Whole-genome sequencing of Bacillus velezensis LS69, a strain with a broad inhibitory spectrum against pathogenic bacteria

Bacillus velezensis LS69 was found to exhibit antagonistic activity against a diverse spectrum of pathogenic bacteria. It has one circular chromosome of 3,917,761bp with 3,643 open reading frames. Genome analysis identified ten gene clusters involved in nonribosomal synthesis of polyketides (macrolactin, bacillaene and difficidin), lipopeptides (surfactin, fengycin, bacilysin and iturin A) and bacteriocins (amylolysin and amylocyclicin). In addition, B. velezensis LS69 was found to contain a series of genes involved in enhancing plant growth and triggering plant immunity. Whole genome sequencing of Bacillus velezensis LS69 will provide a basis for elucidation of its biocontrol mechanisms and facilitate its applications in the future.

Genomic and Functional Characterization of the Endophytic Bacillus subtilis 7PJ-16 Strain, a Potential Biocontrol Agent of Mulberry Fruit Sclerotiniose

Bacillus sp. 7PJ-16, an endophytic bacterium isolated from a healthy mulberry stem and previously identified as Bacillus tequilensis 7PJ-16, exhibits strong antifungal activity and has the capacity to promote plant growth. This strain was studied for its effectiveness as a biocontrol agent to reduce mulberry fruit sclerotiniose in the field and as a growth-promoting agent for mulberry in the greenhouse. In field studies, the cell suspension and supernatant of strain 7PJ-16 exhibited biocontrol efficacy and the lowest disease incidence was reduced down to only 0.80%. In greenhouse experiments, the cell suspension (1.0 × 10⁶ and 1.0 × 10⁵ CFU/mL) and the cell-free supernatant (100-fold and 1000-fold dilution) stimulated mulberry seed germination and promoted mulberry seedling growth. In addition, to accurately identify the 7PJ-16 strain and further explore the mechanisms of its antifungal and growth-promoting properties, the complete genome of this strain was sequenced and annotated. The 7PJ-16 genome is comprised of two circular plasmids and a 4,209,045-bp circular chromosome, containing 4492 protein-coding genes and 116 RNA genes. This strain was ultimately designed as Bacillus subtilis based on core genome sequence analyses using a phylogenomic approach. In this genome, we identified a series of gene clusters that function in the synthesis of non-ribosomal peptides (surfactin, fengycin, bacillibactin, and bacilysin) as well as the ribosome-dependent synthesis of tasA and bacteriocins (subtilin, subtilosin A), which are responsible for the biosynthesis of numerous antimicrobial metabolites. Additionally, several genes with function that promote plant growth, such as indole-3-acetic acid biosynthesis, the production of volatile substances, and siderophores synthesis, were also identified. The information described in this study has established a good foundation for understanding the beneficial interactions between endophytes and host plants, and facilitates the further application of B. subtilis 7PJ-16 as an agricultural biofertilizer and biocontrol agent.

Complete genome sequence of Bacillus velezensis LM2303, a biocontrol strain isolated from the dung of wild yak inhabited Qinghai-Tibet plateau

Bacillus velezensis LM2303 is a biocontrol strain with a broad inhibitory spectrum against plant pathogens, isolated from the dung of wild yak inhabited Qinghai-Tibet plateau, China. Here we present its complete genome sequence, which consists of a single, circular chromosome of 3,989,393bp with a 46.68% G+C content. Genome analysis revealed genes encoding specialized functions for the biosynthesis of antifungal metabolites and antibacterial metabolites, the promotion of plant growth, the alleviation of oxidative stress and nutrient utilization. And the biosynthesis of antimicrobial metabolites in strain LM2303 was confirmed by biochemical analysis, while its plant growth promoting traits were confirmed by inoculation tests. Our results will establish a better foundation for further studies and biocontrol application of B. velezensis LM2303.

Metabolomics investigation of summer mortality in New Zealand Greenshell™ mussels (Perna canaliculus)

Increasing water temperatures due to climate change have resulted in more frequent high mortality events of New Zealand Greenshell™ mussels (Perna canaliculus Gmelin 1791). These events have significant impacts within mussel farms which support a major shellfish industry for New Zealand. The present study investigates metabolic responses of farmed mussels during a summer mortality event in order to identify health impacts and elucidate mechanistic effects of external stressors on mussels. A gas chromatography-mass spectrometry (GC-MS)-based metabolomics approach was used to identify metabolic perturbations and flow cytometry assays were used to assess viability, oxidative stress and apoptosis of haemocytes from healthy and unhealthy mussels during a summer mortality event. The results showed significantly higher mortality and apoptosis of haemocytes in unhealthy mussels compared to healthy mussels. Reactive oxygen species (ROS) production, which is an indicator of oxidative stress was very high in both mussel groups, but no differences were observed between the two mussel groups. Metabolomics revealed alterations of many metabolites in both haemolymph and hepatopancreas (digestive gland) of unhealthy mussels compared to healthy mussels, reflecting perturbations in several molecular pathways, including energy metabolism, amino acid metabolism, protein degradation/tissue damage and oxidative stress. An increased level of itaconic acid which is an antimicrobial metabolite and biomarker of pathogen infection was observed in haemolymph, but not in hepatopancreas samples. This investigation provides the first detailed metabolic characterization of mussel immune responses to a summer mortality event and illustrates the benefits of using an integrated metabolomics and flow cytometry workflow for mussel health assessment and biomarker identification for summer mortality early detection.

Molecular characterization of an endophytic Phomopsisliquidambaris CBR-15 from Cryptolepis buchanani Roem. and impact of culture media on biosynthesis of antimicrobial metabolites

An endophytic fungus Phomopsis liquidambaris CBR-15, was isolated from Cryptolepis buchanani Roem. (Asclepiadaceae) and identified by its characteristic culture morphology and molecular analysis of the ITS region of rDNA and intervening 5.8S rRNA gene. The impact of different culture media on biosynthesis of antimicrobial metabolites was tested by disc diffusion assay. Polyketide synthase gene (PKS) of the endophytic fungus was investigated using three pairs of degenerate primers LC1-LC2c, LC3-LC5c and KS3-KS4c by PCR. TLC-bioautography method was employed to detect the antimicrobial metabolites. Antimicrobial metabolites fractionated with ethyl acetate extract showed significant antimicrobial activity against the test bacteria and fungi. Biosynthesis of antimicrobial metabolites was optimum as depicted by zone of inhibition from ethyl acetate extract cultured in potato dextrose broth. Strain CBR-15 was identified as Phomopsisliquidambaris and PKS genes of the fungus were amplified with LC3-LC5c and KS3-KS4c sets of degenerate primers. These findings suggest that endophytic P.liquidambaris CBR-15 harbor iterative type I fungal PKS gene domain which indicates the biosynthetic potential of endophytic fungi as producers of natural antimicrobial metabolites. The study also demonstrates the utilization and optimization of different culture media which best supports for the biosynthesis of the antimicrobial metabolites from P.liquidambaris.

Extracellular and intracellular phenol production by microalgae during photoautotrophic batch cultivation

Understanding the mechanisms of phenol production by microalgae can contribute to the development of microalgal biorefinery processes with higher economic and environmental sustainability. However, little is known about how phenols are produced and accumulate during microalgal cultivation. In this study, both extracellular and intracellular phenol production by two microalgal strains (Tetradesmus obliquus and Chlorella sp.) were investigated throughout a conventional photoautotrophic batch cultivation. The highest intracellular phenol content (10-25 mg g^-1) and productivity (12-18 mg L^-1 d^-1) were attained for both strains in the first part of the batch, indicating a positive relation with nutrient availability and biomass productivity. Extracellular phenol production was 2-20 fold lower than intracellular phenols, but reached up to 27 mg L^-1 for T. obliquus and 13 mg L^-1 for Chlorella sp. The latter finding highlights relevant issues about the management of the exhausted culture medium, due to likely antimicrobial effects.

Effects of Pichia manshurica yeast supplementation on ruminal fermentation, nutrient degradability, and greenhouse gas emissions in aflatoxin B1 contaminated diets

Yeast feed additives present a natural approach for mitigating ruminal greenhouse gases (GHG) in an environmentally sustainable manner. This study aimed to isolate yeast strains from ruminal fluids capable of reducing GHG from Aflatoxin (AFB1) contaminated diets. Two isolates of Pichia manchuria (FFNLYFC1 and FFNLYFC2) were isolated and identified from the ruminal contents of dairy Zaraibi goats. An in vitro gas production assay was conducted to evaluate the impact of the yeast supplementations on a basal diet contaminated with AFB1 or not. The treatments were control (-AFB1; basal diet without supplements), control with AFB1 contamination (+ AFB1; basal diet containing 20 ppb AFB1), and yeast-supplemented diets (basal diet supplemented with Saccharomyces cerevisiae, and three treatments of P. manchuria [FFNLYFC1, FFNLYFC2, and their mixture at 1:1 ratio (Mix)]. High biological components were detected in abundance of both FFNLYFC1, FFNLYFC2 filtrates (e.g., diisooctyl phthalate). The Mix and FFNLYFC2 of P. manchuria reduced (P < 0.05) methane by 23.5 and 20.8%, respectively, while only Mix inhibited carbon dioxide by 44% compared to the + AFB1 diet. All yeast diets improved (P < 0.05) ammonia concentration, total protozoal and Entodinium spp. counts compared to + AFB1 diet. The Mix exhibited higher (P < 0.05) values of ruminal degraded cellulose, total short-chain fatty acids, acetate and propionate compared to the individual isolates diets. The results suggest synergistic interactions among P. manshurica isolates, leading to enhanced ruminal fermentation and reduced GHG emissions while alleviating the adverse effects of AFB1. Therefore, we recommended the Mix of P. Manchuria as a novel feed additive to ruminant diets.

Data on annotation and analysis of genome sequence of Paenibacillus elgii YSY-1.2, a promising chitinase-producing, plant-growth-promoting, and biocontrol agent

The bacterium Paenibacillus elgii YSY-1.2 was recently isolated from soil collected from Yok Don National Park in Vietnam. Previous experiments showed this bacterium possesses high chitin-degrading activity, plant-growth promotion, and biocontrol capacity. Here, we report the draft genome sequence of strain YSY-1.2 for further characterizations related to crop production. The genome sequencing was performed using the DNBSeq-G99 with the Illumina platform. The draft genome of P. elgii YSY-1.2 has 8,240,519 bp in length and comprises 135 contigs. It has an N50 of 315,408 bp and a GC% of 52.8%. The genome contains 7498 protein-coding genes, 87 tRNA genes, and 1 rRNA gene. Among the protein-coding sequences, 6610 were assigned by COG, while 3230 were assigned by KEGG. The genome possesses at least 61 genes involved in environmental adaptation and plant growth promotion. Additionally; there are 258 carbohydrate-active enzymes deduced from the genome; among them, at least 14 may contribute to the biocontrol capacity. The chitin-degrading system of strain YSY-1.2 contains 16 chitinolytic enzymes, comprising 10 chitinases, 4 β-N-acetylhexosaminidases, and 2 auxiliary activities. Furthermore, 32 gene clusters encoding antimicrobial metabolites were identified from the genome, with 17 showing no sequence similarities to reported clusters. Data provide an insight into the genomic information of strain YSY-1.2 and could lead to valuable further explorations and applications in crop production. This is the first report describing the genome sequence of P. elgii isolated from Vietnam.

The genus Acrophialophora: History, phylogeny, morphology, beneficial effects and pathogenicity

The genus Acrophialophora is a thermotolerant fungus, which is widely distributed in temperate and tropical zones. This fungus is classified in Ascomycota and belongs to the Chaetomiaceae family and the genera of Parathielavia, Pseudothielavia and Hyalosphaerella are closely related to Acrophialophora. For this genus have been reported 28 species so far, which two species of Acrophialophora jodhpurensis and Acrophialophora teleoafricana produce only sexual phase and other species produce asexual form. Therefore, producing both sexual and asexual forms were not reported by any species. Many applications were reported by some species in agriculture, pharmacy and industry. Production of enzymes, antimicrobial metabolites and plant growth-promoting factors were reported by some species. The species of A. nainiana is used in the industries of textile, fruit juice, pulp and paper due to extracellular enzyme production. Also, other species produce extracellular enzymes that can be used in various industries. The species Acrophialophora are used in the composting industry due to the production of various enzymes and to be thermotolerant. In addition, some species were isolated from hostile environmental conditions. Therefore has been suggested that it can be used for mycoremediation. Also, antimicrobial metabolites of Acrophialophora have been reported to be effective against human and plant pathogens. In contrast to the beneficial effects described, the Acrophialophora pathogenicity has been rarely reported. Two species A. fusispora and A. levis are opportunistic fungi and have been reported as pathogens in humans, animals and plants. Currently, the development and applications of Acrophialophora species have increased more than past. To our knowledge, there is no report with comprehensive information on the species of Acrophialophora, which include their disadvantage and beneficial effects, particularly in agriculture. Therefore, it seems necessary to pay more in-depth attention to the application of this genus as a beneficial fungus in agriculture, pharmaceutical and industry. This review is focused on the history, phylogeny, morphology, valuable roles of Acrophialophora and pathogenicity.

Monitoring and assessment of the therapeutic impact of metabolites extracted from sponge-associated bacteria screened from Gulf of Mannar, southeast coast of India

The present study aimed to assess and monitor the therapeutic potential of antimicrobial metabolites from marine sponge-associated bacteria collected from the southeast coast of India against multidrug-resistant clinical bacterial isolates. Five sponge samples were collected and the metabolite-producing bacteria were screened from the Gulf of Mannar, India, and their antibacterial potential was studied against drug-resistant clinical bacterial isolates obtained from the hospitals. The two metabolite-producing bacteria (IS1 and IS2) were characterized by standard microbiology protocols and 16S rRNA sequencing. The antibacterial metabolites were characterized by liquid chromatography mass spectrometry (LCMS) analysis. The study suggested that marine sponges such as Spheciospongia spp., Haliclona spp., Mycale spp., Tedania spp., and SS-01 were associated with 30 ± 2, 26 ± 2, 23 ± 3, 21 ± 2, and 20 ± 2% of antibacterial metabolite-producing bacteria, respectively. The LCMS analysis of metabolites extracted from IS1 (4,6-dimethyl-2-pyrimidinamine; 4,5-dimethyl-2-propylsilyl-1H-imidazole) and IS2 (caproyl amide, 2-imidazoline) associated with Spheciospongia spp. exhibited significant antibacterial properties against drug-resistant bacteria. IS1 showed antimicrobial potential against the clinical isolates of Proteus spp., and IS2 showed antibacterial potential against isolates of both Proteus mirabilis and Salmonella typhi. IS1 and IS2 were identified by 16S rRNA sequencing and designated as Klebsiella spp. DSCE-bt01 and Pseudomonas spp. DSCE-bt02, respectively. The current study concluded that the assessment and monitoring of novel isolates from sponge-associated bacteria from marine coastal areas probably offer latest breakthrough in curtailing the global antimicrobial resistance and the study of such ecosystems adds value addition to the searching of novel bioactive compounds from terrestrial ecosystems.

Role of iturin from Bacillus velezensis DMW1 in suppressing growth and pathogenicity of Plectosphaerella cucumerina in tomato by reshaping the rhizosphere microbial communities

Plant-associated microbiomes play a crucial role in suppressing plant and soil pathogens. However, the mechanisms by which pathogen invasion influences the interaction between bacteria and fungi remain unknown and warrant further investigation. In this study, Bacillus spp. was found to be more abundant in diseased rhizosphere in the presence of the soil-borne fungus Plectosphaerella cucumerina. Most of the isolated Bacillus spp. exhibited a robust ability to balance reactive oxygen species (ROS) and demonstrated broad-spectrum antagonistic activity against P. cucumerina, Phytophthora capsica, Fusarium oxysporum, and Ralstonia solanacearum. The secondary metabolite iturin was identified as the key antifungal compound produced by the representative strain Bacillus velezensis DMW1, which effectively inhibits fungal growth and disrupts cell structures. Transcriptome analysis revealed that fungi treated with iturin (28.67 µg/mL) exhibited 4995 differentially expressed genes (DEGs), including 2611 upregulated genes and 2384 downregulated genes, compared to the control group. Furthermore, the application of DMW1 and return-deficient mutant (Δitu) significantly altered microbial diversity and enriched beneficial microorganisms in the rhizosphere soil. The overall findings highlight the potential of DMW1 as a promising biological agent for controlling soil-borne diseases. Its strong antimicrobial properties, ability to colonize host plants effectively, and capacity to reshape the soil microbiota make it a valuable resource for enhancing microbial ecosystems and providing long-term benefits to plants.

Bioactive volatiles of brewer's yeasts: Antifungal action of compounds produced during wort fermentation on Aspergillus sp

Previous investigations proved the potential of Saccharomyces cerevisiae MBELGA62 and Pichia kudriavzevii MBELGA61 as suitable biocontrolling agents against Aspergillus sp. through the production of soluble and volatile bioactive antifungal compounds. The present study delves into those finding by means of the identification of the volatile compounds produced by brewer's strains that demonstrated fungistatic and fungicidal effects against Aspergillus flavus and A. parasiticus when cultured in brewer's wort agar plates. Traditional brewer's yeasts such as S. cerevisiae MBELGA62 and Saccharomyces pastorianus SAFS235 synthetize volatiles that fully inhibited mycelial development for up to 9 days at 30 °C. The non-conventional brewer's strains P. kudriavzevii MBELGA61 and Meyerozyma guilliermondii MUS122 increased the lag phase by >100% and significantly reduced the fungal growth rate by 27.5-43.0% and 15.4-31.4%, respectively. In this context, 2-phenylethanol, 2-phenylethyl acetate and benzyl alcohol were identified as the main antifungal agents involved in Aspergillus sp.'s inhibition.

Functional and mechanistic studies of a phytogenic formulation, Shrimp Best, in growth performance and vibriosis in whiteleg shrimp

Climate change and disease threaten shrimp farming. Here, we studied the beneficial properties of a phytogenic formulation, Shrimp Best (SB), in whiteleg shrimp. Functional studies showed that SB dose-dependently increased shrimp body weight and decreased feed conversion ratio. We found that SB protected against Vibrio parahaemolyticus as evidenced by survival rate, bacterial load, and hepatopancreatic pathology in shrimp. Finally, we explored the likely mechanism by which SB affects growth performance and vibriosis in shrimp. The 16S rRNA sequencing data showed that SB increased 6 probiotic genera and decreased 6 genera of pathogenic bacteria in shrimp. Among these, SB increased the proportion of Lactobacillus johnsonii and decreased that of V. parahaemolyticus in shrimp guts. To dissect the relationship among SB, Lactobacillus and Vibrio, we investigated the in vitro regulation of Lactobacillus and Vibrio by SB. SB at ≥ 0.25 μg/mL promoted L. johnsonii growth. Additionally, L. johnsonii and its supernatant could inhibit V. parahaemolyticus. Furthermore, SB could up-regulate five anti-Vibrio metabolites of L. johnsonii, which caused bacterial membrane destruction. In parallel, we identified 3 fatty acids as active compounds from SB. Overall, this work demonstrated that SB improved growth performance and vibriosis protection in shrimp via the regulation of gut microbiota.

Whole genome sequence data of Paenibacillus tyrfis YSS-72.2.G2, a chitinolytic bacterium newly isolated from a National Park of Vietnam

Paenibacillus tyrfis YSS-72.2.G2 is a soil chitinolytic bacterium newly isolated from Yok Don National Park of Vietnam. Our previous results demonstrated that this bacterium was a strong chitinase producer, possessed plant growth promotion, and had high activity against phytopathogenic fungi. However, the genome sequence of this strain is unknown. This work aimed to establish data on the genome sequence of P. tyrfis YSS-72.2.G2 and its chitinase system for further assessments regarding biocontrol mechanisms and plant growth promotion. The P. tyrfis YSS-72.2.G2 genome is 7,756,121 bp in size and 53.4 % G+C. It harbors 6,948 protein-coding genes, 5 rRNA genes, 82 tRNA genes, 4 ncRNA genes, 99 pseudo genes, and 5 CRISPR arrays. Genes involved in heavy metal resistance (5 genes), iron acquisition (5 genes), and IAA biosynthesis (5 genes) were predicted in the genome. There were 234 carbohydrate-active enzymes found in this genome; among them, 13 enzymes possibly possess activity against phytopathogens. Chitin-degrading system of YSS-72.2.G2 contains 15 chitinolytic enzymes. In addition, 28 gene clusters coding for antimicrobial metabolites were identified, of these, 14 show no sequence similarities to the known clusters. The raw sequences were submitted to the Sequence Read Archive on the National Center for Biotechnology Information with accession number PRJNA946889. The genome sequence of P. tyrfis YSS-72.2.G2 has been deposited in the DDBJ/GenBank/EMBL database under accession number NZ_BSDJ00000000. Data provide insight into the genomic information of strain YSS-72.2.G2. This is the first work reporting data on the genome sequence of P. tyrfis isolated from Vietnam.