Bacillus-based bionematicides: development,modes of action and commercialisation

Agricultural crops are severely damaged by root-knot nematodes causing extensive financial losses globally. Historically, agrochemicals have been the preferred method to combat these pests; however, threats to humans and the environment posed by these agrochemicals led to the need for developing new biocontrol agents. Importantly, the latter should adhere to biosafety regulations while being highly effective. Root-knot nematodes live in soil and thus the use of rhizobacteria such as Bacillus for biocontrol development have shown potential. Although various Bacillus species have been tested in this capacity, little is known about their secondary metabolites and the mechanisms of action responsible for their nematicidal activity. If these secondary metabolites can be qualitatively and quantitatively characterised, metabolic features could be synthetically engineered and used to combat root-knot nematodes. Although there is great potential for bionematicides, the commercialisation and development of such products can be difficult. This review summarises the importance of Bacillus species as natural antagonists of root-knot nematodes through the production of secondary metabolites. It provides an overview of the significance of root-knot nematodes in agriculture and the advances of chemical nematicides in recent years. The potential of Bacillus species as biocontrol agents, the known mechanisms of action responsible for the nematicidal activity demonstrated by Bacillus species, non-target effects of biocontrol agents and the commercialisation of Bacillus-based bionematicides are discussed.     

Function and application of a non-ester-hydrolyzing carboxylesterase discovered in tulip

Plants have evolved secondary metabolite biosynthetic pathways of immense rich diversity. The genes encoding enzymes for secondary metabolite biosynthesis have evolved through gene duplication followed by neofunctionalization, thereby generating functional diversity. Emerging evidence demonstrates that some of those enzymes catalyze reactions entirely different from those usually catalyzed by other members of the same family; e.g. transacylation catalyzed by an enzyme similar to a hydrolytic enzyme. Tuliposide-converting enzyme (TCE), which we recently discovered from tulip, catalyzes the conversion of major defensive secondary metabolites, tuliposides, to antimicrobial tulipalins. The TCEs belong to the carboxylesterase family in the α/β-hydrolase fold superfamily, and specifically catalyze intramolecular transesterification, but not hydrolysis. This non-ester-hydrolyzing carboxylesterase is an example of an enzyme showing catalytic properties that are unpredictable from its primary structure. This review describes the biochemical and physiological aspects of tulipalin biogenesis, and the diverse functions of plant carboxylesterases in the α/β-hydrolase fold superfamily.     

The use of secondary metabolite profiling in chemotaxonomy of filamentous fungi

A secondary metabolite is a chemical compound produced by a limited number of fungal species in a genus, an order, or even phylum. A profile of secondary metabolites consists of all the different compounds a fungus can produce on a given substratum and includes toxins, antibiotics and other outward-directed compounds. Chemotaxonomy is traditionally restricted to comprise fatty acids, proteins, carbohydrates, or secondary metabolites, but has sometimes been defined so broadly that it also includes DNA sequences. It is not yet possible to use secondary metabolites in phylogeny, because of the inconsistent distribution throughout the fungal kingdom. However, this is the very quality that makes secondary metabolites so useful in classification and identification. Four groups of organisms are particularly good producers of secondary metabolites: plants, fungi, lichen fungi, and actinomycetes, whereas yeasts, protozoa, and animals are less efficient producers. Therefore, secondary metabolites have mostly been used in plant and fungal taxonomy, whereas chemotaxonomy has been neglected in bacteriology. Lichen chemotaxonomy has been based on few biosynthetic families (chemosyndromes), whereas filamentous fungi have been analysed for a wide array of terpenes, polyketides, non-ribosomal peptides, and combinations of these. Fungal chemotaxonomy based on secondary metabolites has been used successfully in large ascomycete genera such as Alternaria, Aspergillus, Fusarium, Hypoxylon, Penicillium, Stachybotrys, Xylaria and in few basidiomycete genera, but not in Zygomycota and Chytridiomycota.     

<Emphasis Type="Italic">In silico</Emphasis> analysis of methyltransferase domains involved in biosynthesis of secondary metabolites

Background  

Secondary metabolites biosynthesized by polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) family of enzymes constitute several classes of therapeutically important natural products like erythromycin, rapamycin, cyclosporine etc. In view of their relevance for natural product based drug discovery, identification of novel secondary metabolite natural products by genome mining has been an area of active research. A number of different tailoring enzymes catalyze a variety of chemical modifications to the polyketide or nonribosomal peptide backbone of these secondary metabolites to enhance their structural diversity. Therefore, development of powerful bioinformatics methods for identification of these tailoring enzymes and assignment of their substrate specificity is crucial for deciphering novel secondary metabolites by genome mining.     

Root bacteria from nematicidal plants and their biocontrol potential against trichodorid nematodes in potato

Trichodorid nematodes (Nematoda: Trichodoridae) are vectors of tobacco rattle virus (TRV), one of the causal agents of spraing disease in potato. Root bacteria from nematicidal plants and their control potential against Trichodoridae were the focus of this study. Bacteria isolated from the roots of 12 nematicidal plants and potato were characterized for their production of hydrolytic enzymes, hydrogen cyanide, phenol oxidation ability and antifungal activity towards the potato pathogen Rhizoctonia solani. Based on these functional traits, bacteria isolates were selected and tested in greenhouse conditions on potato (cv. Saturna) for their effect on plant growth, and screened for nematicidal activity against Paratrichodorus pachydermus and Trichodorus primitivus in naturally infested soil. Sixteen bacteria isolates out of 44 reduced nematode densities by 50–100%. Nine selected isolated were further tested by bacterizing potato tubers (cv. King Edward) which were planted in a trichodorid and TRV-infested soil. Four bacterial isolates consistently reduced nematode densities (by 56.7–74.4%) with no visual negative effect on plant growth. These isolates were tentatively identified, partly by fatty acid methyl ester (FAME) analysis as: Stenotrophomonas maltophilia, Bacillus mycoides, Pseudomonas sp., and one unidentified bacterium. The isolates originated from potato, Plantago major, Thymus vulgaris and Asparagus officinalis, respectively. Two Pseudomonas isolates obtained from Zinnia elegans and selected for their strong nematicidal activity in soil screening tests, did not reduce the nematode population when tested on potato. It is concluded that plants releasing nematicidal compounds may harbour nematode-antagonistic bacteria as well.     

Comparative studies on the in vitro properties of phytases from various microbial origins

The physical and chemical properties of six crude phytase preparations were compared. Four of these enzymes (Aspergillus A, Aspergillus R, Peniophora and Aspergillus T) were produced at commercial scale for the use as feed additives while the other two (E. coli and Bacillus) were produced at laboratory scale. The encoding genes of the enzymes were from different microbial origins (4 of fungal origin and 2 of bacterial origin, i.e., E. coli and Bacillus phytases). One of the fungal phytases (Aspergillus R) was expressed in transgenic rape. The enzymes were studied for their pH behaviour, temperature optimum and stability and resistance to protease inactivation. The phytases were found to exhibit different properties depending on source of the phytase gene and the production organism. The pH profiles of the enzymes showed that the fungal phytases had their pH optima ranging from 4.5 to 5.5. The bacterial E. coli phytase had also its pH optimum in the acidic range at pH 4.5 while the pH optimum for the Bacillus enzyme was identified at pH 7.0. Temperature optima were at 50 and 60°C for the fungal and bacterial phytases, respectively. The Bacillus phytase was more thermostable in aqueous solutions than all other enzymes. In pelleting experiments performed at 60, 70 and 80°C in the conditioner, Aspergillus A, Peniophora (measurement at pH 5.5) and E. coli phytases were more heat stable compared to other enzymes (Bacillus enzyme was not included). At a temperature of 70°C in the conditioner, these enzymes maintained a residual activity of approximately 70% after pelleting compared to approximately 30% determined for the other enzymes. Incubation of enzyme preparations with porcine proteases revealed that only E. coli phytase was insensitive against pepsin and pancreatin. Incubation of the enzymes in digesta supernatants from various segments of the digestive tract of hens revealed that digesta from stomach inactivated the enzymes most efficiently except E. coli phytase which had a residual activity of 93% after 60 min incubation at 40°C. It can be concluded that phytases of various microbial origins behave differently with respect to their in vitro properties which could be of importance for future developments of phytase preparations. Especially bacterial phytases contain properties like high temperature stability (Bacillus phytase) and high proteolytic stability (E. coli phytase) which make them favourable for future applications as feed additives.     

Alkaline cellulases from alkaliphilic Bacillus: Enzymatic properties, genetics, and application to detergents

We have isolated a number of alkaliphilic Bacillus that produce alkaline exoenzymes and found a possible use for alkaline cellulase (carboxymethylcellulase) as an additive for improving the cleaning effect of detergents. Enzymatic properties of some candidate cellulases fulfilled the essential requirements for enzymes to be used practically in laundry detergents. Here I describe the properties and possible catalytic mechanism of the hydrolytic reaction and the gene for the industrial alkaline cellulase produced by one of the isolates, Bacillus sp. KSM-635. Received: October 4, 1996 / Accepted: December 2, 1996     

Expression of bacterial tyrosine ammonia-lyase creates a novel p-coumaric acid pathway in the biosynthesis of phenylpropanoids in Arabidopsis

Some flavonoids are considered as beneficial compounds because they exhibit anticancer or antioxidant activity. In higher plants, flavonoids are secondary metabolites that are derived from phenylpropanoid biosynthetic pathway. A large number of phenylpropanoids are generated from p-coumaric acid, which is a derivative of the primary metabolite, phenylalanine. The first two steps in the phenylpropanoid biosynthetic pathway are catalyzed by phenylalanine ammonia-lyase and cinnamate 4-hydroxylase, and the coupling of these two enzymes forms a rate-limiting step in the pathway. For the generation of p-coumaric acid, the conversion from phenylalanine to p-coumaric acid that is catalyzed by two enzymes can be theoretically performed by a single enzyme, tyrosine ammonia-lyase (TAL) that catalyzes the conversion of tyrosine to p-coumaric acid in certain bacteria. To modify the p-coumaric acid pathway in plants, we isolated a gene encoding TAL from a photosynthetic bacterium, Rhodobacter sphaeroides, and introduced the gene (RsTAL) in Arabidopsis thaliana. Analysis of metabolites revealed that the ectopic over-expression of RsTAL leads to higher accumulation of anthocyanins in transgenic 5-day-old seedlings. On the other hand, 21-day-old seedlings of plants expressing RsTAL showed accumulation of higher amount of quercetin glycosides, sinapoyl and p-coumaroyl derivatives than control. These results indicate that ectopic expression of the RsTAL gene in Arabidopsis enhanced the metabolic flux into the phenylpropanoid pathway and resulted in increased accumulation of flavonoids and phenylpropanoids.     

Isolation and characterization of PRA1, a trypsin-like protease from the biocontrol agent <Emphasis Type="Italic">Trichoderma harzianum</Emphasis> CECT 2413 displaying nematicidal activity

Mycoparasitic Trichoderma strains secrete a complex set of hydrolytic enzymes under conditions related to antagonism. Several proteins with proteolytic activity were detected in culture filtrates from T. harzianum CECT 2413 grown in fungal cell walls or chitin and the protein responsible for the main activity (PRA1) was purified to homogeneity. The enzyme was monomeric, its estimated molecular mass was 28 kDa (SDS-PAGE), and its isoelectric point 4.7–4.9. The substrate specificity and inhibition profile of the enzyme correspond to a serine-protease with trypsin activity. Synthetic oligonucleotide primers based on N-terminal and internal sequences of the protein were designed to clone a full cDNA corresponding to PRA1. The protein sequence showed <43% identity to mammal trypsins and 47–57% to other fungal trypsin-like proteins described thus far. Northern analysis indicated that PRA1 is induced by conditions simulating antagonism, is subject to nitrogen and carbon derepression, and is affected by pH in the culture media. The number of hatched eggs of the root-knot nematode Meloidogyne incognita was significantly reduced after incubation with pure PRA1 preparations. This nematicidal effect was improved using fungal culture filtrates, suggesting that PRA1 has additive or synergistic effects with other proteins produced during the antagonistic activity of T. harzianum CECT 2413. A role for PRA1 in the protection of plants against pests and pathogens provided by T. harzianum CECT 2413 is proposed.     

Secondary metabolite profiling of Alternaria dauci, A. porri, A. solani, and A. tomatophila

Chemotaxonomy (secondary metabolite profiling) has been shown to be of great value in the classification and differentiation in Ascomycota. However, few studies have investigated the use of metabolite production for classification and identification purposes of plant pathogenic Alternaria species. The purpose of the present study was to describe the methodology behind metabolite profiling in chemotaxonomy using A. dauci, A. porri, A. solani, and A. tomatophila strains as examples of the group. The results confirmed that A. dauci, A. solani, and A. tomatophila are three distinct species each with their own specific metabolite profiles, and that A. solani and A. tomatophila both produce altersolanol A, altertoxin I, and macrosporin. By using automated chemical image analysis and other multivariate statistic analyses, three sets of species-specific metabolites could be selected, one each for A. dauci, A. solani, and A. tomatophila.     

Physiological implications of metabolite biosynthesis for net assimilation and heat-stress tolerance of sugarcane (<Emphasis Type="Italic"> Saccharum officinarum</Emphasis>) sprouts

Global increase in ambient temperature is a critical factor for plant growth. In order to study the changes in growth over short intervals, various primary and secondary metabolites, and their relationships with thermotolerance, 1-month-old sugarcane (Saccharum officinarum) sprouts were grown under control conditions (28°C) or under heat-stress conditions (40°C), and measurements were made at six 12-h intervals. Heat stress greatly reduced dry matter and leaf area of sprouts initially but only nominally later on. Changes in the rates of relative growth and net assimilation were greater than relative leaf expansion, indicating an adverse effect of heat on assimilation of nutrients and CO₂ in producing dry matter. Although reduction in leaf water potential was an immediate response to heat, this effect was offset by early synthesis of free proline, glycinebetaine and soluble sugars (primary metabolites). Among secondary metabolites, anthocyanin synthesis was similar to primary metabolites; carotenoids and soluble phenolics accumulated later while chlorophyll remained unaffected. Relationships of growth attributes and metabolite levels, not seen in the controls, were evident under heat stress. In summary, observed changes in metabolite levels were spread over time and space and were crucial in improving net assimilation and heat tolerance of sugarcane.     

Effect of the entomopathogenic fungus,Beauveria bassiana,and its secondary metabolite on detoxifying enzyme activities and acetylcholinesterase (AChE) of the Sunn pest,Eurygaster integriceps (Heteroptera: Scutellaridae)

The effects of Beauveria bassiana spores and its secondary metabolite on insect resistance to an organophosphorus insecticide, fenitrothione and secondary metabolite effects on acetylcholine esterase inhibition were investigated. Findings showed that fungal spores and its secondary metabolite increase total esterase and glutathione S-transferase activities in the hemolymph of infected and treated adults of Eurygaster integriceps. But the fungal secondary metabolite had an adverse effect on AChE activity of adults that decreased its activity level and isoforms of this enzyme in polyacrylamide gel electrophoresis. Fungal infection decreased the susceptibility of E. integriceps adults to fenitrothione, in comparison with uninfected individuals. Possible involvement of detoxifying enzymes in the development of insect resistance to fenitrothione should be considered in combined usage of chemicals and microbial agents for integrated pest management programs.     

一株深海热液口嗜热芽孢杆菌SY27F代谢产物活性的研究

【目的】对一株来源于深海热液口嗜热芽孢杆菌的次生代谢产物进行抑菌活性和抗肿瘤活性的初步研究。【方法】采用纸片法和微量肉汤稀释法检测嗜热芽孢杆菌SY27F次生代谢产物的抑菌活性,采用CCK-8法测定其次生代谢产物的抗肿瘤活性。【结果】抑菌实验表明,嗜热芽孢杆菌代谢产物对大肠杆菌、金黄色葡萄球菌均有抑菌作用,其最低抑菌浓度分别为1.56 mg/mL和3.13 mg/mL;细胞实验表明,其代谢产物对肿瘤细胞A549、HepG2、HeLa、MCF-7均有一定的抑制作用,其半致死浓度分别为0.390、0.451、0.704、1.105 mg/mL;与人肝肿瘤细胞(HepG2)相比,其对人正常肝细胞(L02)表现出良好的生物相容性。【结论】嗜热芽孢杆菌SY27F次生代谢产物具有一定的抑菌和抗肿瘤活性,可为寻找新型抑菌抗肿瘤活性物质提供优质资源。     

The intracellular equilibrium thermodynamic and steady-state concentrations of metabolites

A new model for the organization and flow of metabolites through a metabolic pathway is presented. The model is based on four major findings. (1) The intracellular concentrations of enzyme sites exceed the concentrations of intermediary metabolites that bind specifically to these sites. (2) The concentration of the excessive enzyme sites in the cell is sufficiently high so that nearly all the cellular intermediary metabolites are enzyme-bound. (3) Enzyme conformations are perturbed by the interactions with substrates and products; the conformations of enzyme-substrate and enzyme-product complexes are different. (4) Two enzymes, catalyzing reactions that are sequential in a metabolic pathway, transfer the common metabolite back and forth via an enzyme-enzyme complex without the intervention of the solvent environment. The model proposes that the enzyme-enzyme recognition is ligand-induced. Conversion of E₂S and E₂P results in the loss of recognition of E₂ by E₁ and the concomitant recognition of E₂ by E₃. This model substantially alters existent views of the bioenergetics and the kinetics of intracellular metabolism. The rates of direct transfer of metabolite from enzyme to enzyme are comparable to the rates of interconversion between substrate and product within an individual enzyme. Consequently, intermediary metabolites are nearly equipartitioned among their high-affinity enzyme sites within a metabolic pathway. Metabolic flux involves the direct transfer of metabolite from enzyme to enzyme via a set of low and nearly equal energy barriers.     

Cold-adapted Bacilli isolated from the Qinghai–Tibetan Plateau are able to promote plant growth in extreme environments

Nearly 1400 Bacillus strains growing in the plant rhizosphere were sampled from different sites on the Qinghai–Tibetan Plateau. Forty-five of the isolates, selected due to their biocontrol activity, were genome-sequenced and their taxonomic identification revealed that they were representatives of the Bacillus subtilis species complex (20) and the Bacillus cereus group (9). Majority of the remaining strains were found closely related to Bacillus pumilus, but their average nucleotide identity based on BLAST and electronic DNA/DNA hybridization values excluded closer taxonomic identification. A total of 45 different gene clusters involved in synthesis of secondary metabolites were detected by mining the genomes of the 45 selected strains. Except eight mesophilic strains, the 37 remaining strains were found either cold-adapted or psychrophilic, able to propagate at 10°C and below (Bacillus wiedmannii NMSL88 and Bacillus sp. RJGP41). Pot experiments performed at 10°C with winter wheat seedlings revealed that cold-adapted representatives of B. pumilus, B. safensis and B. atrophaeus promoted growth of the seedlings under cold conditions, suggesting that these bacilli isolated from a cold environment are promising candidates for developing of bioformulations useful for application in sustainable agriculture under environmental conditions unfavourable for the mesophilic bacteria presently in use.     

PCR detection of novel non-ribosomal peptide synthetase genes in lipopeptide-producing Pseudomonas

Bacterial lipopeptides (LPs) are a diverse group of secondary metabolites synthesized through one or more non-ribosomal peptide synthetases (NRPSs). In certain genera, such as Pseudomonas and Bacillus, these enzyme systems are often involved in synthesizing biosurfactants or antimicrobial compounds. Several different types of LPs have been reported for non-pathogenic plant-associated Pseudomonas. Focusing on this group of bacteria, we devised and validated a PCR method to detect novel LP-synthesizing NRPS genes by targeting their lipoinitiation and tandem thioesterase domains, thus avoiding amplification of genes for non-LP metabolites, such as the pyoverdine siderophores present in all fluorescent Pseudomonas. This approach enabled detection of as yet unknown NRPS genes in strains producing viscosin, viscosinamide, WLIP, or lokisin. Furthermore, it proved valuable to identify novel candidate LP producers among Pseudomonas rhizosphere isolates. By phylogenetic analysis of these amplicons, several of the corresponding NRPS genes can be tentatively assigned to the viscosin, amphisin, or entolysin biosynthetic groups, while some others may represent novel NRPS systems.     

<Emphasis Type="Italic">Agrobacterium tumefaciens</Emphasis>-mediated transformation of a medicinal plant <Emphasis Type="Italic">Taraxacum platycarpum</Emphasis>

Dandelion plants, the genus Taraxacum, are used in herbal medicine owing to their choleretic, diuretic and anti-carcinogenic activities and several medicinal compounds have been isolated from the roots of these plants. Metabolic manipulation of secondary metabolite biosynthesis is a potential strategy to improve the production of high-value secondary metabolites. The enzyme 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) is known to control a key regulatory step in the isoprenoid pathway. We report an efficient transformation protocol for stable introduction of HMGR into dandelion plants (Taraxacum platycarpum H. Dablstaed), which is essential for the biotechnological approach. The Agrobacterium tumefaciens strain EHA105 containing the binary vector, pCAMBIA1301, with GUS and HMGR genes, showed high transformation efficiency after 3–5 week hygromycin selection. Southern blotting, GUS staining and RT-PCR analyses demonstrated stable integration of one copy of the HMGR gene into the dandelion genome. Expression of the integrated genes was particularly eminent in root tissues of primary transformant plants. The establishment of an efficient transformation method may facilitate the improvement of medicinal plant in terms of the accumulation levels of secondary metabolites.     

Enzymes from thermophiles

The most frequently used sources of more stable enzymes are thermophilic bacteria, e.g. Bacillus, Closrridium, and Therrnus strains, occurring in natural as well as man-made habitats. They grow from 55 to 88°C with a specific growth rate of up to 2.6 h^? and a yield coefficient of up to 0.4 gram of dry cell weight per gram of carbohydrate consumed. Several thermophilic strains, e.g. Bacillus sp. TP32, rapidly and effectively produce enzymes having a higher thermal stability and resistance to chemical denaturants in comparison to their mesophilic counterparts. Therefore, thermostable enzymes are of importance for bioorganic syntheses. For the further optimization of enzyme production, genetic engineering is applied.     

Biocontrol Potential of Soybean Bacterial Endophytes Against Charcoal Rot Fungus, <Emphasis Type="Italic">Rhizoctonia bataticola</Emphasis>

A total of 137 bacterial isolates from surface sterilized root, stem, and nodule tissues of soybean were screened for their antifungal activity against major phytopathogens like Rhizoctonia bataticola, Macrophomina phaseolina, Fusarium udam, and Sclerotium rolfsii. Nine bacterial endophytes suppressed the pathogens under in vitro plate assay. These were characterized biochemically and identified at the genus level based on their partial sequence analysis of 16S rDNA. Eight of the isolates belonged to Bacillus and one to Paenibacillus. The phylogenetic relationship among the selected isolates was studied and phylogenetic trees were generated. The selected isolates were screened for biocontrol traits like production of hydrogen cyanide (HCN), siderophore, hydrolytic enzymes, antibiotics, and plant growth promoting traits like indole 3-acetic acid production, phosphate solubilization, and nitrogen fixation. A modified assessment scheme was used to select the most efficient biocontrol isolates Paenibacillus sp. HKA-15 (HKA-15) and Bacillus sp. HKA-121 (HKA-121) as potential candidates for charcoal rot biocontrol as well as soybean plant growth promotion.