Actinomycetota, a central constituent microbe during long-term exposure to diazinon, an organophosphorus insecticide.

Microbial biodegradation is a primary pesticide remediation pathway. Despite diazinon is one of the most frequently used organophosphate insecticides worldwide, its effect on soil microbial community remains obscure. We hypothesize that diazinon exposure reshapes microbial community, among them increased microbes may play a crucial role in diazinon degradation. To investigate this, we collected soil from an organic farming environment, introduced diazinon, cultivated it in a greenhouse, and then assessed its effects on soil microbiomes at three distinct time points: 20, 40, and 270 days after treatment (DAT). Results from HPLC showed that the level of diazinon was gradually degraded by 98.8% at 270 DAT when compared with day zero, whereas 16S rRNA gene analysis exhibited a significant reduction in the bacterial diversity, especially at the early two time points, indicating that diazinon may exert selection pressure to the bacteria community. Here, the relative abundance of phylum Actinomycetota increased at 20 and 40 DATs. In addition, the bacterial functional gene profile employing PICRUSt2 prediction also revealed that diazinon exposure induced the genomic function related to xenobiotics biodegradation and metabolism in soil, such as CYB5B, hpaC, acrR, and ppkA. To validate if bacterial function is caused by increased relative abundance in diazinon enriched soil, further bacteria isolation resulted in obtaining 25 diazinon degradation strains out of 103 isolates. Notably, more than 70% (18 out of 25) isolates are identified as phylum Actinomycetota, which empirically confirms and correlates microbiome and PICRUSt2 results. In conclusion, this study provides comprehensive information from microbiome analysis to obtaining several bacteria isolates responsible for diazinon degradation, revealing that the phylum Actinomycetota is as a key taxon that facilitates microbial biodegradation in diazinon spoiled soil. This finding may assist in developing a strategy for microbial detoxification of diazinon, such as using an Actinomycetota rich synthetic community (SynCom).

Mycobiota community and fungal species response to development stage and fire blight disease in apples.

Fire blight disease, caused by the bacterial pathogen Erwinia amylovora, has been a significant concern for over 50 countries worldwide. The efficacy of chemical pesticides currently available for disease control is limited. To address this issue, research is being conducted to explore environmentally friendly control methods, particularly biological control using beneficial microorganisms. However, there is limited research on the apple microbiota community and minimal research has been conducted on fungal communities that may exhibit reliable performance in apple trees. Therefore, our objective was to analyze the fungal communities present in apples at different developmental stages and in different tissues, aiming to identify potential biological control agents for fire blight disease. Our findings indicate that the fungal communities present in apple buds, flowers and leaves play an important role in inhibiting the invasion of E. amylovora. Specifically, we propose GS11 and Lipomyces starkeyi as potential keystone taxa that respond to fire blight disease. These findings provide insights into the continuity and discontinuity of fungal community structure in different developmental stages of apples and offer predictions for potential biological control agents for fire blight disease.

Analysis of Endophytic Bacterial Communities and Investigation of Core Taxa in Apple Trees.

ire blight disease, caused by Erwinia amylovora, is a devastating affliction in apple cultivation worldwide. Chemical pesticides have exhibited limited effectiveness in controlling the disease, and biological control options for treating fruit trees are limited. Therefore, a relatively large-scale survey is necessary to develop microbial agents for apple trees. Here we collected healthy apple trees from across the country to identify common and core bacterial taxa. We analyzed the endophytic bacterial communities in leaves and twigs and discovered that the twig bacterial communities were more conserved than those in the leaves, regardless of the origin of the sample. This finding indicates that specific endophytic taxa are consistently present in healthy apple trees and may be involved in vital functions such as disease prevention and growth. Furthermore, we compared the community metabolite pathway expression rates of these endophyte communities with those of E. amylovora infected apple trees and discovered that the endophyte communities in healthy apple trees not only had similar community structures but also similar metabolite pathway expression rates. Additionally, Pseudomonas and Methylobacterium-Methylorobrum were the dominant taxa in all healthy apple trees. Our findings provide valuable insights into the potential roles of endophytes in healthy apple trees and inform the development of strategies for enhancing apple growth and resilience. Moreover, the similarity in cluster structure and pathway analysis between healthy orchards was mutually reinforcing, demonstrating the power of microbiome analysis as a tool for identifying factors that contribute to plant health.

Dynamics of Bacterial Communities by Apple Tissue: Implications for Apple Health.

Herein, we explored the potential of the apple's core microbiota for biological control of Erwinia amylovora, which causes fire blight disease, and analyzed the structure of the apple's bacterial community across different tissues and seasons. Network analysis results showed distinct differences in bacterial community composition between the endosphere and rhizosphere of healthy apples, and eight taxa were identified as negatively correlated with E. amylovora, indicating their potential key role in a new control strategy against the pathogen. This study highlights the critical role of the apple's bacterial community in disease control and provides a new direction for future research in apple production. In addition, the findings suggest that using the composition of the apple's core taxa as a biological control strategy could be an effective alternative to traditional chemical control methods, which have been proven futile and environmentally harmful.

Transition from Ginseng Root Rot Disease-Conducive Soil to -Suppressive Soil Mediated by Pseudomonadaceae.

Ginseng is a popular medicinal herb with established therapeutic effects such as cardiovascular disease prevention, anticancer effects, and anti-inflammatory effects. However, the slow growth of ginseng due to soilborne pathogens has been a challenge for establishing new plantations. In this study, we investigated root rot disease associated with the microbiota in a ginseng monoculture model system. Our results showed that a collapse of the early microbiota community inhibiting root rot disease was observed before the disease became severe, and nitrogen fixation was necessary to support the initial microbiota community structure. Furthermore, changes in the nitrogen composition were essential for the suppression of pathogen activity in early monoculture soils. We hypothesize that Pseudomonadaceae, a population built up by aspartic acid, can inhibit the occurrence of root rot disease in ginseng and that specific management practices that maintain a healthy microbiome can be implemented to prevent and mitigate the disease. Our findings provide insights into the potential use of specific members of the microbiota for controlling root rot disease in ginseng cultivation. IMPORTANCE Understanding the initial soil microbiota and community shifts in a monoculture system is critical for developing disease-suppressive soils for crop production. The lack of resistance genes against soilborne pathogens in plants highlights the need for effective management strategies. Our investigation of root rot disease and initial microbiota community shifts in a ginseng monoculture model system provides valuable insight into the development of conducive soil into specific suppressive soil. With a thorough understanding of the microbiota in disease-conducive soil, we can work toward the development of disease-suppressive soil to prevent outbreaks and ensure sustainable crop production.

Effect of Scenedesmus sp. CHK0059 on Strawberry Microbiota Community.

Microalgae are photosynthetic cyanobacteria and eukaryotic microorganisms, mainly living in the water. In agriculture, numerous studies have been conducted to utilize microalgae as a biostimulant resource. Scenedesmus has been known to be one such microalga that can promote plant growth by secretion of auxin or cytokinin hormone analogs. However, no research has been performed on the effect of microalgae treatment on plant microbiota communities. This study was conducted to investigate the mode of action of microalgae as biostimulants in a plant microbiota perspective by using Scenedesmus sp. CHK0059 (also known as species Chlorella fusca), which has been well documented as a biostimulant for strawberries. The strawberry cultivar Keumsil was bred with Seolhyang and Maehyang as the parent cultivars. Using these three cultivars, microbiota communities were evaluated for changes in structural composition according to the CHK0059 treatment. CHK0059-treated Seolhyang, and CHK0059-untreated Maehyang were similar in microbial diversity in the endosphere. From a microbiota community perspective, the diversity change showed that CHK0059 was affected by the characteristics of the host. Conversely, when CHK0059 treatment was applied, populations of Streptomyces and Actinospica were observed in the crown endosphere.

Exploration of Mycobiota in Cypripedium japonicum, an Endangered Species.

Orchids live with mycorrhizal fungi in mutualism. This symbiotic relationship plays an essential role in the overall life cycle of orchids from germination, growth, settlement, and reproduction. Among the 1000 species of the orchid, the Korean lady's slipper, Cypripedium japonicum, is known as an endangered species. Currently, only five natural habitats of the Korean lady's slipper remain in South Korea, and the population of Korean lady's slipper in their natural habitat is not increasing. To prevent extinction, this study was designed to understand the fungal community interacting in the rhizosphere of the Korean lady's slipper living in the native and artificial habitats. In-depth analyses were performed to discover the vital mycorrhizal fungi contributing to habitat expansion and cultivation of the endangered orchid species. Our results suggested that Lycoperdon nigrescens contributed most to the increase in natural habitats and Russula violeipes as a characteristic of successful cultivation. And the fungi that helped L. nigrescens and R. violeipes to fit into the rhizosphere community in Korean lady's slipper native place were Paraboeremia selaginellae and Metarhizium anisopliae, respectively. The findings will contribute to restoring and maintaining the endangered orchid population in natural habitats.

Genetic Variation of Strawberry Fusarium Wilt Pathogen Population in Korea.

Strawberries are a popular economic crop, and one of the major plantations and exporting countries is Korea in the world. The Fusarium oxysporum species complex (FOSC) is a soil-borne pathogen with genetic diversity, resulting in wilt disease in various crops. In Korea, strawberries wilt disease was first reported in the 1980s due to the infection of FOSC, causing significant economic damage every year. The causal agent, F. oxysporum f. sp. fragariae, is a soil-borne pathogen with a characteristic of FOSC that is difficult to control chemically and mutates easily. This study obtained genetic polymorphism information that was based on AFLP, of F. oxysporum f. sp. fragariae 91 strains, which were isolated from strawberry cultivation sites in Gyeongsangnam-do and Chungcheongnam-do, and compared strains information, which was the isolated location, host variety, response to chemical fungicide, and antagonistic bacteria, and mycelium phenotype. As a result, AFLP phylogeny found that two groups were mainly present, and group B was present at a high frequency in Gyeongsangnam-do. Group B proved less sensitive to tebuconazole than group A through Student's t-test. In addition, the fractions pattern of AFLP was calculated by comparing the strain information using PCA and PERMANOVA, and the main criteria were separated localization and strawberry varieties (PERMANOVA; p < 0.05). And tebuconazole was different with weak confidence (PERMANOVA; p < 0.10). This study suggests that the F. oxysporum f. sp. fragariae should be continuously monitored and managed, including group B, which is less chemically effective.

Glutamic acid reshapes the plant microbiota to protect plants against pathogens.

BACKGROUND: Plants in nature interact with other species, among which are mutualistic microorganisms that affect plant health. The co-existence of microbial symbionts with the host contributes to host fitness in a natural context. In turn, the composition of the plant microbiota responds to the environment and the state of the host, raising the possibility that it can be engineered to benefit the plant. However, technology for engineering the structure of the plant microbiome is not yet available. RESULTS: The loss of diversity and reduction in population density of Streptomyces globisporus SP6C4, a core microbe, was observed coincident with the aging of strawberry plants. Here, we show that glutamic acid reshapes the plant microbial community and enriches populations of Streptomyces, a functional core microbe in the strawberry anthosphere. Similarly, in the tomato rhizosphere, treatment with glutamic acid increased the population sizes of Streptomyces as well as those of Bacillaceae and Burkholderiaceae. At the same time, diseases caused by species of Botrytis and Fusarium were significantly reduced in both habitats. We suggest that glutamic acid directly modulates the composition of the microbiome community. CONCLUSIONS: Much is known about the structure of plant-associated microbial communities, but less is understood about how the community composition and complexity are controlled. Our results demonstrate that the intrinsic level of glutamic acid in planta is associated with the composition of the microbiota, which can be modulated by an external supply of a biostimulant. Video Abstract.

Investigation of Fungal Strains Composition in Fruit Pollens for Artificial Pollination.

Plants pollination are conducted through various pollinators such as wind, animals, and insects. Recently, the necessity for artificial pollination is drawing attention as the proportion of natural pollinators involved is decreasing over the years. Likewise, the trade in pollen for artificial pollination is also increasing worldwide. Through these imported pollens, many unknown microorganisms can flow from foreign countries. Among them, spores of various fungi present in the particles of pollen can be dispersed throughout the orchard. Therefore, in this study, the composition of fungal communities in imported pollen was revealed, and potential ecological characteristics of the fungi were investigated in four types of imported pollen. Top 10 operational taxonomic unit (OTU) of fungi were ranked among the following groups: Alternaria sp., Cladosporium sp., and Didymella glomerata which belong to many pathogenic species. Through FUNGuild analysis, the proportion of OTUs, which is assumed to be potentially plant pathogens, was higher than 50%, except for apple pollen in 2018. Based on this study of fungal structure, this information can suggest the direction of the pollen quarantine process and contribute to fungal biology in pollen.

Bacterial Community Structure and the Dominant Species in Imported Pollens for Artificial Pollination.

Pollination is an essential process for plants to carry on their generation. Pollination is carried out in various ways depending on the type of plant species. Among them, pollination by insect pollinator accounts for the most common. However, these pollinators have be decreasing in population density due to environmental factors. Therefore, use of artificial pollination is increasing. However, there is a lack of information on microorganisms present in the artificial pollens. We showed the composition of bacteria structure present in the artificial pollens of apple, kiwifruit, peach and pear, and contamination of high-risk pathogens was investigated. Acidovorax spp., Pantoea spp., Erwinia spp., Pseudomonas spp., and Xanthomonas spp., which are classified as potential high-risk pathogens, have been identified in imported pollens. This study presented the pollen-associated bacterial community structure, and the results are expected to be foundation for strengthening biosecurity in orchard industry.

Draft genome sequence data of Paenibacillus Polymyxa strain TH2H2, isolated from a tomato flower in Korea.

Members of the genus Paenibacillus are known for their production of useful substances, and some species of the genus are recognized to be plant growth-promoting rhizobacteria. Paenibacillus polymyxa TH2H2, isolated from a tomato flower, had antifungal activity. Here, the draft genome sequence of Paenibacillus polymyxa TH2H2 is reported. The 5,983,104-bp genome, with a G+C content of 45.31%, comprised 5,221 protein-coding genes, 64 ribosomal RNA and 100 transfer RNA. Three intact antibiotic biosynthesis gene clusters were identified using antiSMASH. These encoded the antifungal agent fusaricidin and two antibacterial agents, tridecaptin and polymyxin. Sequence data have been deposited in the DDBJ/ENA/GenBank database under the accession number RPDG01000000. The version described in this paper is RPDG00000000.1. The BioProject ID in the GenBank database is PRJNA505713.

Genome-Wide Investigation of 2,4-Diacetylphloroglucinol Protection Genes in Arabidopsis thaliana.

The compound 2,4-diacetylphloroglucinol (DAPG) is a well-known secondary metabolite produced by Pseudomonas spp. that are used as biocontrol agents. DAPG displays a remarkably broad spectrum of toxic activity against pathogens of plants. Yet high concentrations of DAPG may also have negative effect on plants, but the phytotoxicity of DAPG is not clearly understood. Here, we used genome-wide activation, tagging Arabidopsis plants as the model plant to investigate the plant response to DAPG. A total of 15 lines were selected as DAPG-tolerant plants from among 62,000 lines investigated. The DAPG-responsible genes were then identified via thermal asymmetric interlaced PCR and quantitative reverse transcription PCR, and the gene ontology analysis showed the distribution of these genes having different biological processes, cellular regulations, and molecular functional properties. Collectively, these findings suggest that plants may rely on several pathways to prevent DAPG phytotoxicity.

Comparison of Microbial Community of Rhizosphere and Endosphere in Kiwifruit.

Understanding the microbial community and function are crucial knowledge for crop management. In this study, bacterial and fungal community structures both rhizosphere and endosphere in kiwifruit were analyzed to gain our knowledge in kiwifruit microbiome. Microbial community in rhizosphere was less variation than endosphere community. Functional prediction results demonstrated that abundance of saprotrophic fungi was similar in both rhizosphere and endosphere, but potential pathogenic fungi was more abundance in endosphere than in rhizosphere. This finding suggested that maintain healthy soil is the first priority to protect the host plant against biotic stresses.

A mutualistic interaction between Streptomyces bacteria, strawberry plants and pollinating bees.

Microbes can establish mutualistic interactions with plants and insects. Here we track the movement of an endophytic strain of Streptomyces bacteria throughout a managed strawberry ecosystem. We show that a Streptomyces isolate found in the rhizosphere and on flowers protects both the plant and pollinating honeybees from pathogens (phytopathogenic fungus Botrytis cinerea and pathogenic bacteria, respectively). The pollinators can transfer the Streptomyces bacteria among flowers and plants, and Streptomyces can move into the plant vascular bundle from the flowers and from the rhizosphere. Our results present a tripartite mutualism between Streptomyces, plant and pollinator partners.

Characterization of Antibacterial Strains against Kiwifruit Bacterial Canker Pathogen.

Kiwifruit (Actinidia spp.) is an economically important crop and a bacterial canker disease, caused by Pseudomonas syringae pv. actinidiae (Psa), is the most destructive disease in kiwifruit production. Therefore, prevent and control of the disease is a critical issue in kiwifruit industry worldwide. Unfortunately, there is no reliable control methods have been developed. Recently, interest in disease control using microbial agents is growing. However, kiwifruit microbiota and their roles in the disease control is mainly remaining unknown. In this study, we secured bacterial libraries from kiwifruit ecospheres (rhizosphere, endospere, and phyllosphere) and screened reliable biocontrol strains against Psa. As the results, Streptomyces racemochromogenes W1SF4, Streptomyces sp. W3SF9 and S. parvulus KPB2 were selected as anti-Psa agents from the libraries. The strains showed forcible antibacterial activity as well as exceptional colonization ability on rhizosphere or phyllosphere of kiwifruit. Genome analyses of the strains suggested that the strains may produce several anti-Psa secondary metabolites. Our results will contribute to develop biocontrol strains against the kiwifruit canker pathogen and the disease management strategies.

Evolution of Antibiotic Synthesis Gene Clusters in the Streptomyces globisporus TFH56, Isolated from Tomato Flower.

Streptomyces species are known to produce various bioactive metabolites that can prevent plant diseases. Previously, the Streptomyces strain TFH56 was found to inhibit the gray mold pathogen, Botrytis cinerea, in tomato flower. In this study, the genome sequence of strain TFH56 was acquired using the Pacific Biosciences RS II platform. Three linear sequences (7.67 Mbp in total) were obtained. Based on average nucleotide identity, strain TFH56 was classified as Streptomyces globisporus, which is consistent with the presence of a linear chromosome and linear plasmids. Moreover, as with other examples of S. globisporus, the genome of strain TFH56 included a caryolan-1-ol synthase gene, a conprimycin synthetic gene cluster, and a lidamycin synthetic gene cluster.

Comparison of Endophytic Microbial Community in Kiwifruit Plant Cultivars.

The microbiome makes a significant contribution to plant health and endophytes may generate positive effects for the host. However, there is a limited knowledge available concerning the kiwifruit endophyte. Therefore, we discuss endophyte microbiome community structures among the kiwifruit cultivars. Total reads numbered 17620 in cv. Hayward, 11515 in cv. Haegeum and 13613 in cv. Jecygold. The number of OTUs was follows: 112 in cv. Hageum; and 87 in cvs. Hayward and Jecygold. Most of the identified OTUs were phylum Proteobacteria and it emerged that Actinobacteria, Firmicute and Bacteroidetes were mainly present. While the largest difference in Proteobacteria content is between cv. Haegeum and cv. Jecygold, they shared more OTUs than cv. Hayward. As well, this study revealed the presence of remarkably dominated OTU of Pseudomonas spp. in kiwifruit sap regardless of cultivars. To the best of our knowledge, this study is the first tone to investigate the kiwifruit endophyte-microbiome community.

Development qRT-PCR Protocol to Predict Strawberry Fusarium Wilt Occurrence.

Strawberry Fusarium wilt disease, caused by Fusarium oxysporum f. sp. fragariae, is the most devastating disease in strawberry production. The pathogen produces chlamydospores which tolerate against harsh environment, fungicide and survive for decades in soil. Development of detection and quantification techniques are regarded significantly in many soilborne pathogens to prevent damage from diseases. In this study, we improved specific-quantitative primers for F. oxysporum f. sp. fragariae to reveal correlation between the pathogen density and the disease severity. Standard curve r2 value of the specific-quantitative primers for qRT-PCR and meting curve were over 0.99 and 80.5°C, respectively. Over pathogen 105 cfu/g of soil was required to cause the disease in both lab and field conditions. With the minimum density to develop the wilt disease, the pathogen affected near 60% in nursery plantation. A biological control microbe agent and soil solarization reduced the pathogen population 2-fold and 1.5-fold in soil, respectively. The developed F. oxysporum f. sp. fragariae specific qRT-PCR protocol may contribute to evaluating soil healthiness and appropriate decision making to control the disease.