to-light transition. This restriction represents a form of photosynthetic control that causes diminished electron flow to PSI and thereby prevents PSI photodamage but does not appear to rely on a ΔpH. Furthermore, when electron flow is restricted, the plastid alternative oxidase (PTOX) becomes active, functioning as an electron valve that dissipates some excitation energy absorbed by PSII and allows the formation of a proton motive force (PMF) that would drive some ATP production (potentially sustaining PSII repair and nonphotochemical quenching [NPQ]). The restriction at the Cyt b6f complex can be gradually relieved with continued illumination. This study provides insights into how PET responds to a marked reduction in availability of downstream electron acceptors and the protective mechanisms involved.

Upside down sulphate dynamics in a saline inland lake

The sulphur cycle has a key role on the fate of nutrients through its several interconnected reactions. Although sulphur cycling in aquatic ecosystems has been thoroughly studied since the early 70’s, its characterisation in saline endorheic lakes still deserves further exploration. Gallocanta Lake (NE Spain) is an ephemeral saline inland lake whose main sulphate source is found on the lake bed minerals and leads to dissolved sulphate concentrations higher than those of seawater. An integrative study including geochemical and isotopic characterization of surface water, porewater and sediment has been performed to address how sulphur cycling is constrained by the geological background. In freshwater and marine environments, sulphate concentration decreases with depth are commonly associated with bacterial sulphate reduction (BSR). However, in Gallocanta Lake sulphate concentrations in porewater increase from 60 mM at the water–sediment interface to 230 mM at 25 cm depth. This extreme increase could be caused by dissolution of the sulphate rich mineral epsomite (MgSO4·7H2O). Sulphur isotopic data was used to validate this hypothesis and demonstrate the occurrence of BSR near the water–sediment interface. This dynamic prevents methane production and release from the anoxic sediment, which is advantageous in the current context of global warming. These results underline that geological context should be considered in future biogeochemical studies of inland lakes with higher potential availability of electron acceptors in the lake bed compared to the water column.

Respiration-induced biofilm formation as a driver for bacterial niche colonization.

Depending on their physiology and metabolism, bacteria can carry out diverse redox processes for energy acquisition, which facilitates adaptation to environmental or host-associated niches. Of these processes, respiration, using oxygen or alternative terminal electron acceptors, is energetically the most favorable in heterotrophic bacteria. The biofilm lifestyle, a coordinated multicellular behavior, is ubiquitous in bacteria and is regulated by a variety of intrinsic and extrinsic cues. Respiration of distinct electron acceptors has been shown to induce biofilm formation or dispersal. The notion of biofilm formation regulation by electron acceptor availability and respiration has often been considered species-specific. However, recent evidence suggests that this phenomenon can be strain-specific, even in strains sharing the same functional respiratory pathways, thereby implying subtle regulatory mechanisms. On this basis, I argue that induction of biofilm formation by sensing and respiration of electron acceptors might direct subgroups of redox-specialized strains to occupy certain niches. A palette of respiration and electron-transfer-mediated microbial social interactions within biofilms may broaden ecological opportunities. The strain specificity of this phenomenon represents an important opportunity to identify key molecular mechanisms and their ecophysiological significance, which in turn may lay the ground for applications in areas ranging from biotechnology to the prevention of antimicrobial resistance.

Electron Accepting Capacities of a Wide Variety of Peat Materials From Around the Globe Similarly Explain CO2 and CH4 Formation

AbstractIn organic soils, the availability of terminal electron acceptors (TEAs) determines the ratio of CO2 to CH4 formation under anoxic conditions. While the importance of electron accepting capacities (EACs) of organic matter is increasingly acknowledged, redox properties of organic matter have only been investigated in a limited set of peat and reference materials. Therefore, we incubated 60 peat samples from 15 sites covering a variety of both bog and poor to intermediate fen samples and characterized their capacities to serve as TEA for anaerobic CO2 formation. We quantified CO2 and CH4 formation and changes in available EAC in anoxic incubations of 56 days. In our experiment, on average 36.5% of CO2 could be attributed to CH4 formation, assuming an CO2:CH4 ratio for methanogenesis of 1:1. Regarding the remaining CO2 formed, for which a corresponding TEA would be needed, we could on average explain 70.8% by corresponding consumption of EAC from both organic and inorganic TEAs, the latter contributing less than 0.1%. When the initial EAC was high, CO2 formation from the apparent consumption of EAC was high and outweighed CO2 formation from methanogenesis. Rapid depletion of available EAC, especially in reactive peat, resulted in a higher share of CO2 from CH4 formation. Our study demonstrates that EAC provides the most important redox buffer for competitive suppression of methanogenesis in peat soils, particularly under fluctuating water table levels, when EAC is repeatedly regenerated. Moreover, electron budgets including EAC of organic matter could largely explain anaerobic CO2 production.

Bacteroides fragilis Maintains Concurrent Capability for Anaerobic and Nanaerobic Respiration.

Bacteroides species can use fumarate and oxygen as terminal electron acceptors during cellular respiration. In the human gut, oxygen diffuses from intestinal epithelial cells supplying "nanaerobic" oxygen levels. Many components of the anaerobic respiratory pathway have been determined, but such analyses have not been performed for nanaerobic respiration. Here, we present genetic, biochemical, enzymatic, and mass spectrometry analyses to elucidate the nanaerobic respiratory pathway in Bacteroides fragilis. Under anaerobic conditions, the transfer of electrons from NADH to the quinone pool has been shown to be contributed by two enzymes, NQR and NDH2. We find that the activity contributed by each under nanaerobic conditions is 77 and 23%, respectively, similar to the activity levels under anaerobic conditions. Using mass spectrometry, we show that the quinone pool also does not differ under these two conditions and consists of a mixture of menaquinone-8 to menaquinone-11, with menaquinone-10 predominant under both conditions. Analysis of fumarate reductase showed that it is synthesized and active under anaerobic and nanaerobic conditions. Previous RNA sequencing data and new transcription reporter assays show that expression of the cytochrome bd oxidase gene does not change under these conditions. Under nanaerobic conditions, we find both increased CydA protein and increased cytochrome bd activity. Reduced-minus-oxidized spectra of membranes showed the presence of heme d when the bacteria were grown in the presence of protoporphyrin IX and iron under both anaerobic and nanaerobic conditions, suggesting that the active oxidase can be assembled with or without oxygen. IMPORTANCE By performing a comprehensive analysis of nanaerobic respiration in Bacteroides fragilis, we show that this organism maintains capabilities for anaerobic respiration on fumarate and nanaerobic respiration on oxygen simultaneously. The contribution of the two NADH:quinone oxidoreductases and the composition of the quinone pool are the same under both conditions. Fumarate reductase and cytochrome bd are both present, and which of these terminal enzymes is active in electron transfer depends on the availability of the final electron acceptor: fumarate or oxygen. The synthesis of cytochrome bd and fumarate reductase under both conditions serves as an adaptation to an environment with low oxygen concentrations so that the bacteria can maximize energy conservation during fluctuating environmental conditions or occupation of different spatial niches.

Isotopic Evidence for Anaerobic Oxidation of Methane in the Freshwater Sediments of Reservoirs: The Impact of Selected Environmental Factors

This paper presents the results of research conducted in 2018–2019 on the anaerobic oxidation of methane (AOM) in reservoir sediments. Located in SE Poland, Maziarnia, Nielisz and Rzeszów Reservoirs were selected for the purposes of the research. Rates of AOM were determined via 50-day incubation of sediment from the 0–5, 5–10 and 10–15 cm layers, to which a 13CH4 isotope tracer was added. The sediments had been collected from a single station at each reservoir in places that had earlier reported high levels of emission of CH4 to the atmosphere. Results demonstrate ongoing AOM processes in the kinds of freshwater ecosystem represented by reservoirs, further implying the existence of an important sink for CH4. More specifically, however, AOM rates were found to differ among both the reservoirs, and the layers of sediment, studied. Preliminary analysis of selected environmental factors capable of affecting AOM failed to suggest the availability of electron acceptors (NO3−, SO42−, Fe3+) as key controlling factors. Important factors also proved to be sediment pH, the quality of organic matter (especially the content of organic electron acceptors), the salinity of pore water, and—primarily—the presence of the microorganisms actually responsible for AOM. The results here are important, given the low level of knowledge of AOM process in reservoirs. They therefore help supply key information on the functioning of these ecosystems and the role in global climate change they play.