Many bacterial processes are powered by the sodium motive force (smf) and in case of pathogens, the smf contributes to virulence. Vibrio cholerae, the causative agent of Cholera disease, possesses a ...Na+-translocating NADH:quinone oxidoreductase (NQR), a six-subunit membrane protein assembly. The 3D structure of NQR revealed the arrangement of the six subunits NqrABCDEF, the position of all redox cofactors (four flavins, two 2Fe-2S centers) and the binding sites for the substrates NADH (in NqrF) and ubiquinone (in NqrB). Upon oxidation of NADH, electrons are shuttled twice across the membrane, starting with cytoplasmic FADNqrF and electron transfer to the 2Fe2S clusterNqrF and from there to an intra-membranous 2Fe-2S clusterNqrDE, periplasmic FMNNqrC, FMNNqrB and from there to riboflavinNqrB. This riboflavin is located at the cytoplasmic entry site of the sodium channel in NqrB, and it donates electrons to ubiquinone-8 positioned at the cytoplasmic side of NqrB. Targeting the substrate binding sites of NQR is a promising strategy to identify new inhibitors against many bacterial pathogens. Detailed structural information on the binding mode of natural inhibitors and small molecules in the active sites of NQR is now available, paving the way for the development of new antibiotics. The NQR shows different conformations as revealed in recent cryo-EM and crystallographic studies combined with spectroscopic analyses. These conformations represent distinct steps in the catalytic cycle. Considering the structural and functional data available, we propose a mechanism of Na+-NQR based on conformational coupling of electron transfer and Na+ translocation reaction steps.
•In pathogenic Vibrio cholerae, the NADH:quinone oxidoreductase (Na+-NQR) generates a sodium gradient.•The Na+-NQR is a six-subunit membrane protein assembly with four flavins and two 2Fe2S clusters.•A Na+ binding site was identified in the membrane-bound NqrB subunit of Na+-NQR.•Distinct 3D structures of Na+-NQR indicate that electron transfer and Na+ transport are conformationally coupled.
Intestinal inflammation is frequently associated with an alteration of the gut microbiota, termed dysbiosis, which is characterized by a reduced abundance of obligate anaerobic bacteria and an ...expansion of facultative Proteobacteria such as commensal E. coli. The mechanisms enabling the outgrowth of Proteobacteria during inflammation are incompletely understood. Metagenomic sequencing revealed bacterial formate oxidation and aerobic respiration to be overrepresented metabolic pathways in a chemically induced murine model of colitis. Dysbiosis was accompanied by increased formate levels in the gut lumen. Formate was of microbial origin since no formate was detected in germ-free mice. Complementary studies using commensal E. coli strains as model organisms indicated that formate dehydrogenase and terminal oxidase genes provided a fitness advantage in murine models of colitis. In vivo, formate served as electron donor in conjunction with oxygen as the terminal electron acceptor. This work identifies bacterial formate oxidation and oxygen respiration as metabolic signatures for inflammation-associated dysbiosis.
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•Genes encoding respiratory pathways are overrepresented in the dysbiotic microbiome•Utilization of microbiota-derived formate enhances E. coli fitness in the inflamed gut•Formate concentrations in the gut are elevated during inflammation-associated dysbiosis•During gut inflammation, formate utilization by E. coli requires oxygen respiration
Intestinal inflammation is associated with changes in the microbiota composition (dysbiosis), such as the expansion of the commensal Enterobacteriaceae population. Hughes and Winter et al. show that utilization of microbiota-derived formate as electron donor and oxygen as terminal electron acceptor contribute to the bloom of Enterobacteriaceae in the inflamed gut.
By leveraging the ability of Shewanella oneidensis MR‐1 (S. oneidensis MR‐1) to anaerobically catabolize lactate through the transfer of electrons to metal minerals for respiration, a lactate‐fueled ...biohybrid (Bac@MnO2) was constructed by modifying manganese dioxide (MnO2) nanoflowers on the S. oneidensis MR‐1 surface. The biohybrid Bac@MnO2 uses decorated MnO2 nanoflowers as electron receptor and the tumor metabolite lactate as electron donor to make a complete bacterial respiration pathway at the tumor sites, which results in the continuous catabolism of intercellular lactate. Additionally, decorated MnO2 nanoflowers can also catalyze the conversion of endogenous hydrogen peroxide (H2O2) into generate oxygen (O2), which could prevent lactate production by downregulating hypoxia‐inducible factor‐1α (HIF‐1α) expression. As lactate plays a critical role in tumor development, the biohybrid Bac@MnO2 could significantly inhibit tumor progression by coupling bacteria respiration with tumor metabolism.
MnO2 nanoflowers were modified on the cell surface of electrochemically active bacteria, S. oneidensis MR‐1. The biohybrids, which couple bacterial respiration with tumor metabolism, can catabolize intercellular lactate and prevent intracellular lactate production in the tumor, thereby inducing significant tumor inhibition.
•Biochar addition stimulated soil microbial biomass (MB) and respiration (MR).•MB and MR decreased with increasing pyrolysis temperature in calcareous soils.•Positive effects of corn biochar on MB ...were much greater in sandy than clayey soils.•Beneficial effects of biochar on MR were much higher in clayey than sandy soils.•Biochar impact on soil microbial performance was larger at 1% than 0.5% rates.
Biochar can be used as an organic amendment to improve soil physical and chemical attributes, with a potentially significant influence on soil microbial performance. However, this effect of biochar is poorly understood for arid soils with low organic matter content. The main objective of this study was to quantify the response of microbial attributes to corn biochar in two calcareous soils with different texture. Three slow pyrolysis biochars were prepared at 200, 400 and 600°C from corn feedstocks. The biochars were added to sandy and clayey soils at 0.5 and 1% (w/w) and the mixtures were incubated for 90days under standard laboratory conditions (25±1°C and 70% of soil field capacity). Soils amended with raw (uncharred) feedstock and unamended (without biochar and raw residue) as the control were also considered in the experiment. The soil properties measured included microbial respiration during 60days, microbial biomass carbon (C), substrate-induced respiration (SIR), fungal (FR) and (BR) bacterial respiration at the end of the incubation. Compared with the unamended control, the addition of corn raw feedstock or its biochar significantly increased cumulative microbial respiration (62–462%), MBC (66–169%), SIR (50–216%), BR (129–308%) and FR (42–200%), but tended to decrease FR/BR ratio (5–90%), depending largely upon its production temperature and application rate as well as soil texture. The positive effects of biochar addition on increasing microbial properties were more pronounced at 1% than 0.5% application rates for all the attributes and in sandy than clayey soils for MBC, SIR and FR attributes. Overall, the measured microbial attributes were all greater in uncharred than charred feedstock treatments and tended to decline with increasing pyrolysis temperature. The relative abundance of soil bacteria increased with biochar addition and pyrolysis temperature, while that of soil fungi decreased. Biochar addition increased microbial performance potentially due to an increase in soil C content while increasing pyrolysis temperature altered biochar chemistry and properties which may have contributed to the decreased microbial performance. It is concluded that although biochar application may improve microbial processes and attributes in calcareous soils with low organic matter content, its effects on microbiological properties are mainly meditated by soil texture, pyrolysis temperature for biochar production and application rate. The greatest response by the microbial indicators can occur when corn biochars produced at low temperatures were added to less fertile sandy soils at 1% addition rate. The study provided clear evidence that application of low temperature corn biochars at 45–50tha−1 to calcareous soils may have a great potential for improvements in the microbial indicators of soil quality.
The nutrient supply to the freshwater system may be changed by rainfall, which also encourages the cyclic succession of microorganisms. However, in a highly dynamic land-water reservoir, the ...microbial metabolic changes brought on by the changes of water nutrients following rainfall are not clearly documented. The study selected the Three Gorges Reservoir (TGR) backwater region during algal bloom seasons as the study area and time, and used the Biolog-EcoPlates technique to examine the heterotrophic metabolism conditions of the water before and after rain. The field monitoring assessed how biotic and abiotic variables affected CO2 flux at the water-air interface. The tests conducted in the laboratory investigated the water-integrated metabolic process was affected by post-rainfall environmental changes. The results showed that the average flux of CO2 at the water-air interface before rainfall was −489.17 ± 506.66 mg·(m2·d)−1, while the average CO2 flux reached 393.35 ± 793.49 mg·(m2·d)−1 after rainfall. This is mostly explained by the heterotrophic metabolic variability of plankton in response to changes in the aqueous environment brought on by precipitation. These discoveries help us better understand how biological metabolisms after rain affect the CO2 flux at the water-air interface and reservoir greenhouse gas (GHG) emission equivalents can be evaluated more accurately.
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•Rainfall changes the structure and level of nutrients in the reservoir.•Certain rainfall can change the abundance structure of algae and bacteria.•The metabolic capabilities of plankton were regulated by nutrients and light levels.•Carbon sinks became carbon sources one day after rainfall during algal blooms.
In oxidative phosphorylation, respiratory complex I serves as an entry point in the electron transport chain for electrons generated in catabolic processes in the form of NADH. An ancestral version ...of the complex, lacking the NADH-oxidising module, is encoded in a significant number of bacterial genomes. Amongst them is Desulfitobacterium hafniense , a strict anaerobe capable of conserving energy via organohalide respiration. This study investigates the role of the complex I-like enzyme in D. hafniense energy metabolism using rotenone as a specific complex I inhibitor under different growth conditions. The investigation revealed that the complex I-like enzyme was essential for growth with lactate and pyruvate but not in conditions involving H 2 as an electron donor. In addition, a previously published proteomic dataset of strain DCB-2 was analysed to reveal the predominance of the complex under different growth conditions and to identify potential redox partners. This approach revealed seven candidates with expression patterns similar to Nuo homologues, suggesting the use of diverse electron sources. Based on these results, we propose a model where the complex I-like enzyme serves as an electron entry point into the respiratory chain for substrates delivering electrons within the cytoplasm, such as lactate or pyruvate, with ferredoxins shuttling electrons to the complex.
IntroductionThe maintenance of planted forests in arid and semi-arid lands is important. Soil formation in forest ecosystems is different with different tree species. Tree species have a direct and ...indirect effect on soil organisms. Forest ecosystems change their species composition and abundance of microorganisms, and consequently their biogeochemical cycles. The accumulation of vegetation biomass and the improvement of soil fertility can play a significant role in soil restoration.Materials and MethodsIn order to investigate the biological characteristics of the soil from 5 treatments, including agricultural (dry farming and relatively poor lands that are usually cultivated barley and wheat and have low productivity), pasture (pastures with minimal vegetation and high slopes that are affected by overgrazing have been changed to barren lands), forest with Acacia type (under and outside the crown), forest with the Cupressus arizonica type (under and outside the crown) and forest with the Pinus brutia type (under and outside the crown) randomly. Sampling was done in 3 repetitions from the 0 to 5 cm layer. The statistical sampling design of this research was completely random, in which, according to the type of afforested species, two types of coniferous forest stands (including Cupressus arizonica and Pinus brutia) and one broadleaf stand (Acacia species) were selected. Also, the area under the crown trees and outside the crown trees was also investigated. Soil samples were sampled with sterile equipment and crushed through a 4-mm sieve. Fresh and moist soil was kept at 4 °C temperature for soil biological tests. Microbial biomass carbon, soil basal respiration (197 days), substrate-induced respiration, and metabolic quotient were measured. Streptomycin sulfate was used to measure fungal respiration and cycloheximide was used to measure bacterial respiration. The activities of urease, acid, and alkaline phosphatase enzymes were determined. After measuring the biological properties of the soil, the normality of the data was checked by the Anderson–Darling test, and the homogeneity of the variance of the treatments was checked by using Levene's test. Analysis of data variance was done using One-Way ANOVA and average data comparison was done using Duncan's test at 5 and 1% probability levels (SAS 9.4 and SPSS 26).Results and DiscussionThe results of soil biological characteristics analysis showed that the highest values of soil respiration and amount of consumed organic matter, substrate-induced respiration, microbial biomass carbon, enzyme activities, and fungal respiration were measured in conifers. Although the amount of these features was also significant in broadleaf trees, they had significant differences. In this study, the high soil respiration rate in coniferous covers compared to broadleaf can be due to the high organic carbon content of the soil in this cover. According to the results of substrate-induced respiration in different coatings, likely the activity of microorganisms involved in the decomposition of organic matter in the studied habitats had a significant difference; Therefore, different coatings can affect the population of soil microorganisms as the main source of decomposition and emission of carbon dioxide by changing the quantity and quality of organic matter and other factors. Also, the highest values of metabolic quotient and bacterial respiration were observed in agricultural and pasture covers. A higher metabolic quotient in these covers indicates a decrease in the efficiency of the use of leaf litter by the soil microbial community. In general, the metabolic quotient in the bacterial community is higher than the fungal community; Therefore, it seems that the predominance of the bacterial population in agricultural and pasture cover has caused this index to increase, although plowing and cultivation, and disturbance of these covers have caused stress to this bacterial community and as a result increased the metabolic quotient deficit in these covers.ConclusionThe results of this research showed that the type of planted tree species causes significant changes in the biological characteristics of the soil. The current research shows that the forest, whether coniferous or broadleaf, had the highest values of enzyme activities, basal respiration, substrate-induced respiration, microbial biomass carbon, and the lowest values of metabolic quotient compared to agricultural and pasture covers. Afforestation increases biological activity and possibly the number and diversity of microorganisms, and improves soil characteristics in the long term. In agriculture and pasture land, due to the destruction of soil and aggregates by agricultural activities such as plowing or excessive livestock grazing, the amount of organic carbon and the activity of microorganisms decreases, and with the decrease of other soil characteristics, the quality of the soil decreases over time. From this research, it can be concluded that the planting of forest species in the soils of degraded areas in the long term can increase soil organic carbon due to high-quality leaf litter, and as a result, increase permeability and soil moisture. Increasing soil organic carbon increases the activity of microorganisms, and in the long term, it will improve various soil characteristics. Planting forest plants in the natural areas of the country, which were destroyed due to the change of use to agriculture and indiscriminate cultivation and finally abandoned, can improve the characteristics of the soil and, as a result, establish the native vegetation of the region, and increase the permeability of water in the soil, the risk of soil erosion, floods, etc. reduce.
The imbalance of gut microbiota, such as dysbiotic expansion of Enterobacteriaceae, is strongly associated with the progress of inflammatory bowel disease (IBD) via exacerbating gut inflammation and ...disturbing intestinal mucosal barrier. Recently, a microbiota-based strategy is an attractive paradigm for IBD therapy. Here, we explored the therapeutic potential of tungsten oxide nanoparticles (WO3NPs) against DSS-induced acute colitis mice. WO3NPs (47.9 nm in diameter) significantly reduced intestinal inflammation, attenuated bacterial translocation, restored the colonic epithelium barriers, and remodeled gut microbiota homeostasis in inflamed colon, compared with the free tungsten (sodium tungstate). The element quantification and mapping results showed WO3NPs could increase the adherence of tungsten with Enterobacteriaceae in colonic mucus layer, which inhibited Enterobacteriaceae growth by microbial metabolic reprogramming and ameliorate colitis. This nano-enabled approach for tungsten reduced its deposition in the main organ except for the colon thereby improve the therapeutic efficacy with good biosafety. Together, our results provide insights into the potential nanotherapeutics of WO3NPs against the invasion processes of microbiota in the treatment of IBD.
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•Reprogramming of microbial metabolism by tungsten oxide nanoparticles contributes to ameliorate IBD.•Tungsten oxide nanoparticles target intestinal microbial respiration and blunt the dysbiotic bloom of Enterobacteriaceae in acute colitis mice.•Tungsten oxide nanoparticles act as a microbe-based therapy against IBD by remodeling gut microbiota homeostasis and recovering intestinal mucosal immune barrier.
Staphylococcus aureus is an opportunistic pathogen and one of the most frequent causes for community acquired and nosocomial bacterial infections. Even so, its energy metabolism is still under ...explored and its respiratory enzymes have been vastly overlooked. In this work, we unveil the dihydroorotate:quinone oxidoreductase (DHOQO) from S. aureus, the first example of a DHOQO from a Gram-positive organism. This protein was shown to be a FMN containing menaquinone reducing enzyme, presenting a Michaelis-Menten behaviour towards the two substrates, which was inhibited by Brequinar, Leflunomide, Lapachol, HQNO, Atovaquone and TFFA with different degrees of effectiveness. Deletion of the DHOQO coding gene (Δdhoqo) led to lower bacterial growth rates, and effected in cell morphology and metabolism, most importantly in the pyrimidine biosynthesis, here systematized for S. aureus MW2 for the first time. This work unveils the existence of a functional DHOQO in the respiratory chain of the pathogenic bacterium S. aureus, enlarging the understanding of its energy metabolism.
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•Dihydroorotate:quinone oxidoreductase from S. aureus is a flavoprotein containing FMN.•The enzyme shows a Michaelis-Menten behaviour towards dihydroorotate and quinone.•The enzyme binds dihydroorotate and quinone at different sites.•The DHOGO knockout mutant affects the pyrimidine the energy biosynthesis rather than the energy metabolism.
•Pronounced seasonality in plankton community respiration and bacterial production but not in bacterial respiration.•Bacterial carbon demand independent of the amount of dissolved organic carbon ...produced by phytoplankton.•Plankton contributed more to CO2 export to the atmosphere than to off-shelf export.
The seasonal variability of plankton metabolism indicates how much carbon is cycling within a system, as well as its capacity to store carbon or export organic matter and CO2 to the deep ocean. Seasonal variability between November 2014, April 2015 and July 2015 in plankton respiration and bacterial (Bacteria + Archaea) metabolism is reported for the upper and bottom mixing layers at two stations in the Celtic Sea, UK. Upper mixing layer (UML, >75 m in November, 41–70 m in April and ∼50 m in July) depth-integrated plankton metabolism showed strong seasonal changes with a maximum in April for plankton respiration (1.2- to 2-fold greater compared to November and July, respectively) and in July for bacterial production (2-fold greater compared to November and April). However UML depth-integrated bacterial respiration was similar in November and April and 2-fold lower in July. The greater variability in bacterial production compared to bacterial respiration drove seasonal changes in bacterial growth efficiencies, which had maximum values of 89% in July and minimum values of 5% in November. Rates of respiration and gross primary production (14C-PP) also showed different seasonal patterns, resulting in seasonal changes in 14C-PP:CRO2 ratios. In April, the system was net autotrophic (14C-PP:CRO2 > 1), with a surplus of organic matter available for higher trophic levels and export, while in July balanced metabolism occurred (14C-PP:CRO2 = 1) due to an increase in plankton respiration and a decrease in gross primary production. Comparison of the UML and bottom mixing layer indicated that plankton respiration and bacterial production were higher (between 4 and 8-fold and 4 and 7-fold, respectively) in the UML than below. However, the rates of bacterial respiration were not statistically different (p > .05) between the two mixing layers in any of the three sampled seasons. These results highlight that, contrary to previous data from shelf seas, the production of CO2 by the plankton community in the UML, which is then available to degas to the atmosphere, is greater than the respiratory production of dissolved inorganic carbon in deeper waters, which may contribute to offshore export.
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