Development of a new broad-spectrum microencapsulation-based spray drying formulation of Bacillus thuringiensis subsp. kurstaki IMBL-B9 for the control of moths.

Certain Bacillus thuringiensis (Bt) strains such as Bt subsp. kurstaki and Bt subsp. aizawai have been widely used for pest management in agricultural practices. However, each strain only shows high specificity for pest control against a narrow range of lepidopteran species, and numerous lepidopteran pests have developed resistance to commercialized Bt strains. Therefore, there is a need for the development of novel Bt bioinsecticides which allow for potent and broad-spectrum insecticidal activity against lepidopteran species, including Spodoptera spp. (Noctuidae) and Plutella xylostealla (Plutellidae). In order to develop a novel bioinsecticide using Bt subsp. kurstaki IMBL-B9 (Btk IMBL-B9) that exhibits excellent insecticidal activity against three different lepidopteran species, we have developed a viable microencapsulation-based spray drying Btk IMBL-B9 formulation. The spore-crystal complex of Btk IMBL-B9 was microencapsulated using coating materials such as gum arabic, maltodextrin, and corn starch via spray drying. The encapsulated formulation of Btk IMBL-B9 presented an increased survival rate and storage stability at 54 ± 2°C for up to 6 weeks. The formulation showed similar insecticidal activity as the commercial bioinsecticide XenTari® against P. xylostella. Under controlled greenhouse conditions, the Btk IMBL-B9 formulation was more effective against Lepidoptera spp. S. frugiperda and P. xylostella, than XenTari®. These results suggest that the microencapsulation-based spray drying formulation of Btk IMBL-B9 can be used effectively for the control of a wide range of moths.

Enhancement of osmotic stress tolerance in soybean seed germination by bacterial bioactive extracts.

Soybean (Glycine max (L.) Merr.) is important to the global food industry; however, its productivity is affected by abiotic stresses such as osmosis, flooding, heat, and cold. Here, we evaluated the bioactive extracts of two biostimulant bacterial strains, Bacillus butanolivorans KJ40 and B. siamensis H30-3, for their ability to convey tolerance to osmotic stress in soybean seeds during germination. Soybean seeds were dip-treated in extracts of KJ40 (KJ40E) or H30-3 (H30-3E) and incubated with either 0% or 20% polyethylene glycol 6000 (PEG), simulating drought-induced osmotic stress. We measured malondialdehyde content as a marker for lipid peroxidation, as well as the activity of antioxidant enzymes, including catalase, glutathione peroxidase, and glutathione reductase, together with changes in sugars content. We also monitored the expression of genes involved in the gibberellic acid (GA)-biosynthesis pathway, and abscisic acid (ABA) signaling. Following osmotic stress in the extract-treated seeds, malondialdehyde content decreased, while antioxidant enzyme activity increased. Similarly, the expression of GA-synthesis genes, including GmGA2ox1 and GmGA3 were upregulated in KJ40E-dipped seeds at 12 or 6 h after treatment, respectively. The ABA signaling genes GmABI4 and GmDREB1 were upregulated in H30-3E- and KJ40E-treated seeds at 0 and 12 h after treatment under osmotic stress; however, GmABI5, GmABI4, and GmDREB1 levels were also elevated in the dip-treated seeds in baseline conditions. The GA/ABA ratio increased only in KJ40E-treated seeds undergoing osmotic stress, while glucose content significantly decreased in H30-3E-treated seeds at 24 h after treatment. Collectively, our findings indicated that dip-treatment of soybean seeds in KJ40E and H30-3E can enhance the seeds' resistance to osmotic stress during germination, and ameliorate cellular damage caused by secondary oxidative stress. This seed treatment can be used agriculturally to promote germination under drought stress and lead to increase crop yield and quality.

Effects of di-(2-ethylhexyl) phthalate on growth, metabolism, and virulence of the plant pathogenic bacterium Acidovorax citrulli.

Acidovorax citrulli is a seed-borne bacterial pathogen that causes bacterial fruit blotch in cucurbits and severely affects the production of cucumbers and watermelons globally. In this study, we investigated the effects of di-(2-ethylhexyl) phthalate (DEHP) on the growth, metabolism, and virulence of A. citrulli. Bacterial population was not affected by DEHP exposure; moreover, significant changes were not observed in lipid peroxidation, membrane permeability, and nucleic acid leakage. However, palmitoleic acid content was increased in the cell membrane of DEHP-exposed A. citrulli. Further, DEHP exposure increased the activity of TCA cycle-related enzymes, including α-ketoglutarate dehydrogenase and succinyl-CoA synthetase, along with increase in the content of glutamate, succinate, fumarate, and malate in TCA cycle. Additionally, total 270 genes were differentially expressed by the treatment, of which 28 genes were upregulated and 242 genes, including those related to translation, flagellum-dependent cell motility, and flagellum assembly, were downregulated. Regarding virulence traits, swimming activity was decreased in DEHP-exposed A. citrulli; however, biofilm formation was not affected in in vitro assay. Moreover, relative expression of pathogenicity genes, including hrpX and hrpG, were decreased in DEHP-exposed A. citrulli compared to that of unexposed A. citrulli. Therefore, these results suggest that DEHP accumulation in soil could potentially influence the metabolism and virulence traits of A. citrulli.

Low-density polyethylene microplastics alter chemical properties and microbial communities in agricultural soil.

Microplastic (MP) pollution in agricultural soils, resulting from the use of plastic mulch, compost, and sewage sludge, jeopardizes the soil microbial populations. However, the effects of MPs on soil chemical properties and microbial communities remain largely unknown. Here, we investigated the effects of different concentration levels (0, 0.1, 1, 3, 5, and 7%; w:w) of low-density polyethylene (LDPE) MPs on the chemical properties and bacterial communities of agricultural soil in an incubation study. The addition of LDPE MPs did not drastically change soil pH (ranging from 8.22 to 8.42). Electrical conductivity increased significantly when the LDPE MP concentrations were between 1 and 7%, whereas the total exchangeable cations (Na+, K+, Mg2+, and Ca2+) decreased significantly at higher LDPE MP concentrations (3-7%). The highest available phosphorus content (2.13 mg kg-1) was observed in 0.1% LDPE MP. Bacterial richness (Chao1 and Ace indices) was the lowest at 0.1% LDPE MP, and diversity indices (Shannon and Invsimpson) were higher at 0 and 1% LDPE MP than at other concentrations. The effect of LDPE MP concentrations on bacterial phyla remained unchanged, but the bacterial abundance varied. The relative abundance of Proteobacteria (25.8-33.0%) was the highest in all treatments. The abundance of Acidobacteria (15.8-17.2%) was also high, particularly in the 0, 0.1, and 1% LDPE MPs. With the increase in LDPE MP concentration, the abundance of Actinobacteria gradually increased from 7.80 to 31.8%. Our findings suggest that different MP concentration levels considerably alter soil chemical properties and microbial composition, which may potentially change the ecological functions of soil ecosystems.

Identification of isomeric cyclo(leu-pro) produced by Pseudomonas sesami BC42 and its differential antifungal activities against Colletotrichum orbiculare.

Pseudomonas spp. produce various antimicrobial substances, including cyclic peptides, which have been shown to suppress fungal pathogens. In a previous study, Pseudomonas sesami BC42 was selected to control anthracnose caused by Colletotrichum orbiculare in cucumber plants, and the bioactive extract of strain BC42 inhibited fungal growth and development. In this work, preparative thin-layer chromatography was conducted to identify the antifungal compounds in the extract of strain BC42, and the portion of the extract that exhibited antifungal activity was further analyzed by gas chromatography-mass spectrometry. Three different isomers of the cyclic dipeptide, cyclo(Leu-Pro), were identified: cyclo(l-Leu-l-Pro), cyclo(d-Leu-d-Pro), and cyclo(d-Leu-l-Pro). Among these, 100 µg/mL of cyclo(l-Leu-l-Pro) significantly and more effectively inhibited the germination of conidia and appressorium formation and reduced leaf lesion size caused by C. orbiculare, relative to the control; cyclo(d-Leu-d-Pro) significantly reduced conidia germination and lesion occurrence, however, cyclo(d-Leu-l-Pro) did not exhibit antifungal activity. Therefore, the cyclo(l-Leu-l-Pro) and cyclo(d-Leu-d-Pro) derived from P. sesami BC42 may be a promising candidate for biocontrol applications in agriculture.

Changes in the Composition and Microbial Community of the Pepper Rhizosphere in Field with Bacterial Wilt Disease.

Bacterial wilt caused by Ralstonia solanacearum is considered one of the most harmful diseases of pepper plants. Recently, research on plant disease control through the rhizosphere microbiome has been actively conducted. In this study, the relationship with disease occurrence between the neighboring plant confirmed by analyzing the physicochemical properties of the rhizosphere soil and changes in the microbial community. The results confirmed that the microbial community changes significantly depending on the organic matters, P2O5, and clay in the soil. Despite significant differences in microbial communities according to soil composition, Actinobacteriota at the phylum level was higher in healthy plant rhizosphere (mean of relative abundance, D: 8.05 ± 1.13; H: 10.06 ± 1.59). These results suggest that Actinobacteriota may be associated with bacterial wilt disease. In this study, we present basic information for constructing of healthy soil in the future by presenting the major microbial groups that can suppress bacterial wilt.

Suppressive Effect of Bioactive Extracts of Bacillus sp. H8-1 and Bacillus sp. K203 on Tomato Wilt Caused by Clavibacter michiganensis subsp. michiganensis.

Tomatoes are cultivated worldwide, and are economically important. Clavibacter michiganensis subsp. michiganensis (Cmm) is a pathogen that causes canker and wilting in tomatoes, resulting in serious damage to tomato plants. We aimed to control Cmm proliferation using substances produced by useful microorganisms. The water extracts of strains H8-1 and K203 inhibited wilting caused by Cmm and slowed the pathogenic colonization in tomato plants. The relative expressions of celA, celB, pat1, and pelA of Cmm treated with the bacterial water extracts were reduced by 0.41-, 0.01-, 0.15-, and 0.14-fold for H8-1, respectively, and 0.45-, 0.02-, 0.13-, and 0.13-fold for K203, respectively, compared to controls at 72 h after treatments. In tomato plants inoculated with Cmm, when water extracts of H8-1 and K203 were treated, relative expression of ACO encoding 1-aminocyclopropane-1-carboxylic acid oxidase was suppressed by 0.26- and 0.23-fold, respectively, while PR1a was increased by 1.94- and 2.94-fold, respectively; PI2 expression was increased by 3.27-fold in water extract of H8-1-treated plants. As antioxidant enzymes of plants inoculated with Cmm, peroxidase and glutathione peroxidase levels were increased in K203-water-extract-treated plants, and catalase was increased in the case of the H8-1 water extract at 10 days after inoculation. In terms of soil enzyme activity, each water extract tended to increase urease activity and microbial diversity; in addition, K203 water extract increased plant growth. Thus, H8-1 and K203 water extracts can be used as potential biocontrol agents against Cmm.

Biochar alters chemical and microbial properties of microplastic-contaminated soil.

The occurrence of microplastics (MPs) in soils can negatively affect soil biodiversity and function. Soil amendments applied to MP-contaminated soil can alter the overall soil properties and enhance its functions and processes. However, little is known about how soil amendments improve the quality of MP-contaminated soils. Thus, the present study used a microcosm experiment to explore the potential effects of four types of biochar on the chemical and microbial properties of low-density polyethylene (LDPE) MP-contaminated soil under both drought and well-watered conditions. The results show that the biochars altered soil pH, electrical conductivity (EC), available phosphorous, and total exchangeable cations (TEC) with some variability depending on the biochar type. Oilseed rape straw (OSR)-derived biochars increased soil pH, EC, and TEC under both water conditions with the highest values of 7.94, 0.54 dS m-1 and 22.0 cmol(+) kg-1, respectively. Soil enzyme activities varied under all treatments; in particular, under drought conditions, the fluorescein diacetate activity increased in soils with high temperature (700 °C) biochar. The application of soft wood pellet biochar (700 °C) to MP-contaminated soil increased urease activity by 146% under well-watered conditions. OSR-derived biochars significantly reduced soil acid phosphatase activity under both water conditions. With biochar supplementation, the diversity indices of the bacterial community increased in well-watered soil but not in soil under drought conditions. The abundance of bacterial phyla, such as Firmicutes, Proteobacteria, Actinobacteria, Dictyoglomi, and Gemmatimonadetes, was relatively high in all treatments. Biochar application resulted in negligible variations in bacterial communities under drought conditions but significant variations under well-watered conditions. The findings of this study imply that biochar can be used as a soil amendment to improve the overall soil quality of MP-contaminated soil, but its impact varies depending on the pyrolysis feedstock and temperature. Thus, selecting a suitable biochar is important for improving the soil quality in MP-contaminated soils.

Effects of microplastics on the terrestrial environment: A critical review.

Microplastics are emerging contaminants and there has been growing concern regarding their impacts on aquatic and terrestrial environments. This review provides a comprehensive overview of the current knowledge regarding the sources, occurrences, fates, and risks associated with microplastic contamination in terrestrial environments. This contamination occurs via multiple sources, including primary microplastics (including synthetic materials) and secondary microplastics (derived from the breakdown of larger plastic particles). Microplastic contamination can have both beneficial and detrimental effects on soil properties. Additionally, microplastics have been shown to interact with a wide array of contaminants, including pesticides, persistent organic pollutants, heavy metals, and antibiotics, and may act as a vector for contaminant transfer in terrestrial environments. Microplastics and their associated chemicals can be transferred through food webs and may accumulate across multiple trophic levels, resulting in potential detrimental health effects for humans and other organisms. Although several studies have focused on the occurrence and impacts of microplastic contamination in marine environments, their sources, fate, transport, and effects in terrestrial environments are less studied and not well understood. Therefore, further research focusing on the fate, transport, and impacts of microplastics in relation to soil properties, polymer composition and forms, and land-use types is needed. The development of standardized and harmonized methods for analyzing microplastics in soil-plant ecosystems is essential. Future work should also consider the many interactions of microplastics with soil quality and ecotoxicological impacts on biota in the context of global environmental change.

Inhibition of Oomycetes by the Mixture of Maleic Acid and Copper Sulfate.

Since the protective activity of the Bordeaux mixture against plant disease caused by oomycetes was discovered, copper compounds have been used for more than a century as an effective plant protection strategy. However, the application of excessive copper can cause adverse effects through long-term heavy metal accumulation in soils. Therefore, it is necessary to develop new strategies to reduce or replace copper in pesticides based on organic and low-input farming systems. Organic acids are eco-friendly. In this study, we tested the antifungal and anti-oomycete activity of maleic acid (MA) and copper sulfate (CS) against 13 plant pathogens. Treatment with a mixture of MA and CS showed strong anti-oomycetes activity against Phytophthora xcambivora, P. capsici, and P. cinnamomi. Moreover, the concentration of CS in the activated mixture of MA and CS was lower than that in the activated CS only, and the mixture showed synergy or partial synergy effects on the anti-oomycete activity. Application of a wettable powder formulation of MA and CS mixture (MCS 30WP; 26.67% MA and 3.33% CS) had excellent protective activity in pot experiments with control values of 73% Phytophthora blight on red pepper, 91% damping-off on cucumber, and 84% Pythium blight on creeping bentgrass, which are similar to those of the CS wettable powder formulation (6.67% CS) containing two times the CS content of MCS 30WP. These observations suggest that the synergistic effect of the MA and CS combination is a sustainable alternative for effective management of destructive oomycete diseases.

Antifungal Activity of Thymol against Aspergillus awamori and Botrytis aclada Isolated from Stored Onion Bulbs.

The antifungal activity of thymol against Aspergillus awamori F23 and Botrytis aclada F15 in onions was examined through direct treatment with amended media and gaseous treatment with I-plates (plastic plates containing central partitions). The protective and curative control efficacy of thymol was examined 24 h before and after the inoculation of onion bulbs with the fungal isolates. Mycelial growth, sporulation, and spore germination of the isolates were inhibited on potato dextrose agar amended with various concentrations of thymol or acetic acid (positive control). Overall, thymol produced a stronger inhibitory effect on the mycelial growth and development of the isolates than acetic acid. Following gaseous treatment in I-plates, mycelial growth, sporulation, and spore germination of the isolates were inhibited at higher concentrations of thymol or acetic acid; however, acetic acid showed a little effect on the sporulation and spore germination of the isolates. Following the treatment of onion bulbs with 1000 mg L-1 of thymol 24 h before and after fungal inoculation, lesion diameter was greatly reduced compared with that following treatment with 0.5% ethanol (solvent control). Onion bulbs sprayed with thymol 24 h before fungal inoculation generally showed reduced lesion diameters by isolate F23 but not in isolate F15 compared with those sprayed 24 h after fungal inoculation. Collectively, thymol effectively inhibited the growth and development of A. awamori and B. aclada on amended media and in I-plates. In addition, spraying or fumigation of thymol is more desirable for effectively controlling these postharvest fungal pathogens during long-term storage conditions.

Effect of Bacillus mesonae H20-5 Treatment on Rhizospheric Bacterial Community of Tomato Plants under Salinity Stress.

Plant growth-promoting bacteria improve plant growth under abiotic stress conditions. However, their effects on microbial succession in the rhizosphere are poorly understood. In this study, the inoculants of Bacillus mesonae strain H20-5 were administered to tomato plants grown in soils with different salinity levels (EC of 2, 4, and 6 dS/m). The bacterial communities in the bulk and rhizosphere soils were examined 14 days after H20-5 treatment using Illumina MiSeq sequencing of the bacterial 16S rRNA gene. Although the abundance of H20-5 rapidly decreased in the bulk and rhizosphere soils, a shift in the bacterial community was observed following H20-5 treatment. The variation in bacterial communities due to H20-5 treatment was higher in the rhizosphere than in the bulk soils. Additionally, the bacterial species richness and diversity were greater in the H20-5 treated rhizosphere than in the control. The composition and structure of the bacterial communities varied with soil salinity levels, and those in the H20-5 treated rhizosphere soil were clustered. The members of Actinobacteria genera, including Kineosporia, Virgisporangium, Actinoplanes, Gaiella, Blastococcus, and Solirubrobacter, were enriched in the H20-5 treated rhizosphere soils. The microbial co-occurrence network of the bacterial community in the H20-5 treated rhizosphere soils had more modules and keystone taxa compared to the control. These findings revealed that the strain H20-5 induced systemic tolerance in tomato plants and influenced the diversity, composition, structure, and network of bacterial communities. The bacterial community in the H20-5 treated rhizosphere soils also appeared to be relatively stable to soil salinity changes.

Chemical Fungicides and Bacillus siamensis H30-3 against Fungal and Oomycete Pathogens Causing Soil-Borne Strawberry Diseases.

Chemical and biological agents were evaluated to inhibit Colletotrichum fructicola, Phytophthora cactorum, and Lasiodiplodia theobromae causing strawberry diseases. Mycelial growths of C. fructicola were gradually arrested by increasing concentrations of fungicides pyraclostrobin and iminoctadine tris (albesilate). P. cactorum and L. theobromae were more sensitive to pyraclostrobin compared to C. fructicola, but iminoctadine tris (albesilate) was not or less effective to limit P. cactorum or L. theobromae, respectively. Bacillus siamensis H30-3 was antagonistic against the three pathogens by diffusible as well as volatile molecules, and evidently reduced aerial mycelial formation of P. cactorum. B. siamensis H30-3 growth was declined by at least 0.025 mg/ml of pyraclostrobin. The two fungicides additively inhibited mycelial growths of C. fructicola, but not of P. cactorum and L. theobromae. B. siamensis H30-3 volatiles led to less growth of C. fructicola than one reduced by the fungicides. Taken together, in vitro antimicrobial activities of the two fungicides together with or without B. siamensis H30-3 volatiles may be cautiously incorporated into integrated management of strawberry diseases dependent on causal pathogens.

The Bacillus zanthoxyli HS1 Strain Renders Vegetable Plants Resistant and Tolerant against Pathogen Infection and High Salinity Stress.

Various management systems are being broadly employed to minimize crop yield loss resulting from abiotic and biotic stresses. Here we introduce a Bacillus zanthoxyli HS1 strain as a potent candidate for managing manifold stresses on vegetable plants. Considering 16S rDNA sequence and biochemical characteristics, the strain is closely related to B. zanthoxyli. The B. zanthoxyli HS1's soil-drench confers disease resistance on tomato and paprika plants against infection with Ralstonia solanacearum and Phytophthora capsici, respectively. Root and shoot growths are also increased in B. zanthoxyli HS1-treated cabbage, cucumber, and tomato plants, compared with those in mock-treated plants, after application of high salinity solution. Moreover, the pretreatment of B. zanthoxyli HS1 on cabbage plants inhibits the degradation of chloroplast pigments caused by high salinity stresses, whereas the inhibitory effect is not observed in cucumber plants. These findings suggest that B. zanthoxyli HS1 stain inhibits disease development and confers tolerance to salinity stress on vegetable plants.

Arachidicoccus soli sp. nov., a bacterium isolated from soil.

A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium, designated KIS59-12T, was isolated from a soil sample collected on Hodo island, Boryeong, Republic of Korea. The strain grew at 10-33 °C, pH 6.0-7.5 and with 0-4 % NaCl (w/v). Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain KIS59-12T was in the same clade as Arachidicoccus rhizosphaerae Vu-144T and Arachidicoccus ginsenosidivorans Gsoil809T with 97.5 and 97.2 % sequence similarity, respectively. Comparative genome analysis between strain KIS59-12T and A. rhizosphaerae Vu-144T showed that average nucleotide identity value was 69.4 % and the digital DNA-DNA hybridization value was 19.1 %. The major respiratory quinone was menaquinone-7. The major polar lipids were phosphatidylethanolamine and an unknown polar lipid. The predominant cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH, which supported the affiliation of strain KIS59-12T with the genus Arachidicoccus. The major polyamines were homospermidine and putrescine. The genomic DNA G+C content was 36.4 mol%. On the basis of phylogenetic, physiological and chemotaxonomic characteristics, strain KIS59-12T represents a novel species of the genus Arachidicoccus, for which the name Arachidicoccus soli sp. nov. is proposed. The type strain of Arachidicoccus soli is KIS59-12T (=KACC 17340T=NBRC 113161T).

Chitinophaga agri sp. nov., a bacterium isolated from soil of reclaimed land.

A Gram-negative, aerobic, and long rod-shaped bacterium, designated as H33E-04T, was isolated from the soil of reclaimed land, Republic of Korea. The strain grew at a temperature range of 15-40 °C, pH 5.0-10.0, and 0-2% NaCl (w/v). The phylogenetic analysis based on 16S rRNA gene sequences showed that strain H33E-04T was in the same clade with Chitinophaga pinensis DSM 2588T, Chitinophaga filiformis IFO 15056T, and Chitinophaga ginsengisoli Gsoil 052T with 98.4%, 97.9%, and 97.8% sequence similarities, respectively. The de novo genome assembly revealed that the DNA G + C content of the strain was 46.2 mol%. Comparative genome analysis between strain H33E-04T and C. pinensis DSM 2588 T showed that the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were 79.9% and 23.4%, respectively. The major respiratory quinone was menaquinone-7 (MK-7) and the predominant cellular fatty acids were iso-C15:0 (31.7%), C16:1 ω5c (31.2%), and iso-C17:0 3-OH (11.8%), supporting the affiliation of strain H33E-04T with the genus Chitinophaga. Based on phylogenetic, physiological, and chemotaxonomic characteristics, strain H33E-04T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga agri sp. nov. is proposed. The type strain of Chitinophaga agri is H33E-04T (= KACC 21303T = NBRC114512T).

Xylophilus rhododendri sp. nov., Isolated from Flower of Royal Azalea, Rhododendron schlippenbachii.

A bacterial strain, designated CJ1-R5T, was isolated from the flower of the royal azalea plant (Rhododendron schlippenbachii) collected in Jeju Island, Republic of Korea. The strain was a Gram-negative, strictly aerobic, motile, rod-shaped bacterium, growing at a temperature range of 4-33 °C (optimum 28-30 °C), pH 5.0-9.0 (optimum pH 7.0-8.0), and 0-1% NaCl (optimum 0%). The 16S rRNA sequence analysis of strain CJ1-R5T revealed the highest sequence similarity (97.9%) with Xylophilus ampelinus ATCC 33914T, and sequence similarities of less than 97.2% with other validly named species. Phylogenetic tree analysis based on the 16S rRNA gene sequences showed that strain CJ1-R5T clustered with Xylophilus ampelinus ATCC 33914T and two uncultured bacterial clones. The only quinone observed in strain CJ1-R5T was ubiquinone-8. The polar lipids observed were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminophospholipid and two unidentified lipids. The major fatty acids were C16:0, C17:0 cyclo, and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). The genome size of strain CJ1-R5T was 5.85 Mbp. The genomic G + C content was 68.4 mol%. ANI and dDDH values between strain CJ1-R5T and Xylophilus ampelinus ATCC 33914T were 79.0% and 22.5%, respectively. Based on the polyphasic taxonomic data, strain CJ1-R5T is considered to represent a novel species, for which the name Xylophilus rhododendri sp. nov. is proposed. The type strain is CJ1-R5T (= KACC 21265T = CCTCC AB2020030T).

Paenibacillus lycopersici sp. nov. and Paenibacillus rhizovicinus sp. nov., isolated from the rhizosphere of tomato (Solanum lycopersicum).

Two Gram-stain-positive, rod-shaped, endospore-forming bacteria, designated 12200R-189T and 14171R-81T were isolated from the rhizosphere of tomato plants. The 16S rRNA gene sequence similarity between strains 12200R-189T and 14171R-81T were 97.2%. Both strains showed the highest 16S rRNA gene sequence similarities to Paenibacillus sacheonensis SY01T (96.3% and 98.0%, respectively). The genome of strain 12200R-189T was approximately 6.7 Mb in size with 5,750 protein-coding genes (CDSs) and the G + C content was 58.1 mol%, whereas that of strain 14171R-81T comprised one chromosome of 7.0 Mb and two plasmids (0.2 Mb each) with 6,595 CDSs and the G + C content was 54.5 mol%. Comparative genome analysis revealed that average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among 12200R-189T, 14171R-81T, and other closely related species were below the cut-off levels 95% and 70%, respectively. Strain 12200R-189T grew at a temperature range of 15-40°C, pH 6.0-9.0, and 0-3% NaCl (w/v), whereas strain 14171R-81T grew at a temperature range of 10-37°C, pH 6.0-8.0, and 0-1% NaCl (w/v). Menaquinone-7 (MK-7) was the only isoprenoid quinone detected in both strains. The predominant cellular fatty acids (> 10%) were iso-C15:0, anteiso-C15:0, and iso-C16:0. The polar lipids of strain 12200R-189T were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), aminophospholipid (APL), phospholipid (PL), phosphatidylglycolipid (PGL), and four aminophosphoglycolipids (APGLs) and those of strain 14171R-81T were DPG, PG, PE, APL, three PLs, two PGLs, and three APGLs. Based on phylogenetic, genomic, phenotypic, and chemotaxonomic analyses, strains 12200R-189T and 14171R-81T represent two novel species of the genus Paenibacillus, for which the names Paenibacillus lycopersici sp. nov. and Paenibacillus rhizovicinus sp. nov. are proposed. The type strains are 12200R-189T (= KACC 19916T = CCTCC AB 2020027T) and 14171R-81T (= KACC 19915T = CCTCC AB 2020026T).

Complete genome sequence data of Flavobacterium anhuiense strain GSE09, a volatile-producing biocontrol bacterium isolated from cucumber (Cucumis sativus) root.

Flavobacterium anhuiense (previously identified as Flavobacterium johnsoniae) strain GSE09 is a volatile-producing bacterium that exhibits significant biocontrol activity against an oomycete pathogen, Phytophthora capsici, on pepper plants. Here, we report the complete genome sequence data of strain GSE09, isolated from surface-sterilized cucumber root. The genome consists of a circular 5,109,718-bp chromosome with a G + C content of 34.30%. A total of 4,138 complete coding sequences including 15 rRNA, 66 tRNA, 3 ncRNA, and 51 pseudogene sequences were retrieved. Thus, the genome sequence data of F. anhuiense GSE09 may facilitate the elucidation of many biological traits related to the biocontrol against plant pathogens.

A preliminary examination of bacterial, archaeal, and fungal communities inhabiting different rhizocompartments of tomato plants under real-world environments.

Plant microbiota is a key determinant of plant health and productivity. The composition and structure of plant microbiota varies according to plant tissue and compartment, which are specific habitats for microbial colonization. To investigate the structural composition of the microbiome associated with tomato roots under natural systems, we characterized the bacterial, archaeal, and fungal communities of three belowground compartments (rhizosphere, endosphere, and bulk soil) of tomato plants collected from 23 greenhouses in 7 geographic locations of South Korea. The microbial diversity and structure varied by rhizocompartment, with the most distinctive community features found in the endosphere. The bacterial and fungal communities in the bulk soil and rhizosphere were correlated with soil physicochemical properties, such as pH, electrical conductivity, and exchangeable cation levels, while this trend was not evident in the endosphere samples. A small number of core bacterial operational taxonomic units (OTUs) present in all samples from the rhizosphere and endosphere represented more than 60% of the total relative abundance. Among these core microbes, OTUs belonging to the genera Acidovorax, Enterobacter, Pseudomonas, Rhizobium, Streptomyces, and Variovorax, members of which are known to have beneficial effects on plant growth, were more relatively abundant in the endosphere samples. A co-occurrence network analysis indicated that the microbial community in the rhizosphere had a larger and more complex network than those in the bulk soil and endosphere. The analysis also identified keystone taxa that might play important roles in microbe-microbe interactions in the community. Additionally, profiling of predicted gene functions identified many genes associated with membrane transport in the endospheric and rhizospheric communities. Overall, the data presented here provide preliminary insight into bacterial, archaeal, and fungal phylogeny, functionality, and interactions in the rhizocompartments of tomato roots under real-world environments.