Applied Microbiology

Arbuscular mycorrhizal (AM) fungi play a crucial role in maintaining sustainable agroecosystems by forming mutualistic relationships with plant roots, improving soil health, facilitating nutrient uptake, and enhancing resilience to abiotic stresses. The mutualistic relationship between AM fungi and plants promotes a balanced microbial community and improves soil structure by forming stable soil aggregates. Additionally, AM fungi can lower the adverse effects of high soil phosphorus (P) while also enhancing plant tolerance to drought, salinity, and heavy metal toxicity through osmotic regulation and antioxidant production. Arbuscular mycorrhizal fungi also support beneficial microorganisms, such as potassium (K)-solubilizing microbes and nitrogen (N)-transforming bacteria, which enhance the nutrient dynamics in soil. However, intensive agricultural practices, including heavy tillage and continuous monoculture, disrupt AM fungal networks and reduce microbial diversity, impairing their effectiveness. Adopting conservation practices such as reduced tillage, crop rotation, and organic amendments supports AM fungal growth. Incorporating mycorrhizal crops and utilizing native fungal inoculants can enhance AM fungal colonization and plant growth. These strategies collectively bolster soil health, crop productivity, and resilience, offering a promising solution to the environmental and agricultural challenges posed by intensive farming. By promoting AM fungi growth and colonization, agroecosystems can achieve long-term productivity and increased sustainability. Full article

This review explores the diverse applications and therapeutic potential of endophytic microbes, emphasizing both fungal and bacterial endophytes. These microorganisms reside within plant tissues without causing harm and play an important role in enhancing plant growth, nutrient acquisition, and resistance to pathogens. They produce phytohormones, facilitate nutrient uptake, solubilize essential nutrients, fix nitrogen, and improve stress tolerance. Furthermore, endophytes contribute to agricultural sustainability by producing plant growth regulators, providing biocontrol against pathogens through antimicrobial compounds, and competing for resources. Integrating endophytic microbes into agricultural practices can reduce reliance on chemical fertilizers and pesticides, promoting eco-friendly and sustainable farming. This review highlights the dual role of endophytic microbes in fostering sustainable agriculture and providing novel therapeutic applications. By minimizing dependence on chemical inputs, endophytes support environmental health while boosting crop yields. The synthesis underscores the importance of leveraging endophytic microbes to tackle global food security and sustainability challenges. Full article

The expression of the rhizobial symbiotic genes is controlled by various transcriptional regulators. After induction with appropriate plant flavonoids, NodD is responsible for the activation of the expression of genes related to Nod factor synthesis and secretion, but also, in most rhizobia harbouring a symbiotic type III secretion system (T3SS), the expression of ttsI. The ttsI gene encodes the positive regulator of the expression of T3SS-related genes, including those coding for structural components and for type III-secreted effector proteins. However, besides this general role among T3SS-harbouring rhizobia, different works have shown additional functions of TtsI in the regulation (positive or negative) of other bacterial traits such as the production of modified lipopolysaccharides or different types of motility (swimming or surface spreading). Interestingly, these additional functions appear to be rather specific than general among rhizobia. Moreover, in Sinorhizobium fredii HH103, TtsI affects the expression of various genes belonging to the nod regulon, including several transcriptional regulators. This review summarizes all the well-known bacterial traits affected by TtsI and describes other rhizobial genes that are regulated by TtsI but whose function remains to be established. Full article

Contamination of coastal-marine environment with multidrug-resistant Escherichia coli has resulted in such bacteria increasingly being detected in the seafood chain. This study aimed to determine the quinolone and colistin resistance genes in extended spectrum-β-lactamase (ESBL)-producing E. coli from seafood. ESBL-producing E. coli isolates (n = 269) were tested for quinolones and colistin resistance phenotypes by disk diffusion and broth microdilution methods, respectively. The isolates were further PCR screened for the plasmid-mediated quinolone resistance (PMQR) genes qnrA, qnrB, and qnrS, genomic mutations in gyrA and parC genes, and the colistin resistance genes mcr-1 and mcr-2. Phylogroup was determined by PCR using the Clermont E. coli phylotyping method. Of 269 isolates tested, 73.60% of E. coli isolates were resistant to moxifloxacin and 8.55% to ofloxacin, the least of all the quinolones tested. Further, 150 (55.76%) E. coli isolates carried at least one of the three PMQR genes tested, where qnrS was the most prevalent gene (53.90%). The colistin resistance gene (mcr-2) was detected in 38 (14.12%) isolates. Twenty-one of these isolates (55.26%) had a colistin minimum inhibitory concentration (MIC) of 16 µg/mL. Based on the Clermont E. coli phylotyping of the isolates harboring at least one of the qnr genes, 66 (44%) belonged to the phylogroup B1, followed by 23 (15.33%) to phylogroup A. Among 38 E. coli isolates carrying colistin resistance gene mcr-2, 27 (71.05%) isolates belonged to phylogroup B1, followed by 4 (10.52%) isolates to phylogroup A. The results suggest that E. coli phylogroups B1 and A harboring plasmid-mediated quinolone and colistin resistance genes are predominant in the seafood supply chain. Full article

Ralstonia solanacearum is a bacterial pathogen that causes bacterial wilt in plants, resulting in significant economic losses worldwide. Biological control that mainly utilizes Bacillus spp. is one of the most effective methods to prevent this disease. In this work, a strain of Bacillus stercoris TY-12 with an obvious antagonism effect on R. solanacearum was screened, and the inhibition diameter against R. solanacearum reached 2.18 cm by the plate antagonism test. Furthermore, an antimicrobial protein was isolated and purified from the fermentation supernatant of TY-12. The LC-MS/MS analysis results indicated that the purified antimicrobial protein is a member of the M42 family metallopeptidase with a molecular weight of approximately 40 kDa and named MP-TY12. After co-culture with MP-TY12 for 4 h, the cell surface of R. solanacearum was disrupted under SEM, indicating that MP-TY12 may inhibit R. solanacearum growth by enzymatically cleaving peptide bonds within the cell wall or membrane structure via hydrolysis. To evaluate the potential application of TY-12 in disease control during crop production, the biocontrol efficacy of TY-12 on the capsicum infected by R. solanacearum was investigated and achieved 84.18%. The growth promotion tests showed that the dry weight, fresh weight, stem diameter, stem length, root length, and the chlorophyll content of capsicum using TY-12 was obviously increased compared to the blank control. It is suggested that TY-12 could be used as a new biocontrol microbial strain in crop production and MP-TY12 might be developed as an antimicrobial agent. Full article

The high sensitivity of living organic forms to space radiation remains the critical issue during spaceflight, to which they will be chronically exposed during months of interplanetary or even decades of interstellar spaceflight. In the human body, all actively dividing and poorly differentiated cells are always close to being damaged by radiological or chemical agents. The chronic exposure to ionizing radiation primarily causes changes in blood counts and intestinal damage such as fibrosis, obliterative vasculitis, changes in the gut microbiota, and atrophy or degeneration of muscle fibers. The project “MISS: Microbiome Induced Space Suit” was presented at the Giant Jamboree of the International Genetically Engineered Machine Competition 2021, with the aim to investigate the ability of the novel microbiota-mediated approach to enhance human resistance to ionizing radiation. The key innovative part of the project was the idea to create a novel radioprotector delivery mechanism based on human gut microbiota with the function of outer membrane vesicles (OMVs) secretion. The project concept proposed the feasibility of genetically modifying the human microbiota in situ through the delivery of genetic constructs to the host’s crypts using silicon nanoparticles with chemically modified surfaces. In this perspective, we discuss the advances in modifying microbiota-mediated secretory activity as a promising approach for radioprotection and as an alternative to hormone therapy and other health conditions that currently require continuous drug administration. Future clinical trials of in situ methods to genetic engineering the crypt microbiota may pave the way for indirect regulation of human cells. Full article

Hard yellow maize is a crucial crop in Peruvian agriculture that plays a significant role in food security and livestock production. However, intensive fertilization practices in agronomic management have negatively impacted soil health. To explore more sustainable agricultural technologies, researchers investigated solutions using microorganisms to enhance plant growth. This study assessed the synergistic effects of microbial inoculants and mineral fertilization on INIA 619 and Dekal B-7088 maize varieties’ yield and nutritional quality. A split-plot design was employed, incorporating four inoculation treatments—no inoculant, Bacillus subtilis, Trichoderma viride, and Pseudomonas putida—combined with fertilization levels of 0%, 50%, 75%, and 100%. The findings revealed that Bacillus subtilis boosted yields by 13.1% in INIA 619 and 55.5% in Dekal B-7088. Additionally, combined with 100% fertilization, microbial inoculation increased protein content by 47% and carbohydrates by 6% in INIA 619 while maintaining nutritional quality with 75% fertilization. Similarly, in Dekal B-7088, inoculation with total fertilization enhanced protein content by 54% and fiber by 27%. These results demonstrated that microbial inoculation could reduce mineral fertilization by up to 25% while sustaining high yields and improving the nutritional quality of maize. Full article

Light is a crucial factor that influences algal production. Red and blue light have been widely utilized in two-stage cultivation approaches due to their significant roles in promoting algal growth and pigment accumulation. To investigate the effects of light on the growth of an isolated wild strain of Haematococcus pluvialis (H. pluvialis) and its astaxanthin production, white light (30 μmol photons m⁻² s⁻¹) mixed with various light intensities of red or blue light were applied to the algal culture during the stationary phase. The results indicate that white light combined with low-intensity red light (5 μmol photons m⁻² s⁻¹) significantly enhanced algal growth, achieving a maximum biomass of 0.43 g/L. The pH values in cultures exposed to all treatments involving red-light intensities were lower than those under solely white light conditions. Furthermore, the combination of white light and low-intensity red light improved photosynthetic efficiency, carbonic anhydrase (CA) activity, and the rate of CO₂ fixation. In contrast, the mixture of white light with blue light at 15 μmol photons m⁻² s⁻¹ facilitated astaxanthin production, resulting in a maximum astaxanthin content of 6.75 mg/L. Blue light was found to increase reactive oxygen species levels, leading to elevated malondialdehyde (MDA) concentrations and enhanced catalase (CAT) activity. These findings suggest that red light plays a crucial role in activating CA activity and promoting cellular CO₂ fixation, which helps maintain the stability of the culture medium pH and ultimately supports algal growth. Conversely, blue light contributes to photoprotective processes by accumulating protective pigments and enhancing the activity of protective enzymes; together, these mechanisms mitigate reactive oxygen species generated by blue light exposure. Our experimental results provide valuable insights for optimizing two-stage cultivation practices for isolated strains of H. pluvialis. Full article

Salmonella enterica is a globally important zoonotic microorganism that affects pigs and can enter the farm through various routes. This study aimed to determine the prevalence of S. enterica in water sources and pigs at Colombian pig farms, and to characterize the antimicrobial resistance of the isolates phenotypically and genotypically. Samples were collected from 103 farms including source water (n = 104), storage tank water (n = 103), drinking water (n = 103), and individual rectal swab samples (n = 1025). The presence of Salmonella was detected/identified using MDS-3M™ agar culture medium. Isolates were serotyped, and their antibiotic susceptibility was determined by minimum inhibitory concentration (MIC). Whole genome sequencing (WGS) was performed using Illumina NovaSeq, and bioinformatics analysis focused on serovar confirmation, MLST determination, and resistance gene detection. The overall between-farm prevalence of Salmonella enterica including all types of samples was 52.4% (54/103), with 6.4% of rectal swab samples and 21.3% of water samples found to be positive. Thirty serovars were identified using WGS, with the most common being S. Typhimurium var. monophasic (1,4,[5],12:i:-) (41.2%), S. Schwarzengrund (4.2%), and S. Saintpaul (4.2%). Salmonella Typhimurium and its monophasic variant were more commonly found in rectal swabs than the remaining serotypes (relative risk = 2.9, p < 0.0001), which were commonly found in the water samples (relative risk = 5.2, p < 0.0001). High levels of phenotypic resistance were observed, particularly to amikacin (99.2%), tetracycline (59.7%), chloramphenicol (55.5%), and ampicillin (42%). All isolates carried genes conferring resistance to aminoglycosides (aac(6′)-Iaa), quinolones (qnrB19), and tetracyclines (tetA). In conclusion, S. enterica is prevalent in Colombian pig farms including the water supply, with the S. Typhimurium monophasic variant being predominant, and antimicrobial resistance is widespread. Full article

Prodigiosin is a fascinating compound that has been gaining attention in the scientific community for its diverse range of potential applications. From its vibrant red color to its unique chemical properties, prodigiosin has captured the interest of researchers looking for innovative solutions in various fields. Prodigiosin, a red pigment produced by certain bacteria such as Serratia marcescens, has attracted interest from pharmaceutical researchers due to its promising potential in various therapeutic applications. A number of studies have demonstrated the potential of prodigiosin as an antimicrobial agent. With the rise of antibiotic resistance in the environment, prodigiosin is a promising solution to combat resistant strains and improve the effectiveness of existing antibiotic therapy. Moreover, different studies have shown that this natural pigment has anticancer properties by inhibiting the growth and proliferation of cancer cells. Prodigiosin exerts its anticancer effects by inducing apoptosis in cancer cells without causing significant damage to healthy cells. In this review, we will attempt to summarize the capabilities of prodigiosin and its prospects as a valuable tool in pharmaceutical research, and also review recent studies focusing on the various industries in which prodigiosin can be applied and the exciting possibilities it holds in the future. Full article

Background: Autism spectrum disorder is a multifactorial phenomenon whose genetic, biological, environmental, and nutritional factors outline the heterogeneous phenotype of the disease. A limitation in social connections with others, stereotyped reactions, and specific interests and preferences characterize the behavioral manifestations of a person with autism. Also, weaknesses are found in emotional, cognitive, and metacognitive development, significantly burdening the individual’s quality of life. Lately, it has gained widespread acceptance that the gut microbiome and neurotransmission constitute two decisive etiological factors of autism both in the prenatal period and postnatally. This study aims to investigate data on the interaction between the quantitative and qualitative composition of the gut flora and neurotransmission in humans, as well as their influences on the appearance and progression of the symptoms of autism spectrum disorder. At the same time, it captures the role of digital technology in diagnosing and intervening in autism, which is mainly related to the individual subjects under study. Methods: The current research employs an exploratory review to provide a concise overview of the complex neuronal functions associated with neurotransmitter action and the homeostasis mechanisms that allow the brain and the human body to survive and perform optimally. Results: A review of 111 sources highlighted the connection of dietary habits with synthesizing and releasing neurotransmitters and their influence on the emergence of autism-related behaviors. Conclusions: The literature review’s findings revealed the importance and influence of nutritional factors on neurotransmission performance and behavioral, social, and cognitive development among individuals with autism. Moreover, it is noteworthy that combining a healthy lifestyle and the targeted use of digital tools can improve the intensity of autism symptoms. Full article

Soil microorganisms play a significant role in the dynamic regulation of organic matter in soils. To assess the influence of agricultural practices on soil functional profiling, we examined the effect of soil disturbance and plant sequence with different levels of mycotrophy on wheat microbiomes metabolism. Soil samples were analyzed with community-level physiological profiles (CLPP) using Biolog™ Ecoplates. The results of average well color development (AWCD) showed that the degree of mycotrophy of preceding crop and soil disturbance affected the soil microbiome, although no impact on Shannon Evenness Index was observed during the experiment. The Shannon–Wiener Diversity Index showed variations among the different preceding plants, but not in wheat analysis. The pattern of the C sources metabolism also changed differentially regarding plant type and soil disturbance during the experiment, being also different within the highly mycotrophic plants (legume and grass). In the legume, an increase in the metabolism of amine/amides and phenolic acids was observed, whilst in the grass, an increase in the metabolism of phosphate-carbons (P carbon) and carbohydrates was more evident. Principal component analysis showed that a grouping in the distinct phases of the experiment correlated with the widening of the metabolism of amino acids, carboxylic acids, and carbohydrates. The results indicate that soil functional community structure reflects soil agricultural practice conditions. Previous plant types and soil disturbance impacted the soil microbiome metabolic response (AWCD) in wheat, generating different patterns of carbon metabolism related to previous plant mycotrophy. Full article

Anorexia nervosa (AN) is a psychiatric illness with harmful physical consequences. Studies have observed differences in the faecal microbiota of patients with AN compared to healthy controls. Diet has an impact on the gut microbiota, facilitating an altered community, such changes could impact the gut–brain axis. In this study, a three-stage gut model system that mimics the luminal microbiology of the large intestine was conducted to identify relationships between diet and gut microbiota. A microbial medium was developed to provide nutrients more appropriate to restricting subtype AN (R-AN). The model was inoculated with faeces and samples were taken to compare differences in the microbiota and end products following the fermentation of healthy control medium (HC) compared to R-AN medium. Then, 16S amplicon sequencing along with flow cytometry–fluorescence in situ hybridisation were used to ascertain changes in the microbiota. Gas chromatography (GC) was used to assess changes in microbial metabolites. There were reduced levels of SCFA following the fermentation of R-AN medium. The fermentation of R-AN media led to fewer total bacteria numbers, along with less bifidobacteria and Rumincoccus proximally, but more Clostridium and Enterobacteriaceae. Nutrient-deficient medium resulted in reduced neurotransmitter-producing bacteria, reduced butyrate-producing bacteria, and increased protein-utilising bacteria, all of which could be maintaining factors in AN. The model system provides a novel tool for exploring how extreme dietary changes impact the microbiota and could therefore could be useful for assessing appropriate gut–brain targeted treatments. Full article

With the increase in mercury pollution around the world, several bacteria have been identified that are capable of resisting mercury toxicity. With this in mind, the aim of this review was to determine which genes are involved in mercury resistance, which bacterial genera exhibit this resistance, and which bacterial isolation sources have been most reported. To answer these questions, the PICO method (population, intervention, comparison, and outcome) was used, three databases were searched, and 17 relevant articles were included. As a result, resistance is due to a set of mer genes that transcribe mer proteins. The most important genes identified were merA and merR, and their proteins confer resistance by reducing Hg to Hg⁺² or Hg⁰. Among the bacteria studied, those of the genera Pseudomonas, Escherichia, and the phylum Cyanobacteria stand out, the most important being Escherichia coli and Synechocystis sp., which are highly efficient and fast at reducing Hg. Based on the results, Escherichia coli and Synechocystis sp. are promising candidates for reducing environmental Hg, especially in aquatic environments. However, there is a lack of studies on the mechanism of bioremediation carried out by cyanobacteria and the influence of abiotic factors on the presence and/or expression of mer genes. Full article

The global food security crisis is emphasized by the alarming amount of food waste, where about one-third of the world’s food production, roughly 1.3 billion metric tons, is lost annually. Pathogens, such as Botrytis cinerea, contribute significantly to this loss by attacking stored agricultural produce. These attacks typically start when pathogens infiltrate small fruit wounds, remain dormant, and then switch to an aggressive necrotrophic stage upon ripening, causing significant postharvest food losses. In response to this challenge, this study presents an innovative application of Reverse Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP). This method is increasingly recognized for its simplicity and effectiveness, distinguishing itself from more complex molecular diagnostic techniques. This study focuses on developing a heat-dry RT-LAMP desiccation method designed to be simple, robust, rapid, sensitive, and specific in detecting Botrytis cinerea. This method lies in its utilization of a desiccation process, where heat is utilized to preserve crucial components such as primers and enzymes in the presence of trehalose. A 5% trehalose with an amplification time of 1 h and 40 min was optimal for the assay detection of latent Botrytis cinerea. This method exhibited a sensitivity of 10 femtograms and was tailored specifically to the Botrytis cinerea PLF marker. Validation was performed using RNA extracted from an infected tomato, establishing a detection threshold of 1 ng/µL, approximately 500 pg of synthesized DNA target marker. This discovery holds significant implications, suggesting the potential for developing dry RT-LAMP kits that are adaptable for both laboratory and field usage. Furthermore, this method shows promise as a diagnostic tool for other neglected pathogenic diseases, representing a substantial advancement in agricultural pathology and supporting endeavors to enhance food security. Full article

Host genetics and environmental factors have been associated with effects on the mouse fecal microbiome; however, the commercial source of mice remains the dominant factor. Increasing evidence indicates that supplier-specific microbiomes confer differences in disease susceptibility in models of inflammatory conditions, as well as baseline behavior and body morphology. However, current knowledge regarding the compositional differences between suppliers is based on targeted-amplicon sequencing data, and functional differences between these communities remain poorly defined. We applied a multi-omic (metagenomic and metatranscriptomic) approach to biomolecules extracted from murine feces representative of two U.S. suppliers of research mice, which differ in composition, and influence baseline physiology and behavior as well as disease severity in models of intestinal disease. We reconstructed high-quality metagenome-assembled genomes, frequently containing genomic content unique to each supplier. Transcriptional activity and pathway analyses revealed key functional differences between the metagenomes associated with each supplier including carbohydrate, fatty acid, and sulfite metabolism. These data provide a detailed characterization of the baseline differences in the fecal metagenome of mice from two U.S. commercial suppliers, suggesting that these functional differences are influenced by differences in the initial inoculum of colony founders, as well as additional taxa gained during growth of the production colony. Full article

On commercial banana (Musa spp.) plantations, soils are often supplemented with phosphorus (P) fertiliser to optimise production. Such additions may influence the diversity and function of soil microbial communities, which play important roles in P cycling and affect plant fitness. Here, we characterised the effects of P addition on the diversity and function of banana-associated microbial communities. P addition was associated with significant increases in soil P and the activities of alpha-glucosidase, chitinase, arylsulphatase, and acid phosphatase, but not beta-glucosidase or xylosidase. P addition also expedited bunch emergence and harvest, but did not influence fruit yield, plant height, or foliar P. There were no significant effects of P addition on the alpha or beta diversity of bacterial, fungal, and nematode communities, including members of the core microbiome. The only exceptions to this was an increase in the relative abundance of a Fusarium population in roots. These results indicate that phosphorus application to banana soils may stimulate microbial enzyme activities with minor or negligible effects on microbial diversity. Full article

Staphylococcus aureus is a leading cause of bloodstream infection (SAB), with up to 30% mortality. Despite treatment with standard antibiotics, one in three patients develops a persistent infection, which portends a five-fold increase in the risk of death. Persistent SAB has been attributed in part to the inability of antistaphylococcal antibiotics to eradicate intracellular S. aureus surviving inside macrophages. (-)- Epigallocatechin gallate (EGCG) is a catechin found in green tea that has been widely studied for its broad biological activities, ranging from anticancer to antibacterial activity. However, EGCG is greatly limited by its poor drug-like properties in terms of stability, membrane permeability, and bioavailability. In this study, we established through a series of in vitro experiments that structural modifications of EGCG enhanced drug-like properties while maintaining or improving its antistaphylococcal activity. Our lead EGCG analogs (MCC-1 and MCC-2) showed improved biochemical properties along with increased potency against extracellular S. aureus and restored susceptibility of β-lactam agents to methicillin-resistant S. aureus (MRSA). Importantly, the lead analogs but not EGCG potentiated macrophage- and antibiotic-mediated clearance of intracellular bacteria. Overall, EGCG analogs showed promise for further development as adjunctive therapy candidates for the treatment of SAB. Full article

The rhizosphere, a narrow region of soil surrounding plant roots, is an environment rich in microbial diversity that profoundly influences plants’ health, growth, and agricultural productivity. This microbial community, known as the rhizosphere microbiome, consists of a complex array of bacteria, fungi, archaea, and other microorganisms that engage in complex interactions with plant roots. These microorganisms contribute to nutrient cycling, mineral uptake facilitation, and protection against soil-borne pathogens, thereby promoting plant growth and resilience towards biotic and abiotic stresses. Additionally, microbial signaling molecules, including phytohormones such as auxins, cytokinin, gibberellins, ethylene, and abscisic acid, play a pivotal role in regulating these interactions by modulating plants’ responses to environmental stressors. Recent advancements in microbiomics have enabled a deeper understanding of the rhizosphere’s diversity, composition, and functions, paving the way for more sustainable agricultural practices. By harnessing the potential of the rhizosphere microbiome, innovative strategies can be developed to reduce dependency on synthetic agrochemicals, enhance soil fertility, and increase crop yields. This review discusses the diversity and mechanisms of plant–microbe interactions, focusing on the role of microbial signaling molecules, and explores their applications in promoting agricultural sustainability. The insights gained from microbiomics studies can revolutionize farming practices by reducing dependency on chemical inputs, enhancing crop productivity, and nurturing soil health and environmental sustainability. Full article