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The mammalian intestinal tract is colonized by trillions of beneficial commensal bacteria that are anatomically restricted to specific niches. However, the mechanisms that regulate anatomical containment remain unclear. Here, we show that interleukin-22 (IL-22)-producing innate lymphoid cells (ILCs) are present in intestinal tissues of healthy mammals. Depletion of ILCs resulted in peripheral dissemination of commensal bacteria and systemic inflammation, which was prevented by administration of IL-22. Disseminating bacteria were identified as Alcaligenes species originating from host lymphoid tissues. Alcaligenes was sufficient to promote systemic inflammation after ILC depletion in mice, and Alcaligenes-specific systemic immune responses were associated with Crohn's disease and progressive hepatitis C virus infection in patients. Collectively, these data indicate that ILCs regulate selective containment of lymphoid-resident bacteria to prevent systemic inflammation associated with chronic diseases.

Hydrogen (H 2 ) energy has garnered significant attention due to its numerous advantages. Nonetheless, for future commercialization, it is imperative to screen and identify strains with enhanced H 2 -producing capacities. In order to attain a high and consistent production performance, the conversion of biomass sources into H 2 requires careful selection of the most appropriate H 2 -producing bacteria. This study aimed to isolate and identify a highly effective H 2 producing bacteria from local sewage sludge and assess its fermentability for H 2 production. The isolate was first identified by means of morphological, phenotypic, biological, and 16 S rRNA investigations. A facultative anaerobe that produces H 2 and is gram-negative was identified as Alcaligenes ammonioxydans strain SRAM. For the purpose of determining whether the isolate could produce H 2 using glucose as the substrate, its fermentability was evaluated in 500 mL serum bottles. This strain demonstrated the ability to produce H 2 from glucose under anaerobic environment, achieving a maximum H 2 yield of 2.9 mol H₂/mol of glucose. The highest rate of H 2 production, 9.261 mmol H₂/ g dry cell weight per hr, was attained at 37 °C and an initial pH of 6.8. This work effectively illustrated the use of a novel locally isolated strain in the biotechnological conversion of glucose to H 2 . This strategy offers an effective remedy for the world’s energy instability in addition to addressing environmental issues related to industrial operations. Highlights Novel hydrogen producing bacterial strain was isolated from local sewage sludge and identified. Isolated bacterial strain have been screened for hydrogen productivity. Alcaligenes ammonioxydans Strain SRAM utilized glucose yielding 2.9 mol H₂/mol glucose. It was a potential hydrogen producer in slightly alkaline condition. Graphical Abstract Biohydrogen Production via Dark Fermentation Using a Newly Isolated Strain: An Overview

Direct ammonia oxidation (Dirammox) might be of great significance to advance the innovation of biological nitrogen removal process in wastewater treatment systems. However, it remains unknown whether Dirammox bacteria can be selectively enriched in activated sludge. In this study, a lab-scale bioreactor was established and operated for 2 months to treat synthetic wastewater with hydroxylamine as a selection pressure. Three Dirammox strains ( Alcaligenes aquatilis SDU_AA1, Alcaligenes aquatilis SDU_AA2, and Alcaligenes sp. SDU_A2) were isolated from the activated sludge, and their capability to perform Dirammox process was confirmed. Although these three Dirammox bacteria were undetectable in the seed sludge (0%), their relative abundances rapidly increased after a month of operation, reaching 12.65%, 0.69%, and 0.69% for SDU_A2, SDU_AA1, and SDU_AA2, respectively. Among them, the most dominant Dirammox (SDU_A2) exhibited higher nitrogen removal rate (32.35%) than the other two strains (13.57% of SDU_AA1 and 14.52% of SDU_AA2). Comparative genomic analysis demonstrated that the most dominant Dirammox bacterium (SDU_A2) possesses fewer complete metabolic modules compared to the other two less abundant Alcaligenes strains. Our findings expanded the understanding of the application of Dirammox bacteria as key functional microorganisms in a novel biological nitrogen and carbon removal process if they could be well stabilized. Key points • Dirammox-dominated microbial community was enriched in activated sludge bioreactor. • The addition of hydroxylamine played a role in Dirammox enrichment. • Three Dirammox bacterial strains, including one novel species, were isolated. Graphical abstract

A novel heterotrophic nitrification-aerobic denitrification bacterium, Alcaligenes sp. TB (GenBank accession no. JQ044686), was isolated from a rotating drum biofilter for NO removal. Its characteristics and metabolic pathway for NO removal were comprehensively investigated. Experimental results showed that the nitrification and denitrification efficiency reached 99.42 and 96.44 %, respectively, after 44 h under the conditions of pH 7.2, 30 °C, and 120 rpm. The tests with the addition of Pb 2+ and Na 2 WO 4 as the reductase inhibitor revealed that nitrite was the key intermediate to produce the nitrogen gas as the final product in the simultaneous heterotrophic nitrification and denitrification by strain TB. Based on the experimental results, the metabolic pathway of strain TB has been proposed that it carries out shortcut/complete simultaneous nitrification and denitrification with nitrite as an intermediate and nitrogen gas as a final product. The two potential metabolic pathways existing in strain TB can be described as NH 4 +  → NH 2 OH → NO 2 −  → N 2 O → N 2 and NH 4 +  → NH 2 OH → NO 2 −  → NO 3 −  → NO 2 −  → N 2 O → N 2 . This work indicates that the strain TB may be a good candidate for the denitrification of the sewage.

Intensification of sodic soil due to increasing pH is an emerging environmental issue. The present study aimed to isolate and characterise alkaline stress-tolerant and plant growth-promoting bacterial strains from moderately alkaline soil (pH 8–9), strongly alkaline soil (pH 9–10), and very strongly alkaline soil (> 10). Total 68 bacteria were isolated, and screened for multiple plant growth promoting (PGP) attributes. Out of total, 42 isolates demonstrating at least three plant growth promoting PGP traits selected for further assays. Then out of 42, 15 bacterial isolates were selected based on enhanced maize plant growth under greenhouse experiment, and 16S rRNA gene sequencing revealed Bacillus spp. as a dominant genus. Furthermore, based on improved seed germination percentage and biomass of maize (Zea mays L.) under alkaline stress conditions Alcaligenes sp. NBRI NB2.5, Bacillus sp. NBRI YE1.3, and Bacillus sp. NBRI YN4.4 bacterial strains were selected, and evaluated for growth-promotion and alkaline stress amelioration under greenhouse condition. Amongst the selected 3 plant growth promoting rhizobacterial (PGPR) strains, Bacillus sp. NBRI YN4.4 significantly improved the photosynthetic pigments and soluble sugar content, and decreased proline level in inoculated maize plants as compared to uninoculated control under stress conditions. Moreover, significantly enhanced soil enzymes such as dehydrogenase, alkaline phosphatase and betaglucosidase due to inoculation of Bacillus sp. NBRI YN4.4 in maize plants grown in alkaline soil attributes to its role in improving the soil health. Therefore, alkaline stress-tolerant PGPR NBRI YN4.4 can be useful for developing strategies for the reclamation of saline/sodic soils and improving the plant growth and soil health in sustainable manner.

Environmental contamination with hydrocarbons though natural and anthropogenic activities is a serious threat to biodiversity and human health. Microbial bioremediation is considered as the effective means of treating such contamination. This study describes a biosurfactant producing bacterium capable of utilizing crude oil and various hydrocarbons as the sole carbon source. Strain BU33N was isolated from hydrocarbon polluted sediments from the Bizerte coast (northern Tunisia) and was identified as Alcaligenes aquatilis on the basis of 16S rRNA gene sequence analysis. When grown on crude oil and phenanthrene as sole carbon and energy sources, isolate BU33N was able to degrade ~86%, ~56% and 70% of TERHc, n-alkanes and phenanthrene, respectively. The draft genome sequence of the A. aquatilis strain BU33N was assembled into one scaffold of 3,838,299 bp (G+C content of 56.1%). Annotation of the BU33N genome resulted in 3,506 protein-coding genes and 56 rRNA genes. A large repertoire of genes related to the metabolism of aromatic compounds including genes encoding enzymes involved in the complete degradation of benzoate were identified. Also genes associated with resistance to heavy metals such as copper tolerance and cobalt-zinc-cadmium resistance were identified in BU33N. This work provides insight into the genomic basis of biodegradation capabilities and bioremediation/detoxification potential of A. aquatilis BU33N.

For the first time, this study reports extracellular uricase enzyme isolation and characterization from strain UR1 of spp. from Western Saudi Arabia. The strain efficiently produced highly active extracellular uricase for therapeutic applications. It offers a simplified enzyme purification approach rather than complicated intracellular enzyme purification from other microbes. Strain UR1 exhibited significantly higher uricase synthesis potential [916 U/mg (specific activities) and 275 U/ml (volume)]. The study optimized the conditions (37°C and pH 7.4) for 10% enhanced uricase production in the BT medium where sucrose served as the carbon source. Uricase enzyme remained stable at various pH levels (5–9) up to 50°C, however, the optimal activity was noted at 40°C and pH 7.5. The strain was sensitive to EDTA-like inhibitors. Ca improved the strain activity, which could yield potent formulations for clinical and industrial applications. This novel aspect presents spp. strain UR1 as a promising candidate for the treatment of hyperuricemia and gout. It offers an efficient and inexpensive alternative for uricase synthesis at the industrial scale. These findings encourage further investigations regarding genetic aspects of uricase for improved bioprocessing and therapeutic applications.

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.

Although an environmental contaminant, Alcaligenes sp. are now increasingly reported in clinical infections. Here, we present a whole-genome sequence of an extended spectrum beta-lactamase (ESBL) Alcaligenes nematophilus strain EBU-23 encoding beta-lactamase, bla gene, isolated from the stool of a hospitalized infant with acute gastroenteritis in a tertiary hospital in Nigeria. Antibiotics susceptibility test revealed that the isolate was resistant to the β-lactams, cephalosporins, and penicillin, β-lactam combination, and the fluoroquinolones. Genomic analysis exposed the presence of a class A beta-lactam hydrolase gene and multiple multidrug efflux permease which may be responsible for the beta-lactamase and multidrug resistance observed with the isolate. To the best our knowledge, we describe the first whole-genome sequence of a multidrug-resistant A. nematophilus implicated in acute childhood gastroenteritis in Nigeria.

Alcaligenes sp. ECU0401 has been isolated from soil samples with high nitrilase activity against glycolonitrile using the enrichment culture technique. The preferred carbon/nitrogen sources and metal ions were sodium acetate, a composite of peptone and yeast extract, and Cu²⁺, respectively. Glycolic acid was obtained in a yield of 96.5% after 14 h of biotransformation from a total of 200 mM glycolonitrile in the mode of sequential addition during the cultivation of Alcaligenes sp. ECU0401 in a 5-L jar fermenter. Fifty micromolars of glycolonitrile could be hydrolyzed in a yield of 94.1% by resting cells after 36 h. The microbial nitrilase system could hydrolyze various nitriles with high activity, and no amidase activity and glycolic acid were observed in hydrolyzing glycolamide. It significantly exhibited high enantioselectivity in the hydrolysis of mandelonitrile and 2-chloromandelonitrile (>99.9% e.e. p ). Efficient biocatalyst recycling was achieved as a result of immobilization in glutaraldehyde/polyethylenimine cross-linked carrageenan with immobilized cells exhibiting a biocatalyst productivity of 1,042.2 g glycolic acid per gram dry cell weight after 29 batch recycles.