A Novel Rhizospheric Bacterium: Bacillus velezensis NKMV-3 as a Biocontrol Agent Against Alternaria Leaf Blight in Tomato

A scientific version of understanding "Why did the chickens cross the road"? - A guided journey through Bacillus spp. towards sustainable agriculture, circular economy and biofortification

The world, a famished planet with an overgrowing population, requires enormous food crops. This scenario compelled the farmers to use a high quantity of synthetic fertilizers for high food crop productivity. However, prolonged usage of chemical fertilizers results in severe adverse effects on soil and water quality. On the other hand, the growing population significantly consumes large quantities of poultry meats. Eventually, this produces a mammoth amount of poultry waste, chicken feathers. Owing to the protein value of the chicken feathers, these wastes are converted into protein hydrolysate and further extend their application as biostimulants for sustained agriculture. The protein profile of chicken feather protein hydrolysate (CFPH) produced through Bacillus spp. was the maximum compared to physical and chemical protein extraction methods. Several studies proved that the application of CFPH and active Bacillus spp. culture to soil and plants results in enhanced plant growth, phytochemical constituents, crop yield, soil nutrients, fertility, microbiome and resistance against diverse abiotic and biotic stresses. Overall, "CFPH - Jack of all trades" and "Bacillus spp. - an active camouflage to the surroundings where they applied showed profound and significant benefits to the plant growth under the most adverse conditions. In addition, Bacillus spp. coheres the biofortification process in plants through the breakdown of metals into metal ions that eventually increase the nutrient value of the food crops. However, detailed information on them is missing. This can be overcome by further real-world studies on rhizoengineering through a multi-omics approach and their interaction with plants. This review has explored the best possible and efficient strategy for managing chicken feather wastes into protein-rich CFPH through Bacillus spp. bioconversion and utilizing the CFPH and Bacillus spp. as biostimulants, biofertilizers, biopesticides and biofortificants. This paper is an excellent report on organic waste management, circular economy and sustainable agriculture research frontier.

Analysis of antimicrobial biological activity of a marine Bacillus velezensis NDB

A new strain of Bacillus velezensis NDB was isolated from Xiangshan Harbor and antibacterial test revealed antibacterial activity of this strain against 12 major pathogenic bacteria. The whole genome of the bacterium was sequenced and found to consist of a 4,214,838 bp circular chromosome and a 7410 bp circular plasmid. Furthermore, it was predicted by AntiSMASH and BAGEL4 to have 12 clusters of secondary metabolism genes for the synthesis of the inhibitors, fengycin, bacillomycin, macrolactin H, bacillaene, and difficidin, and there were also five clusters encoding potentially novel antimicrobial substances, as well as three bacteriocin biosynthesis gene clusters of amylocyclicin, ComX1, and LCI. qRT-PCR revealed significant up-regulation of antimicrobial secondary metabolite synthesis genes after 24 h of antagonism with pathogenic bacteria. Furthermore, MALDI-TOF mass spectrometry revealed that it can secrete surfactin non-ribosomal peptide synthase and polyketide synthase to exert antibacterial effects. GC-MS was used to analyze methanol extract of B. velezensis NDB, a total of 68 compounds were identified and these metabolites include 16 amino acids, 17 acids, 3 amines, 11 sugars, 11 alcohols, 1 ester, and 9 other compounds which can inhibit pathogenic bacteria by initiating the antibiotic secretion pathway. A comparative genomic analysis of gene families showed that the specificity of B. velezensis NDB was mainly reflected in environmental adaptability. Overall, this research on B. velezensis NDB provides the basis for elucidating its biocontrol effect and promotes its future application as a probiotic.

Evaluation of Bacillus isolates as a biological control agents against soilborne phytopathogenic fungi

Pesticides, used in agriculture to control plant diseases, pose risks to the environment and human health. To address this, there's a growing focus on biocontrol, using microorganisms instead of chemicals. In this study, we aimed to identify Bacillus isolates as potential biological control agents. We tested 1574 Bacillus isolates for antifungal effects against pathogens like Botrytis cinerea, Fusarium solani, and Rhizoctonia solani. Out of these, 77 isolates formed inhibition zones against all three pathogens. We then investigated their lytic enzyme activities (protease, chitinase, and chitosanase) and the production of antifungal metabolites (siderophore and hydrogen cyanide). Coagulase activity was also examined to estimate potential pathogenicity in humans and animals. After evaluating all mechanisms, 19 non-pathogenic Bacillus isolates with significant antifungal effects were chosen. Molecular identification revealed they belonged to B. subtilis (n = 19) strains. The 19 native Bacillus strains, demonstrating strong antifungal effects in vitro, have the potential to form the basis for biocontrol product development. This could address challenges in agricultural production, marking a crucial stride toward sustainable agriculture.

Soil nutrient management influences diversity, community association and functional structure of rhizosphere bacteriome under vegetable crop production

Introduction

Rhizosphere bacterial communities play a crucial role in promoting plant and soil ecosystem health and productivity. They also have great potential as key indicators of soil health in agroecosystems. Various environmental factors affect soil parameters, which have been demonstrated to influence soil microbial growth and activities. Thus, this study investigated how rhizosphere bacterial community structure and functions are affected by agronomic practices such as organic and conventional fertiliser application and plant species types.

Methods

Rhizosphere soil of vegetable crops cultivated under organic and conventional fertilisers in different farms was analysed using high-throughput sequencing of the 16S rRNA gene and co-occurrence network pattern among bacterial species. The functional structure was analysed with PICRUSt2 pipeline.

Results

Overall, rhizosphere bacterial communities varied in response to fertiliser type, with soil physicochemical parameters, including NH4, PO4, pH and moisture content largely driving the variations across the farms. Organic farms had a higher diversity richness and more unique amplicon sequence variants than conventional farms. Bacterial community structure in multivariate space was highly differentiated across the farms and between organic and conventional farms. Co-occurrence network patterns showed community segmentation for both farms, with keystone taxa more prevalent in organic than conventional farms.

Discussion

Module hub composition and identity varied, signifying differences in keystone taxa across the farms and positive correlations between changes in microbial composition and ecosystem functions. The organic farms comprised functionally versatile communities characterised by plant growth-promoting keystone genera, such as Agromyces, Bacillus and Nocardioides. The results revealed that organic fertilisers support high functional diversity and stronger interactions within the rhizosphere bacterial community. This study provided useful information about the overall changes in soil microbial dynamics and how the changes influence ecosystem functioning under different soil nutrient management and agronomic practices.

Endophytes and Plant Extracts as Potential Antimicrobial Agents against Candidatus Liberibacter Asiaticus, Causal Agent of Huanglongbing

Huanglongbing (HLB), also known as citrus greening, is an insidious disease in citrus and has become a threat to the sustainability of the citrus industry worldwide. In the U.S., Candidatus Liberibacter asiaticus (CLas) is the pathogen that is associated with HLB, an unculturable, phloem-limited bacteria, vectored by the Asian Citrus Psyllid (ACP, Diaphorina citri). There is no known cure nor treatment to effectively control HLB, and current control methods are primarily based on the use of insecticides and antibiotics, where effectiveness is limited and may have negative impacts on beneficial and non-target organisms. Thus, there is an urgent need for the development of effective and sustainable treatment options to reduce or eliminate CLas from infected trees. In the present study, we screened citrus-derived endophytes, their cell-free culture supernatants (CFCS), and crude plant extracts for antimicrobial activity against two culturable surrogates of CLas, Sinorhizobium meliloti and Liberibacter crescens. Candidates considered high-potential antimicrobial agents were assessed directly against CLas in vitro, using a propidium monoazide-based assay. As compared to the negative controls, statistically significant reductions of viable CLas cells were observed for each of the five bacterial CFCS. Subsequent 16S rRNA gene sequencing revealed that each of the five bacterial isolates were most closely related to Bacillus amyloliquefaciens, a species dominating the market of biological control products. As such, the aboveground endosphere of asymptomatic survivor citrus trees, grown in an organic orchard, were found to host bacterial endophytes capable of effectively disrupting CLas cell membranes. These results concur with the theory that native members of the citrus microbiome play a role in the development of HLB. Here, we identify five strains of Bacillus amyloliquefaciens demonstrating notable potential to be used as sources of novel antimicrobials for the sustainable management of HLB.

Antagonistic transcriptome profile reveals potential mechanisms of action on Xanthomonas oryzae pv. oryzicola by the cell-free supernatants of Bacillus velezensis 504, a versatile plant probiotic bacterium

Bacterial leaf streak (BLS) of rice is a severe disease caused by the bacterial pathogen Xanthomonas oryzae pv. oryzicola (Xoc) that has gradually become the fourth major disease on rice in some rice-growing regions in southern China. Previously, we isolated a Bacillus velezensis strain 504 that exhibited apparent antagonistic activity against the Xoc wild-type strain RS105, and found that B. velezensis 504 was a potential biocontrol agent for BLS. However, the underlying mechanisms of antagonism and biocontrol are not completely understood. Here we mine the genomic data of B. velezensis 504, and the comparative transcriptomic data of Xoc RS105 treated by the cell-free supernatants (CFSs) of B. velezensis 504 to define differentially expressed genes (DEGs). We show that B. velezensis 504 shares over 89% conserved genes with FZB42 and SQR9, two representative model strains of B. velezensis, but 504 is more closely related to FZB42 than SQR9, as well as B. velezensis 504 possesses the secondary metabolite gene clusters encoding the essential anti-Xoc agents difficidin and bacilysin. We conclude that approximately 77% of Xoc RS105 coding sequences are differentially expressed by the CFSs of B. velezensis 504, which significantly downregulates genes involved in signal transduction, oxidative phosphorylation, transmembrane transport, cell motility, cell division, DNA translation, and five physiological metabolisms, as well as depresses an additional set of virulence-associated genes encoding the type III secretion, type II secretion system, type VI secretion system, type IV pilus, lipopolysaccharides and exopolysaccharides. We also show that B. velezensis 504 is a potential biocontrol agent for bacterial blight of rice exhibiting relative control efficiencies over 70% on two susceptible cultivars, and can efficiently antagonize against some important plant pathogenic fungi including Colletotrichum siamense and C. australisinense that are thought to be the two dominant pathogenic species causing leaf anthracnose of rubber tree in Hainan province of China. B. velezensis 504 also harbors some characteristics of plant growth-promoting rhizobacterium such as secreting protease and siderophore, and stimulating plant growth. This study reveals the potential biocontrol mechanisms of B. velezensis against BLS, and also suggests that B. velezensis 504 is a versatile plant probiotic bacterium.

Effects of Bacillus amyloliquefaciens XJ-BV2007 on Growth of Alternaria alternata and Production of Tenuazonic Acid

Large amounts of processing tomato are grown in Xinjiang, China. Tomato black spot disease, caused by Alternaria spp., and the produced alternaria toxins in tomato products are posing risks to human health. In this study, we isolated a rhizospheric bacterium, XJ-BV2007, from tomato (Solanum lycopersicum) fields, which we identified as Bacillus amyloliquefaciens. We found that this bacterium has a strong antagonistic effect against Alternaria alternata and reduces the accumulation of alternaria toxins in tomatoes. According to the antifungal activity of the bacteria-free filtrate, we revealed that B. amyloliquefaciens XJ-BV2007 suppresses A. alternata by the production of antifungal metabolites. Combining semi-preparative high-performance liquid chromatography, we employed UPLC-QTOF-MS analysis and the Oxford cup experiment to find that fengycin plays an important role in inhibiting A. alternata. This paper firstly reported that B. amyloliquefaciens efficiently controls tomato black spot disease and mycotoxins caused by A. alternata. B. amyloliquefaciens XJ-BV2007 may provide an alternative biocontrol strain for the prevention of tomato black spot disease.

Biocontrol activity and action mechanism of Bacillus velezensis strain SDTB038 against Fusarium crown and root rot of tomato

Fusarium crown and root rot of tomato is a soilborne diseases that has brought serious harm and economic losses to tomato production in facilities in recent years. The disease has been reported in more than 30 countries worldwide, but there are few reports on its biological control. A Bacillus velezensis strain SDTB038 with biocontrol effects was isolated and identified in a previous study and is considered one of the most important PGPRs. Seven secondary metabolite biosynthesis gene clusters were found in strain SDTB038 by whole genome sequencing, explaining its biocontrol effects. Results indicated that different concentrations of SDTB038 fermentation broth inhibited the mycelial growth of Fusarium crown and root rot of tomato. Strain SDTB038 could generate indole acetic acid and promote healthy growth of tomatoes, while the effect of 108 CFU/ml SDTB038 concentration on promoting tomato growth was the most obvious. B. velezensis SDTB038 significantly reduced the accumulation of ROS in tomato plants, induced the up-regulation of antifreeze genes, and promoted the rapid recovery of tomato plants at low temperatures in a pot experiment. At the same time, SDTB038 had good control effect on Fusarium crown and root rot of tomato, and 108 CFU/ml SDTB038 fermentation broth had the best control effect, which was 42.98%. In summary, the strain B. velezensis SDTB038 may be a promising bacterial agent for biological control of Fusarium crown and root rot of tomato, and an important source of potential antimicrobial compounds.

Exploring Marine as a Rich Source of Bioactive Peptides: Challenges and Opportunities from Marine Pharmacology

This review highlights the underexplored potential and promises of marine bioactive peptides (MBPs) with unique structural, physicochemical, and biological activities to fight against the current and future human pathologies. A particular focus is given to the marine environment as a significant source to obtain or extract high-value MBPs from touched/untouched sources. For instance, marine microorganisms, including microalgae, bacteria, fungi, and marine polysaccharides, are considered prolific sources of amino acids at large, and peptides/polypeptides in particular, with fundamental structural sequence and functional entities of a carboxyl group, amine, hydrogen, and a variety of R groups. Thus, MBPs with tunable features, both structural and functional entities, along with bioactive traits of clinical and therapeutic value, are of ultimate interest to reinforce biomedical settings in the 21st century. On the other front, as the largest biome globally, the marine biome is the so-called "epitome of untouched or underexploited natural resources" and a considerable source with significant potentialities. Therefore, considering their biological and biomedical importance, researchers around the globe are redirecting and/or regaining their interests in valorizing the marine biome-based MBPs. This review focuses on the widespread bioactivities of MBPs, FDA-approved MBPs in the market, sustainable development goals (SDGs), and legislation to valorize marine biome to underlying the impact role of bioactive elements with the related pathways. Finally, a detailed overview of current challenges, conclusions, and future perspectives is also given to satisfy the stimulating demands of the pharmaceutical sector of the modern world.