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Consumption of heavy metals, especially lead (Pb) contaminated food is a serious threat to human health. Higher Pb uptake by the plant affects the quality, growth and yield of crops. However, inoculation of plant growth-promoting rhizobacteria (PGPR) along with a mixture of organic amendments and biochar could be an effective way to overcome the problem of Pb toxicity. That’s why current pot experiment was conducted to investigate the effect of compost mixed biochar (CB) and ACC deaminase producing PGPR on growth and yield of spinach plants under artificially induced Pb toxicity. Six different treatments i.e., control, Alcaligenes faecalis (PGPR1), Bacillus amyloliquefaciens (PGPR2), compost + biochar (CB), PGPR1 + CB and PGPR2 + CB were applied under 250 mg Pb kg -1 soil. Results showed that inoculation of PGPRs ( Alcaligenes faecalis and Bacillus amyloliquefaciens ) alone and along with CB significantly enhanced root fresh (47%) and dry weight (31%), potassium concentration (11%) in the spinach plant. Whereas, CB +  Bacillus amyloliquefaciens significantly decreased (43%) the concentration of Pb in the spinach root over control. In conclusion, CB +  Bacillus amyloliquefaciens has the potential to mitigate the Pb induced toxicity in the spinach. The obtained result can be further used in the planning and execution of rhizobacteria and compost mixed biochar-based soil amendment.

Dimethyl disulfide (DMDS) is an important volatile organic sulfur compound with diverse applications and substantial demand in the chemical, agricultural, and food industries. The challenges associated with their chemical synthesis have spurred exploration of biological synthesis as an alternative route. Nevertheless, there is limited research on the biosynthesis of DMDS, and the yield remains low. In this study, strain W2-3, exhibiting high DMDS production, was isolated from aged tobacco leaves collected in Hubei Province, China. Based on morphological characteristics, 16S rRNA gene sequencing and phylogenetic analysis, the strain was identified as Alcaligenes faecalis . Through single-factor experimental methods, an initial pH of 7 and temperature ranging from 19.5 to 30 °C were demonstrated to be the optimal fermentation conditions for DMDS production. Under these optimized conditions, the maximum yield of DMDS reached 213.49 mg/L, which was a 1.34-fold increase from the pre-optimization yield of 159.86 mg/L. Moreover, optimization of sulfur sources and concentrations showed that increasing methionine concentration led to higher DMDS production. Under sufficient Met conditions, W2-3 achieved a peak of 2440.71 mg/L DMDS, representing an increase of 11.43-fold compared to the control group without methionine supplementation. This yield significantly surpassed the highest yield reported in the literature (40.06 mg/L) by 60.93-fold, establishing a new record for the highest yield currently known. This study identifies A. faecalis W2-3 as a promising microbial chassis for the biosynthesis of DMDS, characterized by a high yield and strong temperature adaptability. It offers insights into the metabolic pathways and fermentation conditions for industrial-scale DMDS production. As the first systematic optimization research aimed at enhancing DMDS production, it fills a gap in the literature. Our findings pave the way for sustainable and efficient DMDS biosynthesis, with significant implications for promoting its application in agriculture, industry, and environmental management.

In this study, a bacterial strain exhibiting high selenite (Na2SeO3) tolerance and reduction capacity was isolated from the gut of Monochamus alternatus larvae and identified as Alcaligenes faecalis Se03. The isolate exhibited extreme tolerance to selenite (up to 120 mM) when grown aerobically. In the liquid culture medium, it was capable of reducing nearly 100% of 1.0 and 5.0 mM Na2SeO3 within 24 and 42 h, respectively, leading to the formation of selenium nanoparticles (SeNPs). Electron microscopy and energy dispersive X-ray analysis demonstrated that A. faecalis Se03 produced spherical electron-dense SeNPs with an average hydrodynamic diameter of 273.8 ± 16.9 nm, localized mainly in the extracellular space. In vitro selenite reduction activity and real-time PCR indicated that proteins such as sulfite reductase and thioredoxin reductase present in the cytoplasm were likely to be involved in selenite reduction and the SeNPs synthesis process in the presence of NADPH or NADH as electron donors. Finally, using Fourier transform infrared spectroscopy, protein and carbohydrate residues were detected on the surface of the biogenic SeNPs. Based on these observations, A. faecalis Se03 has the potential to be an eco-friendly candidate for the bioremediation of selenium-contaminated soil/water and a bacterial catalyst for the biogenesis of SeNPs.

A new heterotrophic nitrifying bacterium was isolated from the compost of swine manure and rice husk and identified as Alcaligenes faecalis SDU20. Strain SDU20 had heterotrophic nitrification potential and could remove 99.7% of the initial NH4+–N. Nitrogen balance analysis revealed that 15.9 and 12.3% of the NH4+–N were converted into biological nitrogen and nitrate nitrogen, respectively. The remaining 71.44% could be converted into N2 or N2O. Single-factor experiments showed that the optimal conditions for ammonium removal were the carbon source of sodium succinate, C/N ratio 10, initial pH 8.0, and temperature 30 °C. Nitrification genes were determined to be upregulated when sodium succinate was used as the carbon source analyzed by quantitative real-time polymerase chain reaction (qRT-PCR). Strain SDU20 could tolerate 4% salinity and show resistance to some heavy metal ions. Strain SDU20 removed 72.6% high concentrated NH4+–N of 2000 mg/L within 216 h. In a batch experiment, the highest NH4+–N removal efficiency of 98.7% and COD removal efficiency of 93.7% were obtained in the treatment of unsterilized swine wastewater. Strain SDU20 is promising in high-ammonium wastewater treatment.

Proton-coupled electron transfer (PCET), a ubiquitous phenomenon in biological systems, plays an essential role in copper nitrite reductase (CuNiR), the key metalloenzyme in microbial denitrification of the global nitrogen cycle. Analyses of the nitrite reduction mechanism in CuNiR with conventional synchrotron radiation crystallography (SRX) have been faced with difficulties, because X-ray photoreduction changes the native structures of metal centers and the enzyme–substrate complex. Using serial femtosecond crystallography (SFX), we determined the intact structures of CuNiR in the resting state and the nitrite complex (NC) state at 2.03- and 1.60-Å resolution, respectively. Furthermore, the SRX NC structure representing a transient state in the catalytic cycle was determined at 1.30-Å resolution. Comparison between SRX and SFX structures revealed that photoreduction changes the coordination manner of the substrate and that catalytically important His255 can switch hydrogen bond partners between the backbone carbonyl oxygen of nearby Glu279 and the side-chain hydroxyl group of Thr280. These findings, which SRX has failed to uncover, propose a redox-coupled proton switch for PCET. This concept can explain how proton transfer to the substrate is involved in intramolecular electron transfer and why substrate binding accelerates PCET. Our study demonstrates the potential of SFX as a powerful tool to study redox processes in metalloenzymes.

High lead (Pb) concentration in soils is becoming a severe threat to human health. It also deteriorates plants, growth, yield and quality of food. Although the use of plant growth-promoting rhizobacteria (PGPR), biochar and compost can be effective environment-friendly amendments for decreasing Pb stress in crop plants, the impacts of their simultaneous co-application has not been well documented. Thus current study was carried, was conducted to investigate the role of rhizobacteria and compost mixed biochar (CB) under Pb stress on selected soil properties and agronomic parameters in mint ( Mentha piperita L.) plants. To this end, six treatments were studied: Alcaligenes faecalis , Bacillus amyloliquefaciens , CB, PGPR1 + CB, PGPR2 + CB and control. Results showed that the application A. faecalis  + CB significantly decreased soil pH and EC over control. However, OM, nitrogen, phosphorus and potassium concentration were significantly improved in the soil where A. faecalis  + CB was applied over control. The A. faecalis  + CB treatment significantly improved mint plant root dry weight (58%), leaves dry weight (32%), chlorophyll (37%), and N (46%), P (39%) and K (63%) leave concentration, while also decreasing the leaves Pb uptake by 13.5% when compared to the unamended control. In conclusion, A. faecalis  + CB has a greater potential to improve overall soil quality, fertility and mint plant productivity under high Pb soil concentration compared to the sole application of CB and A. faecalis .

Heterotrophic nitrification remains a mystery for decades. It has been commonly hypothesized that heterotrophic nitrifiers oxidize ammonia to hydroxylamine and then to nitrite in a way similar to autotrophic AOA and AOB. Recently, heterotrophic nitrifiers from Alcaligenes were found to oxidize ammonia to hydroxylamine and then to N2 (“dirammox”, direct ammonia oxidation) by the gene cluster dnfABC with a yet-to-be-reported mechanism. The role of a potential glutamine amidotransferase DnfC clues the heterotrophic ammonia oxidation might involving in glutamine. Here, we found Alcaligenes faecalis JQ135 could oxidize amino acids besides ammonia. We discovered that glutamine is an intermediate of the dirammox pathway and the glutamine synthetase gene glnA is essential for both A. faecalis JQ135 and the Escherichia coli cells harboring dnfABC gene cluster to oxidize amino acids and ammonia. Our study expands understanding of heterotrophic nitrifiers and challenges the classical paradigm of heterotrophic nitrification.

Endophytic bacteria, recognized as eco-friendly biofertilizers, have demonstrated the potential to enhance crop growth and yield. While the plant growth-promoting effects of endophytic bacteria have been extensively studied, the impact of weed endophytes remains less explored. In this study, we aimed to isolate endophytic bacteria from native weeds and assess their plant growth-promoting abilities in rice under varying chemical fertilization. The evaluation encompassed measurements of mineral phosphate and potash solubilization, as well as indole-3-acetic acid (IAA) production activity by the selected isolates. Two promising strains, tentatively identified as Alcaligenes faecalis (BTCP01) from Eleusine indica (Goose grass) and Metabacillus indicus (BTDR03) from Cynodon dactylon (Bermuda grass) based on 16S rRNA gene phylogeny, exhibited noteworthy phosphate and potassium solubilization activity, respectively. BTCP01 demonstrated superior phosphate solubilizing activity, while BTDR03 exhibited the highest potassium (K) solubilizing activity. Both isolates synthesized IAA in the presence of L-tryptophan, with the detection of nifH and ipdC genes in their genomes. Application of isolates BTCP01 and BTDR03 through root dipping and spraying at the flowering stage significantly enhanced the agronomic performance of rice variety CV. BRRI dhan29. Notably, combining both strains with 50% of recommended N, P, and K fertilizer doses led to a substantial increase in rice grain yields compared to control plants receiving 100% of recommended doses. Taken together, our results indicate that weed endophytic bacterial strains BTCP01 and BTDR03 hold promise as biofertilizers, potentially reducing the dependency on chemical fertilizers by up to 50%, thereby fostering sustainable rice production.

Phototrophy and chemotrophy are two dominant modes of microbial metabolism. To date, non-phototrophic microorganisms have been excluded from the solar light-centered phototrophic metabolism. Here we report a pathway that demonstrates a role of light in non-phototrophic microbial activity. In lab simulations, visible light-excited photoelectrons from metal oxide, metal sulfide, and iron oxide stimulated the growth of chemoautotrophic and heterotrophic bacteria. The measured bacterial growth was dependent on light wavelength and intensity, and the growth pattern matched the light absorption spectra of the minerals. The photon-to-biomass conversion efficiency was in the range of 0.13–1.90‰. Similar observations were obtained in a natural soil sample containing both bacteria and semiconducting minerals. Results from this study provide evidence for a newly identified, but possibly long-existing pathway, in which the metabolisms and growth of non-phototrophic bacteria can be stimulated by solar light through photocatalysis of semiconducting minerals. Microbial metabolism is usually considered to be phototrophic or chemotrophic. By showing that light-induced photoelectrons from metal oxide and metal sulfides can stimulate the growth of chemoautotrophic and heterotrophic bacteria, this study indicates that light may be involved in non-phototrophic microbial activity.

Abstract Quinolinic acid (QA) is a pyridine derivative that can be found in many organisms and is widely used in the chemical industry. However, QA possesses excitotoxic properties. To date, the catabolism of QA mediated by microorganisms has rarely been reported. In this study, a QA-degrading strain (JQ191) was isolated from sewage sludge. Based on phenotypic and 16S rRNA gene phylogenetic analysis, the strain was identified as Alcaligenes faecalis. Strain JQ191 was able to utilize QA as the sole source of carbon and nitrogen for growth. QA-cultured cells of JQ191 completely degrade 200 mg/L QA within 2 days in a mineral salt medium, whereas the LB-cultured cells experienced a 2-day lag period before degrading QA, indicating that the catabolic enzymes involved in QA degradation were induced by QA. 6-Hydroxypicolinic acid (6HPA) was identified as an intermediate of QA degradation by strain JQ191. A 6HPA monooxygenase gene picB was cloned, genetically disrupted, and heterologously expressed, and the results show that picB was responsible for catalyzing 6HPA to 3,6DHPA in JQ191. A new QA mineralization pathway was proposed. This study identifies a new bacterium candidate that has a potential application prospect in the bioremediation of QA-polluted environment, as well as provides new insights into the bacterial catabolism of QA. A new bacterium that can degrade neurotoxic quinolinic acid(QA).