Bacteria, Volume 4, Issue 3 (September 2025) – 12 articles

Common bean (Phaseolus vulgaris L.) is a critical protein-rich legume supporting food and nutritional security globally. However, Fusarium wilt, caused by Fusarium solani, remains a major constraint to production, with yield losses reaching up to 84%. While biocontrol strategies have been explored, most microbial agents are sourced from mesophilic environments and show limited effectiveness under abiotic stress. Here, we report the isolation and characterization of extremophilic Bacillus spp. from the hypersaline Lake Bogoria, Kenya, and their biocontrol potential against F. solani. From 30 isolates obtained via serial dilution, 9 exhibited antagonistic activity in vitro, with mycelial inhibition ranging from 1.07-1.93 cm 16S rRNA sequencing revealed taxonomic diversity within the Bacillus genus, including unique extremotolerant strains. Molecular screening identified genes associated with the biosynthesis of antifungal metabolites such as 2,4-diacetylphloroglucinol, pyrrolnitrin, and hydrogen cyanide. Enzyme assays confirmed substantial production of chitinase (1.33–3160 U/mL) and chitosanase (10.62–28.33 mm), supporting a cell wall-targeted antagonism mechanism. In planta assays with the lead isolate (B7) significantly reduced disease incidence (8–35%) and wilt severity (1–5 affected plants), while enhancing root colonization under pathogen pressure. These findings demonstrate that extremophile-derived Bacillus spp. possess robust antifungal traits and highlight their potential as climate-resilient biocontrol agents for sustainable bean production in arid and semi-arid agroecosystems. Full article

Plant growth-promoting rhizobacteria (PGPRs) are well known for their capacity to enhance the growth and survival of in vitro-grown plants. However, their effect on Nardostachys jatamansi (D. Don) DC., a critically endangered medicinal plant in the Indian Himalayan Region, is still unknown. In this study, a simple, reproducible protocol for in vitro propagation of N. jatamansi was established using shoot tip explants, cultured on Murashige and Skoog (MS) medium supplemented with different plant growth regulators, including N6-benzylaminopurine, thidiazuron (TDZ), and naphthalene acetic acid (NAA). MS media supplemented with 2.0 μM TDZ and 0.5 µM NAA created a significant shoot induction with an average of 6.2 shoots per explant. These aseptically excised individual shoots produced roots on MS medium supplemented with Indole Butyric Acid or NAA within 14 days of the transfer. The PGPR, viz., Bacillus subtilis and Pseudomonas corrugata, inoculation resulted in improved growth, higher chlorophyll content, and survival of in vitro-rooted plants (94.6%) after transfer to the soil. Moreover, the PGPRs depicted a two-fold higher total phenolics (45.87 mg GAE/g DW) in plants. These results clearly demonstrate the beneficial effects of P. corrugata and B. subtilis on the growth, survival, and phytochemical content of N. jatamansi. Full article

Leather biodegradation is a complex microbial process with increasing relevance for sustainable waste management. In this study, we investigated bacterial communities responsible for the degradation of leather treated with different tanning agents (chrome, Zeolite, Biole^®) using high-throughput 16S rRNA gene sequencing and metatranscriptomic analysis. Proteobacteria, Bacteroidetes, and Patescibacteria emerged as the dominant phyla, while genera such as Acinetobacter, Pseudomonas, and Sphingopyxis were identified as key contributors to enzymatic activity and potential metal resistance. A total of 1302 enzymes were expressed across all the conditions, including 46 proteases, with endopeptidase La, endopeptidase Clp, and methionyl aminopeptidase being the most abundant. Collagen samples exhibited the highest functional diversity and total enzyme expression, whereas chrome-treated samples showed elevated protease activity, indicating selective pressure from heavy metals. Differential enzyme expression patterns were linked to both the microbial identity and tanning chemistry, revealing genus- and treatment-specific enzymatic signatures. These findings deepen our understanding of how tanning agents modulate the microbial structure and function and identify proteases with potential applications in the bioremediation and eco-innovation of leather waste processing. Full article

Azospirillum is a well-studied genus of plant growth-promoting rhizobacteria (PGPR) and one of the most extensively researched diazotrophs. This genus can colonize rhizosphere soil and enhance plant growth and productivity by supplying essential nutrients to the host. Azospirillum–plant interactions involve multiple mechanisms, including nitrogen fixation, the production of phytohormones (auxins, cytokinins, indole acetic acid (IAA), and gibberellins), plant growth regulators, siderophore production, phosphate solubilization, and the synthesis of various bioactive molecules, such as flavonoids, hydrogen cyanide (HCN), and catalase. Thus, Azospirillum is involved in plant growth and development. The genus Azospirillum also enhances membrane activity by modifying the composition of membrane phospholipids and fatty acids, thereby ensuring membrane fluidity under water deficiency. It promotes the development of adventitious root systems, increases mineral and water uptake, mitigates environmental stressors (both biotic and abiotic), and exhibits antipathogenic activity. Biological nitrogen fixation (BNF) is the primary mechanism of Azospirillum, which is governed by structural nif genes present in all diazotrophic species. Globally, Azospirillum spp. are widely used as inoculants for commercial crop production. It is considered a non-pathogenic bacterium that can be utilized as a biofertilizer for a variety of crops, particularly cereals and grasses such as rice and wheat, which are economically significant for agriculture. Furthermore, Azospirillum spp. influence gene expression pathways in plants, enhancing their resistance to biotic and abiotic stressors. Advances in genomics and transcriptomics have provided new insights into plant-microbe interactions. This review explored the molecular mechanisms underlying the role of Azospirillum spp. in plant growth. Additionally, BNF phytohormone synthesis, root architecture modification for nutrient uptake and stress tolerance, and immobilization for enhanced crop production are also important. A deeper understanding of the molecular basis of Azospirillum in biofertilizer and biostimulant development, as well as genetically engineered and immobilized strains for improved phosphate solubilization and nitrogen fixation, will contribute to sustainable agricultural practices and help to meet global food security demands. Full article

The genus Turicibacter is a common inhabitant of the small intestine of numerous animal species, including chickens. However, little is known about the phenotypic and genetic diversity of the genus. Within the chicken small intestine, bile and its primary components, bile acids, are involved in nutrient absorption and modulating microbial community structure. Here, we compare T. sanguinis MOL361 (type strain of the genus), with three strains of the recently described species T. bilis, two from chicken and one from swine. Multiple bile salt hydrolase (BSH) genes, responsible for modification of host-derived bile acids, were identified in each strain and were compared to other Turicibacter BSH with known activities. The bile acid deconjugation ability of individual strains were assessed using chicken bile, as well as the primary bile acids taurochenodeoxycholic acid and taurocholic acid. Both chicken isolates, T. bilis MMM721 and T. bilis ISU324, as well as T. sanguinis MOL361, significantly reduced the concentrations of the tauro-conjugated bile acids. Overall, this work identifies the context-dependent nature of Turicibacter BSH activity. Full article

Grass carp in aquaculture exhibited symptoms of bacterial infection leading to mortality. To investigate the cause of the disease and control grass carp infections, samples from diseased grass carp were collected, and a bacterial strain named XH-1 was isolated from the internal organs of the infected fish. Artificial infection experiments were conducted to determine whether the isolated strain XH-1 was the pathogenic bacterium. The biological characteristics of the isolated strain were studied through a 16S rRNA sequence analysis, physiological and biochemical identification, and phylogenetic tree construction. Extracts from 14 traditional Chinese herbs were tested to evaluate their bacteriostatic and bactericidal effects on the isolated strain. The regression infection experiment confirmed that the isolated strain XH-1 was the pathogenic bacterium causing the grass carp disease. Biological characterization studies identified the bacterium as Aeromonas veronii, which is clustered with A. veronii MW116767.1 on the phylogenetic tree. Among the 14 Chinese herbal extracts, Lignum sappa, Pericarpium granna, Artemisia argyi, Scutellaria baicalensis Georgi, Coptis chinensis, and Artemisiacapillaris thunb exhibited significant bacteriostatic effects on XH-1. Lignum sappa showed the highest sensitivity to A. veronii, with the largest inhibition zone diameter, and its minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were 7.813 mg/mL and 15.625 mg/mL, respectively. As the concentration of Lignum sappa extract increased, its bacteriostatic and bactericidal effects strengthened. When the concentration exceeded 14 mg/mL, it maintained strong bactericidal activity over 32 h. This study on A. veronii XH-1 provides theoretical insights for the prevention of grass carp aquaculture diseases and the use of traditional Chinese herbs for treatment. Full article

Nitrifying bacteria, including ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), are players in the nitrogen cycle but pose serious health risks when colonizing drinking water distribution networks (DWDNs). While the global impact of these bacteria is increasingly recognized, a significant research gap remains concerning their effects in tropical regions, particularly in developing countries. This study aims to bridge that gap by systematically reviewing the existing literature on nitrifying bacteria in DWDNs, their behavior in biofilms, and associated public health risks, particularly in systems reliant on surface water sources in tropical climates. Using the PRISMA guidelines for systematic reviews, 51 relevant studies were selected based on content validity and relevance to the research objective. The findings highlight the critical role of nitrifying bacteria in the formation of nitrogenous disinfection by-products (N-DBPs) and highlight specific challenges faced by developing countries, including insufficient monitoring and low public awareness regarding safe water storage practices. Additionally, this review identifies key surrogate indicators, such as ammonia, nitrite, and nitrate concentrations, that influence the formation of DBPs. Although health risks from nitrifying bacteria are reported in comparable studies, there is a lack of epidemiological data from tropical regions. This underscores the urgent need for localized research, systematic monitoring, and targeted interventions to mitigate the risks associated with nitrifying bacteria in DWDNs. Addressing these challenges is essential for enhancing water safety and supporting sustainable water management in tropical developing countries. Full article

Background: Helicobacter pylori infection is widely prevalent across the globe and is a major etiological agent of various gastric pathologies. This bacterium colonizes the human stomach, where it induces a range of mucosal abnormalities observable upon clinical examination. Accordingly, the present study aimed to assess the prevalence and clinical implications of H. pylori infection among patients undergoing endoscopic evaluation. Method: A cross-sectional study was conducted from January to May 2019 at endoscopy service-providing health institutions. Sociodemographic and clinical data were collected. Gastric biopsies were collected during endoscopic procedures and immediately inoculated into brain–heart infusion broth and plated out. Then, phenotypic bacterial identification was done. The collected data have been analyzed using SPSS version 23. A logistic regression model was used for association determination. Result: Among the 135 individuals enrolled in the study, 59.3% are male, and 40.7% are female, with a mean age of 45 years. H. pylori is isolated in 17.8% of participants (24/135). Notably, the majority of these isolates 71% (17/24) are from male participants, while 29% (7/24) are from females. A statistically significant association is identified between H. pylori infection and both high salt intake [AOR = 3.3; 95% CI: 1.5–10.8; p = 0.04] and the presence of duodenal ulcers [AOR = 3.8; 95% CI: 1.2–11.9; p = 0.02]. The highest prevalence of H. pylori is observed among patients diagnosed with atrophic pangastritis. Conclusions: The prevalence of H. pylori among the study participants is comparatively low. However, a significant association was observed between H. pylori infection and both high dietary salt intake and the presence of duodenal ulcers. Full article

In the African Sahel, fonio (Digitaria sp.) is a cereal crop that alleviates mid-season hunger before other main crops are harvested. As fonio is valued for its ability to grow under low nutrient and drought conditions, it was hypothesized that it may contain endophytic bacteria that can tolerate such extreme stress. White fonio seeds were obtained from a dry environment (Mali) and a moderate rainfall environment (Guinea). Plants were grown indoors on field soil mixed with sand to mimic Sahelian soils, grown at 30 °C, and exposed to drought, optimal water, and low nitrogen stress conditions. In total, 73 cultured bacteria were classified using full-length 16S rRNA sequencing followed by searching three 16S reference databases. Selected strains were tested in vitro for tolerance to relevant abiotic stresses. Including nine isolates from seeds, the candidate root/shoot endophytes spanned 27 genera and 18–39 top-match species. Several well-known nitrogen-fixing bacteria were cultured, including Ensifer. Leaves were dominated by Bacilli (spore-formers known to withstand dry conditions). There were five root isolates of Variovorax. Leifsonia was isolated from the leaves and showed 100% sequence identity with seed isolates, suggestive of transmission from seed to shoot. In vitro experiments showed that seed isolates, including Leifsonia, survived diverse abiotic stresses relevant to the Sahel. Combined, these results suggest that white fonio hosts stress-tolerant microbiota, and points to Leifsonia as a candidate seed-to-plant transmitted endophyte, pending confirmation by future whole genome sequencing. This microbial collection serves as a starting point for long-term experiments to understand stress tolerance in this under-studied crop. Full article

The oral microbiome, a highly diverse and intricate ecosystem of microorganisms, plays a pivotal role in the maintenance of systemic health. With the oral cavity housing over 700 different bacterial species, the body’s second most diverse microbial community, periodontal pathogens often lead to the dysregulation of immune responses and consequently, neuropsychiatric disorders. Emerging evidence suggests a significant link between the dysbiosis of oral taxa and the progression of neurogenic disorders such as depression, schizophrenia, bipolar disorders, and more. In this paper, we show the relationship between mental health conditions and shifts in the oral microbiome by highlighting inflammatory responses and neuroactive pathways. The connection between the central nervous system and the oral cavity highlights its role as a modulator of mental health. Clinically, these findings have significant importance as dysbiosis could compromise quality of life. The weight of mental health is often compounded with treatment resistance, non-adherence, and relapse, causing a further need for treatment development. This review seeks to underscore the crucial role of the proposed oral–brain axis in hopes of increasing its presence in future intervention strategies and mental health therapies. Full article

Postharvest losses of Solanaceae crops, which include potatoes (Solanum tuberosum), tomatoes (Solanum lycopersicum), bell peppers (Capsicum annuum), and others, are one of the major challenges in agriculture throughout the world, impacting food security and economic viability. Agrochemicals have been successfully employed to prevent postharvest losses in agriculture. However, the excessive use of agrochemicals may cause detrimental effects on consumer health, the emergence of pesticide-resistant pathogens, increased restrictions on existing pesticides, environmental harm, and the decline of beneficial microorganisms, such as natural antagonists to pests and pathogens. Hence, there is a need to search for a safer and more environmentally friendly alternative. Microbial antagonists have gained more attention in recent years as substitutes for the management of pests and pathogens because they minimize the excessive applications of toxic substances while providing a sustainable approach to plant health management. However, more research is required to make microbial agents more stable and effective and less toxic before they can be used in commercial settings. Therefore, research is being conducted to develop new biological control agents and obtain knowledge of the mechanisms of action that underlie biological disease control. To accomplish this objective, the review aims to investigate microbial antagonists’ modes of action, potential future applications for biological control agents, and difficulties encountered during the commercialization process. We also highlight earlier publications on the function of microbial biological control agents against postharvest crop diseases. Therefore, we can emphasize that the prospects for biological control are promising and that the use of biological control agents to control crop diseases can benefit the environment. Full article

Soil microbes are important for maintaining agricultural ecosystems by promoting nutrient cycling, plant growth, and soil resilience. Microbial-based inoculants, such as bio-inoculants and bioremediation agents, have been identified as suitable means to promote soil health, reduce environmental deterioration, and achieve sustainable agriculture. Bio-inoculants, such as biofertilizers and biopesticides, promote nutrient availability, plant growth, and chemical input dependency reduction. Diverse microbial populations, especially plant growth-promoting bacteria (PGPB), enhance resistance by promoting a symbiotic association with plants and inducing natural resistance against insects. Bioremediation, the second significant microbial intervention, is the use of microorganisms for detoxifying and rehabilitating polluted soils. Methods effectively degrade organic pollutants, immobilize heavy metals, and mitigate the toxic effects of industrial and agricultural pollutants. Recent advances in microbial ecology and biotechnology, such as metagenomics, have transformed the knowledge of microbial soil communities, and tailor-made microbial formulations and monitoring equipment may be developed to maximize their activity. Though promising, environmental heterogeneity, scalability, and lack of field-based evidence constrain their widespread application. Multidimensional applications of microbial solutions in agroecology are explored in this review, with a focus on their potential in maintaining soil health, crop production, and environmental sustainability. It also addresses the application of bioremediation and microbial inoculants in agroecosystems and technological innovations with future research objectives. Microbial innovation to shape the soil microbiome offers a valid tool for addressing global challenges in agriculture, food security, and ecological resilience in the context of climate change. Full article