Taxonomic study on nonpathogenic streptomycetes isolated from common scab lesions on potato tubers

Exploring the Potentiality of Native Actinobacteria to Combat the Chilli Fruit Rot Pathogens under Post-Harvest Pathosystem

Chilli is an universal spice cum solanaceous vegetable crop rich in vitamin A, vitamin C, capsaicin and capsanthin. Its cultivation is highly threatened by fruit rot disease which cause yield loss as high as 80-100% under congenial environment conditions. Currently actinobacteria are considered as eco-friendly alternatives to synthetic fungicides at pre and post-harvest pathosystems. Hence, this research work focuses on the exploitation of rhizospheric, phyllospheric and endophytic actinobacteria associated with chilli plants for their antagonistic activity against fruit rot pathogens viz., Colletotrichum scovillei, Colletotrichum truncatum and Fusarium oxysporum. In vitro bioassays revealed that the actinobacterial isolate AR26 was found to be the most potent antagonist with multifarious biocontrol mechanisms such as production of volatile, non-volatile, thermostable compounds, siderophores, extracellular lytic enzymes. 16S rRNA gene sequence confirmed that the isolate AR26 belongs to Streptomyces tuirus. The results of detached fruit assay revealed that application of liquid bio-formulation of Stretomyces tuirus @ 10 mL/L concentration completely inhibited the development of fruit rot symptoms in pepper fruits compared to methanol extracts. Hence, the present research work have a great scope for evaluating the biocontrol potential of native S. tuirus AR26 against chilli fruit rot disease under field condition as well against a broad spectrum of post-harvest plant pathogens.

Efficacy of bioagents against Pythium deliense Meurs associated with yellowing of black pepper

Yellowing and wilting of black pepper vines is a serious concern in many black pepper growing tracts where Pythium deliense was recently emerged as a pathogen from the rhizosphere of affected vines, which is proved to be pathogenic by Koch's postulates. As a measure to manage the symptoms, bioagents were evaluated against infection by P. deliense. Among the seven bioagents tested, Trichoderma harzianum and Streptomyces albulus showed 100% inhibition in vitro followed by one Streptomyces sp. and S. rimosus (75.33%). The potential ones were further evaluated under the hydroponic system in vivo by challenge inoculation. No root infection was noticed with T. harzianum and S. albulus inoculation, instead, the inoculated plants showed root regeneration. This suggests the efficiency of these bioagents on plant growth promotion as well as on disease suppression. Biochemical analysis of the hydroponic medium showed an increase in membrane conductivity in all the treatments except in T. harzianum. The release of phenolic compounds into the medium was lowest with T. harzianum indicating the prevention of pathogen invasion. In planta evaluation under greenhouse condition and field evaluation also showed the protective effect of T. harzianum and S. albulus with a reduction in the intensity of yellowing to an extent of 73.1% and 71.2%, respectively. The study revealed that T. harzianum and the actinomycete S. albulus had the potential to prevent the root rot caused by P. deliense.

Diversity of prokaryotic community at a shallow marine hydrothermal site elucidated by Illumina sequencing technology

To investigate the prokaryotic community structure and composition in an active hydrothermal site, named Black Point, off Panarea Island (Eolian Islands, Italy), we examined sediment and fluid samples, differing in temperature, by a massive parallel sequencing (Illumina) technique targeting the V3 region of the 16S rRNA gene. The used technique enabled us to detect a greater prokaryotic diversity than that until now observed and to reveal also microorganisms occurring at very low abundance (≤0.01 %). Most of sequences were assigned to Bacteria while Archaea were a minor component of the microbial community in both low- and high-temperature samples. Proteobacteria (mainly consisting of Alpha-, Gamma-, and Epsilonproteobacteria) dominated among all samples followed by Actinobacteria and Bacteroidetes. Analyzed DNA obtained from samples taken at different temperatures indicated the presence of members of different dominant genera. The main differences were observed between sediment samples where Rhodovulum and Thiohalospira prevailed at high temperature, while Thalassomonas and Sulfurimonas at low temperature. Chlorobium, Acinetobacter, Sulfurimonas, and Brevundimonas were abundant in both low- and high-temperature fluid samples. Euryarchaeota dominated the archaeal community in all samples. Classes of Euryarchaeota embracing hyperthermophilic members (Thermococci and Thermoplasmata) and of Crenarchaeota (Thermoprotei) were more abundant in high-temperature samples. A great number of sequences referred to Bacteria and Archaea still remained unaffiliated, indicating that Black Point site represents a rich source of so-far uncharted prokaryotic diversity.

Field efficacy of nonpathogenic Streptomyces species against potato common scab

AIMS

The primary objective of these experiments was to reduce pathogenicity and virulence of endemic soil pathogenic Streptomyces strains that cause potato common scab (CS) using nonpathogenic Streptomyces strains to suppress CS in a field situation.

METHODS AND RESULTS

Nonpathogenic Streptomyces strains that had shown potential for mitigating CS in greenhouse assays were used in Michigan and Pennsylvania fields known to have high CS disease pressure. Five biocontrol (BC) strains and three potato cultivars were used in 2009, and three BC strains and three cultivars were used in 2010 in each location. The effects of BC strains on CS disease incidence and severity differed between locations, years and potato cultivars. When overall means of individual BC treatments were compared with nontreated controls, CS incidence and severity were decreased by all BC strains in PA2009, PA2010 and MI2010, particularly in cultivar 'Yukon Gold' in MI. Biocontrol treatments also significantly shifted the proportions of superficial, raised and pitted lesion types in some cultivar/biocontrol treatment combinations.

CONCLUSIONS

All BC strains significantly reduced CS incidence and severity on 'Yukon Gold' in three of four trials, and one BC strain significantly improved the lesion severity profile in cultivar 'Atlantic'. No BC strain significantly reduced CS incidence and severity on all potato cultivars in the different years and locations.

SIGNIFICANCE AND IMPACT OF THE STUDY

Several nonpathogenic Streptomyces strains showed potential to reduce CS incidence and severity on two important potato-chipping cultivars in the field. These results can be further applied to reduce CS disease severity in potatoes.

Detection of potential suberinase-encoding genes in Streptomyces scabiei strains and other actinobacteria

Streptomyces scabiei causes common scab, an economically important disease of potato tubers. Some authors have previously suggested that S. scabiei penetration into host plant tissue is facilitated by secretion of esterase enzymes degrading suberin, a lipidic biopolymer of the potato periderm. In the present study, S. scabiei EF-35 showed high esterase activity in suberin-containing media. This strain also exhibited esterase activity in the presence of other biopolymers, such as lignin, cutin, or xylan, but at a much lower level. In an attempt to identify the esterases involved in suberin degradation, translated open reading frames of S. scabiei 87-22 were examined for the presence of protein sequences corresponding to extracellular esterases of S. scabiei FL1 and of the fungus Coprinopsis cinerea VTT D-041011, which have previously been shown to be produced in the presence of suberin. Two putative extracellular suberinase genes, estA and sub1, were identified. The presence of these genes in several actinobacteria was investigated by Southern blot hybridization, and both genes were found in most common-scab-inducing strains. Moreover, reverse transcription - polymerase chain reaction performed with S. scabiei EF-35 showed that estA was expressed in the presence of various biopolymers, including suberin, whereas the sub1 gene appeared to be specifically expressed in the presence of suberin and cutin.

ATP modulates the growth of specific microbial strains

The regulatory function of extracellular ATP (exATP) in bacteria is unknown, but recent studies have demonstrated exATP induced enhanced secondary metabolite production and morphological differentiation in Streptomyces coelicolor. The growth of Streptomyces coelicolor, however, was unaffected by exATP, although changes in growth are common phenotypes. To identify bacteria whose growth is altered by exATP, we measured exATP-induced population changes in fast-growing microbes and actinomycetes in compost. Compared with the water-treated control, the addition of 10 ml 100 μM ATP to 10 g of compost enhanced the actinomycetes population by 30% and decreased fast-growing microbial numbers by 20%. Eight microbes from each group were selected from the most populated colony, based on appearance. Of the eight isolated fast-growing microbes, the 16S rRNA sequences of three isolates were similar to the plant pathogens Serratia proteamaculans and Sphingomonas melonis, and one was close to a human pathogen, Elizabethkingia meningoseptica. The growth of all fast-growing microbes was inhibited by ATP, which was confirmed in Pseudomonas syringae DC3000, a pathogenic plant bacterium. The growth of six of eight isolated actinomycetes strains, all of which were identified as close to Streptomyces neyagawaensis, was enhanced by ATP treatment. This study suggests that exATP regulates bacterial physiology and that the exATP response system is a target for the control of bacterial ecology.

Effect of potato suberin on Streptomyces scabies proteome

Two-dimensional (2D) PAGE was used to detect proteins induced in Streptomyces scabies by potato suberin, a lipidic plant polymer. Nineteen up-regulated proteins were excised from 2D gels and analysed by N-terminal sequencing or tandem mass spectrometry (MS/MS). Four of the up-regulated proteins could be linked to the bacterial response to stress (AldH, GroES, TerD and LexA). Specific metabolic pathways seemed to be activated in the presence of suberin, as shown by the increased expression of specific transporters and of enzymes related not only to glycolysis, but also to nucleotide and amino acid metabolism. Suberin also appeared to influence secondary metabolism as it also caused the overproduction of the BldK proteins that are known to be involved in differentiation and secondary metabolism.

High proportions of nonpathogenic Streptomyces are associated with common scab-resistant potato lines and less severe disease

Streptomyces isolates were obtained from potato tubers with common scab lesions from 2 fields over a 3 year period in Minnesota and a 5 year period in Maine. Isolates were obtained from different potato cultivars or breeding lines and types of scab lesions. A majority of isolates could be classified as putative pathogens based on the presence of genes for biosynthesis of the pathogenicity determinant, thaxtomin, but large numbers of streptomycetes lacking genes for thaxtomin biosynthesis (presumably nonpathogenic) were also recovered. Most Streptomyces isolates recovered from raised and pitted lesions were pathogens, whereas mostly nonpathogenic isolates were recovered from unblemished potato skin or nonscab lesions. Fewer pathogenic than nonpathogenic isolates were recovered from the most resistant potato lines. The proportion and diversity of nonpathogenic isolates recovered was higher in Maine than in Minnesota. The association between greater numbers of nonpathogenic Streptomyces and less severe common scab suggests that the interaction between plant genotype and Streptomyces microbial community is important in determining the severity of common scab on potato, and emphasizes the role of complex interactions between plants and microbial populations on and near plant roots in plant disease outcomes.

Phylogenetic analysis of bacteria preserved in a permafrost ice wedge for 25,000 years

Phylogenetic analysis of bacteria preserved within an ice wedge from the Fox permafrost tunnel was undertaken by cultivation and molecular techniques. The radiocarbon age of the ice wedge was determined. Our results suggest that the bacteria in the ice wedge adapted to the frozen conditions have survived for 25,000 years.

A survey of genetic variation in streptomyces isolates causing potato common scab in the United States

ABSTRACT Common scab is a serious disease of potatoes and other root and tuber crops, affecting crop quality and market value. The disease is caused by gram positive soil bacteria in the genus Streptomyces. Disease incidence and severity vary in different locations and years; this is due in part to variation in the environment (weather) and genetic variation in potato cultivars. Little information is available on the contribution of genetic variation by the pathogen. To examine genetic diversity in different locations within the United States, streptomycetes were isolated from lesions on field-grown potatoes from six states. Isolates were classified into species based on sequence of variable regions in the 16s rRNA gene. The presence of genes associated with the recently described S. turgidiscabies pathogenicity island (PAI) was also determined. About half of the isolates belonged to S. scabies or S. europaeiscabiei based on 16s rDNA sequence, and had characteristic features of the PAI. They were found in all six states, and were pathogenic on potato and radish. The remaining isolates included pathogens and nonpathogens. They were varied in appearance, and represent several species, including one pathogenic species not previously reported. Some pathogenic isolates lacked one or more genes characteristic of the PAI, although all had genes for biosynthesis of the pathogenicity determinant thaxtomin. In this relatively small survey, regional differences in scab-causing streptomycetes were seen. This report furnishes tools and baseline data for population genetic study of scab-causing streptomycetes in the United States.

Competing factors of compost concentration and proximity to root affect the distribution of streptomycetes

Streptomycetes are important members of soil microbial communities and are particularly active in the degradation of recalcitrant macromolecules and have been implicated in biological control of plant disease. Using a streptomycetes-specific polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (PCR-DGGE) methodology coupled with band excision and sequence analysis, we examined the effect of grape marc compost amendment to soil on cucumber plant-associated streptomycetes community composition. We observed that both compost amendment and proximity to the root surface influenced the streptomycetes community composition. A strong root selection for a soil-derived Streptomycete, most closely related to Streptomyces thermotolerans, S. iakyrus, and S. thermocarboxydus, was independent of compost amendment rate. However, while the impact of compost amendment was mitigated with increasing proximity to the root, high levels of compost amendment resulted in the detection of compost-derived species on the root surface. Conversely, in rhizosphere and non-rhizosphere soils, the community composition of streptomycetes was affected strongly even by modest compost amendment. The application of a streptomycetes-specific PCR primer set combined with DGGE analysis provided a rapid means of examining the distribution and ecology of streptomycetes in soils and plant-associated environments.

Microscopic examination of chitosan-polyphosphate beads with entrapped spores of the biocontrol agent, Streptomyces melanosporofaciens EF-76

Spores of the biocontrol agent, Streptomyces melanosporofaciens EF-76, were entrapped by complex coacervation in beads composed of a macromolecular complex (MC) of chitosan and polyphosphate. A proportion of spores entrapped in beads survived the entrapment procedure as shown by treating spores from chitosan beads with a dye allowing the differentiation of live and dead cells. The spore-loaded chitosan beads could be digested by a chitosanase, suggesting that, once introduced in soil, the beads would be degraded to release the biocontrol agent. Spore-loaded beads were examined by optical and scanning electron microscopy because the release of the biological agent depends on the spore distribution in the chitosan beads. The microscopic examination revealed that the beads had a porous surface and contained a network of inner microfibrils. Spores were entrapped in both the chitosan microfibrils and the bead lacuna.

Analysis of the endophytic actinobacterial population in the roots of wheat (Triticum aestivum L.) by terminal restriction fragment length polymorphism and sequencing of 16S rRNA clones

The endophytic actinobacterial population in the roots of wheat grown in three different soils obtained from the southeast part of South Australia was investigated by terminal restriction fragment length polymorphism (T-RFLP) analysis of the amplified 16S rRNA genes. A new, validated approach was applied to the T-RFLP analysis in order to estimate, to the genus level, the actinobacterial population that was identified. Actinobacterium-biased primers were used together with three restriction enzymes to obtain terminal restriction fragments (TRFs). The TRFs were matched to bacterial genera by the T-RFLP Analysis Program, and the data were analyzed to validate and semiquantify the genera present within the plant roots. The highest diversity and level of endophytic colonization were found in the roots of wheat grown in a dark loam from Swedes Flat, and the lowest were found in water-repellent sand from Western Flat. This molecular approach detected a greater diversity of actinobacteria than did previous culture-dependent methods, with the predominant genera being Mycobacterium (21.02%) in Swedes Flat, Streptomyces (14.35%) in Red Loam, and Kitasatospora (15.02%) in Western Flat. This study indicates that the soil that supported a higher number of indigenous organisms resulted in wheat roots with higher actinobacterial diversity and levels of colonization within the plant tissue. Sequencing of 16S rRNA clones, obtained using the same actinobacterium-biased PCR primers that were used in the T-RFLP analysis, confirmed the presence of the actinobacterial diversity and identified a number of Mycobacterium and Streptomyces species.

Identification of Streptomyces coelicolor proteins that are differentially expressed in the presence of plant material

Streptomyces coelicolor and Lemna minor were used as a model to study the modulation of bacterial gene expression during plant-streptomycete interactions. S. coelicolor was grown in minimal medium with and without L. minor fronds. Bacterial proteomes were analyzed by two-dimensional gel electrophoresis, and a comparison of the two culture conditions resulted in identification of 31 proteins that were induced or repressed by the presence of plant material. One-half of these proteins were identified by peptide mass fingerprinting by using matrix-assisted laser desorption ionization-time of flight mass spectrometry. The induced proteins were involved in energetic metabolism (glycolysis, pentose phosphate pathway, oxidative phosphorylation), protein synthesis, degradation of amino acids, alkenes, or cellulose, tellurite resistance, and growth under general physiological or oxidative stress conditions. The repressed proteins were proteins synthesized under starvation stress conditions. These results suggest that root exudates provide additional carbon sources to the bacteria and that physiological adaptations are required for efficient bacterial growth in the presence of plants.