Isolation and characterization of endophytic streptomycete antagonists of Fusarium wilt pathogen from surface-sterilized banana roots

Selection of Streptomyces against soil borne fungal pathogens by a standardized dual culture assay and evaluation of their effects on seed germination and plant growth

Background

In the search for new natural resources for crop protection, streptomycetes are gaining interest in agriculture as plant growth promoting bacteria and/or biological control agents. Because of their peculiar life cycle, in which the production of secondary metabolites is synchronized with the development of aerial hyphae and sporulation, the commonly used methods to screen for bacterial antagonists need to be adapted.

Results

The dual culture assay was standardized in terms of inoculation timing of Streptomyces antagonist and pathogen, and growth rate of different fungal pathogens. In case of fast-growing fungi, inoculation of the antagonist 2 or 3 days prior to the pathogen resulted in significantly stronger inhibition of mycelium growth. One hundred and thirty Streptomyces strains were evaluated against six destructive soil borne pathogens. The activity of strains varied from broad-spectrum to highly specific inhibition of individual pathogens. All strains inhibited at least one tested pathogen. Three strains, which combined the largest broad-spectrum with the highest inhibition activity, were selected for further characterization with four vegetable species. All of them were able to colonize seed surface of all tested vegetable crops. They mostly improved radicle and hypocotyl growth in vitro, although no statistically significant enhancement of biomass weight was observed in vivo. Occasionally, transient negative effects on germination and plant growth were observed.

Conclusions

The adapted dual culture assay allowed us to compare the inhibition of individual Streptomyces strains against six fungal soil borne pathogens. The best selected strains were able to colonize the four vegetable crops and have a potential to be developed into biocontrol products. Although they occasionally negatively influenced plant growth, these effects did not persist during the further development. Additional in vivo studies are needed to confirm their potential as biological control or plant growth promoting agents.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0886-1) contains supplementary material, which is available to authorized users.

Diversity, bioactivities, and metabolic potentials of endophytic actinomycetes isolated from traditional medicinal plants in Sichuan, China

The present study was designed to determine the taxonomic diversity and metabolic activity of the actinomycetes community, including 13 traditional medicinal plants collected in Sichuan province, China, using multiple approaches such as morphological and molecular identification methods, bioactivity assays, and PCR screening for genes involved in antibiotics biosynthesis. 119 endophytic actinomycetes were recovered; 80 representative strains were chosen for 16S rRNA gene partial sequence analyses, with 66 of them being affiliated to genus Streptomyces and the remaining 14 strains being rare actinomycetes. Antimicrobial tests showed that 12 (15%) of the 80 endophytic actinomycetes displayed inhibitory effects against at least one indicator pathogens, which were all assigned to the genus Streptomyces. In addition, 87.5% and 58.8% of the isolates showed anticancer and anti-diabetic activities, respectively. Meanwhile, the anticancer activities of the isolates negatively correlated with their anti-diabetic activities. Based on the results of PCR screening, five genes, PKS-I, PKS-II, NRPS, ANSA, and oxyB, were detected in 55.0%, 58.8%, 90.0%, 18.8% and 8.8% of the 80 actinomycetes, respectively. In conclusion, the PCR screening method employed in the present study was conducive for screening and selection of potential actinomycetes and predicting potential secondary metabolites, which could overcome the limitations of traditional activity screening models.

Distribution and Identification of Endophytic Streptomyces Species from Schima wallichii as Potential Biocontrol Agents against Fungal Plant Pathogens

The prospective of endophytic microorganisms allied with medicinal plants is disproportionally large compared to those in other biomes. The use of antagonistic microorganisms to control devastating fungal pathogens is an attractive and eco-friendly substitute for chemical pesticides. Many species of actinomycetes, especially the genus Streptomyces, are well known as biocontrol agents. We investigated the culturable community composition and biological control ability of endophytic Streptomyces sp. associated with an ethanobotanical plant Schima wallichi. A total of 22 actinobacterial strains were isolated from different organs of selected medicinal plants and screened for their biocontrol ability against seven fungal phytopathogens. Seven isolates showed significant inhibition activity against most of the selected pathogens. Their identification based on 16S rRNA gene sequence analysis, strongly indicated that all strains belonged to the genus Streptomyces. An endophytic strain BPSAC70 isolated from root tissues showed highest percentage of inhibition (98.3 %) against Fusarium culmorum with significant activity against other tested fungal pathogens. Phylogenetic analysis based on 16S rRNA gene sequences revealed that all seven strains shared 100 % similarity with the genus Streptomyces. In addition, the isolates were subjected to the amplification of antimicrobial genes encoding polyketide synthase type I (PKS-I) and nonribosomal peptide synthetase (NRPS) and found to be present in most of the potent strains. Our results identified some potential endophytic Streptomyces species having antagonistic activity against multiple fungal phytopathogens that could be used as an effective biocontrol agent against pathogenic fungi.

Continous application of bioorganic fertilizer induced resilient culturable bacteria community associated with banana Fusarium wilt suppression

Fusarium wilt of banana always drives farmers to find new land for banana cultivation due to the comeback of the disease after a few cropping years. A novel idea for solving this problem is the continuous application of bioorganic fertilizer (BIO), which should be practiced from the beginning of banana planting. In this study, BIO was applied in newly reclaimed fields to pre-control banana Fusarium wilt and the culturable rhizobacteria community were evaluated using Biolog Ecoplates and culture-dependent denaturing gradient gel electrophoresis (CD-DGGE). The results showed that BIO application significantly reduced disease incidences and increased crop yields, respectivly. And the stabilized general bacterial metabolic potential, especially for the utilization of carbohydrates, carboxylic acids and phenolic compounds, was induced by BIO application. DGGE profiles demonstrated that resilient community structure of culturable rhizobacteria with higher richness and diversity were observed in BIO treated soils. Morever, enriched culturable bacteria affiliated with Firmicutes, Gammaproteobacteria and Actinobacteria were also detected. In total, continuous application of BIO effectively suppressed Fusarium wilt disease by stabilizing culturable bacterial metabolic potential and community structure. This study revealed a new method to control Fusarium wilt of banana for long term banana cultivation.

Isolation and identification of biocontrol agent Streptomyces rimosus M527 against Fusarium oxysporum f. sp. cucumerinum

Actinomycetes have received considerable attention as biocontrol agents against fungal plant pathogens and as plant growth promoters. In this study, a total of 320 actinomycetes were isolated from various habitats in China. Among which, 77 strains have been identified as antagonistic activities against Fusarium oxysporum f. sp. cucumerinum which usually caused fusarium wilt of cucumber. Of these, isolate actinomycete M527 not only displayed broad-spectrum antifungal activity but also showed the strongest antagonistic activity against the spore germination of F. oxysporum f. sp. cucumerinum. In pot experiments, the results indicated that isolate M527 could promote the shoot growth and prevent the development of the disease on cucumber caused by F. oxysporum f. sp. cucumerinum. The control efficacy against seedling fusarium wilt of cucumber after M527 fermentation broth root-irrigation was up to 72.1% as compared to control. Based on 16S rDNA sequence analysis, the isolate M527 was identified as Streptomyces rimosus.

Illumina-based analysis of core actinobacteriome in roots, stems, and grains of rice

Seed-borne microbiota can transmit vertically from generation to generation and be a favour mutualism between the endosymbionts and hosts. The aim of this study was to investigate the rice-associated actinobacterial taxa in roots, stems, and grains and explore vertically transmitted core actinobacteriome of rice plants. Illumina sequencing analyses of samples of rice grains, stems, and roots showed that the roots contained the most diverse actinobacteria among the tissues. The grains contained 78 actinobacterial operational taxonomic units (OTUs), among which 44 were shared with those in the stems, 30 shared with those in the roots. The coexisted OTUs in the three types of samples mainly belong to genera of Pseudonocardia, Dietzia, Nocardioides, Streptomyces, Mycobacterium, Corynebacterium, Citricoccus, Salinibacterium, and Agrococcus, and other unclassified taxa. The dominant actinobacterial genera Pseudonocardia and Dietzia in the stems and roots were still detected in relatively high abundance in the grains. The Streptomyces isolated from surface sterilized grains could improve nitrogen use efficiency of rice seedlings and the resistance to rice blast fungus. The results suggested that the rice grains contained diverse actinobacterial taxa deriving from stems and roots and showed intimate correlation with the host plants.

Actinomycetes from Eucalyptus and their biological activities for controlling Eucalyptus leaf and shoot blight

In Thailand, Eucalyptus plantations rapidly expand across the country. Leaf and shoot blight caused by Cryptosporiopsis eucalypti, Cylindrocladium sp. and Teratosphaeria destructans is a serious disease in Eucalyptus plantations. In this study, a total of 477 actinomycete strains were successfully isolated from roots and rhizosphere soil of Eucalyptus. Four hundred and thirty nine isolates were classified as streptomycetes and 38 isolates were non-streptomycetes. Among these isolates, 272 (57.0%), 118 (24.7%) and 241 (50.5%) isolates were antagonistic to Cryptosporiopsis eucalypti, Cylindrocladium sp. and Teratosphaeria destructans, respectively. All isolates were tested for their abilities to produce siderophores, indole acetic acid (IAA) and solubilise phosphate. Most isolates (464, 97.3%) produced siderophores. The majority of isolates (345, 72.3%) solubilised phosphate. In addition, almost half of these isolates (237, 49.7%) produced indole acetic acid. Strain EUSKR2S82 which showed the strongest inhibitory effect against all tested fungi with plant growth promoting ability was selected to test with Eucalyptus. This strain could colonize plant roots and increase Eucalyptus roots length. In a detached leaves bioassay, the disease severity of EUSKR2S82-inoculated Eucalyptus leaves was only 30% compared to 95% in the control treatment. The 16S rRNA gene sequence analysis revealed that the strain EUSKR2S82 was related to Streptomyces ramulosus NRRL-B 2714(T) (99.44% similarity). Identification of non-streptomycete isolates using 16S rRNA gene sequences classified them into 9 genera: Actinoallomurus, Actinomadura, Amycolatopsis, Cryptosporangium, Microbispora, Micromonospora, Nocardia, Nonomuraea and Pseudonocardia. It is evident that Eucalyptus tree harbored several genera of actinomycetes. The selected isolate, EUSKR2S82 showed potential as a candidate for biocontrol agent of leaf and shoot blight of Eucalyptus and to promote growth.

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.

Endophytic Actinobacteria and the Interaction of Micromonospora and Nitrogen Fixing Plants

For a long time, it was believed that a healthy plant did not harbor any microorganisms within its tissues, as these were often considered detrimental for the plant. In the last three decades, the numbers of studies on plant microbe-interactions has led to a change in our view and we now know that many of these invisible partners are essential for the overall welfare of the plant. The application of Next Generation Sequencing techniques is a powerful tool that has permitted the detection and identification of microbial communities in healthy plants. Among the new plant microbe interactions recently reported several actinobacteria such as Micromonospora are included. Micromonospora is a Gram-positive bacterium with a wide geographical distribution; it can be found in the soil, mangrove sediments, and freshwater and marine ecosistems. In the last years our group has focused on the isolation of Micromonospora strains from nitrogen fixing nodules of both leguminous and actinorhizal plants and reported for the first time its wide distribution in nitrogen fixing nodules of both types of plants. These studies have shown how this microoganism had been largely overlooked in this niche due to its slow growth. Surprisingly, the genetic diversity of Micromonospora strains isolated from nodules is very high and several new species have been described. The current data indicate that Micromonospora saelicesensis is the most frequently isolated species from the nodular tissues of both leguminous and actinorhizal plants. Further studies have also been carried out to confirm the presence of Micromonospora inside the nodule tissues, mainly by specific in situ hybridization. The information derived from the genome of the model strain, Micromonospora lupini, Lupac 08, has provided useful information as to how this bacterium may relate with its host plant. Several strategies potentially necessary for Micromonospora to thrive in the soil, a highly competitive, and rough environment, and as an endophytic bacterium with the capacity to colonize the internal plant tissues which are protected from the invasion of other soil microbes were identified. The genome data also revealed the potential of M. lupini Lupac 08 as a plant growth promoting bacterium. Several loci involved in plant growth promotion features such as the production of siderophores, phytohormones, and the degradation of chitin (biocontrol) were also located on the genome and the functionality of these genes was confirmed in the laboratory. In addition, when several host plants species were inoculated with Micromonospora strains, the plant growth enhancing effect was evident under greenhouse conditions. Unexpectedly, a high number of plant-cell wall degrading enzymes were also detected, a trait usually found only in pathogenic bacteria. Thus, Micromonospora can be added to the list of new plant-microbe interactions. The current data indicate that this microorganism may have an important application in agriculture and other biotechnological processes. The available information is promising but limited, much research is still needed to determine which is the ecological function of Micromonospora in interaction with nitrogen fixing plants.

Six New Polyketide Decalin Compounds from Mangrove Endophytic Fungus Penicillium aurantiogriseum 328

Six new compounds with polyketide decalin ring, peaurantiogriseols A–F (1–6), along with two known compounds, aspermytin A (7), 1-propanone,3-hydroxy-1-(1,2,4a,5,6,7,8,8a-octahydro-2,5-dihydroxy-1,2,6-trimethyl-1-naphthalenyl) (8), were isolated from the fermentation products of mangrove endophytic fungus Penicillium aurantiogriseum 328#. Their structures were elucidated based on their structure analysis. The absolute configurations of compounds 1 and 2 were determined by ¹H NMR analysis of their Mosher esters; the absolute configurations of 3–6 were determined by using theoretical calculations of electronic circular dichroism (ECD). Compounds 1–8 showed low inhibitory activity against human aldose reductase, no activity of inducing neurite outgrowth, nor antimicrobial activity.

In Vitro and In Vivo Plant Growth Promoting Activities and DNA Fingerprinting of Antagonistic Endophytic Actinomycetes Associates with Medicinal Plants

Endophytic actinomycetes have shown unique plant growth promoting as well as antagonistic activity against fungal phytopathogens. In the present study forty-two endophytic actinomycetes recovered from medicinal plants were evaluated for their antagonistic potential and plant growth-promoting abilities. Twenty-two isolates which showed the inhibitory activity against at least one pathogen were subsequently tested for their plant-growth promoting activities and were compared genotypically using DNA based fingerprinting, including enterobacterial repetitive intergenic consensus (ERIC) and BOX repetitive elements. Genetic relatedness based on both ERIC and BOX-PCR generates specific patterns corresponding to particular genotypes. Exponentially grown antagonistic isolates were used to evaluate phosphate solubilization, siderophores, HCN, ammonia, chitinase, indole-3-acetic acid production, as well as antifungal activities. Out of 22 isolates, the amount of indole-3-acetic acid (IAA) ranging between 10–32 μg/ml was produced by 20 isolates and all isolates were positive for ammonia production ranging between 5.2 to 54 mg/ml. Among 22 isolates tested, the amount of hydroxamate-type siderophores were produced by 16 isolates ranging between 5.2 to 36.4 μg/ml, while catechols-type siderophores produced by 5 isolates ranging from 3.2 to 5.4 μg/ml. Fourteen isolates showed the solubilisation of inorganic phosphorous ranging from 3.2 to 32.6 mg/100ml. Chitinase and HCN production was shown by 19 and 15 different isolates, respectively. In addition, genes of indole acetic acid (iaaM) and chitinase (chiC) were successively amplified from 20 and 19 isolates respectively. The two potential strains Streptomyces sp. (BPSAC34) and Leifsonia xyli (BPSAC24) were tested in vivo and improved a range of growth parameters in chilli (Capsicum annuum L.) under greenhouse conditions. This study is the first published report that actinomycetes can be isolated as endophytes from within these plants and were shown to have antagonistic and plant growth promoting abilities. These results clearly suggest the possibility of using endophytic actinomycetes as bioinoculant for plant growth promotion, nutrient mobilization or as biocontrol agent against fungal phytopathogens for sustainable agriculture.

Identification of an Endophytic Antifungal Bacterial Strain Isolated from the Rubber Tree and Its Application in the Biological Control of Banana Fusarium Wilt

Banana Fusarium wilt (also known as Panama disease) is one of the most disastrous plant diseases. Effective control methods are still under exploring. The endophytic bacterial strain ITBB B5-1 was isolated from the rubber tree, and identified as Serratia marcescens by morphological, biochemical, and phylogenetic analyses. This strain exhibited a high potential for biological control against the banana Fusarium disease. Visual agar plate assay showed that ITBB B5-1 restricted the mycelial growth of the pathogenic fungus Fusarium oxysporum f. sp. cubense race 4 (FOC4). Microscopic observation revealed that the cell wall of the FOC4 mycelium close to the co-cultured bacterium was partially decomposed, and the conidial formation was prohibited. The inhibition ratio of the culture fluid of ITBB B5-1 against the pathogenic fungus was 95.4% as estimated by tip culture assay. Chitinase and glucanase activity was detected in the culture fluid, and the highest activity was obtained at Day 2 and Day 3 of incubation for chitinase and glucanase, respectively. The filtrated cell-free culture fluid degraded the cell wall of FOC4 mycelium. These results indicated that chitinase and glucanase were involved in the antifungal mechanism of ITBB B5-1. The potted banana plants that were inoculated with ITBB B5-1 before infection with FOC4 showed 78.7% reduction in the disease severity index in the green house experiments. In the field trials, ITBB B5-1 showed a control effect of approximately 70.0% against the disease. Therefore, the endophytic bacterial strain ITBB B5-1 could be applied in the biological control of banana Fusarium wilt.

Endophytic actinobacteria of medicinal plants: diversity and bioactivity

Endophytes are the microorganisms that exist inside the plant tissues without having any negative impact on the host plant. Medicinal plants constitute the huge diversity of endophytic actinobacteria of economical importance. These microbes have huge potential to synthesis of numerous novel compounds that can be exploited in pharmaceutical, agricultural and other industries. It is of prime importance to focus the present research on practical utilization of this microbial group in order to find out the solutions to the problems related to health, environment and agriculture. An extensive characterization of diverse population of endophytic actinobacteria associated with medicinal plants can provide a greater insight into the plant-endophyte interactions and evolution of mutualism. In the present review, we have discussed the diversity of endophytic actinobacteria of from medicinal plants their multiple bioactivities.

A critical review on properties and applications of microbial l-asparaginases

l-Asparaginase is one of the main drugs used in the treatment of acute lymphoblastic leukemia (ALL), a commonly diagnosed pediatric cancer. Although several microorganisms are found to produce l-asparaginase, only the purified enzymes from E. coli and Erwinia chrysanthemi are employed in the clinical and therapeutic applications in humans. However, their therapeutic response seldom occurs without some evidence of hypersensitivity and other toxic side effects. l-Asparaginase is also of prospective use in food industry to reduce the formation of acrylamide in fried, roasted or baked food products. This review is an attempt to compile information on the properties of l-asparaginases obtained from different microorganisms. The complications involved with the therapeutic use of the currently available l-asparaginases, and the enzyme's potential application as a food processing aid to mitigate acrylamide formation have also been reviewed. Further, avenues for searching alternate sources of l-asparaginase have been discussed, highlighting the prospects of endophytic microorganisms as a possible source of l-asparaginases with varied biochemical and pharmacological properties.

Isolation, abundance and phylogenetic affiliation of endophytic actinomycetes associated with medicinal plants and screening for their in vitro antimicrobial biosynthetic potential

Microorganisms associated with medicinal plants are of interest as the producers of important bioactive compounds. To date, the diversity of culturable endophytic actinomycetes associated with medicinal plants is in its initial phase of exploration. In this study, 42 endophytic actinomycetes were isolated from different organs of seven selected medicinal plants. The highest number of isolates (n = 22, 52.3%) of actinomycetes was isolated from roots, followed by stems (n = 9, 21.4%), leaves (n = 6, 14.2%), flowers (n = 3, 7.1%), and petioles (n = 2, 4.7%). The genus Streptomyces was the most dominant among the isolates (66.6%) in both the locations (Dampa TRF and Phawngpuii NP, Mizoram, India). From a total of 42 isolates, 22 isolates were selected for further studies based on their ability to inhibit one of the tested human bacterial or fungal pathogen. Selected isolates were identified based on 16S rRNA gene analysis and subsequently the isolates were grouped to four different genera; Streptomyces, Brevibacterium, Microbacterium, and Leifsonia. Antibiotic sensitivity assay was performed to understand the responsible antimicrobials present in the isolates showing the antimicrobial activities and revealed that the isolates were mostly resistant to penicillin G and ampicillin. Further, antimicrobial properties and antibiotic sensitivity assay in combination with the results of amplification of biosynthetic genes polyketide synthase (PKS-I) and non-ribosomal peptide synthetase (NRPS) showed that the endophytic actinomycetes associated with the selected medicinal plants have broad-spectrum antimicrobial activity. This is the first report of the isolation of Brevibacterium sp., Microbacterium sp., and Leifsonia xyli from endophytic environments of medicinal plants, Mirabilis jalapa and Clerodendrum colebrookianum. Our results emphasize that endophytic actinomycetes associated with medicinal plants are an unexplored resource for the discovery of biologically active compounds.

The role of the chi1 gene from the endophytic bacteria Serratia proteamaculans 336x in the biological control of wheat take-all

Take-all, a disease caused by the fungus Gaeumannomyces graminis var. tritici, is the most important root disease of wheat and causes severe yield losses worldwide. Using microorganisms as biological agents to control the disease is important because no resistant cultivars or effective chemical fungicides are available. In this study, we tested the biological control capability of a chitinase produced by the endophytic bacterium Serratia proteamaculans 336x against wheat take-all. The chitinase gene chi1 of S. proteamaculans 336x was cloned and heterologously expressed in Escherichia coli. The recombinant protein exhibited chitinase activity and in vitro antifungal activity against G. graminis var. tritici. With in-frame deletion of the chi1 gene by homologous recombination, the chi1-deleted mutant was devoid of chitinase activity and the biocontrol efficacy was reduced by 42.5%. The complementation of the Δchi1 mutant strain by the chi1 gene resulted in the partial restoration of the chitinase activity and biocontrol efficacy. These results support a role for the Chi1 protein in the biocontrol process of S. proteamaculans 336x against wheat take-all.

Siderophore production by actinobacteria

Produced by bacteria, fungi and plants, siderophores are low-molecular-weight chelating agents (200-2,000 Da) to facilitate uptake of iron (Fe). They play an important role in extracellular Fe solubilization from minerals to make it available to microorganisms. Siderophores have various chemical structures and form a family of at least 500 different compounds. Some antibiotics (i.e., albomycins, ferrimycins, danomycins, salmycins, and tetracyclines) can bind Fe and some siderophores showed diverse biological activities. Functions and applications of siderophores derived from actinobacteria were reviewed to better understand the diverse metabolites.

Endophytic microorganisms--promising applications in bioremediation of greenhouse gases

Bioremediation is a technique that uses microbial metabolism to remove pollutants. Various techniques and strategies of bioremediation (e.g., phytoremediation enhanced by endophytic microorganisms, rhizoremediation) can mainly be used to remove hazardous waste from the biosphere. During the last decade, this specific technique has emerged as a potential cleanup tool only for metal pollutants. This situation has changed recently as a possibility has appeared for bioremediation of other pollutants, for instance, volatile organic compounds, crude oils, and radionuclides. The mechanisms of bioremediation depend on the mobility, solubility, degradability, and bioavailability of contaminants. Biodegradation of pollutions is associated with microbial growth and metabolism, i.e., factors that have an impact on the process. Moreover, these factors have a great influence on degradation. As a result, recognition of natural microbial processes is indispensable for understanding the mechanisms of effective bioremediation. In this review, we have emphasized the occurrence of endophytic microorganisms and colonization of plants by endophytes. In addition, the role of enhanced bioremediation by endophytic bacteria and especially of phytoremediation is presented.

Greek indigenous streptomycetes as biocontrol agents against the soil-borne fungal plant pathogen Rhizoctonia solani

AIMS

To examine the biocontrol potential of multiactive Greek indigenous Streptomyces isolates carrying antifungal activity against Rhizoctonia solani that causes damping-off symptoms on beans.

METHODS AND RESULTS

A total of 605 Streptomyces isolates originated from 12 diverse Greek habitats were screened for antifungal activity against R. solani DSM843. Almost one-third of the isolates proved to be antagonistic against the fungus. From the above isolates, six were selected due to their higher antifungal activity, identified by analysing their 16S rRNA gene sequence and studied further. The obtained data showed the following: firstly, the isolates ACTA1383 and ACTA1557 exhibited the highest antagonistic activity, and therefore, they were selected for in vivo experiments using bean seeds as target; secondly, in solid and liquid culture experiments under optimum antagonistic conditions, the medium extracts from the isolates OL80, ACTA1523, ACTA1551 and ACTA1522 suppressed the growth of the fungal mycelium, while extracts from ACTA 1383 and ACTA1557 did not show any activity.

CONCLUSIONS

These results corresponded important indications for the utility of two Greek indigenous Streptomyces isolates (ACTA1557 and ACTA1383) for the protection of the bean crops from R. solani damping-off symptoms, while four of them (isolates OL80, ACTA1523, ACTA1551 and ACTA1522) seem to be promising producers of antifungal metabolites.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study on the biocontrol of R. solani using multiactive Streptomyces isolates originated from ecophysiologically special Greek habitats. Our study provides basic information to further explore managing strategies to control this critical disease.

Thaxtomin A-deficient endophytic Streptomyces sp. enhances plant disease resistance to pathogenic Streptomyces scabies

Each plant species in nature harbors endophytes, a community of microbes living within host plants without causing any disease symptom. However, the exploitation of endophyte-based phytoprotectants is hampered by the paucity of mechanistic understandings of endophyte-plant interaction. We here reported two endophytic Streptomyces isolates IFB-A02 and IFB-A03 recovered from a stress-tolerant dicotyledonous plant Artemisia annua L. After the determination of their non-pathogenicity at the genomic level and from the toxin (thaxtomin A, TXT) level, the endophytism of both isolates was supported by their successful colonization in planta. Of the two endophytes, IFB-A03 was further studied for the mechanism of endophyte-conferred phytoprotection owing to its plant growth promotion in model eudicot Arabidopsis thaliana. Using the endophyte-Arabidopsis co-cultivation system into which pathogenic Streptomyces scabies was introduced, we demonstrated that IFB-A03 pre-inoculation could activate the salicylic acid (SA)-mediated plant defense responses upon pathogen challenge. Moreover, IFB-A03 was shown to partially rescue the defense deficiency in eds5 (enhanced disease susceptibility 5) Arabidopsis mutants, putatively acting at the upstream of SA accumulation in the defense signaling pathway associated with the systemic acquired resistance (SAR). These data suggest that endophytic Streptomyces sp. IFB-A03 could be a promising candidate for biocontrol agents against S. scabies--a causative pathogen of common scab diseases prevailing in agronomic systems.

Abundant and diverse endophytic actinobacteria associated with medicinal plant Maytenus austroyunnanensis in Xishuangbanna tropical rainforest revealed by culture-dependent and culture-independent methods

Endophytes are now considered as an important component of biodiversity. However, the diversity of endophytic actinobacteria associated with tropical rainforest native medicinal plants is essentially unknown. In this study, the diversity of endophytic actinobacteria residing in root, stem and leaf tissues of medicinal plant Maytenus austroyunnanensis collected from tropical rainforest in Xishuangbanna, China was investigated with a combination of cultivation and culture-independent analysis on the basis of 16S rRNA gene sequencing. By using different selective isolation media and methods, a total of 312 actinobacteria were obtained, and they were affiliated with the order Actinomycetales (distributed into 21 genera). Based on a protocol for endophytes enrichment, three 16S rRNA gene clone libraries were constructed and 84 distinct operational taxonomic units were identified and they distributed among the orders Actinomycetales and Acidimicrobiales, including eight suborders and at least 38 genera with a number of rare actinobacteria genera. Phylogenetic analysis showed that 32% of the clones in the libraries had lower than 97% similarities with related type strains. Interestingly, six genera from the order Actinomycetales and uncultured clones from Acidimicrobiales have not, to our knowledge, been previously reported as endophytes. Our study confirms abundant endophytic actinobacterial consortium in tropical rainforest native plant and suggests that this special habitat represents an underexplored reservoir of diverse and novel actinobacteria of potential interest for bioactive compounds discovery.

Control of Fusarium wilt in banana with Chinese leek

The inhibitory effects of Chinese leek(Allium tuberosum) on Fusarium oxysporum f. sp. cubense (Foc) and on Fusarium wilt incidence were studied in order to identify a potential efficient way to control the disease. Adopting the rotation system of Chinese leek-banana reduced the Fusarium wilt incidence and disease severity index by 88 %-97 % and 91 %-96 %, respectively, improved the crop value by 36 %-86 %, in an area heavily infested by Foc between 2007 and 2009. As a result of inoculation in the greenhouse, Chinese leek treatment reduced disease incidence and the disease severity index by 58 % and 62 %, respectively in the variety Baxi (AAA) and by 79 % and 81 %, respectively in the variety Guangfen NO.1 (ABB). Crude extracts of Chinese leek completely inhibited the growth of Foc race 4 on Petri dishes, suppressed the proliferation of the spores by 91 % and caused 87 % spore mortality. The findings of this study suggest that Chinese leek has the potential to inhibit Foc growth and Fusarium wilt incidence. This potential may be developed into an environmentally friendly treatment to control Fusarium wilt of banana.

Study in vitro of the impact of endophytic bacteria isolated from Centella asiatica on the disease incidence caused by the hemibiotrophic fungus Colletotrichum higginsianum

Thirty-one endophytic bacteria isolated from healthy leaves of Centella asiatica were screened in vitro for their ability to reduce the growth rate and disease incidence of Colletotrichum higginsianum, a causal agent of anthracnose. Isolates of Cohnella sp., Paenibacillus sp. and Pantoea sp. significantly stimulated the growth rate of C. higginsianum MUCL 44942, while isolates of Achromobacter sp., Acinetobacter sp., Microbacterium sp., Klebsiella sp. and Pseudomonas putida had no influence on this plant pathogen. By contrast, Bacillus subtilis BCA31 and Pseudomonas fluorescens BCA08 caused a marked inhibition of C. higginsianum MUCL 44942 growth by 46 and 82 %, respectively. Cell-free culture filtrates of B. subtilis BCA31 and P. fluorescens BCA08 were found to contain antifungal compounds against C. higginsianum MUCL 44942. Inoculation assays on in vitro-cultured plants of C. asiatica showed that foliar application of B. subtilis BCA31, three days before inoculation with C. higginsianum MUCL 44942, significantly reduced incidence and severity of the disease. The role of endophytic bacteria in maintaining the apparent inactivity of C. higginsianum MUCL 44942 in C. asiatica grown in the wild is discussed.

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.

Diversity and chemotaxis of soil bacteria with antifungal activity against Fusarium wilt of banana

The chemotactic response of bacteria to root exudates plays an important role in the colonization of bacteria in the rhizosphere. In this study, 420 strains of antifungal bacteria against Fusarium oxysporum f. sp. cubense (Foc) were screened for chemotaxis based on a cheA molecular diagnostic method. A total of 124 strains with antifungal efficiencies of 27.26-67.14 % generated a characteristic band of cheA. The chemotaxis of 97 bacterial strains producing a cheA band was confirmed using the drop assay and swarm plate assay using catechol, p-hydroxybenzoic acid, salicylic acid, and asparagine as the attractants. A phylogenetic analysis based on restriction fragment length polymorphisms (RFLPs) and 16S rDNA sequences indicated that the 124 chemotactic antagonists of Foc were affiliated with 18 species of Paenibacillaceae, Bacillaceae, Streptomycineae, Enterobacteriaceae, and Pseudomonadaceae. The chemical composition of banana root exudates were analyzed by GC-MS, and 62 compounds, including alkanes, alkenes, naphthalenes, benzenes, and alcohols, were evaluated. Five representative antagonists of Foc showed 1.76- to 7.75-fold higher chemotactic responses than the control to seven compounds in banana root exudates, as determination by capillary assays.

Isolation of a strong promoter fragment from endophytic Enterobacter cloacae and verification of its promoter activity when its host strain colonizes banana plants

To engineer endophytic Enterobacter cloacae as a biocontrol agent against banana fusarium wilt, a promoter-probe plasmid pUCK was constructed to identify a strong promoter to express disease resistance genes. Using a kanamycin resistance gene for selection, 10 fragments with strong promoter activity were identified from the genome of the E. cloacae KKWB-10 strain. The regions of these 10 fragments that were the primary contributors to the promoter function were identified, and their promoter activities were further evaluated using green fluorescent protein (GFP) as a reporter gene. Fragment 132a″ drove the highest level of GFP activity when the bacteria bearing the fragments were cultured in Luria-Bertani and banana stem extract media. The GFP-expressing strain harboring fragment 132a″ (K-pUCK7-132a″-GT) was then inoculated into banana plantlets (about 1 × 10(7) CFU per plant) to verify the activity of fragment 132a″ in planta. Ten days after inoculation, tissue sections of these banana plantlets were observed by laser confocal scanning microscope. Green fluorescence was observed in the tissues of banana plantlets inoculated with K-pUCK7-132a″-GT but not in uninoculated controls. These results suggest that fragment 132a″ possesses strong promoter activity when its host strain colonizes the banana plants and can be used to engineer endophytic E. cloacae KKWB-10 for biocontrol.

Streptomyces youssoufiensis sp. nov., isolated from a Moroccan phosphate mine

A novel actinomycete, strain X4T, was isolated from a phosphate mine in Youssoufia, 100 km north of Marrakesh, Morocco. The taxonomic status of this strain was evaluated by a polyphasic approach. Strain X4Thad white aerial mycelium withRectiflexibilesspore chains bearing smooth-surfaced spores and did not produce diffusible pigments. Chemotaxonomic analysis showed that the cell wall of strain X4Tcontainedll-diaminopimelic acid and glycine. Phylogenetic analysis based on the almost complete 16S rRNA gene sequence indicated that strain X4Tbelongs to the Group I streptomycetes, branching off next toStreptomyces ramulosusNRRL B-2714TandStreptomyces kasugaensisM338-M1T. DNA–DNA relatedness and phenotypic data enabled strain X4Tto be distinguished from the phylogenetically most closely related type strains. It is therefore proposed that strain X4Trepresents a novel species of the genusStreptomyces, for which the nameStreptomyces youssoufiensissp. nov. is proposed; the type strain is X4T( = CCMM B709T = DSM 41920T).

Biosynthetic potential of phylogenetically unique endophytic actinomycetes from tropical plants

The culturable diversity of endophytic actinomycetes associated with tropical, native plants is essentially unexplored. In this study, 123 endophytic actinomycetes were isolated from tropical plants collected from several locations in Papua New Guinea and Mborokua Island, Solomon Islands. Isolates were found to be prevalent in roots but uncommon in leaves. Initially, isolates were dereplicated to the strain level by ribotyping. Subsequent characterization of 105 unique strains by 16S rRNA gene sequence analysis revealed that 17 different genera were represented, and rare genera, such as Sphaerisporangium and Planotetraspora, which have never been previously reported to be endophytic, were quite prevalent. Phylogenetic analyses grouped many of the strains into clades distinct from known genera within Thermomonosporaceae and Micromonosporaceae, indicating that they may be unique genera. Bioactivity testing and liquid chromatography-mass spectrometry (LC-MS) profiling of crude fermentation extracts were performed on 91 strains. About 60% of the extracts exhibited bioactivity or displayed LC-MS profiles with spectra indicative of secondary metabolites. The biosynthetic potential of 29 nonproductive strains was further investigated by the detection of putative polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) genes. Despite their lack of detectable secondary metabolite production in fermentation, most were positive for type I (66%) and type II (79%) PKS genes, and all were positive for NRPS genes. These results suggest that tropical plants from New Guinea and the adjacent archipelago are hosts to unique endophytic actinomycetes that possess significant biosynthetic potential.

Anti-phytopathogen potential of endophytic actinobacteria isolated from tomato plants (Lycopersicon esculentum) in southern Brazil, and characterization of Streptomyces sp. R18(6), a potential biocontrol agent

Tomato plants (Lycopersicon esculentum) are highly susceptible to phytopathogen attack. The resulting intensive application of pesticides on tomato crops can affect the environment and health of humans and animals. The objective of this study was to select potential biocontrol agents among actinobacteria from tomato plants, in a search for alternative phytopathogen control. We evaluated 70 endophytic actinobacteria isolated from tomato plants in southern Brazil, testing their antimicrobial activity, siderophore production, indoleacetic acid production, and phosphate solubility. The actinomycete isolate with the highest antimicrobial potential was selected using the agar-well diffusion method, in order to optimize conditions for the production of compounds with antimicrobial activity. For this study, six growth media (starch casein-SC, ISP2, Bennett's, Sahin, Czapek-Dox, and TSB), three temperatures (25 degrees C, 30 degrees C, and 35 degrees C) and different pH were tested. Of the actinobacteria tested, 88.6% showed antimicrobial activity against at least one phytopathogen, 72.1% showed a positive reaction for indoleacetic acid production, 86.8% produced siderophores and 16.2% showed a positive reaction for phosphate solubility. Isolate R18(6) was selected due to its antagonistic activity against all phytopathogenic microorganisms tested in this study. The best conditions for production were observed in the SC medium, at 30 degrees C and pH 7.0. The isolate R18(6) showed close biochemical and genetic similarity to Streptomyces pluricolorescens.

Culturable bacterial populations associated with ectomycorrhizae of Norway spruce stands with different degrees of decline in the Czech Republic

The aim of this study was to determine which species of culturable bacteria are associated with ectomycorrhizae (ECM) of Norway spruce (Picea abies (L.) Karst) in the Sudety Mountains, exposed for years to atmospheric pollutants, acid rain, and climatic stress, and to identify particular species that have adapted to those conditions. Biolog identification was performed on bacterial species from ECM of adult spruce trees and seedlings of stands with low, intermediate, and high forest decline. Bacterial diversity in ECM associated with adult spruce trees, seedlings, and seedlings grown on monoliths was calculated; although the expected values appeared to vary widely, no significant differences among sites were observed. Dendrograms based on the identified bacterial species showed that stands with low forest decline clustered separately from the others. Principal component analysis of the normalized data for ECM-associated species showed a clear separation between stands with high forest decline and stands with low forest decline for seedlings and a less evident separation for adult spruce trees. In conclusion, shifts in ECM-associated culturable bacterial populations seem to be associated with forest decline in Norway spruce stands. Some bacterial species were preferentially associated with mycorrhizal roots depending on the degree of forest decline; this was more evident in seedlings where the species Burkholderia cepacia and Pseudomonas fluorescens were associated with, respectively, ECM of the most damaged stands and those with low forest decline.

Isolation, diversity, and antimicrobial activity of rare actinobacteria from medicinal plants of tropical rain forests in Xishuangbanna, China

Endophytic actinobacteria are relatively unexplored as potential sources of novel species and novel natural products for medical and commercial exploitation. Xishuangbanna is recognized throughout the world for its diverse flora, especially the rain forest plants, many of which have indigenous pharmaceutical histories. However, little is known about the endophytic actinobacteria of this tropical area. In this work, we studied the diversity of actinobacteria isolated from medicinal plants collected from tropical rain forests in Xishuangbanna. By the use of different selective isolation media and methods, a total of 2,174 actinobacteria were isolated. Forty-six isolates were selected on the basis of their morphologies on different media and were further characterized by 16S rRNA gene sequencing. The results showed an unexpected level of diversity, with 32 different genera. To our knowledge, this is the first report describing the isolation of Saccharopolyspora, Dietzia, Blastococcus, Dactylosporangium, Promicromonospora, Oerskovia, Actinocorallia, and Jiangella species from endophytic environments. At least 19 isolates are considered novel taxa by our current research. In addition, all 46 isolates were tested for antimicrobial activity and were screened for the presence of genes encoding polyketide synthetases and nonribosomal peptide synthetases. The results confirm that the medicinal plants of Xishuangbanna represent an extremely rich reservoir for the isolation of a significant diversity of actinobacteria, including novel species, that are potential sources for the discovery of biologically active compounds.

Diversities within genotypes, bioactivity and biosynthetic genes of endophytic actinomycetes isolated from three pharmaceutical plants

One hundred and fifty endophytic actinomycetes were isolated from three pharmaceutical plants, Annonaceae squamosal, Camptotheca acuminate and Taxus chinensis. Bioactivity test showed that 72.4% of the endophytic actinomycetes displayed inhibition against more than one indicator microorganism. In total, 9.3 and 10.7% showed the cytotoxicity and antioxidant activity, respectively. 3-Amino-5-hydroxybenzoic acid synthase (AHBA), ketosynthase (KS), cytochrome P450 hydroxylases (CYPs) and epoxidase (ES) encoding genes were found in 8.8, 23.8, 2.8 and 11.7% isolates, respectively, by genes screening. The identification based on traditional and molecular methods indicated that diverse genotypes of Streptomyces were distributed in the three pharmaceutical plants, and a few strains of Amycolatopsis were also found in the root of T. chinensis. These results indicated that endophytic actinomycetes associated with pharmaceutical plants could be a promising source of drug leads.

Multiple, novel biologically active endophytic actinomycetes isolated from upper Amazonian rainforests

Microbial biodiversity provides an increasingly important source of medically and industrially useful compounds. We have isolated 14 actinomycete species from a collection of approximately 300 plant stem samples from the upper Amazonian rainforest in Peru. All of the cultured isolates produce substances with inhibitory activity directed at a range of potential fungal and bacterial pathogens. For some organisms, this activity is very broad in spectrum while other organisms show specific activity against a limited number of organisms. Two of these organisms preferentially inhibit bacterial test organisms over eukaryotic organisms. rDNA sequence analysis indicates that these organisms are not equivalent to any other cultured deposits in GenBank. Our results provide evidence of the untapped biodiversity in the form of biologically active microbes present within the tissues of higher plants.

Streptomyces thinghirensis sp. nov., isolated from rhizosphere soil of Vitis vinifera

A novel actinomycete, strain S10(T), was isolated from rhizosphere soil of wild Vitis vinifera in Thinghir, Ouarzazate Province, Southern Morocco. The taxonomic status of this strain was established using a polyphasic approach. Strain S10(T) had white-grey aerial mycelium with long, spiral spore chains bearing smooth surfaced spores and produced a yellow diffusible pigment. Chemotaxonomic analyses showed that the cell wall of strain S10(T) contained ll-diaminopimelic acid and glycine. Phylogenetic analysis based on the almost complete 16S rRNA gene sequence indicated that strain S10(T) belonged to the Group I streptomycetes, branching off next to Streptomyces marokkonensis LMG 23016(T) from the Streptomyces violaceoruber group. DNA-DNA relatedness and phenotypic data distinguished strain S10(T) from the phylogenetically closest related type strains. It is therefore proposed that strain S10(T) (=CCMM B35(T)=DSM 41919(T)) represents the type strain of a novel species of the genus Streptomyces, for which the name Streptomyces thinghirensis sp. nov. is proposed.

Isolation and characterization of actinomycetes from healthy goat faeces

AIMS

To isolate and characterize actinomycetes with probiotic activities from healthy goat faeces.

METHODS AND RESULTS

Faecal actinomycetes were isolated by dilution methods and identified by 16S rRNA gene sequence analysis. The hydrolytic enzyme activities were analysed by clear zone formation. The antimicrobial activities and resistance to heavy metals were tested by growth inhibition methods. The isolates belong to a small group of actinobacterial genera, including Streptomyces, Nocardiopsis and Oerskovia. The Oerskovia was the most widely distributed genus among the cultures. The proportion of streptomycete-like strains producing amylase or protease is significantly higher than those of other actinomycetes (P < 0.05). Compared with streptomycete-like strains, a higher proportion of (alpha- or beta-) galactase-producing other actinomycetes was found in goat faeces. More than 50% of streptomycete-like strains showed activities against test fungi. Streptomycetes could tolerate 0.25 mmol l(-1) Cr(2)O(7)(2-), 2 mmol l(-1) Ni(2+); however, other actinomycetes are liable to 40 mmol l(-1) Fe(3+) and 0.25 mmol l(-1) Cr(2)O(7)(2-) and resistant to 5 mmol l(-1) Ni(2+) and 2 mmol l(-1) Cu(2+).

CONCLUSIONS

The different physiological characteristics of the actinomycetes suggested that the cooperation in the actinomycetes might be involved in their association with goat.

SIGNIFICANCE AND IMPACT OF THE STUDY

Probiotic mixtures based on faecal actinomycetes showed potentials in animal production.