Chitinolytic activity of endophytic Streptomyces and potential for biocontrol

Cactus Endophytic Fungi and Bioprospecting for their Enzymes and Bioactive Molecules: A Systematic Review

Endophytic fungi are associated with plant health and represent a remarkable source of potential of enzymes and bioactive compounds, but the diversity of endophytes remains uncertain and poorly explored, especially in Cactaceae, one of the most species-rich families adapted to growing in arid and semi-arid regions. The aim of this study was to conduct a systematic review on the diversity and bioprospecting of endophytic fungi from Cactaceae. We analysed peer-reviewed articles from seven databases using PRISMA guidelines. The results showed that the Cactaceae family is a source of new taxa, but the diversity of endophytic fungi of Cactaceae is little explored, mainly the diversity among tissues and by metagenomics. Bioprospecting studies have shown that these microorganisms can be used in the production of enzymes and larvicidal and antifungal compounds. Our results are relevant as a starting point for researchers to develop studies that expand the knowledge of plant mycobiota in arid and semi-arid ecosystems, as well as comprising a remarkable source of fungal compounds with several biotechnological applications.

Current Scenario and Future Prospects of Endophytic Microbes: Promising Candidates for Abiotic and Biotic Stress Management for Agricultural and Environmental Sustainability

Globally, substantial research into endophytic microbes is being conducted to increase agricultural and environmental sustainability. Endophytic microbes such as bacteria, actinomycetes, and fungi inhabit ubiquitously within the tissues of all plant species without causing any harm or disease. Endophytes form symbiotic relationships with diverse plant species and can regulate numerous host functions, including resistance to abiotic and biotic stresses, growth and development, and stimulating immune systems. Moreover, plant endophytes play a dominant role in nutrient cycling, biodegradation, and bioremediation, and are widely used in many industries. Endophytes have a stronger predisposition for enhancing mineral and metal solubility by cells through the secretion of organic acids with low molecular weight and metal-specific ligands (such as siderophores) that alter soil pH and boost binding activity. Finally, endophytes synthesize various bioactive compounds with high competence that are promising candidates for new drugs, antibiotics, and medicines. Bioprospecting of endophytic novel secondary metabolites has given momentum to sustainable agriculture for combating environmental stresses. Biotechnological interventions with the aid of endophytes played a pivotal role in crop improvement to mitigate biotic and abiotic stress conditions like drought, salinity, xenobiotic compounds, and heavy metals. Identification of putative genes from endophytes conferring resistance and tolerance to crop diseases, apart from those involved in the accumulation and degradation of contaminants, could open new avenues in agricultural research and development. Furthermore, a detailed molecular and biochemical understanding of endophyte entry and colonization strategy in the host would better help in manipulating crop productivity under changing climatic conditions. Therefore, the present review highlights current research trends based on the SCOPUS database, potential biotechnological interventions of endophytic microorganisms in combating environmental stresses influencing crop productivity, future opportunities of endophytes in improving plant stress tolerance, and their contribution to sustainable remediation of hazardous environmental contaminants.

Biocontrol Screening of Endophytes: Applications and Limitations

The considerable loss of crop productivity each year due to plant disease or pathogen invasion during pre- or post-harvest storage conditions is one of the most severe challenges to achieving the goals of food security for the rising global population. Although chemical pesticides severally affect the food quality and health of consumers, a large population relies on them for plant disease management. But currently, endophytes have been considered one of the most suitable biocontrol agents due to better colonization and acclimatization potential. However, a very limited number of endophytes have been used commercially as biocontrol agents. Isolation of endophytes and their screening to represent potential characteristics as biocontrol agents are considered challenging by different procedures. Through a web search using the keywords "endophytes as biocontrol agents" or "biocontrol mechanism of endophytes," we have succinctly summarised the isolation strategies and different in vitro and in vivo biocontrol screening methods of endophytic biocontrol agents in the present review. In this paper, biocontrol mechanisms of endophytes and their potential application in plant disease management have also been discussed. Furthermore, the registration and regulatory mechanism of the endophytic biocontrol agents are also covered.

Biocontrol potential of Chitinophaga flava HK235 producing antifungal-related peptide chitinocin

Botrytis cinerea is a necrotrophic fungal pathogen with an extremely broad host range, causing significant economic losses in agricultural production. In this study, we discovered a culture filtrate of bacterial strain HK235, which was identified as Chitinophaga flava, exhibiting high levels of antifungal activity against B. cinerea. From the HK235 culture filtrate, we isolated a new antimicrobial peptide molecule designated as chitinocin based on activity-guided fractionation followed by characterization of the amino acid composition and spectroscopic analyses. The HK235 culture filtrate and chitinocin completely inhibited both conidial germination and mycelial growth of B. cinerea at a concentration of 20% and 200 μg/mL, respectively. In addition to antibiosis against B. cinerea, the active compound chitinocin had a broad antifungal and antibacterial activity in vitro. When tomato plants were treated with the culture filtrate and chitinocin, the treatment strongly reduced the development of gray mold disease in a concentration-dependent manner compared to the untreated control. Here, considering the potent antifungal property in vitro and in vivo, we present the biocontrol potential of C. flava HK235 for the first time.

Development of a Multicomponent Microbiological Soil Inoculant and Its Performance in Sweet Potato Cultivation

The cultivation and consumption of sweet potato (Ipomoea batatas) are increasing globally. As the usage of chemical fertilizers and pest control agents during its cultivation may lead to soil, water and air pollution, there is an emerging need for environment-friendly, biological solutions enabling increased amounts of healthy crop and efficient disease management. Microbiological agents for agricultural purposes gained increasing importance in the past few decades. Our goal was to develop an agricultural soil inoculant from multiple microorganisms and test its application potential in sweet potato cultivation. Two Trichoderma strains were selected: Trichoderma ghanense strain SZMC 25217 based on its extracellular enzyme activities for the biodegradation of plant residues, and Trichoderma afroharzianum strain SZMC 25231 for biocontrol purposes against fungal plant pathogens. The Bacillus velezensis strain SZMC 24986 proved to be the best growth inhibitor of most of the nine tested strains of fungal species known as plant pathogens, therefore it was also selected for biocontrol purposes against fungal plant pathogens. Arthrobacter globiformis strain SZMC 25081, showing the fastest growth on nitrogen-free medium, was selected as a component with possible nitrogen-fixing potential. A Pseudomonas resinovorans strain, SZMC 25872, was selected for its ability to produce indole-3-acetic acid, which is among the important traits of potential plant growth-promoting rhizobacteria (PGPR). A series of experiments were performed to test the selected strains for their tolerance to abiotic stress factors such as pH, temperature, water activity and fungicides, influencing the survivability in agricultural environments. The selected strains were used to treat sweet potato in two separate field experiments. Yield increase was observed for the plants treated with the selected microbial consortium (synthetic community) in comparison with the control group in both cases. Our results suggest that the developed microbial inoculant has the potential to be used in sweet potato plantations. To the best of our knowledge, this is the first report about the successful application of a fungal-bacterial consortium in sweet potato cultivation.

Antagonistic Activity of Pseudomonas fluorescens Strain X1 Against Different Fusaria and it's In Vivo Analysis Against Fusarium udum Infected Pigeon Pea

A plant growth-promoting rhizobacterial strain, Pseudomonas fluorescens X1 isolated from the garden soil was employed for antagonistic activity against different species of fusaria. Strain X1 inhibited four different fusaria (Fusarium moniliforme, Fusarium oxysporum, Fusarium semitectum and Fusarium udum) in dual culture plate assay, and in broth culture using cell-free culture filtrate. Scanning electron microscopic (SEM) analysis revealed deformation and shrinkage in mycelia of fusaria after treatment with strain X1. Confocal micrographs showed degeneration of nuclei inside the cells of fusaria for the same effect. Strain X1 exhibited maximum antifungal activity, when it was grown in nutrient broth yeast (NBY) medium amended with 1 mM NH₄MoO₄ and 1% glucose. The antifungal extracts eluted from thin-layer chromatography (TLC) followed by high performance liquid chromatography (HPLC) showed two fractions active against different fusaria. Liquid chromatography-mass spectrometry (LCMS) analysis of the two fractions 1 and 2 corresponded to molecular ions at m/z 177.16 and m/z 177.09, respectively. Infra-red (IR) analysis showed five similar absorption bands in both the fractions analysed. In vivo analysis of strain X1 alone and along with fungicide inhibited the growth of F. udum and improved the biomass and growth of pigeon pea. These results indicated that strain X1 could be possibly used as a biocontrol agent to inhibit the growth of soil-borne diseases of different fusaria including F. udum that causes wilting in pigeon pea.

Rice leaf endophytic Microbacterium testaceum: Antifungal actinobacterium confers immunocompetence against rice blast disease

Genetic and functional characteristics of rice leaf endophytic actinobacterial member, Microbacterium are described. Morphotyping, multilocus sequence analysis and transmission electron microscopy indicated the species identity of the endophytic bacterium, OsEnb-ALM-D18, as Microbacterium testaceum. The endophytic Microbacterium showed probiotic solubilization of plant nutrients/minerals, produced hydrolytic enzyme/phytohormones, and showed endophytism in rice seedlings. Further, the endophytic colonization by M. testaceum OsEnb-ALM-D18 was confirmed using reporter gene coding for green fluorescence protein. Microbacterium OsEnb-ALM-D18 showed volatilome-mediated antibiosis (95.5% mycelial inhibition) on Magnaporthe oryzae. Chemical profiling of M. testaceum OsEnb-ALM-D18 volatilome revealed the abundance of 9-Octadecenoic acid, Hexadecanoic acid, 4-Methyl-2-pentanol, and 2,5-Dihydro-thiophene. Upon endobacterization of rice seedlings, M. testaceum altered shoot and root phenotype suggestive of activated defense. Over 80.0% blast disease severity reduction was observed on the susceptible rice cultivar Pusa Basmati-1 upon foliar spray with M. testaceum. qPCR-based gene expression analysis showed induction of OsCERK1, OsPAD4, OsNPR1.3, and OsFMO1 suggestive of endophytic immunocompetence against blast disease. Moreover, M. testaceum OsEnb-ALM-D18 conferred immunocompetence, and antifungal antibiosis can be the future integrated blast management strategy.

Streptomyces: Still the Biggest Producer of New Natural Secondary Metabolites, a Current Perspective

There is a real consensus that new antibiotics are urgently needed and are the best chance for combating antibiotic resistance. The phylum Actinobacteria is one of the main producers of new antibiotics, with a recent paradigm shift whereby rare actinomycetes have been increasingly targeted as a source of new secondary metabolites for the discovery of new antibiotics. However, this review shows that the genus Streptomyces is still the largest current producer of new and innovative secondary metabolites. Between January 2015 and December 2020, a significantly high number of novel Streptomyces spp. have been isolated from different environments, including extreme environments, symbionts, terrestrial soils, sediments and also from marine environments, mainly from marine invertebrates and marine sediments. This review highlights 135 new species of Streptomyces during this 6-year period with 108 new species of Streptomyces from the terrestrial environment and 27 new species from marine sources. A brief summary of the different pre-treatment methods used for the successful isolation of some of the new species of Streptomyces is also discussed, as well as the biological activities of the isolated secondary metabolites. A total of 279 new secondary metabolites have been recorded from 121 species of Streptomyces which exhibit diverse biological activity. The greatest number of new secondary metabolites originated from the terrestrial-sourced Streptomyces spp.

Marine Natural Product Antimycin A Suppresses Wheat Blast Disease Caused by Magnaporthe oryzae Triticum

The application of chemical pesticides to protect agricultural crops from pests and diseases is discouraged due to their harmful effects on humans and the environment. Therefore, alternative approaches for crop protection through microbial or microbe-originated pesticides have been gaining momentum. Wheat blast is a destructive fungal disease caused by the Magnaporthe oryzae Triticum (MoT) pathotype, which poses a serious threat to global food security. Screening of secondary metabolites against MoT revealed that antimycin A isolated from a marine Streptomyces sp. had a significant inhibitory effect on mycelial growth in vitro. This study aimed to investigate the inhibitory effects of antimycin A on some critical life stages of MoT and evaluate the efficacy of wheat blast disease control using this natural product. A bioassay indicated that antimycin A suppressed mycelial growth (62.90%), conidiogenesis (100%), germination of conidia (42%), and the formation of appressoria in the germinated conidia (100%) of MoT at a 10 µg/mL concentration. Antimycin A suppressed MoT in a dose-dependent manner with a minimum inhibitory concentration of 0.005 μg/disk. If germinated, antimycin A induced abnormal germ tubes (4.8%) and suppressed the formation of appressoria. Interestingly, the application of antimycin A significantly suppressed wheat blast disease in both the seedling (100%) and heading stages (76.33%) of wheat at a 10 µg/mL concentration, supporting the results from in vitro study. This is the first report on the inhibition of mycelial growth, conidiogenesis, conidia germination, and detrimental morphological alterations in germinated conidia, and the suppression of wheat blast disease caused by a Triticum pathotype of M. Oryzae by antimycin A. Further study is required to unravel the precise mode of action of this promising natural compound for considering it as a biopesticide to combat wheat blast.

Streptomyces spp. Isolated from Marine and Caatinga Biomes in Brazil for the Biological Control of Duponchelia fovealis

Actinobacteria have been drawing attention due to their potential for the development of new pest control products. We hereby assess the effects of Streptomyces isolated from marine and caatinga biomes against Duponchelia fovealis Zeller (Lepidoptera: Crambidae), a pest associated with the strawberry culture at a global scale. To this end, eggs deposited by adults were immersed for 5 s in a bacterial suspension, and the larvae were fed on leaflets placed in glass tubes containing bacterial suspensions. In both treatments, the control was a saline solution. The bioassays demonstrated that the Streptomyces strains were able to cause the death of D. fovealis eggs (≈ 40%) and larvae (≈ 65%) compared to untreated eggs (1.4%) and larvae (2.0%). The crude extract of strain T49 and the chitinase extract of strain T26 affected larval growth when applied directly to the thorax of first-instar larvae (larval-adult lifespan of 65.3 ± 0.5 days and 67.5 ± 0.7 days, respectively; survival of 61.2 ± 1.2%) in relation to the control treatment (larval-adult lifespan of 41.75 ± 0.2 days and survival of 83.7 ± 2.6%). The Streptomyces spp. strains T41, T49, and T50 caused antifeeding activity. Apart from larval mortality, the adults that emerged from the larvae exposed to the extracts presented morphological abnormalities, and the moths' chitin spectra showed clear alterations to the pupa and wings. Our studies show, for the very first time, that Streptomyces isolated from the marine environment and the Caatinga biome are effective at provoking the mortality of D. fovealis and are promising agents for developing new products with biological control properties.

Deciphering the antagonistic effect of Streptomyces spp. and host-plant resistance induction against charcoal rot of sorghum

The findings of this study suggest that the selected five strains of Streptomyces spp. could be used for biological control of charcoal rot disease in sorghum. Two strains each of Streptomyces albus (CAI-17 and KAI-27) and Streptomyces griseus (KAI-26 and MMA-32) and one strain of Streptomyces cavourensis (SAI-13) previously reported to have plant growth-promotion activity in chickpea, rice and sorghum were evaluated for their antagonistic potential against Macrophomina phaseolina, which causes charcoal rot in sorghum. The antagonistic potential of these strains against M. phaseolina was assessed through dual culture assay, metabolite production assay, blotter paper assay in greenhouse and field disease screens. In both dual culture and metabolite production assays, the selected strains significantly inhibited the growth of M. phaseolina (63-74%). In the blotter paper assay, all the five strains of Streptomyces spp. inhibited the pathogen (80-90%). When these five strains were tested for their antagonistic potential under the greenhouse (two times) and field (two seasons) conditions by toothpick method of inoculation, significant differences were observed for charcoal rot severity. Principal component analysis capturing 91.3% phenotypic variations, revealed that the shoot samples treated with both Streptomyces and the pathogen exhibited significantly enhanced antioxidant parameters including superoxide dismutase, catalase, ascorbate peroxidase, guaiacol peroxidase, glutathione reductase, phenylalanine ammonia-lyase, polyphenol oxidase, and total phenolic contents when compared to shoot samples treated with only M. phaseolina. Scanning electron microscope analysis revealed that the phloem and xylem tissues of the Streptomyces treated stem samples were intact compared to that of pathogen inoculated plants. This study indicated that the selected strains of Streptomyces spp. have the potential for biological control of charcoal rot disease in sorghum.

ANTIFUNGAL ACTIVITY SCREENING OF ANTARCTIC ACTINOBACTERIA AGAINST PHYTOPATHOGENIC FUNGI

The extreme weather conditions in the Antarctic have exerted selective pressures favoring differential features in bacteria to survive this untapped environment (i.e., antibiotic molecules). Notably, higher chances of antibiotic discovery from extremophiles have been proposed recently. Althoughnew organic and environmentally friendly sources for helping in the control of plant pathogenic fungi are necessary, the information about anti-phytopathogenic applications of extremophile microorganisms from untapped environments is limited. In this study, we determined the antifungal effect of actinobacterial strains isolated from Antarctic soils and sediments. Co-culture inhibition assays and Minimum Inhibitory Concentration (MIC) determination revealed that all Antarctic strains (x28) can inhibit the growth of at least one phytopathogenic fungi including Fusarium oxysporum,Rhizoctonia solani,Botrytissp. and Phytophthora infestans. Additionally, new novel antagonistic relationships are reported. Our work establishes a precedent on Antarctic actinobacteria strains with the capacity to produce antifungal compounds, and its potential for developing new fungicides or biocontrol agents solving current agriculture problems.

Biocontrol of Cereal Crop Diseases Using Streptomycetes

A growing world population and an increasing demand for greater food production requires that crop losses caused by pests and diseases are dramatically reduced. Concurrently, sustainability targets mean that alternatives to chemical pesticides are becoming increasingly desirable. Bacteria in the plant root microbiome can protect their plant host against pests and pathogenic infection. In particular, Streptomyces species are well-known to produce a range of secondary metabolites that can inhibit the growth of phytopathogens. Streptomyces are abundant in soils and are also enriched in the root microbiomes of many different plant species, including those grown as economically and nutritionally valuable cereal crops. In this review we discuss the potential of Streptomyces to protect against some of the most damaging cereal crop diseases, particularly those caused by fungal pathogens. We also explore factors that may improve the efficacy of these strains as biocontrol agents in situ, as well as the possibility of exploiting plant mechanisms, such as root exudation, that enable the recruitment of microbial species from the soil to the root microbiome. We argue that a greater understanding of these mechanisms may enable the development of protective plant root microbiomes with a greater abundance of beneficial bacteria, such as Streptomyces species.

Actinobacteria associated with Glycyrrhiza inflata Bat. are diverse and have plant growth promoting and antimicrobial activity

Many of the plant associated microbes may directly and indirectly contribute to plant growth and stress resistance. Our aim was to assess the plant growth-promoting and antimicrobial activities of actinobacteria isolated from Glycyrrhiza inflata Bat. plants to find strains that could be applied in agricultural industry, for example in reclaiming saline soils. We isolated 36 and 52 strains that showed morphological characteristics of actinobacteria from one year old and three year old G. inflata plants, respectively. Based on 16S rRNA gene sequence analysis, the strains represented ten actinobacterial genera. Most of the strains had plant growth promoting characteristics in vitro, tolerated 200 mM NaCl and inhibited the growth of at least one indicator organism. The eight selected Streptomyces strains increased the germination rate of G. inflata seeds under salt stress. In addition, the four best seed germination promoters promoted the growth of G. inflata in vivo. The best promoters of G. inflata growth, strains SCAU5283 and SCAU5215, inhibited a wide range of indicator organisms, and may thus be considered as promising candidates to be applied in inoculating G. inflata.

Microbial modulation of bacoside A biosynthetic pathway and systemic defense mechanism in Bacopa monnieri under Meloidogyne incognita stress

Plant-associated beneficial microbes have been explored to fulfill the imperative function for plant health. However, their impact on the host secondary metabolite production and nematode disease management remains elusive. Our present work has shown that chitinolytic microbes viz., Chitiniphilus sp. MTN22 and Streptomyces sp. MTN14 singly as well as in combination modulated the biosynthetic pathway of bacoside A and systemic defense mechanism against Meloidogyne incognita in Bacopa monnieri. Interestingly, expression of bacoside biosynthetic pathway genes (3-Hydroxy-3-methylglutaryl coenzyme A reductase, mevalonate diphosphate decarboxylase, and squalene synthase) were upregulated in plants treated with the microbial combination in the presence as well as in absence of M. incognita stress. These microbes not only augmented bacoside A production (1.5 fold) but also strengthened host resistance via enhancement in chlorophyll a, defense enzymes and phenolic compounds like gallic acid, syringic acid, ferulic acid and cinnamic acid. Furthermore, elevated lignification and callose deposition in the microbial combination treated plants corroborate well with the above findings. Overall, the results provide novel insights into the underlying mechanisms of priming by beneficial microbes and underscore their capacity to trigger bacoside A production in B. monnieri under biotic stress.

Potential for biocontrol of melanized fungi by actinobacteria isolated from intertidal region of Ilha Do Mel, Paraná, Brazil

Actinobacteria occur in many environments and have the capacity to produce secondary metabolites with antibiotic potential. Identification and taxonomy of actinobacteria that produce antimicrobial substances is essential for the screening of new compounds, and sequencing of the 16S region of ribosomal DNA (rDNA), which is conserved and present in all bacteria, is an important method of identification. Melanized fungi are free-living organisms, which can also be pathogens of clinical importance. This work aimed to evaluate growth inhibition of melanized fungi by actinobacteria and to identify the latter to the species level. In this study, antimicrobial activity of 13 actinobacterial isolates from the genus Streptomyces was evaluated against seven melanized fungi of the genera Exophiala, Cladosporium, and Rhinocladiella. In all tests, all actinobacterial isolates showed inhibitory activity against all isolates of melanized fungi, and only one actinobacterial isolate had less efficient inhibitory activity. The 16S rDNA region of five previously unidentified actinobacterial isolates from Ilha do Mel, Paraná, Brazil, was sequenced; four of the isolates were identified as Streptomyces globisporus subsp. globisporus, and one isolate was identified as Streptomyces aureus. This work highlights the potential of actinobacteria with antifungal activity and their role in the pursuit of novel antimicrobial substances.

Purification and Characterization of a New Antifungal Compound 10-(2,2-dimethyl-cyclohexyl)-6,9-dihydroxy-4,9-dimethyl-dec-2-enoic Acid Methyl Ester from Streptomyces hydrogenans Strain DH16

In agriculture, biocontrol agents have been emerged as safe alternative to chemical pesticides where Streptomyces spp. and their metabolites constitute a great potential for their exploration as potent agents for controlling various fungal phytopathogens. The present study reports an antifungal compound purified from Streptomyces hydrogenans strain DH16, a soil isolate, using silica gel chromatography and semi preparative HPLC. The compound was characterized using various spectroscopic techniques (IR, ¹H and ¹³C NMR) and named 10-(2,2-dimethyl-cyclohexyl)-6,9-dihydroxy-4,9-dimethyl-dec-2-enoic acid methyl ester (SH2). Compound (SH2) showed significant inhibitory activity against fungal phytopathogens and resulted in severe morphological aberrations in their structure. Minimal inhibitory and minimal fungicidal concentrations of the compound ranged from 6.25 to 25 μg/ml and 25 to 50 μg/ml, respectively. In vivo evaluation of the compound showed strong control efficacy against Alternaria brassicicola, a seed borne pathogen, on radish seeds. In comparison to mancozeb and carbendazim, the compound was more effective in controlling damping off disease. Additionally, it promoted plant growth with increased rate of seed germination, and displayed no phytotoxicity. The compound retained its antifungal activity after its exposure to temperature of 100°C and sunlight for 1 h. Furthermore, the compound (SH2) when tested for its biosafety was found to be non-cytotoxic, and non-mutagenic against Salmonella typhimurium TA98 and TA100 strains. This compound from S. hydrogenans strain DH16 has not been reported earlier, so this new compound can be developed as an ideal safe and superior biofungicide for the control of various fungal plant diseases.

Taxonomy, Physiology, and Natural Products of Actinobacteria

Actinobacteria are Gram-positive bacteria with high G+C DNA content that constitute one of the largest bacterial phyla, and they are ubiquitously distributed in both aquatic and terrestrial ecosystems. Many Actinobacteria have a mycelial lifestyle and undergo complex morphological differentiation. They also have an extensive secondary metabolism and produce about two-thirds of all naturally derived antibiotics in current clinical use, as well as many anticancer, anthelmintic, and antifungal compounds. Consequently, these bacteria are of major importance for biotechnology, medicine, and agriculture. Actinobacteria play diverse roles in their associations with various higher organisms, since their members have adopted different lifestyles, and the phylum includes pathogens (notably, species of Corynebacterium, Mycobacterium, Nocardia, Propionibacterium, and Tropheryma), soil inhabitants (e.g., Micromonospora and Streptomyces species), plant commensals (e.g., Frankia spp.), and gastrointestinal commensals (Bifidobacterium spp.). Actinobacteria also play an important role as symbionts and as pathogens in plant-associated microbial communities. This review presents an update on the biology of this important bacterial phylum.

Antifungal performance of extracellular chitinases and culture supernatants of Streptomyces galilaeus CFFSUR-B12 against Mycosphaerella fijiensis Morelet

The tropical and mycoparasite strain Streptomyces galilaeus CFFSUR-B12 was evaluated as an antagonist of Mycosphaerella fijiensis Morelet, causal agent of the Black Sigatoka Disease (BSD) of banana. On zymograms of CFFSUR-B12 culture supernatants, we detected four chitinases of approximately 32 kDa (Chi32), 20 kDa (Chi20), and two with masses well over 170 kDa (ChiU) that showed little migration during denaturing electrophoresis at different concentrations of polyacrylamide. The thymol-sulphuric acid assay showed that the ChiU were glycosylated chitinases. Moreover, matrix assisted laser desorption ionization time-of-flight MS analysis revealed that the ChiU are the same protein and identical to a family 18 chitinase from Streptomyces sp. S4 (gi|498328075). Chi32 was similar to an extracellular protein from Streptomyces albus J1074 (gi|478687481) and Chi20 was non-significantly similar to chitinases from five different strains of Streptomyces (P > 0.05). Subsequently, Chi32 and Chi20 were partially purified by anion exchange and hydrophobic interaction chromatography and tested against M. fijiensis. Chitinases failed to inhibit ascospore germination, but inhibited up to 35 and 62% of germ tube elongation and mycelial growth, respectively. We found that crude culture supernatant and living cells of S. galilaeus CFFSUR-B12 were the most effective in inhibiting M. fijiensis and are potential biocontrol agents of BSD.

Biodiversity of genes encoding anti-microbial traits within plant associated microbes

The plant is an attractive versatile home for diverse associated microbes. A subset of these microbes produces a diversity of anti-microbial natural products including polyketides, non-ribosomal peptides, terpenoids, heterocylic nitrogenous compounds, volatile compounds, bacteriocins, and lytic enzymes. In recent years, detailed molecular analysis has led to a better understanding of the underlying genetic mechanisms. New genomic and bioinformatic tools have permitted comparisons of orthologous genes between species, leading to predictions of the associated evolutionary mechanisms responsible for diversification at the genetic and corresponding biochemical levels. The purpose of this review is to describe the biodiversity of biosynthetic genes of plant-associated bacteria and fungi that encode selected examples of antimicrobial natural products. For each compound, the target pathogen and biochemical mode of action are described, in order to draw attention to the complexity of these phenomena. We review recent information of the underlying molecular diversity and draw lessons through comparative genomic analysis of the orthologous coding sequences (CDS). We conclude by discussing emerging themes and gaps, discuss the metabolic pathways in the context of the phylogeny and ecology of their microbial hosts, and discuss potential evolutionary mechanisms that led to the diversification of biosynthetic gene clusters.

Red soils harbor diverse culturable actinomycetes that are promising sources of novel secondary metabolites

Red soils, which are widely distributed in tropical and subtropical regions of southern China, are characterized by low organic carbon, high content of iron oxides, and acidity and, hence, are likely to be ideal habitats for acidophilic actinomycetes. However, the diversity and biosynthetic potential of actinomycetes in such habitats are underexplored. Here, a total of 600 actinomycete strains were isolated from red soils collected in Jiangxi Province in southeast China. 16S rRNA gene sequence analysis revealed a high diversity of the isolates, which were distributed into 26 genera, 10 families, and 7 orders within the class Actinobacteria; these taxa contained at least 49 phylotypes that are likely to represent new species within 15 genera. The isolates showed good physiological potentials for biosynthesis and biocontrol. Chemical screening of 107 semirandomly selected isolates spanning 20 genera revealed the presence of at least 193 secondary metabolites from 52 isolates, of which 125 compounds from 39 isolates of 12 genera were putatively novel. Macrolides, polyethers, diketopiperazines, and siderophores accounted for most of the known compounds. The structures of six novel compounds were elucidated, two of which had a unique skeleton and represented characteristic secondary metabolites of a putative novel Streptomyces phylotype. These results demonstrate that red soils are rich reservoirs for diverse culturable actinomycetes, notably members of the families Streptomycetaceae, Pseudonocardiaceae, and Streptosporangiaceae, with the capacity to synthesize novel bioactive compounds.

Micromonospora from nitrogen fixing nodules of alfalfa (Medicago sativa L.). A new promising Plant Probiotic Bacteria

Biotic interactions can improve agricultural productivity without costly and environmentally challenging inputs. Micromonospora strains have recently been reported as natural endophytes of legume nodules but their significance for plant development and productivity has not yet been established. The aim of this study was to determine the diversity and function of Micromonospora isolated from Medicago sativa root nodules. Micromonospora-like strains from field alfalfa nodules were characterized by BOX-PCR fingerprinting and 16S rRNA gene sequencing. The ecological role of the interaction of the 15 selected representative Micromonospora strains was tested in M. sativa. Nodulation, plant growth and nutrition parameters were analyzed. Alfalfa nodules naturally contain abundant and highly diverse populations of Micromonospora, both at the intra- and at interspecific level. Selected Micromonospora isolates significantly increase the nodulation of alfalfa by Ensifer meliloti 1021 and also the efficiency of the plant for nitrogen nutrition. Moreover, they promote aerial growth, the shoot-to-root ratio, and raise the level of essential nutrients. Our results indicate that Micromonospora acts as a Rhizobia Helper Bacteria (RHB) agent and has probiotic effects, promoting plant growth and increasing nutrition efficiency. Its ecological role, biotechnological potential and advantages as a plant probiotic bacterium (PPB) are also discussed.

Isolation and enzyme bioprospection of endophytic bacteria associated with plants of Brazilian mangrove ecosystem

The mangrove ecosystem is a coastal tropical biome located in the transition zone between land and sea that is characterized by periodic flooding, which confers unique and specific environmental conditions on this biome. In these ecosystems, the vegetation is dominated by a particular group of plant species that provide a unique environment harboring diverse groups of microorganisms, including the endophytic microorganisms that are the focus of this study. Because of their intimate association with plants, endophytic microorganisms could be explored for biotechnologically significant products, such as enzymes, proteins, antibiotics and others. Here, we isolated endophytic microorganisms from two mangrove species, Rhizophora mangle and Avicennia nitida, that are found in streams in two mangrove systems in Bertioga and Cananéia, Brazil. Bacillus was the most frequently isolated genus, comprising 42% of the species isolated from Cananéia and 28% of the species from Bertioga. However, other common endophytic genera such as Pantoea, Curtobacterium and Enterobacter were also found. After identifying the isolates, the bacterial communities were evaluated for enzyme production. Protease activity was observed in 75% of the isolates, while endoglucanase activity occurred in 62% of the isolates. Bacillus showed the highest activity rates for amylase and esterase and endoglucanase. To our knowledge, this is the first reported diversity analysis performed on endophytic bacteria obtained from the branches of mangrove trees and the first overview of the specific enzymes produced by different bacterial genera. This work contributes to our knowledge of the microorganisms and enzymes present in mangrove ecosystems.

Mechanism of phosphate solubilization and antifungal activity of Streptomyces spp. isolated from wheat roots and rhizosphere and their application in improving plant growth

The application of plant-growth-promoting rhizobacteria (PGPR) at field scale has been hindered by an inadequate understanding of the mechanisms that enhance plant growth, rhizosphere incompetence and the inability of bacterial strains to thrive in different soil types and environmental conditions. Actinobacteria with their sporulation, nutrient cycling, root colonization, bio-control and other plant-growth-promoting activities could be potential field bio-inoculants. We report the isolation of five rhizospheric and two root endophytic actinobacteria from Triticum aestivum (wheat) plants. The cultures exhibited plant-growth-promoting activities, namely phosphate solubilization (1916 mg l−1), phytase (0.68 U ml−1), chitinase (6.2 U ml−1), indole-3-acetic acid (136.5 mg l−1) and siderophore (47.4 mg l−1) production, as well as utilizing all the rhizospheric sugars under test. Malate (50–55 mmol l−1) was estimated in the culture supernatant of the highest phosphate solublizer, Streptomyces mhcr0816. The mechanism of malate overproduction was studied by gene expression and assays of key glyoxalate cycle enzymes – isocitrate dehydrogenase (IDH), isocitrate lyase (ICL) and malate synthase (MS). The significant increase in gene expression (ICL fourfold, MS sixfold) and enzyme activity (ICL fourfold, MS tenfold) of ICL and MS during stationary phase resulted in malate production as indicated by lowered pH (2.9) and HPLC analysis (retention time 13.1 min). Similarly, the secondary metabolites for chitinase-independent biocontrol activity of Streptomyces mhcr0817, as identified by GC-MS and 1H-NMR spectra, were isoforms of pyrrole derivatives. The inoculation of actinobacterial isolate mhce0811 in T. aestivum (wheat) significantly improved plant growth, biomass (33 %) and mineral (Fe, Mn, P) content in non-axenic conditions. Thus the actinobacterial isolates reported here were efficient PGPR possessing significant antifungal activity and may have potential field applications.

Bio-prospecting of distillery yeasts as bio-control and bio-remediation agents

This work constitutes a preliminary study in which the capacity of non-Saccharomyces yeasts isolated from ancient distilleries as bio-control agents against moulds and in the treatment of waste waters contaminated by heavy metals-i.e. bio-remediation-is shown. In the first control assays, antagonist effect between non-Saccharomyces yeasts, their extracts and supernatants against some moulds, analysing the plausible (not exhaustive) involved factors were qualitatively verified. In addition, two enzymatic degrading properties of cell wall plant polymers, quitinolitic and pectinolitic, were screened. Finally, their use as agents of bio-remediation of three heavy metals (cadmium, chromium and lead) was analysed semi-quantitatively. The results showed that all isolates belonging to Pichia species effectively inhibited all moulds assayed. Moreover, P. kudriavzevii is a good candidate for both bio-control and bio-remediation because it inhibited moulds and accumulated the major proportion of the three tested metals.

Genetic and functional characterization of culturable plant-beneficial actinobacteria associated with yam rhizosphere

Actinobacteria were isolated from the rhizosphere of yam plants from agricultural fields from Yeoju, South Korea and analyzed for their genetic and plant-beneficial functional diversity. A total of 29 highly occurring actinobacterial isolates from the yam rhizosphere were screened for various plant-beneficial traits such as antimicrobial activity on fungi and bacteria; biocontrol traits such as production of siderophore, protease, chitinase, endo-cellulase, and β-glucanase. The isolates were also screened for plant growth-promoting (PGP) traits such as auxin production, phosphate solubilization, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, and in vitro Arabidopsis growth promotion. 16S rDNA sequence-based phylogenetic analysis was carried out on the actinobacterial isolates to determine their genetic relatedness to known actinobacteria. BOX-PCR analysis revealed high genetic diversity among the isolates. Several isolates were identified to belong to the genus Streptomyces and a few to Kitasatospora. The actinobacterial strains exhibited high diversity in their functionality and were identified as novel and promising candidates for future development into biocontrol and PGP agents.

Taxonomic and functional diversity of Streptomyces in a forest soil

In this work we report the isolation and the characterization of 79 Streptomyces isolates from a French forest soil. The 16S rRNA gene phylogeny indicated that a great diversity of Streptomyces was present in this soil, with at least nine different and potentially new species. Growth plate assays showed that most Streptomyces lineages exhibit cellulolytic and hemicellulolytic capacities and potentially participate in wood decomposition. Molecular screening for a specific hydrogenase also indicated a widespread potential for atmospheric H2 uptake. Co-culture experiments with representative strains showed antagonistic effects between Streptomyces of the same population and between Streptomyces and various fungi. Interestingly, in certain conditions, growth promotion of some fungi also occurred. We conclude that in forest soil, Streptomyces populations exhibit many important functions involved in different biogeochemical cycles and also influence the structure of soil microbial communities.

Purification and characterization of an extracellular chitinase from antagonistic Streptomyces violaceusniger

The actinomycetes Streptomyces violaceusniger showed strong antagonistic activity against various tested wood rotting fungi. An extracellular chitinase, produced by antagonistic S. violaceusniger MTCC 3959, was purified as follows: ammonium sulfate precipitation, chitin affinity and chromatographic separation of Q Sepharose. The molecular mass of the purified chitinase was estimated as 56.5 kDa by SDS-PAGE. Chitinase was optimally active at pH of 5.0 and 50 °C. It retained almost 100% activity at pH 5.0 and also had high thermal tolerance at 50 °C. Enzyme activity was inhibited by Hg(2+) and Ag(+) cations, but was neither substantially inhibited by K(+) cation nor by chelating agent EDTA. The apparent Km and Vmax at 37 °C were 0.1426 mM and 6.6 U/mg, respectively using pNP-(GlcNAc)2 as substrate. The 56.5 kDa chitinase of strain MTCC 3959 represented an exo-type activity. The purified chitinase was further identified by MALDI-TOF. The results of peptide mass fingerprinting showed that 10 tryptic peptides of the chitinase were identical to the chitinase C from Streptomyces albus J1074 (GenBank Accession No. gi|239982330). The sequence of N-terminal amino acid (AA) of the chitinase was determined to be G-D-G-T-G-P-G-P-G-P.

Streptomyces competition and co-evolution in relation to plant disease suppression

High densities of antagonistic Streptomyces are associated with plant disease suppression in many soils. Here we review use of inoculation and organic matter amendments for enriching antagonistic Streptomyces populations to reduce plant disease and note that effective and consistent disease suppression in response to management has been elusive. We argue that shifting the focus of research from short-term disease suppression to the population ecology and evolutionary biology of antagonistic Streptomyces in soil will enhance prospects for effective management. A framework is presented for considering the impacts of short- and long-term management on competitive and coevolutionary dynamics among Streptomyces populations in relation to disease suppression.

Plant growth enhancing effects by a siderophore-producing endophytic streptomycete isolated from a Thai jasmine rice plant (Oryza sativa L. cv. KDML105)

An endophytic Streptomyces sp. GMKU 3100 isolated from roots of a Thai jasmine rice plant (Oryza sativa L. cv. KDML105) showed the highest siderophore production on CAS agar while phosphate solubilization and IAA production were not detected. A mutant of Streptomyces sp. GMKU 3100 deficient in just one of the plant growth promoting traits, siderophore production, was generated by inactivation of a desD-like gene encoding a key enzyme controlling the final step of siderophore biosynthesis. Pot culture experiments revealed that rice and mungbean plants inoculated with the wild type gave the best enhancement of plant growth and significantly increased root and shoot biomass and lengths compared with untreated controls and siderophore-deficient mutant treatments. Application of the wild type in the presence or absence of ferric citrate significantly promoted plant growth of both plants. The siderophore-deficient mutant clearly showed the effect of this important trait involved in plant-microbe interaction in enhancement of growth in rice and mungbean plants supplied with sequestered iron. Our results highlight the value of a substantial understanding of the relationship of the plant growth promoting properties of endophytic actinomycetes to the plants. Endophytic actinomycetes, therefore, can be applied as potentially safe and environmentally friendly biofertilizers in agriculture.

Biotechnological approaches to develop bacterial chitinases as a bioshield against fungal diseases of plants

Fungal diseases of plants continue to contribute to heavy crop losses in spite of the best control efforts of plant pathologists. Breeding for disease-resistant varieties and the application of synthetic chemical fungicides are the most widely accepted approaches in plant disease management. An alternative approach to avoid the undesired effects of chemical control could be biological control using antifungal bacteria that exhibit a direct action against fungal pathogens. Several biocontrol agents, with specific fungal targets, have been registered and released in the commercial market with different fungal pathogens as targets. However, these have not yet achieved their full commercial potential due to the inherent limitations in the use of living organisms, such as relatively short shelf life of the products and inconsistent performance in the field. Different mechanisms of action have been identified in microbial biocontrol of fungal plant diseases including competition for space or nutrients, production of antifungal metabolites, and secretion of hydrolytic enzymes such as chitinases and glucanases. This review focuses on the bacterial chitinases that hydrolyze the chitinous fungal cell wall, which is the most important targeted structural component of fungal pathogens. The application of the hydrolytic enzyme preparations, devoid of live bacteria, could be more efficacious in fungal control strategies. This approach, however, is still in its infancy, due to prohibitive production costs. Here, we critically examine available sources of bacterial chitinases and the approaches to improve enzymatic properties using biotechnological tools. We project that the combination of microbial and recombinant DNA technologies will yield more effective environment-friendly products of bacterial chitinases to control fungal diseases of crops.

Identification, characterization, and expression analyses of class II and IV chitinase genes from Douglas-fir seedlings infected by Phellinus sulphurascens

Laminated root rot (LRR) disease, caused by the fungus Phellinus sulphurascens, is a major threat to coastal Douglas-fir (DF) (Pseudotsuga menziesii) forests in western North America. Understanding host-pathogen interactions of this pathosystem is essential to manage this important conifer root disease. Our research objectives were to identify DF pathogenesis-related (PR) genes and analyze their expression patterns over the course of infection. We constructed a cDNA library of Phellinus sulphurascens-infected DF seedling roots and sequenced a total of 3,600 random cDNA clones from this library. One of the largest groups of identified genes (203 cDNA clones) matched with chitinase genes reported in other plant species. We identified at least three class II and six class IV chitinase genes from DF seedlings. Quantitative reverse-transcriptase polymerase chain reaction analyses showed significant differential expression patterns locally in root tissues and systemically in needle tissues after fungal invasion. Nonetheless, there was a common trend in gene expression patterns for most of the chitinase genes: an upregulation within 12 h of pathogen inoculation followed by down-regulation within 2 to 3 days postinoculation (dpi), and then further upregulation within 5 to 7 dpi. Western immunoblot data showed differential accumulation of class IV chitinases in Phellinus sulphurascens-infected DF seedlings. Further detailed functional analyses will help us to understand the specific role of DF chitinases in defense against Phellinus sulphurascens infection.

Endochitinase CHI2 of the biocontrol fungus Metarhizium anisopliae affects its virulence toward the cotton stainer bug Dysdercus peruvianus

Chitinases have been implicated in fungal cell wall remodeling and play a role in exogenous chitin degradation for nutrition and competition. Due to the diversity of these enzymes, assigning particular functions to each chitinase is still ongoing. The entomopathogenic fungus Metarhizium anisopliae produces several chitinases, and here, we evaluate whether endochitinase CHI2 is involved in the pathogenicity of this fungus. We constructed strains either overexpressing or lacking the CHI2 chitinase. These constructs were validated by Southern, Northern and Western blot analysis, and chitinase production. To access the effects of CHI2 chitinase in virulence, the cotton stainer bug Dysdercus peruvianus was used as a host. CHI2 overexpression constructs showed higher efficiency in host killing suggesting that the production of this chitinase by a constitutive promoter reduces the time necessary to kill the insect. More significantly, the knock out constructs showed decreased virulence to the insects as compared to the wild type strain. The lack of this single CHI2 chitinase diminished fungal infection efficiency, but not any other detectable trait, showing that the M. anisopliae family 18, subgroup B endochitinase CHI2 plays a role in insect infection.