Anaerobic Respiration Processes Research Articles

Single-walled Carbon Nanotubes Wrapped with Charged Polysaccharides Enhance Extracellular Electron Transfer.

Microbial electrochemical systems (MESs) rely on the microbes' ability to transfer charges from their anaerobic respiratory processes to electrodes through extracellular electron transfer (EET). To increase the generally low output signal in devices, advanced bioelectrical interfaces tend to augment this problem by attaching conducting nanoparticles, such as positively charged multiwalled carbon nanotubes (CNTs), to the base carbon electrode to electrostatically attract the negatively charged bacterial cell membrane. On the other hand, some reports point to the importance of the magnitude of the surface charge of functionalized single-walled CNTs (SWCNTs) as well as the size of functional groups for interaction with the cell membrane, rather than their polarity. To shed light on these phenomena, in this study, we prepared and characterized well-solubilized aqueous dispersions of SWCNTs functionalized by either positively or negatively charged cellulose-derivative polymers, as well as with positively charged or neutral small molecular surfactants, and tested the electrochemical performance of Shewanella oneidensis MR-1 in MESs in the presence of these functionalized SWCNTs. By simple injection into the MESs, the positively charged polymeric SWCNTs attached to the base carbon felt (CF) electrode, and as fluorescence microscopy revealed, allowed bacteria to attach to these structures. As a result, EET currents continuously increased over several days of monitoring, without bacterial growth in the electrolyte. Negatively charged polymeric SWCNTs also resulted in continuously increasing EET currents and a large number of bacteria on CF, although SWCNTs did not attach to CF. In contrast, SWCNTs functionalized by small-sized surfactants led to a decrease in both currents and the amount of bacteria in the solution, presumably due to the detachment of surfactants from SWCNTs and their detrimental interaction with cells. We expect our results will help researchers in designing materials for smart bioelectrical interfaces for low-scale microbial energy harvesting, sensing, and energy conversion applications.

FeS-based cascade bioreactors driven by Shewanella oneidensis MR-1 for efficient chemodynamic therapy with augmented antitumor immunity

Chemodynamic therapy (CDT) is an emerging therapeutic approach, which can trigger immune responses by causing tumor cell death and releasing tumor-associated antigens. However, CDT alone is not effective in eliciting a robust immune response. Herein, FeS nanoparticles are in situ fabricated on the surface of Shewanella oneidensis MR-1 (FeS@MR-1) for enhanced CDT to boost antitumor immunity. Under acidic conditions, FeS@MR-1 degrades and simultaneously induces the release of Fe(II) ions and H2S gas. The released H2S can inhibit the activity of catalase, resulting in the accumulation of H2O2, which facilitates the production of highly toxic hydroxyl radical (·OH) through the Fenton reaction catalyzed by Fe(II). Thanks to the iron-reducing ability during the anaerobic respiration process, S. oneidensis MR-1 drives the Fenton reaction to proceed continuously by promoting Fe(III) to Fe(II) conversion to ensure the high efficiency of CDT. Furthermore, FeS@MR-1 can reprogram the immunosuppressive tumor microenvironment by consuming lactate and act as a natural immune adjuvant to enhance immune responses. More importantly, the combined treatment of FeS@MR-1 with immune checkpoint blockade triggers systemic antitumor responses, leading to excellent therapeutic performance against primary, distant, and orthotopic ovarian tumors. This work presents a cascade bioreactor based on S. oneidensis MR-1, which is promising for enhanced CDT and immunotherapy.

Understanding the Warburg Effect Yields New Insights into the Metabolic Control of Cancer

Human cells may use either aerobic or anaerobic cellular respiration processes to produce energy, depending on cellular conditions. When there is enough oxygen, cells respire aerobically, but in case of oxygen deficiency, anaerobic cellular respiration is used, which leads to lactic acidosis and an increased risk of cancer according to Warburg's hypothesis.
 This paper reviews key aspects related to the historical evolutionary origins of metabolic pathways in cancer cells and compares similarities between cancer cells and ancient unicellular organisms to address the origins of metabolic change in cancer cells and provide new insights into the metabolic control of cancer.
 Understanding the main causes of cancer and the biological origin of their behavioral abnormalities is essential for the metabolic control of cancer. Environmental stressors to cells may include lack of essential nutrients, poor oxygenation, excess acids, viruses, infections, and exposure to chemicals, toxins, and radiation. These cellular stressors can cause normal cells to mutate and become cancerous in an attempt to survive in the harsh conditions.
 According to the research findings, creating appropriate conditions at the cellular level in terms of pH, sufficient oxygenation and the availability of good sugars, essential vitamins, minerals, enzymes and coenzymes through a healthy diet can lead to a metabolic switch in cancer cells that controls mutations, which can help prevent and control cancer.

Sinking krill carcasses as hotspots of microbial carbon and nitrogen cycling in the Arctic

Krill represent a major link between primary producers and higher trophic levels in polar marine food webs. Potential links to lower trophic levels, such as heterotrophic microorganisms, are less well documented. Here, we studied the kinetics of microbial degradation of sinking carcasses of two dominant krill species Thysanoessa raschii and Meganyctiphanes norvegica from Southwest Greenland. Degradation experiments under oxic conditions showed that 6.0-9.1% of carbon and 6.4-7.1% of nitrogen were lost from the carcasses after one week. Aerobic microbial respiration and the release of dissolved organic carbon were the main pathways of carbon loss from the carcasses. Ammonium release generally contributed the most to carcass nitrogen loss. Oxygen micro profiling revealed anoxic conditions inside krill carcasses/specimens, allowing anaerobic nitrogen cycling through denitrification and dissimilatory nitrate reduction to ammonium (DNRA). Denitrification rates were up to 5.3 and 127.7 nmol N carcass-1 d-1 for T. raschii and M. norvegica, respectively, making krill carcasses hotspots of nitrogen loss in the oxygenated water column of the fjord. Carcass-associated DNRA rates were up to 4-fold higher than denitrification rates, but the combined activity of these two anaerobic respiration processes did not contribute significantly to carbon loss from the carcasses. Living krill specimens did not harbor any significant denitrification and DNRA activity despite having an anoxic gut as revealed by micro profiling. The investigated krill carcasses sink fast (1500-3000 m d-1) and our data show that only a small fraction of the associated carbon is lost during descent. Based on data on krill distribution, our findings are used to discuss the potential importance of sinking krill carcasses for sustaining benthic food webs in the Arctic.

Summer Dystrophic Criticalities of Non-Tidal Lagoons: The Case Study of a Mediterranean Lagoon

Eutrophication determines algal blooms and the subsequent accumulation of organic matter in sediments, which, in turn, results in the dominance of anaerobic respiratory processes that release toxic gases. Dystrophy is a final dissipative moment that reduces the organic load in the sediment. A case of dystrophy occurring in the Burano lagoon (Tuscany, Italy) in 2021 is reported. The study examined the weather, physico-chemistry of the water, submerged vegetation and sediment labile organic matter. In spring, dissolved oxygen (DO) and pH showed high values, in an abundance of submerged vegetation, while low values had ammonium, nitrate and orthophosphate. In mid-August, as warm and moist sea breezes prevailed, hydrogen sulfide releases were produced, preceded by a sharp rise in ammonium and orthophosphate concentrations, which remained high until November. During dystrophy, DO varied between anoxia and oversaturation, the latter in Cyanobacteria blooms. Dystrophic waters evolved gradually due to microphytes blooms, which changed from Cyanobacteria, in August, to the Dinophyta Alexandrium tamarense, in September, and Bacillariophyta, in November. Sediment labile organic matter varied between 3% and 7%. Ruppia spiralis meadows suffered the total detachment of fronds and stems during the dystrophy and proved to be areas of accumulation of organic detritus, themselves sources of dystrophic phenomena.

Development of a generalised equilibrium modified atmosphere model and its application to the Taleggio cheese

The food metabolic processes influence the gas composition of packaged products: by finely tuning the gas fluxes through the packaging, the aerobic and anaerobic respiration processes can be efficiently exploited to regulate the equilibrium gas concentrations. In this work, we present a generalised model able to predict the evolution of gases in micro-perforated equilibrium MAP, with a detailed evaluation of fluxes through the perforations by means of Computational Fluid Dynamics. It was found that the Sherwood number for the studied micro-perforations is 0.715 and it was confirmed via experiments on packaging with oxygen-depleted atmospheres. The kinetic model was experimentally validated on a smear short-ripened soft cheese (Taleggio) whose complex surface microbiota confer to the product a non-trivial respiration behaviour. Cheese slices were packed with three different micro-perforated solutions (one 120 μm diameter hole, two 90 μm diameter holes, and five 90 μm diameter holes) achieving three different equilibrium gas compositions with good model predictions. The model was applied to literature data with success, thus the model can be deemed general and applicable to many different systems. • A generalised model for equilibrium modified atmosphere packaging (EMAP) with micro-perforation is developed. • Computational fluid dynamics (CFD) is used to predict diffusive fluxes through micro-perforations. • Taleggio cheese EMAP experiments are presented. • The model correctly describes the gas behavior inside the packaging for taleggio cheese and other soft cheese.

Extracellular Electron Transfer Enables Cellular Control of Cu(I)-Catalyzed Alkyne-Azide Cycloaddition.

Extracellular electron transfer (EET) is an anaerobic respiration process that couples carbon oxidation to the reduction of metal species. In the presence of a suitable metal catalyst, EET allows for cellular metabolism to control a variety of synthetic transformations. Here, we report the use of EET from the electroactive bacterium Shewanella oneidensis for metabolic and genetic control over Cu(I)-catalyzed alkyne–azide cycloaddition (CuAAC). CuAAC conversion under anaerobic and aerobic conditions was dependent on live, actively respiring S. oneidensis cells. The reaction progress and kinetics were manipulated by tailoring the central carbon metabolism. Similarly, EET-CuAAC activity was dependent on specific EET pathways that could be regulated via inducible expression of EET-relevant proteins: MtrC, MtrA, and CymA. EET-driven CuAAC exhibited modularity and robustness in the ligand and substrate scope. Furthermore, the living nature of this system could be exploited to perform multiple reaction cycles without regeneration, something inaccessible to traditional chemical reductants. Finally, S. oneidensis enabled bioorthogonal CuAAC membrane labeling on live mammalian cells without affecting cell viability, suggesting that S. oneidensis can act as a dynamically tunable biocatalyst in complex environments. In summary, our results demonstrate how EET can expand the reaction scope available to living systems by enabling cellular control of CuAAC.

New insights into physiological effects of anoxia under darkness on the iconic seagrass Zostera marina based on a combined analysis of transcriptomics and metabolomics

Coastal hypoxia/anoxia is a major emerging threat to global coastal ecosystems. Macroalgae blooms of tens of kilometers are often observed in open waters. These blooms not only cause a lack of oxygen, but also benthic light limitation. We explored the physiological responses of Zostera marina L. to anoxia under darkness. After exposing Z. marina to anoxia under darkness for 72 h, we measured the elongation of leaves and the decrease in maximal quantum yield of photosystem II (Fv/Fm), and investigated the transcriptomic and metabolomic responses to anoxic stress based on RNA-sequencing and liquid chromatography-mass spectrometry (LC-MS) technology. The results showed that anoxic stress significantly reduced the leaf Fv/Fm, and had a significant negative effect on the photosynthesis and growth of Z. marina. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of up-regulated differentially expressed genes (DEGs) showed that glycolysis was the most significant enrichment pathway (p < 0.001), and most of the important products in glycolysis were significantly up-regulated. This indicated that the glycolysis process of anaerobic respiration is promoted under anoxia. The metabolite results also showed that glyceraldehyde 3-phosphate in the glycolysis pathway was significantly up-regulated. Moreover, three genes encoding sucrose synthase (gene-ZOSMA_310G00150, gene-ZOSMA_81G00980, and gene-ZOSMA_8G00730) and one gene encoding alpha-amylase (gene-ZOSMA_95G00270) were significantly up-regulated, providing the sugar basis for the subsequent increase in glycolysis. Furthermore, gene-encoding oxoglutarate dehydrogenase, the rate-limiting step of the tricarboxylic acid (TCA) cycle, was significantly down-regulated, indicating that this cycle was inhibited under anoxia. Metabolomic results showed that L-tryptophan, L-phenylalanine, and DL-leucine were significantly up-regulated. Only significantly decreased glutamate and non-significantly decreased glutamine, substances consumed in alanine and γ-aminobutyric acid (GABA) shunt mechanisms, were detected in the leaves, while GABA and alanine were not detected. The results of this study show that anoxic stress induces a programmed transcriptomic and metabolomic response in seagrass, most likely reflecting a complex strategy of acclimation and adaptation in seagrass to resist anoxic stress.

Differential manganese and iron recycling and transport in continental margin sediments of the Northern Gulf of Mexico

Pore water and solid phase geochemical profiles of sediment cores collected along two transects on the western and eastern sides of the Mississippi River mouth in the northern Gulf of Mexico were incorporated into a reactive transport model to determine the role of manganese and iron in the remineralization of carbon. Reactive transport model calculations indicate that sedimentation rates control the intensity of anaerobic carbon remineralization and select for the dominant anaerobic carbon remineralization pathways. Although sulfate reduction dominates the shelf station (65 m water depth), denitrification and microbial manganese reduction appear equally significant anaerobic respiration processes along the continental slope the closest to the Mississippi River, whereas microbial iron reduction does not represent an important process in these sediments. These findings suggest that the differential kinetics of manganese and iron redox transformations influence carbon remineralization processes on the continental slope. The fast kinetics of Fe2+ oxidation near the sediment-water interface and high sedimentation rates maintain Fe under the form of Fe(III) oxides and thermodynamically prevent sulfate reduction from dominating carbon remineralization processes on the slope, whereas the much slower Mn2+ oxygenation kinetics allows diffusion of Mn2+ across the sediment-water interface of the shelf station closest to the river mouth. Exposure to oxygenated bottom waters and entrainment within mobile muds typical of deltaic sediments during high riverine discharge likely promote the formation and downslope transport of Mn(III/IV) oxides within the nepheloid layer. This phenomenon appears to form a manganese ‘conveyor belt’ that selectively enriches Mn(III/IV) oxides relative to Fe(III) oxides in the deep sediment. In contrast, the intensity of anaerobic carbon remineralization processes along the eastern continental slope the farthest from the Mississippi River plume is much lower due to the low organic and lithogenic inputs, and denitrification dominates anaerobic respiration. Overall, these findings suggest that manganese cycling and its role in carbon remineralization processes in continental slope sediments exposed to large riverine inputs may be more important than previously considered.

Photosynthetic microorganisms (Algae) mediated bioelectricity generation in microbial fuel cell: Concise review

Abstract Since the last century, the search for clean and renewable energy is going on. This process will continue until there is a stable solution available as an alternative to fossil fuels. Several energy-producing products arise from photosynthetic-organisms like biofuel, bioelectricity, and there are various methods also available for the extraction of these products. Microbial fuel cells (MFCs) are energy transducers which convert organic matter directly into electricity, through the process of anaerobic respiration of microorganisms. Now a day’s researchers have taken as a challenge to use algae along with the bacterial communities to provide an organic carbon fuel source for the MFCs. This paper describes the potential application of algal biomass in the field of bioelectricity. Till now, many scientific experiments conducted all around the world to demonstrate how well efficient is this green photosynthetic organism capable of producing electricity along with its other applications like biofuel, demand in the food industry, and much more. The present manuscript aimed to provide an overview of the potential use of algae as a biocatalyst in MFCs. Further, this article also provides the current status of numerous countries which are excelled in the field of bioelectricity generation.

Chemical and mineral comparison of fossil insect cuticles from Crato Konservat Lagerstätte, Lower Cretaceous of Brazil

The Crato Formation palaeoentomofauna from the Lower Cretaceous (Aptian) of northeast Brazil is extremely well preserved. Crato insects are often complete with abdomen, thorax, head, legs, wings articulated and fragile cuticle details observed at the macro and micro scale. The Crato Formation stands out for the high diversity of fossil insects with at least 386 described species, so far. We investigate the preservation pathways through SEM–EDS and Raman spectroscopy, which give fundamental insights regarding the understanding of this complex theme. Our study compared cuticle soft-tissue preservation of Ensifera in different layers of the Crato limestone. The results of our analyses confirmed that the anaerobic bacterial respiration processes influenced the labile-tissues preservation. Ensifera fossils display preservational stages ranging from kerogenization to pyritization. Kerogenization represents the partial or complete chemical transformation of organic material into aliphatic and cyclic hydrocarbons in situ during mesodiagenesis, while pyritization occurs during the decaying of carcass in the early diagenesis. Here, we followed the previous hypothesis of fish tissue preservation that these processes are governed principally by variations in the positioning and residence time of the carcasses in different microbial zones within the sediment column. Besides early/mesodiagenetic modifications, oxidation processes during recent weathering led to some mineral transformations that played a key role in the preservation of Ensifera.

Benthic alkalinity and dissolved inorganic carbon fluxes in the Rhône River prodelta generated by decoupled aerobic and anaerobic processes

Abstract. Estuarine regions are generally considered a major source of atmospheric CO2, as a result of the high organic carbon (OC) mineralization rates in their water column and sediments. Despite this, the intensity of anaerobic respiration processes in the sediments tempered by the reoxidation of reduced metabolites near the sediment–water interface controls the flux of benthic alkalinity. This alkalinity may partially buffer metabolic CO2 generated by benthic OC respiration in sediments. Thus, sediments with high anaerobic respiration rates could contribute less to local acidification than previously thought. In this study, a benthic chamber was deployed in the Rhône River prodelta and the adjacent continental shelf (Gulf of Lion, northwestern Mediterranean) in late summer to assess the fluxes of total alkalinity (TA) and dissolved inorganic carbon (DIC) from the sediment. Concurrently, in situ O2 and pH micro-profiles, voltammetric profiles and pore water composition were measured in surface sediments to identify the main biogeochemical processes controlling the net production of alkalinity in these sediments. Benthic TA and DIC fluxes to the water column, ranging between 14 and 74 and 18 and 78 mmol m−2 d−1, respectively, were up to 8 times higher than dissolved oxygen uptake (DOU) rates (10.4±0.9 mmol m−2 d−1) close to the river mouth, but their intensity decreased offshore, as a result of the decline in OC inputs. In the zone close to the river mouth, pore water redox species indicated that TA and DIC were mainly produced by microbial sulfate and iron reduction. Despite the complete removal of sulfate from pore waters, dissolved sulfide concentrations were low and significant concentrations of FeS were found, indicating the precipitation and burial of iron sulfide minerals with an estimated burial flux of 12.5 mmol m−2 d−1 near the river mouth. By preventing reduced iron and sulfide reoxidation, the precipitation and burial of iron sulfide increases the alkalinity release from the sediments during the spring and summer months. Under these conditions, the sediment provides a net source of alkalinity to the bottom waters which mitigates the effect of the benthic DIC flux on the carbonate chemistry of coastal waters and weakens the partial pressure of CO2 increase in the bottom waters that would occur if only DIC was produced.

Selenite uptake by outer membrane porin ExtI and its involvement in the subcellular localization of rhodanese-like lipoprotein ExtH in Geobacter sulfurreducens

Selenite reduction is a key step in the biogeochemical cycle of selenium—an essential trace element for life. A variety of bacteria can transform selenite into elemental selenium nanoparticles on the cell surface via anaerobic respiration or detoxification processes. However, the proteins associated with the uptake of selenite for these processes are poorly understood. In this study, we investigated the role of an outer membrane porin-like protein, ExtI, in selenite permeation in Geobacter sulfurreducens. We demonstrated that selenite uptake and selenium nanoparticle formation were impaired in an extI-deficient strain. A putative rhodanese-like lipoprotein is encoded by an extH gene located immediately upstream of extI in the genome. We showed that ExtH is translocated into inner and outer membranes and that extI deficiency exclusively affects the localization of ExtH in the outer membrane. Coelution of ExtI and ExtH during gel filtration analysis of the outer membrane fraction of wild-type cells suggests a direct protein-protein interaction between them. Taken together, these results lead us to propose a physiological role for ExtI as a selenite channel associated with ExtH in the outer membrane.

Soil properties impacting denitrifier community size, structure, and activity in New Zealand dairy-grazed pasture

Abstract. Denitrification is an anaerobic respiration process that is the primary contributor of the nitrous oxide (N2O) produced from grassland soils. Our objective was to gain insight into the relationships between denitrifier community size, structure, and activity for a range of pasture soils. We collected 10 dairy pasture soils with contrasting soil textures, drainage classes, management strategies (effluent irrigation or non-irrigation), and geographic locations in New Zealand, and measured their physicochemical characteristics. We measured denitrifier abundance by quantitative polymerase chain reaction (qPCR) and assessed denitrifier diversity and community structure by terminal restriction fragment length polymorphism (T-RFLP) of the nitrite reductase (nirS, nirK) and N2O reductase (nosZ) genes. We quantified denitrifier enzyme activity (DEA) using an acetylene inhibition technique. We investigated whether varied soil conditions lead to different denitrifier communities in soils, and if so, whether they are associated with different denitrification activities and are likely to generate different N2O emissions. Differences in the physicochemical characteristics of the soils were driven mainly by soil mineralogy and the management practices of the farms. We found that nirS and nirK communities were strongly structured along gradients of soil water and phosphorus (P) contents. By contrast, the size and structure of the nosZ community was unrelated to any of the measured soil characteristics. In soils with high water content, the richnesses and abundances of nirS, nirK, and nosZ genes were all significantly positively correlated with DEA. Our data suggest that management strategies to limit N2O emissions through denitrification are likely to be most important for dairy farms on fertile or allophanic soils during wetter periods. Finally, our data suggest that new techniques that would selectively target nirS denitrifiers may be the most effective for limiting N2O emissions through denitrification across a wide range of soil types.

Potentially Active Iron, Sulfur, and Sulfate Reducing Bacteria in Skagerrak and Bothnian Bay Sediments

ABSTRACTIn many marine surface sediments, the reduction of manganese (Mn) and iron (Fe) oxides is obscured by sulfate reduction, which is regarded as the predominant anaerobic microbial respiration process. However, many dissimilatory sulfate and sulfur reducing microorganisms are known to utilize alternative electron acceptors such as metal oxides. In this study, we tested whether sulfate and sulfur reducing bacteria are linked to metal oxide reduction based on biogeochemical modeling of porewater concentration profiles of Mn2+ and Fe2+ in Bothnian Bay (BB) and Skagerrak (SK) sediments. Steady-state modeling of Fe2+ and Mn2+ porewater profiles revealed zones of net Fe (0–9 cm BB; ∼10 and 20 cm SK) and Mn (0–5 cm BB; 2–8 cm SK) species transformations. 16S rRNA pyrosequencing analysis of the in-situ community showed that Desulfobacteraceae, Desulfuromonadaceae and Desulfobulbaceae were present in the zone of Fe-reduction of both sediments. Rhodobacteraceae were also detected at high relative abundance in both sediments. BB sediments appeared to harbor a greater diversity of potential Fe-reducers compared to SK. Additionally, when the upper 10 cm of sediment from the SK was incubated with lepidocrocite and acetate, Desulfuromonas was the dominant bacteria. Real-time quantitative polymerase chain reaction (qPCR) results showed decreasing dsrA gene copy numbers with depth coincided with decreased Fe-reduction activity. Our results support the idea that sulfur and sulfate reducing bacteria contribute to Fe-reduction in the upper centimeters of both sediments.

Usage of ferrum (ІІІ) and manganese (IV) ions as electron acceptors by Desulfuromonas sp. bacteria

The toxicity of metal ions to microorganisms, in particular at high concentrations, is one of the main impediments to their usage in remediation technologies. The purpose of this work is to analyze the possibility of usage by bacteria of the Desulfuromonas genus, isolated by us from Yavorivske Lake, of ferrum (ІІІ) and manganese (IV) ions at concentrations in the medium of 1,74–10,41 mM as electron acceptors of anaerobic respiration to assesss resistance of sulphur reducing bacteria strains to heavy metal compounds. Cells of Desulfuromonas acetoxidans ІМV V-7384, Desulfuromonas sp. Yavor-5 and Desulfuromonas sp. Yavor-7 were cultivated for 10 days at 30 °C under anaerobic conditions in Kravtsov-Sorokin’s medium without sulphate ions, sulphur, with cysteine as the sulphur source (0.2 g/l) and sodium lactate or citrate as the electron donor (17.86 g/l), in which were added sterile 1 M solutions of C6H5O7Fe and C4H4O4 (control) and also weights of MnO2 to their terminal concentrations 1.74, 3.47, 5.21, 6.94, 10.41 mM. Biomass was determined by the turbidimetric method. In the culture liquid the presence of Fe3+ and Mn4+ were qualitatively determined, and the content of Fe2+ in reaction with о-phenanthroline was determined quantitatively. It was established that sulphur reducing bacteria used with different intensity ferrum (ІІІ) and manganese (IV) ions as electron acceptors during the process of anaerobic respiration at concentrations of 1.74–10.41 mM C6H5O7Fe and MnO2 in the medium, which demonstrated the important role of the investigated microorganisms in reductive detoxication of natural and technogenic media from oxidized forms of transitional heavy metals. An insignificant difference in biomass accumulation during usage of 5.21–10.41 mM ferrum (ІІІ) ions and fumarate is caused by toxicity of the metal ions to cells since the high redox potential of the Fe(III)/Fe(ІІ) pair with increase in concentrations of electron acceptors in the medium did not lead to increase in the biomass accumulation level. The greatest biomass of the bacteria accumulated on the 8–10th days in the medium with the lowest concentration of C6H5O7Fe – 1.74 mM (up to 2.77 g/l), and the lowest biomass – with highest concentration – 10.41 mM (up to 2.41 g/l). After 10 days of cultivation the bacteria of all strains had fully used the ferrum (ІІІ) ions present in the medium. A biomass yield almost twice as low was revealed after manganese (IV) oxide was used by bacteria compared with its use of ferrum (ІІІ) citrate and fumarate at all studied concentrations of electron acceptors in the medium. The highest biomass of bacteria accumulated in the medium with the lowest MnO2 content – 1.74 mM (up to 1.35 g/l), and the lowest biomass in the medium with the highest content – 10.41 mM (up to 1.15 g/l). After 10 days of cultivation bacteria of all strains had not fully restored the manganese (IV) ions present in the medium. The greatest biomass compared with other strains after growth in medium with different C6H5O7Fe and MnO2 contents was accumulated by the strain Desulfuromonas sp. Yavor-7. Since sulphur reducing bacteria strains proved to be resistant to Fe3+ and Mn4+ high concentrations (up to10.41 mM) they can be successfully used in technologies of environmenal remediation from sulphur and heavy metal compounds.

Validation of an Integrative Methodology to Assess and Monitor Reductive Dechlorination of Chlorinated Ethenes in Contaminated Aquifers

Bioremediation of tetra-and trichloroethene-contaminated aquifers is frequently hampered due to incomplete dechlorination to the more toxic dichloroethene (DCE) and vinyl chloride (VC), indicating insufficient knowledge about the biological mechanisms related to aquifer functioning. A methodology based on the joint analysis of geochemical and microbiological datasets was developed to assess the presence of the biochemical potential for complete reductive dechlorination to harmless ethene and to explain the reasons for which degradation often stalls at the more toxic intermediates. This methodology is composed of three successive steps, with i) the acquisition of geochemical data including chlorinated ethenes, ii) the detailed analysis of the bacterial community structures as well as the biochemical potential for complete dechlorination using microcosms and molecular detection of organohalide-respiring bacteria and key reductive dehalogenases, and iii) a statistical Multiple Factor Analysis combining the above mentioned abiotic and biotic variables in a functional modelling of the contaminated aquifer. The methodology was validated by analyzing two chlorinated ethenes-contaminated sites. Results from the first site showed that the full biochemical potential for ethene production was present in situ. However, redox potential was overall too high and locally manganese reduction out-competed chlorinated ethenes reduction, explaining the reasons for the local accumulation of DCE and VC to a lesser extent. The second contaminated aquifer was under bioremediation by successive cheese whey injections. Analysis demonstrated that cheese whey additions led to increasingly reduced redox conditions and that hampered reductive dechlorination was not due to competition with other anaerobic respiration processes. Complete reductive dechlorination to ethene was preferentially occurring under methanogenic conditions. DCE and VC accumulation was probably induced first by low pH resulting from whey fermentation and at a later stage by phosphate limitation. In conclusions, the proposed methodology successfully allowed the identification of biogeochemical processes limiting or supporting complete dechlorination in both aquifers. The integrative approach provided fundamental information about the functional heterogeneity of the contaminated aquifers in time and space, and can be used as a reliable tool to support corrective decision-making in the development of remediation strategies based on natural attenuation of chlorinated ethenes.

A physical explanation for the development of redox microzones in hyporheic flow

AbstractRecent observations reveal a paradox of anaerobic respiration occurring in seemingly oxic‐saturated sediments. Here we demonstrate a residence time‐based explanation for this paradox. Specifically, we show how microzones favorable to anaerobic respiration processes (e.g., denitrification, metal reduction, and methanogenesis) can develop in the embedded less mobile porosity of bulk‐oxic hyporheic zones. Anoxic microzones develop when transport time from the streambed to the pore center exceeds a characteristic uptake time of oxygen. A two‐dimensional pore‐network model was used to quantify how anoxic microzones develop across a range of hyporheic flow and oxygen uptake conditions. Two types of microzones develop: flow invariant and flow dependent. The former is stable across variable hydrologic conditions, whereas the formation and extent of the latter are sensitive to flow rate and orientation. Therefore, pore‐scale residence time heterogeneity, which can now be evaluated in situ, offers a simple explanation for anaerobic signals occurring in oxic pore waters.

Dynamic transition of chemolithotrophic sulfur-oxidizing bacteria in response to amendment with nitrate in deposited marine sediments.

Although environmental stimuli are known to affect the structure and function of microbial communities, their impact on the metabolic network of microorganisms has not been well investigated. Here, geochemical analyses, high-throughput sequencing of 16S rRNA genes and transcripts, and isolation of potentially relevant bacteria were carried out to elucidate the anaerobic respiration processes stimulated by nitrate (20 mM) amendment of marine sediments. Marine sediments deposited by the Great East Japan Earthquake in 2011 were incubated anaerobically in the dark at 25∘C for 5 days. Nitrate in slurry water decreased gradually for 2 days, then more rapidly until its complete depletion at day 5; production of N2O followed the same pattern. From day 2 to 5, the sulfate concentration significantly increased and the sulfur content in solid-phase sediments significantly decreased. These results indicated that denitrification and sulfur oxidation occurred simultaneously. Illumina sequencing revealed the proliferation of known sulfur oxidizers, i.e., Sulfurimonas sp. and Chromatiales bacteria, which accounted for approximately 43.5% and 14.8% of the total population at day 5, respectively. These oxidizers also expressed 16S rRNA to a considerable extent, whereas the other microorganisms, e.g., iron(III) reducers and methanogens, became metabolically active at the end of the incubation. Extinction dilution culture in a basal-salts medium supplemented with sulfur compounds and nitrate successfully isolated the predominant sulfur oxidizers: Sulfurimonas sp. strain HDS01 and Thioalkalispira sp. strain HDS22. Their 16S rRNA genes showed 95.2–96.7% sequence similarity to the closest cultured relatives and they grew chemolithotrophically on nitrate and sulfur. Novel sulfur-oxidizing bacteria were thus directly involved in carbon fixation under nitrate-reducing conditions, activating anaerobic respiration processes and the reorganization of microbial communities in the deposited marine sediments.

Key respiratory genes elucidate bacterial community respiration in a seasonally anoxic estuary.

Intense annual spring phytoplankton blooms and thermohaline stratification lead to anoxia in Chesapeake Bay bottom waters. Once oxygen becomes depleted in the system, microbial communities use energetically favourable alternative electron acceptors for respiration. The extent to which changes in respiration are reflected in community gene expression have only recently been investigated. Metatranscriptomes prepared from near-bottom water plankton over a 4-month time series in central Chesapeake Bay demonstrated changes consistent with terminal electron acceptor availability. The frequency of respiration-related genes in metatranscriptomes was examined by BLASTx against curated databases of genes intimately and exclusively involved in specific electron acceptor utilization pathways. The relative expression of genes involved in denitrification and dissimilatory nitrate reduction to ammonium were coincident with changes in nitrate, nitrite and ammonium concentrations. Dissimilatory iron and manganese reduction transcript ratios increase during anoxic conditions and corresponded with the highest soluble reactive phosphate and manganese concentrations. The sulfide concentration peaked in late July and early August and also matched dissimilatory sulfate reduction transcript ratios. We show that rather than abrupt transitions between terminal electron acceptors, there is substantial overlap in time and space of these various anaerobic respiratory processes in Chesapeake Bay.