Isolation and Identification of Bacillus Species From Soil and Evaluation of Their Antibacterial Properties

Metagenomic nanopore sequencing for exploring the nature of antimicrobial metabolites of Bacillus haynesii

Multidrug-resistant (MDR) pathogens are a rising global health worry that imposes an urgent need for the discovery of novel antibiotics particularly those of natural origin. In this context, we aimed to use the metagenomic nanopore sequence analysis of soil microbiota coupled with the conventional phenotypic screening and genomic analysis for identifying the antimicrobial metabolites produced by promising soil isolate(s). In this study, whole metagenome analysis of the soil sample(s) was performed using MinION™ (Oxford Nanopore Technologies). Aligning and analysis of sequences for probable secondary metabolite gene clusters were extracted and analyzed using the antiSMASH version 2 and DeepBGC. Results of the metagenomic analysis showed the most abundant taxa were Bifidobacterium, Burkholderia, and Nocardiaceae (99.21%, followed by Sphingomonadaceae (82.03%) and B. haynesii (34%). Phenotypic screening of the respective soil samples has resulted in a promising Bacillus isolate that exhibited broad-spectrum antibacterial activities against various MDR pathogens. It was identified using microscopical, cultural, and molecular methods as Bacillus (B.) haynesii isolate MZ922052. The secondary metabolite gene analysis revealed the conservation of seven biosynthetic gene clusters of antibacterial metabolites namely, siderophore lichenicidin VK21-A1/A2 (95% identity), lichenysin (100%), fengycin (53%), terpenes (100%), bacteriocin (100%), Lasso peptide (95%) and bacillibactin (53%). In conclusion, metagenomic nanopore sequence analysis of soil samples coupled with conventional screening helped identify B. haynesii isolate MZ922052 harboring seven biosynthetic gene clusters of promising antimicrobial metabolites. This is the first report for identifying the bacteriocin, lichenysin, and fengycin biosynthetic gene clusters in B. haynesii MZ922052.

Bacillus velezensis BVE7 as a promising agent for biocontrol of soybean root rot caused by Fusarium oxysporum

Introduction

Soybean root rot (SRR), caused by Fusarium oxysporum, is a severe soil-borne disease in soybean production worldwide, which adversely impacts the yield and quality of soybean. The most effective method for managing crop soil-borne diseases and decreasing reliance on chemical fungicides, such as Bacillus spp., is via microbial biocontrol agents.

Methods and Results

In this study, a soil-isolated strain BVE7 was identified as B. velezensis, exhibiting broad-spectrum activity against various pathogens causing soybean root rot. BVE7 sterile filtrate, at a concentration of 10%, demonstrated significant antifungal activity by inhibiting the conidial germination, production, and mycelial growth of F. oxysporum by 61.11%, 73.44%, and 85.42%, respectively, causing hyphal malformations. The antifungal compound produced by BVE7 demonstrated adaptability to a standard environment. The pot experiment showed that BVE7 suspension could effectively control soybean root rot, with the highest control efficiency of 75.13%. Furthermore, it considerably enhanced the activity of catalase, phenylalanine ammonia lyase, superoxide dismutase, and peroxidase in soybean roots, while also preventing an increase in malondialdehyde activity. By improving the host resistance towards pathogens, the damage caused by fungi and the severity of soybean root rot have been reduced.

Discussion

This study presents the innovative utilization of B. velezensis, isolated from soybean roots in cold conditions, for effectively controlling soybean root rot caused by F. oxysporum. The findings highlight the remarkable regional and adaptive characteristics of this strain, making it an excellent candidate for combating soybean root rot in diverse environments. In conclusion, B. velezensis BVE7 demonstrated potential in effectively reducing SRR incidence and can be considered as a viable option for SRR management.

Functionality of probiotics on the resistance capacity of shrimp against white spot syndrome virus (WSSV)

Shrimp aquaculture is currently regarded as a significant commercial and food production sector due to its growing importance as a source of human-consumable protein, As shrimp farming has become more intensive, disease outbreaks have become more common, necessitating the overuse of antimicrobial drugs, which has had a number of unintended consequences. The white spot syndrome virus (WSSV) is now recognized as one of the world's most pervasive and potentially fatal diseases affecting shrimp. However, there is currently no cure to prevent the disease's uncontrolled incidence and spread. Probiotics are currently favoured over these antimicrobial substances because of their ability to stimulate disease resilience in shrimp farms by strengthening the immune systems naturally. Probiotics for bacterial infections such as vibriosis are well documented, whereas research is still required to identify the legitimate strains for viral diseases. The utilization of these probiotics as a therapy for and preventative measure against WSSV in shrimp farming is a cutting-edge method that has proven to be effective. Some probiotic strains, such as Bacillus spp, Lactobacillus, and Pediococcus pentosaceus, have been displayed to enhance the innate immunity of shrimp against WSSV, reduce viral load, increase digestibility and growth, and support the gut microbiome of the host in multiple investigations. The present review explores recent developments regarding the function of probiotics in shrimp, with a focus on their anti-WSSV activity.

Unleashing the Potential of Bacterial Isolates from Apple Tree Rhizosphere for Biocontrol of Monilinia laxa: A Promising Approach for Combatting Brown Rot Disease

Monilinia laxa, a notorious fungal pathogen responsible for the devastating brown rot disease afflicting apples, wreaks havoc in both orchards and storage facilities, precipitating substantial economic losses. Currently, chemical methods represent the primary means of controlling this pathogen in warehouses. However, this study sought to explore an alternative approach by harnessing the biocontrol potential of bacterial isolates against brown rot in apple trees. A total of 72 bacterial isolates were successfully obtained from the apple tree rhizosphere and subjected to initial screening via co-cultivation with the pathogen. Notably, eight bacterial isolates demonstrated remarkable efficacy, reducing the mycelial growth of the pathogen from 68.75 to 9.25%. These isolates were subsequently characterized based on phenotypic traits, biochemical properties, and 16S rRNA gene amplification. Furthermore, we investigated these isolates' production capacity with respect to two enzymes, namely, protease and chitinase, and evaluated their efficacy in disease control. Through phenotypic, biochemical, and 16S rRNA gene-sequencing analyses, the bacterial isolates were identified as Serratia marcescens, Bacillus cereus, Bacillus sp., Staphylococcus succinus, and Pseudomonas baetica. In dual culture assays incorporating M. laxa, S. marcescens and S. succinus exhibited the most potent degree of mycelial growth inhibition, achieving 68.75 and 9.25% reductions, respectively. All the bacterial isolates displayed significant chitinase and protease activities. Quantitative assessment of chitinase activity revealed the highest levels in strains AP5 and AP13, with values of 1.47 and 1.36 U/mL, respectively. Similarly, AP13 and AP6 exhibited the highest protease activity, with maximal enzyme production levels reaching 1.3 and 1.2 U/mL, respectively. In apple disease control assays, S. marcescens and S. succinus strains exhibited disease severity values of 12.34% and 61.66% (DS), respectively, highlighting their contrasting efficacy in mitigating disease infecting apple fruits. These findings underscore the immense potential of the selected bacterial strains with regard to serving as biocontrol agents for combatting brown rot disease in apple trees, thus paving the way for sustainable and eco-friendly alternatives to chemical interventions.

Production of Bacillus subtilis soil isolate as biocontrol agent under bioreactor conditions

This study aimed to investigate the biomass production of Bacillus subtilis in flask and bioreactor conditions. It is necessary to carry the culture from the shake flask to the pH, air, temperature and stirring controlled bioreactor in order to reduce the working time and increase the production efficiency and product quality. In this study, Bacillus was isolated from soil and grown under flask and bioreactor conditions as biocontrol agent against Botrytis cinerea and Fusarium oxysporum. In this process, a pH value of 7.5, 100% O₂ saturation, 30% dissolved O₂, at the temperature of 37 °C, total flow of 0.1 Lmin^-1 and mixing speed of 150 min^-1 were preferred for optimal concerning high production yield of B. subtilis in bioreactor. To test whether B. subtilis has antifungal activity on the growth of B. cinerea and F. oxysporum, a dual culture assay in a PDA medium was carried out. Ultimately, high biomass production in a short incubation period by reaching 2.2 µg/mL after 9 h in the bioreactor. It was observed that the bacteria produced in the bioreactor cultivation grew stronger and showed high antifungal activity which resulted 33.33% inhibition percentage against B. cinerea. It was concluded that B. subtilis can be used as a green-fungicide against B. cinerea and F. oxysporum, and bacterial metabolites from B. subtilis could pave the way for the development of next generation green/biopesticides.

Molecular Characterization of Bacterial Isolates from Soil Samples and Evaluation of their Antibacterial Potential against MDRS

Some soil microbes, with their diverse inhabitance, biologically active metabolites, and endospore formation, gave them characteristic predominance and recognition among other microbial communities. The present study collected ten soil samples from green land, agricultural and marshy soil sites of Khyber Pakhtunkhwa, Pakistan. After culturing on described media, the bacterial isolates were identified through phenotypic, biochemical and phylogenetic analysis. Our phylogenetic analysis revealed three bacterial isolates, A6S7, A1S6, and A1S10, showing 99% nucleotides sequence similarity with Brevibacillus formosus, Bacillus Subtilis and Paenibacillus dendritiformis. The crude extract was prepared from bacterial isolates to assess the anti-bacterial potential against various targeted multidrug-resistant strains (MDRS), including Acinetobacter baumannii (ATCC 19606), Methicillin-resistant Staphylococcus aureus (MRSA) (BAA-1683), Klebsiella pneumoniae (ATCC 13883), Pseudomonas aeruginosa (BAA-2108), Staphylococcus aureus (ATCC 292013), Escherichia coli (ATCC25922) and Salmonella typhi (ATCC 14028). Our analysis revealed that all bacterial extracts possess activity against Gram-negative and Gram-positive bacteria at a concentration of 5 mg/mL, efficiently restricting the growth of E. coli compared with positive control ciprofloxacin. The study concluded that the identified species have the potential to produce antimicrobial compounds which can be used to control different microbial infections, especially MDRS. Moreover, the analysis of the bacterial extracts through GC-MS indicated the presence of different antimicrobial compounds such as propanoic acid, oxalic acid, phenol and hexadecanoic acid.

Microbiological quality analysis of inoculants based on Bradyrhizobium spp. and Azospirillum brasilense produced "on farm" reveals high contamination with non-target microorganisms

The use of inoculants carrying diazotrophic and other plant growth-promoting bacteria plays an essential role in the Brazilian agriculture, with a growing use of microorganism-based bioproducts. However, in the last few years, some farmers have multiplied microorganisms in the farm, known as "on farm" production, including inoculants of Bradyrhizobium spp. for soybean (Glycine max L. Merrill.) and Azospirillum brasilense for corn (Zea mays L.) or co-inoculation in soybean. The objective was to assess the microbiological quality of such inoculants concerning the target microorganisms and contaminants. In the laboratory, 18 samples taken in five states were serial diluted and spread on culture media for obtaining pure and morphologically distinct colonies of bacteria, totaling 85 isolates. Molecular analysis based on partial sequencing of the 16S rRNA gene revealed 25 genera of which 44% harbor species potentially pathogenic to humans; only one of the isolates was identified as Azospirillum brasilense, whereas no isolate was identified as Bradyrhizobium. Among 34 isolates belonging to genera harboring species potentially pathogenic to humans, 12 had no resistance to antibiotics, six presented intrinsic resistance, and 18 presented non-intrinsic resistance to at least one antibiotic. One of the samples analyzed with a shotgun-based metagenomics approach to check for the microbial diversity showed several genera of microorganisms, mainly Acetobacter (~ 32% of sequences) but not the target microorganism. The samples of inoculants produced on farm were highly contaminated with non-target microorganisms, some of them carrying multiple resistances to antibiotics.

A biogenic microbial biosurfactin that degrades difenoconazole fungicide with potential antimicrobial and oil displacement properties

Surfactin is a bacterial lipopeptide and an influential biosurfactant mainly known for excellent surfactant ability. The amphiphilic nature of surfactin helps it to sustain under hydrophobic and hydrophilic conditions. In this investigation, a bacterium strain (BTKU3) that produces biosurfactant were isolated from oil-contaminated soil. Based on the blue agar plate (Bap) assay, the BTKU3 strain was found to be promising for biosurfactant production. This strain was later identified as a Lysinibacillus sp. by 16S rRNA sequencing. The characteristics of extracted bacterial surfactin were evidenced by FTIR with the presence of amine, C-H, CO, CC, esters, thiocarbonyl and asymmetric aliphatic C-H stretch molecular structural groups. Further, the extracted bacterial biosurfactant material was subjected to Liquid Chromatography-Mass Spectroscopy (LCMS), and it was identified and confirmed as surfactin with an elution time of 3.1 min and m/z value of 1034. The emulsification and oil displacement tests further proved the surfactin ability with 83% of coconut oil emulsion index and 80 % oil displacement ability with diesel, respectively. Lysinibacillus sp. BTKU3 strain also proved its efficacy in the degradation of difenoconazole by utilizing a capacity of 9.1 μg ml^-1. Thus, it is inferred that the Lysinibacillus sp. BTKU3 strain plays a significant role in the production of surfactin, which positively acts as an antimicrobial agent and reduces contaminants in polluted sites.

Biodiversity of Soil Bacterial Communities from the Sasso Fratino Integral Nature Reserve

The Sasso Fratino Integral Nature Reserve (Italy) aims to protect nature and territory. Since no anthropic activities are allowed, it represents a good model to study the bacterial community of a wild environment. The aim of this work was to characterise the cultivable and the total bacterial community of soil samples from the reserve in terms of taxonomy, composition, and structure. Seven soil samples were collected at different altitudes, and the chemical composition, the total and the cultivable microbiota, and the antibiotic resistance profiles of isolates were investigated. Total bacterial communities, studied through Next Generation Sequences analysis, included 390 genera. Samples differed in terms of microbial composition basing on the different altitude/vegetation of collection points. Random Amplified Polymorphic DNA Analysis (RAPD) allowed to identify 82 haplotypes out of 158 bacterial isolates. The taxonomic identification through 16S rDNA sequencing revealed that the strains were affiliated to 21 genera. Antibiotic resistance profiles of bacteria were also investigated, highlighting a high resistance against streptomycin and kanamycin. This work represents the first description of the soil bacterial community from the Natural Reserve of Sasso Fratino, and it is the first study considering the soil microbiota of an Italian integral nature reserve.

Genome Mining and Comparative Genome Analysis Revealed Niche-Specific Genome Expansion in Antibacterial Bacillus pumilus Strain SF-4

The present study reports the isolation of antibacterial exhibiting Bacillus pumilus (B. pumilus) SF-4 from soil field. The genome of this strain SF-4 was sequenced and analyzed to acquire in-depth genomic level insight related to functional diversity, evolutionary history, and biosynthetic potential. The genome of the strain SF-4 harbor 12 Biosynthetic Gene Clusters (BGCs) including four Non-ribosomal peptide synthetases (NRPSs), two terpenes, and one each of Type III polyketide synthases (PKSs), hybrid (NRPS/PKS), lipopeptide, β-lactone, and bacteriocin clusters. Plant growth-promoting genes associated with de-nitrification, iron acquisition, phosphate solubilization, and nitrogen metabolism were also observed in the genome. Furthermore, all the available complete genomes of B. pumilus strains were used to highlight species boundaries and diverse niche adaptation strategies. Phylogenetic analyses revealed local diversification and indicate that strain SF-4 is a sister group to SAFR-032 and 150a. Pan-genome analyses of 12 targeted strains showed regions of genome plasticity which regulate function of these strains and proposed direct strain adaptations to specific habitats. The unique genome pool carries genes mostly associated with “biosynthesis of secondary metabolites, transport, and catabolism” (Q), “replication, recombination and repair” (L), and “unknown function” (S) clusters of orthologous groups (COG) categories. Moreover, a total of 952 unique genes and 168 exclusively absent genes were prioritized across the 12 genomes. While newly sequenced B. pumilus SF-4 genome consists of 520 accessory, 59 unique, and seven exclusively absent genes. The current study demonstrates genomic differences among 12 B. pumilus strains and offers comprehensive knowledge of the respective genome architecture which may assist in the agronomic application of this strain in future.

Overview of the latest developments in the role of probiotics, prebiotics and synbiotics in shrimp aquaculture

With the growing world population, the demand for food has increased, leading to excessive and intensive breeding and cultivation of fisheries, simultaneously exacerbating the risk of disease. Recently, shrimp producers have faced major losses of stocks due to the prevalence of periodical diseases and inappropriate use of antibiotics for disease prevention and treatment, leading to bacterial resistance in shrimp, along with imposing health hazards on human consumers. Strict regulations have been placed to ban or reduce the use of prophylactic antibiotics to lessen their detrimental effects on aquatic life. Dietary and water supplements have been used as substitutes, among which probiotics, prebiotics, and synbiotics have been the most beneficial for controlling or treating bacterial, viral, and parasitic diseases in shrimp. The present analysis addresses the issues and current progress in the administration of pro-, pre-, and synbiotics as disease controlling agents in the field of shrimp farming. Furthermore, the benefits of pro-, pre-, and synbiotics and their mechanism of action have been identified such as; strengthening of immune responses, growth of antibacterial agents, alteration in gut microflora, competition for nutrients and binding sites, and enzymes related activities. Overall, this study aims to depict the antagonistic action of these supplements against a variety of pathogens and their mode of action to counter diseases and benefit shrimp species.

Implementation of Antibiotic Discovery by Student Crowdsourcing in the Valencian Community Through a Service Learning Strategy

Antibiotic misuse is a public health problem due to the appearance of resistant strains in almost all human pathogens, making infectious diseases more difficult to treat. The search for solutions requires the development of new antimicrobials as well as novel strategies, including increasing social awareness of the problem. The Small World Initiative (SWI) and the Tiny Earth (TE) network are citizen science programs pursuing the discovery of new antibiotics from soil samples and the promotion of scientific culture. Both programs aim to bring scientific culture and microbiological research closer to pre-university students through a crowdsourcing strategy and a Service Learning (SL) educational approach, with a 2-fold objective: to encourage students to pursue careers in science and to involve them in the discovery of soil microorganisms producing new antimicrobials. SWI and TE projects were put into practice in Spain under the common name MicroMundo. MicroMundo@Valencia was implemented at the Universitat de València (UV) during the academic years 2017–2018 and 2018–2019. It trained 140 university students to disseminate this initiative into 23 high/secondary schools, and one primary school, involving about 900 people (teachers and students) as researchers. A total of 7,002 bacterial isolates were obtained from 366 soil samples and tested for antibiosis at UV and high/secondary school centers. About 1 or 7% of them produced inhibition halos for the Escherichia coli or Bacillus cereus target strains, respectively. Geolocation of sampling sites by an application developed ad hoc and Kriging analysis also allowed detection of soil foci of antibiotic-producing bacteria. Evaluation of the project by university, high/secondary, and primary school students revealed their strong positive perception and their increased interest in science, as a consequence of acquiring new scientific and pedagogical concepts and skills that they were able to pass on to other classmates, younger students, or relatives. To further expand the dissemination of the project in the Valencian Community, diverse extramural activities deemed to include a gender perspective and aimed at different age groups, were also carried out, obtaining very satisfactory results, increasing sensitivity and awareness to the global antibiotic crisis.

Isolation and Molecular Characterization of Antibiotic Producing Bacillus licheniformis Strains Isolated from Soil

Currently, there is an increase prevalence of antibiotic-resistant bacteria worldwide. Therefore, the need for characterization of naturally occuring antibiotics with less antibiotic resistance is required. Soil resources contains valuable antibiotic producing microorganisms that increasingly being utilized for the production of suitable antibiotics. Therefore, this study aimed at identifying an antibiotic bacteria with ability of producing antibiotic that is isolated from soil samples collected from Al Zarqa provenance, an arid area in Jordan. Morphological and biochemical characterization of the isolates were carried out and found that all of the isolates belong to Bacillus genus. Further confirmation of the characterization of the bacteria was done by ribosomal RNA and PCR. The results reveal that the isolates represent Basilluslicheniformis. These bacilli were further investigated for antimicrobial activities against 6 ATCC human pathogens viz., S. aureus, S. pneumonia, Salmonella typhi., E. coli, P. mirabels and E. cloacae. Additionally, the results of Gas Chromatography Mass Spectrometry (GCMS) of ethyl acetate extracts for B. licheniformis secondary metabolites showed that they contain two main antimicrobial compounds namely Pyrrolo [1, 2-a] pyrazine-1, 4-dione,hexahydro and Trans-13-octadecenoic acid. The present work maybe suggests that soil isolates from the studied arid area include antibiotic producing strains that can be utilized commercially.

Biosurfactant production by a Bacillus megaterium strain

The aim of the present study was to investigate the ability of Bacillus megaterium IBB_Po17 (GenBank KX499518) cells to produce biosurfactant when the growth was done in the presence of long-chain n-alkane n-hexadecane on medium supplemented with yeast extract, proteose peptone, starch, or cellulose. B. megaterium IBB_Po17 revealed a higher growth in the presence of n-hexadecane when the medium was supplemented with yeast extract, proteose peptone, or starch, compared with cellulose. Biosurfactant production was higher when B. megaterium IBB_Po17 was grown in the presence of n-hexadecane on yeast extract, proteose peptone, or starch supplemented medium, compared with biosurfactant produced on cellulose supplemented medium. A direct correlation between cell growth and biosurfactant production was observed. When the growth of B. megaterium IBB_Po17 cells was higher, the decrease in pH values of the medium was higher too, and more amount of CO₂ was released. Changes in cell morphology, aggregation of the cells in clusters, and biofilm formation were observed when B. megaterium IBB_Po17 was grown in the presence of n-hexadecane on medium supplemented with yeast extract, proteose peptone, starch, or cellulose. Due to its physiological abilities, this Gram-positive bacterium could be a promising candidate for the bioremediation of petroleum hydrocarbon polluted environments.

Biological Control of Aedes albopictus: Obtained from the New Bacterial Candidates with Insecticidal Activity

Vector-borne deadly pathogens cause more than 700,000 deaths annually. They are transmitted by several vectors, among which the mosquito is the most important. Chemical compounds often have devastating side effects, leading to the abandonment of the majority of them. Biological control has been performed by using formulations of Bacillus sphaericus and Bacillus thuringiensis, but their intensive use has led to the emergence of resistance. Currently, the development of new alternative molecules is urgently needed, in order to use them in mosaics or in rotation with already known insecticides for the control of vectors, especially mosquitoes. Here, we attempted to identify bacterial species with potential anti-mosquito actions. Among bacterial strains isolated from dry sandy soil from Senegal, eleven strains from the Bacillales and Actinomycetales orders were chosen for the entomopathogenic activity experiments. Then, we tested their secondary metabolites, which were obtained from the supernatant fraction, and their cell wall and cytoplasmic compounds, which were found in the pellet fraction, in Aedes albopictus larvae, and compared the larval mortality rate with that obtained by using a commercial product. A total of 4/11 (36.36%) of the isolated species exhibited insecticidal activity. B. nealsonii, which is not a well-known bacterium, had the highest larvicidal effect with 70% of the larval mortality, which is highlighted for the first time. The Streptomyces species we isolated seem to be potential new species, and 3/5 (60%) of them exhibited insecticidal activity. Our study reports provide potential candidates for the identification of active molecules to be developed for strengthening the biological control of infectious diseases agents transmitted by mosquitoes.

Insecticidal Activity of Bacteria from Larvae Breeding Site with Natural Larvae Mortality: Screening of Separated Supernatant and Pellet Fractions

Mosquitoes can transmit to humans devastating and deadly pathogens. As many chemical insecticides are banned due to environmental side effects or are of reduced efficacy due to resistance, biological control, including the use of bacterial strains with insecticidal activity, is of increasing interest and importance. The urgent actual need relies on the discovery of new compounds, preferably of a biological nature. Here, we explored the phenomenon of natural larvae mortality in larval breeding sites to identify potential novel compounds that may be used in biological control. From there, we isolated 14 bacterial strains of the phylum Firmicutes, most of the order Bacillales. Cultures were carried out under controlled conditions and were separated on supernatant and pellet fractions. The two fractions and a 1:1 mixture of the two fractions were tested on L3 and early L4 Aedes albopictus. Two concentrations were tested (2 and 6 mg/L). Larvae mortality was recorded at 24, 48 and 72 h and compared to that induced by the commercialized B. thuringiensis subsp. israelensis. Of the 14 strains isolated, 11 were active against the A. albopictus larvae: 10 of the supernatant fractions and one pellet fraction, and mortality increased with the concentration. For the insecticide activity prediction in three strains of the Bacillus cereus complex, PCR screening of the crystal (Cry) and cytolytic (Cyt) protein families characteristic to B. thuringiensis subsp. israelensis was performed. Most of the genes coding for these proteins' synthesis were not detected. We identified bacterial strains that exhibit higher insecticidal activity compared with a commercial product. Further studies are needed for the characterization of active compounds.

Mechanisms and the role of probiotic Bacillus in mitigating fish pathogens in aquaculture

Diseases are natural components of the environment, and many have economic implications for aquaculture and fisheries. Aquaculture is a fast-growing industry with the aim to meet the high protein demand of the ever-increasing global population; however, the emergence of diseases is a major setback to the industry. Probiotics emerged as a better solution to curb the disease problem in aquaculture among many alternatives. Probiotic Bacillus has been proven to better combat a wide range of fish pathogens relative to other probiotics in aquaculture; therefore, understanding the various mechanisms used by Bacillus in combating diseases will help improve their mode of action hence yielding better results in their combat against pathogens in the aquaculture industry. Thus, an overview of the mechanisms (production of bacteriocins, suppression of virulence gene expression, competition for adhesion sites, production of lytic enzymes, production of antibiotics, immunostimulation, competition for nutrients and energy, and production of organic acids) used by Bacillus probiotics in mitigating fish pathogens ranging from Aeromonas, Vibrio, Streptococcus, Yersinia, Pseudomonas, Clostridium, Acinetobacter, Edwardsiella, Flavobacterium, white spot syndrome virus, and infectious hypodermal and hematopoietic necrosis virus proven to be mitigated by Bacillus have been provided.

Optimization of enhanced microbial production of zinc bacitracin by submerged fermentation technology

Bacitracin is one of the most important antibiotics used in different biomedical fields. It helps to achieve sizeable amount of foreign exchange due to its use in the poultry feed. The cheap agricultural wastes are readily available for the preparation of fermentation media used for bacitracin production. The microorganisms could be mutated with different chemicals and UV radiation to improve bacitracin production. Thus, the current study was focused on the synthesis of low-cost and effective bacitracin by mutant strains of Bacillus licheniformis, employing the submerged fermentation technique. The bacteria were exposed to the UV irradiation for various time periods ranging from 5 to 40 min. These mutants were named as BLAA-5-BLAA-40. Mutant strain BLAA-25 produced maximum bacitracin, with significantly high activity (142.81 IU/mg) against Klebsiella pneumoniae but less activity against Escherichia coli (115.19 IU/mg). Several fermentation conditions were investigated to optimize bacitracin production. The highest bacitracin yield was obtained by an inoculum size of 10%, fermentation period 48 hr, pH 7, T = 37°C, using soybean meal as a substrate. Among all substrates, cucumber peel was the substrate showing the highest minimum inhibitory concentration (2.3 mg/ml and 2.7 mg/ml against K. pneumoniae and E. coli respectively). A comparison between commercial and experimentally produced Zn bacitracin showed that commercial bacitracin has a low activity (63.2 IU/mg) as compared with experimental bacitracin. Hence, the agro wastes and mutation could be used to increase the synthesis of Zn bacitracin in B. licheniformis.

Evaluation of the Strain Bacillus amyloliquefaciens YP6 in Phoxim Degradation via Transcriptomic Data and Product Analysis

Phoxim, a type of organophosphorus pesticide (OP), is widely used in both agriculture and fisheries. The persistence of phoxim has caused serious environmental pollution problems. In this study, Bacillus amyloliquefaciens YP6 (YP6), which is capable of promoting plant growth and degrading broad-spectrum OPs, was used to study phoxim degradation. Different culture media were applied to evaluate the growth and phoxim degradation of YP6. YP6 can grow rapidly and degrade phoxim efficiently in Luria-Bertani broth (LB broth) medium. Furthermore, it can also utilize phoxim as the sole phosphorus source in a mineral salt medium. Response surface methodology was performed to optimize the degradation conditions of phoxim by YP6 in LB broth medium. The optimum biodegradation conditions were 40 °C, pH 7.20, and an inoculum size of 4.17% (v/v). The phoxim metabolites, O,O-diethylthiophosphoric ester, phoxom, and α-cyanobenzylideneaminooxy phosphonic acid, were confirmed by liquid chromatography-mass spectrometry. Meanwhile, transcriptome analysis and qRT-PCR were performed to give insight into the phoxim-stress response at the transcriptome level. The hydrolase-, oxidase-, and NADPH-cytochrome P450 reductase-encoding genes were significantly upregulated for phoxim hydrolysis, sulfoxidation, and o-dealkylation. Furthermore, the phoxim biodegradation pathways by YP6 were proposed, for the first time, based on transcriptomic data and product analysis.

A review on the application of Bacillus as probiotics in aquaculture

Probiotics use in aquaculture has gained attention as microbial candidates to maintain the health and the well-being of many aquaculture animals. Among the many microbial candidates, probiotic Bacillus has sporulation capacity that makes them survive harsh environmental conditions, are non-pathogenic and non-toxic when fed to fish, and can produce antimicrobial substances making them more suitable candidates compared to other probiotics. In this review, we discussed the necessity of using the probiotic Bacillus in sustainable aquaculture as a good alternative to improve feed utilization, stress response, immune response and disease resistance, maintenance of tissue integrity, and as well improvement of water quality for sustainable aquaculture. Therefore the findings of current researches about the effects of Bacillus application to improve the culture of aquatic animals for future research and development of Bacillus application in aquaculture have been summarised.

Isolation and characterization of Bacillus sp. strain BC01 from soil displaying potent antagonistic activity against plant and fish pathogenic fungi and bacteria

Fungal and bacterial pathogens infect a diverse range of hosts including various plant and animal species. Fungal and bacterial diseases, especially of plants and aquatic animals, such as fish, lead to significant damage to crops and aquaculture, respectively, worldwide. The present study was conducted to isolate and characterize potent Bacillus strains with significant antagonistic activity against the major plant and fish pathogenic fungi and bacteria. We randomly collected 22 isolates of Bacillus from the soil, rhizosphere, and sediment from different parts of Bangladesh. Initial characterization, based on in vitro antagonistic activity on the culture plate, resulted in the selection of four gram-positive Bacillus sp. isolates. Among these, the isolate BC01, obtained from soil demonstrated the highest broad-spectrum anti-bacterial and anti-fungal activities. We confirmed the genus of BC01 to be Bacillus by morphological and biochemical tests as well as using molecular data analysis tools, including the study of 16s rDNA, phylogenetic relationship, and evolutionary divergence scores. The isolate significantly inhibited the mycelial growth of the plant pathogen, Penicillium digitatum and fish pathogen, Aphanomyces invadans in vitro. The anti-bacterial effect of the isolate was also evaluated against Pseudomonas spp. and Xanthomonas spp., the two deadliest plant pathogens, and Aeromonas veronii, Pseudomonas fluorescens, and Streptococcus iniae, three major fish pathogens that are primarily responsible for global aquaculture loss. The results of the present study could pave the way for developing potent drugs to combat microbial infection of plants and fish.

Non-Covalent Supported of l-Proline on Graphene Oxide/Fe₃O₄ Nanocomposite: A Novel, Highly Efficient and Superparamagnetically Separable Catalyst for the Synthesis of Bis-Pyrazole Derivatives

A superparamagnetic graphene oxide/Fe₃O₄/l-proline nano hybrid that was obtained from the non-covalent immobilization of l-proline on graphene oxide/Fe₃O₄ nanocomposite was used as a new magnetically separable catalyst for the efficient synthesis of 4,4′-(arylmethylene)bis(1H-pyrazol-5-ol) derivatives. The prepared heterogeneous catalyst was characterized using FTIR, TGA, DTG, XRD, TEM, SEM, and elemental analysis techniques. Short reaction times (5–15 min), excellent yields (87–98%), and simple experimental procedure with an easy work-up are some of the advantages of the introduced catalyst.

The role of microbiota, and probiotics and prebiotics in skin health

During the past decade, scientists have made great strides in understanding the microbiome's role in human health. Today, the microbiome has become key in scientific research, therapeutic development, medical treatment, and as a news feature in the media. Most studies have focused on the microbiome of our gut, but recently researchers have turned their attention to other microbiomes, including that of the skin. These studies of gut and skin microbiomes are yielding very informative results, new treatment strategies, and the development of new prebiotic and probiotic products for the treatment of many skin conditions.

Bioprospecting Red Sea Coastal Ecosystems for Culturable Microorganisms and Their Antimicrobial Potential

Microorganisms that inhabit unchartered unique soil such as in the highly saline and hot Red Sea lagoons on the Saudi Arabian coastline, represent untapped sources of potentially new bioactive compounds. In this study, a culture-dependent approach was applied to three types of sediments: mangrove mud (MN), microbial mat (MM), and barren soil (BS), collected from Rabigh harbor lagoon (RHL) and Al-Kharrar lagoon (AKL). The isolated bacteria were evaluated for their potential to produce bioactive compounds. The phylogenetic characterization of 251 bacterial isolates based on the 16S rRNA gene sequencing, supported their assignment to five different phyla: Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Planctomycetes. Fifteen putative novel species were identified based on a 16S rRNA gene sequence similarity to other strain sequences in the NCBI database, being ≤98%. We demonstrate that 49 of the 251 isolates exhibit the potential to produce antimicrobial compounds. Additionally, at least one type of biosynthetic gene sequence, responsible for the synthesis of secondary metabolites, was recovered from 25 of the 49 isolates. Moreover, 10 of the isolates had a growth inhibition effect towards Staphylococcus aureus, Salmonella typhimurium and Pseudomonas syringae. We report the previously unknown antimicrobial activity of B. borstelensis, P. dendritiformis and M. salipaludis against all three indicator pathogens. Our study demonstrates the evidence of diverse cultured microbes associated with the Red Sea harbor/lagoon environments and their potential to produce antimicrobial compounds.