Search Results (33)

Fusarium head blight (FHB), caused mainly by the Fusarium graminearum species complex, is a devastating cereal disease associated with yield losses and mycotoxin contamination. Early infection is closely linked to spore germination and germ tube elongation, yet conventional monitoring methods are labor-intensive and poorly suited for dynamic phenotypic quantification. We present EffiFormer-CGS, a three-module deep learning framework integrating object detection, key point localization, and phenotypic quantification for microscopic images of FHB spores. A dataset of 2381 images was generated from systematic experiments with triazole fungicides (Prochloraz, Prothioconazole, and Tebuconazole) across multiple concentrations and time points. Spores were annotated with bounding boxes and fine-grained geometric key points, enabling calculation of germination degree as the ratio of germ tube length to body length. EffiFormer-CGS achieved 90.8% mAP@0.5:0.95 in object detection and 91.4% mAP@0.5 in key point localization. All fungicides significantly inhibited germination, with Prochloraz showing the strongest effect. Predictions closely matched manual counts, with germination rate errors ≤ 5.18%. EffiFormer-CGS provides an efficient, automated, and high-precision approach for spore germination analysis, supporting high-throughput fungicide screening, resistance monitoring, and sustainable FHB management. Full article

The rhizosphere is a dynamic microenvironment where plants interact with diverse native microbial communities that significantly influence growth, health, and resilience. Among plant-growth-promoting rhizobacteria, Bacillus subtilis stands out as a multifunctional species with exceptional ability to colonize plant roots, form robust biofilm, and confer protection against diseases. Its resilience as a spore-former, genetic ability to produce active compounds such as antibiotics, and phytohormones make it a valuable species for agriculture and forest sustainability. This review reveals the molecular and physiological mechanisms underlying B. subtilis interactions with plants, focusing on biofilm formation, root colonization, biocontrol and disease suppression, and promotion of plant growth. We further examine its role in root colonization, which triggers extensive reprogramming of plant gene expression, thereby integrating growth promotion with enhanced immune competence through a network that regulates plant-beneficial traits. Its genomic regulation supports colonization, stress tolerance, and immune support, while synergistic interactions with other microbes highlight its adaptability. As a versatile bio-fertilizer and biocontrol agent, further study of its strain-specific traits and rhizosphere interactions is key to maximizing its role in sustainable agriculture and forest control under environmental changes. Full article

Edible insects are gaining traction worldwide; however, the existing data regarding their microbiological quality remain inadequate. This study investigated the bacterial communities and microbiological quality of five types of frozen edible insects commercially available in Thailand. Amplicon sequencing revealed Firmicutes (Bacillota) and Proteobacteria (Pseudomonadota) as the main phyla across all samples; Bacteroidota was predominant in house crickets, Actinobacteriota in silkworms, and Desulfobacterota was exclusively found in house and mole crickets. Culture-based assays showed total viable counts, lactic acid bacteria, yeasts–molds, and spore-formers ranging from 3.41–6.58, 2.52–7.41, 1.83–5.62, to 2.00–4.70 log CFU·g⁻¹, respectively. In some samples, Enterobacteriaceae and Escherichia coli, key hygiene indicators, reached 5.05 and 2.70 log CFU·g⁻¹, respectively. Among foodborne pathogens, presumptive Bacillus cereus was found to vary from <1.70 to 3.93 log CFU·g⁻¹, while Clostridium perfringens and Staphylococcus aureus were under the quantitation limit, and Salmonella was absent. Overall, the results indicate significant variation in microbial diversity and quality among different insect types. The high levels of microbial hygiene indicators and foodborne pathogens in some samples raised food safety concerns and point to the need to develop or implement production guidelines and microbiological criteria for frozen edible insects to ensure food safety. 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 fragmentary and whole substitution of wheat flour with flour blends is an alternative approach for producing cheaper, nutrient-rich, and comparatively advantageous gluten-free foods through fermentation. Dry samples of sweet potato, pigeon pea, and maize botanicals were purchased from local vendors, authenticated and processed before spontaneous fermentation at room temperature. The pH and microbiological growth patterns of the fermenting botanicals were evaluated every 12 h for 72 h, using standard test protocols. It revealed that the rates of growth of isolated microorganisms were affected by pH; all the botanicals fermented had a reduction in their pH values. Acids were produced during fermentation, leading to a reduction in pH. Bacteria growth on the fermenting samples on nutrient agar reveals that the bacterial load increased with fermentation time, from 7.52 Log₁₀ CFU/g to 10.6 Log₁₀ CFU/g (sweet potato); 6.3 Log₁₀ CFU/g to 10.54 Log₁₀ CFU/g (pigeon pea), and 6.3 Log₁₀ CFU/g to 10.54 Log₁₀ CFU/g (maize). On MacConkey agar, the bacterial load on all samples started after 24 h of fermentation, peaked at 48 h, and gradually reduced towards 72 h of fermentation. There was increase in fungal growth with time from 0 to 36 h across all samples. The microorganisms isolated can be categorized into lactic acid bacteria, spore formers, Enterobacteriaceae, Staphylococcace, yeast, and molds. Fermentation of botanicals over 72 h results in organic acid formation, which lowers pH; this attribute helps in checkmating undesirable microorganisms capable of affecting the production of gluten-free flours with good keeping qualities. Full article

For years, the Bacillus genus has encompassed a heterogeneous group of individuals whose main common trait was their ability to sporulate in the presence of oxygen. This criterion has been revised, resulting in the reclassification of several species into new genera and to a redefinition of the characteristics of the members of this taxon. Currently, the species of the genus are grouped into the Subtilis clade and the Cereus clade. The former, called Bacillus sensu stricto, initially composed of B. subtilis, B. licheniformis, B. pumilus, and B. amyloliquefaciens, has subsequently incorporated new species related to these. The Cereus clade, Bacillus cereus sensu lato, consists of pathogenic species (B. anthracis, B. cereus, and B. thuringiensis) as well as others of significance in agriculture and industry. Furthermore, identifying these individuals remains complex, requiring alternatives to 16S rRNA sequencing. The ability to form spores resistant to stressful conditions provides a significant advantage over other genera, with observable differences in sporulation rates and spore structure among different species. Additionally, Bacillus spp. are known for their capacity to produce antimicrobial substances, lytic enzymes, and volatile organic compounds, each with diverse applications. Some species are even used as probiotics. This review delves into aspects related to the taxonomy and identification of microorganisms belonging to the genus Bacillus, which often present challenges. The aim is to provide a comprehensive overview of the topic. In addition, it highlights the characteristics and applications of the genus, emphasizing its importance in biotechnology and microbiology. Full article

Bacillus cereus is estimated to be responsible for 1.4–12% of all food poisoning outbreaks worldwide. The objective of this study was to investigate the toxigenic potential of 181 isolates of B. cereus previously recovered from different types of berries and berry products (strawberries, raspberries, blackberries, and blueberries) by assessing the presence of enterotoxin genes (hblA, hblC, hblD, nheA, nheB, nheC, and cytK) and an emetic toxin cereulide synthetase gene (ces). The cytotoxic activity on Caco-2 cells was also evaluated for the two isolates containing the gene cytK. Twenty-three toxigenic profiles were found. The nheABC (91.7%) and hblACD (89.0%) complexes were the most prevalent among the isolates, while the cytK and ces genes were detected in low percentages, 1.1% and 3.3%, respectively. In addition, the nheABC/hblACD complex and ces genes were detected in isolates recovered throughout the production process of blackberries and strawberries. The cytotoxic activity on Caco-2 cells was also observed to be greater than 60% for isolates containing the cytK gene. Full article

Due to its growth under harsh acidic conditions, the microalga Galdieria sulphuraria may offer the opportunity to combine sanitation and the utilization of organic waste streams. To further deepen the knowledge of alternative waste treatment strategies that allow for holistic utilization, the control and removal of microbial contaminants via non-sterile heterotrophic G. sulphuraria on food waste hydrolysate were investigated in a continuous flow bioreactor culture. Furthermore, a substrate reservoir and harvested biomass were stored under non-sterile conditions over a period of 12 days. Despite the non-sterile conditions, the microbial load of the biomass could be kept under control. Neither the pathogen Salmonella sp. nor the coliform bacteria Escherichia coli could be found. Only nine counts per g of biomass were found for species belonging to Enterococcus spp., Enterobacteriacae, and moulds. Aerobic spore formers were counted with 2700 counts per g of biomass. Most of the aerobic mesophilic counts were formed by yeasts (1.5 × 10⁶ vs. 1.3 × 10⁶ counts per g biomass). The results revealed that, when using acidic growth conditions, contamination will not take over the culture; thus, the sterilization of waste materials can be skipped. It is assumed that such an approach can result in efficient processes for future waste-based bioeconomy strategies. Full article

Mycopesticides are living preparations that use fungal cells, such as spores and hyphae, as active ingredients. They mainly include mycoinsecticides, mycofungicides, mycoherbicides and nematophagous fungi. The utilization of fungi for controlling agricultural pests can be traced back to approximately 1880, when entomopathogenic fungi were initially employed for this purpose. However, it was not until 1965 that the world’s first mycopesticide, Beauveria bassiana, was registered as Boverin^® in the former Soviet Union. In past decades, numerous novel mycopesticides have been developed for their lower R&D costs, as well as the environmentally friendly and safe nature. In this review, we investigated the mycopesticides situation of registration in USA, EU, China, Canada and Australia. Superisingly, it was found that the registered mycopesticides are extremely raised in recent years. Currently, the insecticides, fungicides (nematocides) and herbicides were respectively registered 27, 53 and 8 fungal strains. This paper also analyzes the main problems currently faced by mycopesticides and offers suggestions for their future development. Full article

Spore-forming bacteria in silage may reduce dry matter intake or affect dairy product quality when transferred to milk. The present study investigated the effects of three facultative anaerobes (Bacillus cereus, Bacillus subtilis, and Bacillus licheniformis) and two strict anaerobes (Clostridium tyrobutyricum and Clostridium beijerinckii) commonly found in low-quality silage, milk, and cheese. Maize silage was intentionally contaminated with these spore formers in separate mini silos at 1 × 10⁵ CFU spore former per g and treated with commercial silage inoculant Lentilactobacillus buchneri NCIMB 40788 at 4 × 10⁵ CFU per g or left untreated. The microbial and chemical profiles of maize silage, which were determined using Nuclear Magnetic Resonance (NMR), were measured after fermentation for 100 days, and they were also measured for silage exposed to air for 72 h after opening at 100 days. The effect of the inoculant strain L. buchneri NCIMB 40788 on these contaminated silages was investigated to determine if the inoculant could prevent/limit the negative impacts caused by the spore former contaminants. Overall, inoculation improved silage quality and aerobic stability. Acetic acid content was higher in the INOC samples than in the NIS (p < 0.001), while lactic acid content was lower in INOC than in NIS (p < 0.001). Both lactic and acetic acid levels were higher in the silage samples contaminated with B. cereus. Contamination with the spore formers increased the aerobic and anaerobic spore counts of the samples contaminated with B. subtilis and B. licheniformis compared to the control silage after opening. After 3 days of aerobic exposure, the samples contaminated with B. cereus, B. subtilis, and B. licheniformis showed higher aerobic spore counts than the control. The dominant bacterial population was significantly modified by inoculation. Neither inoculation nor contamination types impacted fungal populations upon opening, but a dominance of Wickerhamomyces was observed after aerobic exposure in the B. cereus silages. The γ-aminobutyrate (GABA) content after aerobic exposure was higher than the uncontaminated control for the silage contaminated with B. licheniformis. The samples contaminated with Clostridium species remained largely unchanged compared to the control samples. Physicochemical and bacterial profiles were mainly affected by inoculation, and a limited impact of spore contaminant was noted. Our results show that when L. buchneri inoculation was carried out, higher aerobic and anaerobic spore counts following contamination with bacterial spore formers were mitigated after reaching aerobic stability. Full article

Human zoonotic infection with Campylobacter is a major cause of gastroenteritis in the United States and worldwide. Listeria monocytogenes causes a potentially fatal infection in humans and is often attributed to contaminated food. Genetic typing has demonstrated that Campylobacter infection is often associated with the consumption of contaminated poultry products, with Campylobacter often colonizing the poultry gastrointestinal tract, while listeriosis is commonly associated with the consumption of contaminated ready-to-eat (RTE) foods. In this study, a strain of endospore-forming bacterium (strain NH) that is bactericidal towards the human food pathogens Campylobacter jejuni and Listeria monocytogenes was identified and characterized. Transwell experiments demonstrated that the bactericidal effect on both C. jejuni and L. monocytogenes is due to secretions from the spore former. These foodborne pathogens consistently exhibited 7 log reductions in growth when exposed to the NH cell-free culture filtrate. Sequencing of the 16s rRNA gene V4 variable region and analysis of the full-length 16s rRNA gene sequence from the WGS indicated that strain NH belongs to the species Aneurinibacillus aneurinilyticus. A microplate bioassay demonstrated that a bactericidal substance that is sensitive to protease could be collected from cell-free filtrates by salting out with ammonium sulfate. Gel filtration chromatography indicated a native molecular weight for the bactericidal protein of ca. 50 kDa, consistent with a class III bacteriocin. The active protein bound strongly to a cation-exchange resin and with an isoelectric point of ten, suggesting a positively charged protein. Both cation-exchange chromatography and isoelectric focusing indicated the enrichment of an 11 kDa protein on SDS-PAGE. This protein was identified through mass spectroscopy as the flgM protein, an anti-sigma factor. Analysis of whole genome sequencing (WGS) of the strain NH genome indicated the presence of a number of non-conservative amino acid substitutions in the flgM-gene-derived amino acid sequence of strain NH and A. aneurinilyticus compared to other members of the Aneurinibacillus genus. Further investigation is needed to determine whether these substitutions are correlated with the bactericidal activity. The identified strain may be useful as a feed additive for the pre-harvest control of Campylobacter jejuni in poultry. Full article

Typhulaceae Jülich is one of the cold-adapted fungal families in basidiomycetes. The representative genera, Typhula (Pers.) Fr. and Pistillaria Fr., are distinguished by the discontinuity between stems and hymenia in the former and the continuity in the latter (Fries 1821). This taxonomic criterion is ambiguous, and consequently, the view of Karsten (1882) has been widely accepted: Typhula develops basidiomata from sclerotia, while basidiomata develop directly from substrata in Pistillaris. However, Corner (1970) observed basidiomata of Pistillaria petasitis S. Imai developing from sclerotia in Hokkaido, Japan. We later recognized that P. petasitis basidiomata also emerged directly from substrates on the ground in Hokkaido. An aberrant form of Typhula hyperborea H. Ekstr. was found in Upernavik, West Greenland. This specimen had a stem-like structure on a Poaceae plant, and sclerotia developed on its tip. Similar phenomena were found in other Typhula species in Japan. In this study, we aimed to elucidate the life cycle plasticity in the genera Typhula and Pistillaria through the interactions between their ecophysiological potential and environmental conditions in their localities. We collected and prepared strains of the above fungi from sclerotia or basidiomata, and we elucidated the taxonomical relationship and determined the physiological characteristics of our strains. Our findings imply that both Typhula and Pistillaria have the potential to produce sclerotia as well as the capacity for mycelial growth at ambient air temperatures in each locality where samples were collected. These findings suggest that Typhula spp. develope basidiomata not only from the sclerotia dispersed by the basidiospores but also from mycelia generated by the spore germination, which formed basidiomata multiple times, depending on their growth environments. Full article

A total of thirty-two aerobic spore former strains were isolated from intestinal samples of healthy children and analyzed for their hemolytic and antibiotic-resistant activities. Four strains selected as non-hemolytic and sensitive to all antibiotics recommended as relevant by regulatory agencies were short-listed and evaluated for their in silico and in vitro probiotic potentials. The four selected strains were assigned to the Bacillus velezensis (MV4 and MV11), B. subtilis (MV24), and Priestia megaterium (formerly Bacillus megaterium) (MV30) species. A genomic analysis indicated that MV4, MV11, and MV24 contained a homolog of the gene coding for the fibrinolytic enzyme nattokinase while only MV30 encoded a glutamic acid decarboxylase essential to synthesize the neurotransmitter GABA. All four strains contained gene clusters potentially coding for new antimicrobials, showed strong antioxidant activity, formed biofilm, and produced/secreted quorum-sensing peptides able to induce a cytoprotective stress response in a model of human intestinal (HT-29) cells. Altogether, genomic and physiological data indicate that the analyzed strains do not pose safety concerns and have in vitro probiotic potentials allowing us to propose their use as an alternative to antibiotics. Full article

Resuscitation promoting factors (Rpf), a class of proteins secreted by gram-positive bacteria including actinobacteria, promote the resuscitation of dormant bacteria and spore germination. Here, we describe the reconstitution of the resuscitation promoting activity of the Rpf protein from Nocardiopsis halophila CGMCC 4.1195^T in vitro and in vivo. The Rpf protein was expressed in the host Escherichia coli BL21 codon plus (DE3) and was confirmed to have a significant resuscitation effect on the viable but non-culturable (VBNC) N. halophila. Subsequently, the rpf gene of N. halophila was knocked out. We found that the growth rate of the mutant strain (Δrpf) was slower than that of the wild strain, and the former produced significantly shorter spores than the wild-type strain. Our results confirmed the activity of the Rpf protein in N. halophila to promote dormant bacteria resuscitation. This study will lay the foundation for the application of the Rpf protein from N. halophila to exploit actinomycetes resources. Full article

New detections of thermophiles in psychrobiotic (i.e., bearing cold-tolerant life forms) marine and terrestrial habitats including Arctic marine sediments, Antarctic accretion ice, permafrost, and elsewhere are continually being reported. These microorganisms present great opportunities for microbial ecologists to examine biogeographical processes for spore-formers and non-spore-formers alike, including dispersal histories connecting warm and cold biospheres. In this review, we examine different examples of thermophiles in cryobiotic locations, and highlight exploration of thermophiles at cold temperatures under laboratory conditions. The survival of thermophiles in psychrobiotic environments provokes novel considerations of physiological and molecular mechanisms underlying natural cryopreservation of microorganisms. Cultures of thermophiles maintained at low temperature may serve as a non-sporulating laboratory model for further exploration of metabolic potential of thermophiles at psychrobiotic temperatures, as well as for elucidating molecular mechanisms behind natural preservation and adaptation to psychrobiotic environments. These investigations are highly relevant for the search for life on other cold and icy planets in the Solar System, such as Mars, Europa and Enceladus. Full article