Biocontrol and plant stimulating potential of novel strain Bacillus sp. PPM3 isolated from marine sediment

Whole-genome analysis and secondary metabolites production of a new strain Brevibacillus halotolerans 7WMA2: A potential biocontrol agent against fungal pathogens

The extensive usage of synthetic fungicides against fungal diseases has caused adverse impacts on both human and agricultural crops. Therefore, the current study aims to establish a new bacterium 7WMA2, as a biocontrol agent to achieve better antifungal results. The strain 7WMA2 was isolated from marine sediment, displayed a broad spectrum of several fungi that includes Alternaria alternata, Cladosporium sp., Candida albicans, Fusarium oxysporum, Trichosporon pullulans, and Trichophyton rubrum. The 16S rRNA phylogeny inferred that strain 7WMA2 was a member of Brevibacillus. The phylogenetic and biochemical analyses revealed that the strain 7WMA2 belongs to the species of Brevibacillus halotolerans. The complete genome sequence of Brevibacillus halotolerans 7WMA2 consists of a circular chromosome of 5,351,077 bp length with a GC content of 41.39 mol %, including 4433 CDS, 111 tRNA genes, and 36 rRNA genes. The genomic analysis showed 23 putative biosynthetic secondary metabolite gene clusters responsible for non-ribosomal peptides, polyketides and siderophores. The antifungal compounds concentrated from cell-free fermentation broth demonstrated strong inhibition of fungi, and the compounds are considerably thermal stable and adaptable to pH range 2-12. This complete genome sequence has provided insight for further exploration of antagonistic ability and its secondary metabolite compounds indicated feasibility as biological control agents against fungal infections.

Metabolomics on the study of marine organisms

BACKGROUND

Marine ecosystems are hosts to a vast array of organisms, being among the most richly biodiverse locations on the planet. The study of these ecosystems is very important, as they are not only a significant source of food for the world but also have, in recent years, become a prolific source of compounds with therapeutic potential. Studies of aspects of marine life have involved diverse fields of marine science, and the use of metabolomics as an experimental approach has increased in recent years. As part of the "omics" technologies, metabolomics has been used to deepen the understanding of interactions between marine organisms and their environment at a metabolic level and to discover new metabolites produced by these organisms.

AIM OF REVIEW

This review provides an overview of the use of metabolomics in the study of marine organisms. It also explores the use of metabolomics tools common to other fields such as plants and human metabolomics that could potentially contribute to marine organism studies. It deals with the entire process of a metabolomic study, from sample collection considerations, metabolite extraction, analytical techniques, and data analysis. It also includes an overview of recent applications of metabolomics in fields such as marine ecology and drug discovery and future perspectives of its use in the study of marine organisms.

KEY SCIENTIFIC CONCEPTS OF REVIEW

The review covers all the steps involved in metabolomic studies of marine organisms including, collection, extraction methods, analytical tools, statistical analysis, and dereplication. It aims to provide insight into all aspects that a newcomer to the field should consider when undertaking marine metabolomics.

Isolation of the Novel Strain Bacillus amyloliquefaciens F9 and Identification of Lipopeptide Extract Components Responsible for Activity against Xanthomonas citri subsp. citri

Citrus canker, caused by Xanthomonas citri subsp. citri (Xcc), is a quarantine disease that seriously affects citrus production worldwide. The use of microorganisms and their products for biological control has been proven to be effective in controlling Xanthomonas disease. In this study, a novel Xcc antagonistic strain was isolated and identified as Bacillus amyloliquefaciens F9 by morphological and molecular analysis. The lipopeptide extract of B. amyloliquefaciens F9 (F9LE) effectively inhibited the growth of Xcc in an agar diffusion assay and restrained the occurrence of canker lesions in a pathogenicity test under greenhouse conditions. Consistent with these findings, F9LE treatment significantly inhibited the production of extracellular enzymes in Xcc cells and induced cell wall damage, with leakage of bacterial contents revealed by scanning electron microscopy and transmission electron microscopy analyses. In addition, F9LE also showed strong antagonistic activity against a wide spectrum of plant pathogenic bacteria and fungi. Furthermore, using electrospray ionization mass spectrometry analysis, the main antimicrobial compounds of strain F9 were identified as three kinds of lipopeptides, including homologues of surfactin, fengycin, and iturin. Taken together, our results show that B. amyloliquefaciens F9 and its lipopeptide components have the potential to be used as biocontrol agents against Xcc, and other plant pathogenic bacteria and fungi.

Antimicrobial Bacillus: Metabolites and Their Mode of Action

The agricultural industry utilizes antibiotic growth promoters to promote livestock growth and health. However, the World Health Organization has raised concerns over the ongoing spread of antibiotic resistance transmission in the populace, leading to its subsequent ban in several countries, especially in the European Union. These restrictions have translated into an increase in pathogenic outbreaks in the agricultural industry, highlighting the need for an economically viable, non-toxic, and renewable alternative to antibiotics in livestock. Probiotics inhibit pathogen growth, promote a beneficial microbiota, regulate the immune response of its host, enhance feed conversion to nutrients, and form biofilms that block further infection. Commonly used lactic acid bacteria probiotics are vulnerable to the harsh conditions of the upper gastrointestinal system, leading to novel research using spore-forming bacteria from the genus Bacillus. However, the exact mechanisms behind Bacillus probiotics remain unexplored. This review tackles this issue, by reporting antimicrobial compounds produced from Bacillus strains, their proposed mechanisms of action, and any gaps in the mechanism studies of these compounds. Lastly, this paper explores omics approaches to clarify the mechanisms behind Bacillus probiotics.

Pathogen Biocontrol Using Plant Growth-Promoting Bacteria (PGPR): Role of Bacterial Diversity

A vast microbial community inhabits in the rhizosphere, among which, specialized bacteria known as Plant Growth-Promoting Rhizobacteria (PGPR) confer benefits to host plants including growth promotion and disease suppression. PGPR taxa vary in the ways whereby they curtail the negative effects of invading plant pathogens. However, a cumulative or synergistic effect does not always ensue when a bacterial consortium is used. In this review, we reassess the disease-suppressive mechanisms of PGPR and present explanations and illustrations for functional diversity and/or stability among PGPR taxa regarding these mechanisms. We also provide evidence of benefits when PGPR mixtures, rather than individuals, are used for protecting crops from various diseases, and underscore the critical determinant factors for successful use of PGPR mixtures. Then, we evaluate the challenges of and limitations to achieving the desired outcomes from strain/species-rich bacterial assemblages, particularly in relation to their role for plant disease management. In addition, towards locating additive or synergistic outcomes, we highlight why and how the benefits conferred need to be categorized and quantified when different strains/species of PGPR are used in combinations. Finally, we highlight the critical approaches needed for developing PGPR mixtures with improved efficacy and stability as biocontrols for utilization in agricultural fields.

The salt-tolerant phenazine-1-carboxamide-producing bacterium Pseudomonas aeruginosa NF011 isolated from wheat rhizosphere soil in dry farmland with antagonism against Fusarium graminearum

Fusarium head blight (FHB) disease caused by Fusarium graminearum (Fg) seriously affects the yield and quality of wheat. In this study, after bacterial community analysis of two wheat rhizosphere soils, the genus Pseudomonas was shown to be enriched in normal dry farmland (maize-wheat rotation) compared to that observed nearby paddy farmland (rice-wheat rotation) with serious FHB disease. Subsequently, a P. aeruginosa strain, NF011 with the highest antagonistic activity against Fg and excellent tolerance to 8.0 % of NaCl was isolated from the wheat rhizosphere soil in the normal dry farmland. Dual culture assay results showed that NF011 is a broad-spectrum fungicide for controlling six wheat pathogenic fungi. The major antifungal compound produced by NF011 was identified as phenazine-1-carboxamide (PCN) by LC-MS and nuclear magnetic resonance. 1.0 × 10⁸ CFU/mL of NF011 or 32 mg/L of PCN could completely inhibit Fg spore germination and resulted in the destruction of Fg hypha vacuoles. Mannitol, peanut meal, beef extract, metal ions (Mn²⁺, Ca²⁺, Fe²⁺, and Mg²⁺), and amino acids (Arg and Lys) could promote the production of PCN by NF011, moreover, the optimal pH and temperature was 6.0 and 20 °C. The PCN produced by NF011 under the optimized culture conditions reached 436.55 ± 11.06 mg/L, 4.90-fold higher than that observed under the basic culture conditions. Finally, infection experiment results showed that NF011 can effectively prevent Fg spores from infecting wheat spikes and wheat grains and suppress the production of deoxynivalenol (DON). Therefore, the salt-tolerant PCN-producing NF011 has the potential to control wheat fungal disease.

Fungichromin production by Streptomyces sp. WP-1, an endophyte from Pinus dabeshanensis, and its antifungal activity against Fusarium oxysporum

In this study, we isolated an endophytic Streptomyces sp. strain, WP-1, from surface-sterilized barks of Pinus dabeshanensis, an endangered Chinese plant. WP-1 showed strong antifungal activity against diverse pathogenic fungi, such as Fusarium oxysporum, Rhizoctonia solani, Phytophthora infestan, and Candida albicans. Based on phylogenetic analyses, preliminary identification suggested that the WP-1 strain belonged to the genus Streptomyces. Column chromatogram and HPLC were employed to isolate the primary antifungal component from the culture medium of WP-1, and it was identified as the methylpentaene macrolide antibiotic, fungichromin (FC). In this study, for the first time, using in vitro bioassay studies, we revealed that FC strongly inhibited mycelial growth and conidia germination in Fusarium oxysporum. The median inhibitory concentration of FC was found to be 3.80 mg/L. The fermentation conditions of the WP-1 strain were further investigated to improve FC production. We found that supplementation of the synthetic medium with oils (soybean oil, oleic acid, and so on), particularly during the initial stage of fermentation, significantly increased the FC yield. Ammonium-trapping agent (magnesium phosphate) was used as an additive to increase FC yield to 5741.7 mg/L. It was 2.9-fold more as compared to the highest FC yield reported so far where Streptomyces padanus PMS-702 was used for FC production. KEY POINTS: • Isolation and identification of a fungichromin-producing endophytic actinomycete WP-1 strain. • Fungichromin production was significantly improved via oils and ammonium-trapping agents addition. • Discovery of the antifungal activity of fungichromin against Fusarium oxysporum.