Spatial and Temporal Shifts of Endophytic Bacteria in Conifer Seedlings of Abies religiosa (Kunth) Schltdl. & Cham.

Endophytes play an important role in plant development, survival, and establishment, but their temporal dynamics in young conifer plants are still largely unknown. In this study, the bacterial community was determined by metabarcoding of the 16S rRNA gene in the rhizoplane, roots, and aerial parts of 1- and 5-month-old seedlings of natural populations of Abies religiosa (Kunth) Schltdl. & Cham. In 1-month-old seedlings, Pseudomonas dominated aerial parts (relative abundance 71.6%) and roots (37.9%). However, the roots exhibited significantly higher bacterial species richness than the aerial parts, with the dissimilarity between these plant sections mostly explained by the loss of bacterial amplification sequence variants. After 5 months, Mucilaginibacter dominated in the rhizoplane (9.0%), Streptomyces in the roots (12.2%), and Pseudomonas in the aerial parts (18.1%). The bacterial richness and community structure differed significantly between the plant sections, and these variations were explained mostly by 1-for-1 substitution. The relative abundance of putative metabolic pathways significantly differed between the plant sections at both 1 and 5 months. All the dominant bacterial genera (e.g., Pseudomonas and Burkholderia-Caballeronia-Paraburkholderia) have been reported to have plant growth-promoting capacities and/or antagonism against pathogens, but what defines their role for plant development has still to be determined. This investigation improves our understanding of the early plant-bacteria interactions essential for natural regeneration of A. religiosa forest.

Endophytic Aspergillus fumigatiaffinis: Novel paclitaxel production and optimization insights.

This study investigated the potential of endophytic fungi to produce paclitaxel (Taxol®), a potent anticancer compound widely employed in chemotherapy. This research aimed to identify, confirm, and characterize endophytic fungi capable of paclitaxel (PTX) production and assess their paclitaxel yield. Additionally, it aimed to investigate factors influencing paclitaxel production. A total of 100 endophytic fungal isolates were collected and identified from the roots of Artemisia judaica. Aspergillus fumigatiaffinis exhibited the highest PTX production (26.373 µg L-1) among the isolated endophytic fungi. The strain was identified as A. fumigatiaffinis (Accession No. PP235788.1). Molecular identification confirmed its novelty, representing the first report of PTX production by A. fumigatiaffinis, an endophyte of Artemisia judaica. Optimization through full factorial design of experiments (DOE) and response surface methodology (RSM) significantly enhanced PTX production to 110.23 µg L-1 from 1 g of dry weight of the fungal culture under optimal conditions of pH 8.0, 150 µg L-1 becozyme supplementation, and 18 days of fermentation in potato dextrose broth. The presence of paclitaxel was confirmed using thin layer chromatography, high performance liquid chromatography, and gas chromatography-mass spectrometry. These findings maximize the role of endophytic fungus to produce a secondary metabolite that might be able to replace the chemically produced PTX and gives an opportunity to provide a sustainable source of PTX eco-friendly at high concentrations. KEY POINTS: • Endophytic fungi, like A. fumigatiaffinis, show promise for eco-friendly paclitaxel production • Optimization strategies boost paclitaxel yield significantly, reaching 110.23 µg L -1 • Molecular identification confirms novelty, offering a sustainable PTX source.

Spatial distribution and community composition of endophytic fungi within Mussaenda pubescens stems.

Endophytic fungi, pivotal in facilitating plant co-evolution, significantly enhance plant growth, stress resistance, and environmental adaptability. Despite their importance, the spatial distribution of stem endophytic fungi (SEF) within host plants remains poorly characterized. Here, we employed high-throughput sequencing to conduct a comparative analysis of SEF communities in Mussaenda pubescens on a regional scale. Our findings reveal that whole-SEF communities were overwhelmingly dominated by members of the phylum Ascomycota, accounting for 85.9 %, followed by Basidiomycota at 13.9 %, and that alpha diversity within the whole-SEF community of M. pubescens remains relatively consistent across sampling sites. However, significant variation was observed within conditionally abundant taxa (CAT), conditionally rare or abundant taxa (CRAT), and conditionally rare taxa (CRT). Climatic factors emerged as the primary influence on SEF community distribution, followed by spatial distance and stem chemical properties. Neutral community modeling results suggested that both stochastic and deterministic processes play a role in shaping whole-SEF communities, with deterministic processes having a stronger influence on CRT subcommunities. Furthermore, the CRT co-occurrence network exhibited a more complex structure, characterized by higher values of network betweenness and degree relative to CAT and CRAT subcommunities. These findings enhance our understanding of community assembly and ecological interactions between stem fungal endophytes, presenting opportunities for harnessing fungal resources for the benefit of humanity.

Antagonistic potential of endophytic fungal isolates of tomato (Solanum lycopersicum L.) fruits against post-harvest disease-causing pathogens of tomatoes: An in vitro investigation.

Post-harvest decay of fresh agricultural produce is a major threat to food security globally. Synthetic fungicides, commonly used in practice for managing the post-harvest losses, have negative impacts on consumers' health. Studies have reported the effectiveness of fungal isolates from plants as biocontrol agents of post-harvest diseases, although this is still poorly established in tomatoes (Solanum lycopersicum L. cv. Jasmine). In this study, 800 endophytic fungi were isolated from mature green and ripe untreated and fungicide-treated tomato fruits grown in open soil and hydroponics systems. Of these, five isolates (Aureobasidium pullulans SUG4.1, Coprinellus micaceus SUG4.3, Epicoccum nigrum SGT8.6, Fusarium oxysporum HTR8.4, Preussia africana SUG3.1) showed antagonistic properties against selected post-harvest pathogens of tomatoes (Alternaria alternata, Fusarium solani, Fusarium oxysporum, Geotrichum candidum, Rhizopus stolonifera, Rhizoctonia solani), with Lactiplantibacillus plantarum as a positive control. P. africana SUG3.1 and C. micaceus SUG4.3 significantly inhibited growth of all the pathogens, with antagonistic capabilities comparable to that exhibited by L. plantarum. Furthermore, the isolates produced an array of enzymes, including among others, amylase, cellulose and protease; and were able to utilize several carbohydrates (glucose, lactose, maltose, mannitol, sucrose). In conclusion, P. africana SUG3.1 and C. micaceus SUG4.3 may complement L. plantarum as biocontrol agents against post-harvest pathogens of tomatoes.

Endophytic fungal isolates from apple tissue: Latent pathogens lurking within?

Fungal endophytes inhabit a similar ecological niche to that occupied by many phytopathogens, with several pathogens isolated from healthy tissues in their latent phase. This study aimed to evaluate the pathogenicity, the colonisation ability, and the enzyme activity of 37 endophytic fungal isolates recovered from apparently healthy apple shoot and leaf tissues. The pathogenicity of the isolates was assessed on 'Royal Gala' and 'Braeburn' fruit and detached 'Royal Gala' shoots. For the non-pathogenic isolates, their ability to endophytically colonise detached 'Royal Gala' shoots was evaluated. Enzyme activity assays were undertaken to determine whether the pathogenicity of the endophytes was related to the production of the extracellular enzymes, amylase, cellulase, pectinase, protease, and xylanase. Of the 37 isolates studied, eight isolates, representing the genera Colletotrichum, Diaporthe, Fusarium, and Penicillium, were shown to be pathogenic on both apple shoots and fruit. Two isolates identified as Trichoderma atroviride, were pathogenic only on shoots, and three isolates, representing the genus Diaporthe, were pathogenic only on fruit. Of the remaining 24 isolates, 22 (Biscogniauxia (n = 8), Chaetomium (n = 4), Trichoderma (n = 3), Epicoccum (n = 2), Neosetophoma (n = 2), Xylaria (n = 1), Daldinia (n = 1), and Paraphaeosphaeria (n = 1)) were recovered from the inoculated apple shoots but two failed to colonise the shoot tissues. Of the isolates tested, 20 produced amylase, 15 cellulase, 25 pectinase, 26 protease, and 13 xylanase. There was no correlation between the range and type of enzymes produced by the isolates and their pathogenicity or ability to endophytically colonise the shoot tissue. The study showed that approximately one-third (13/37) of the isolates recovered from the apparently healthy apple shoot tissues were observed as latent pathogens. The isolates that did not cause disease symptoms may have the ability to reduce colonisation of apple tissues by pathogens including Neonectria ditissima associated with European canker of apple.

Streptomyces mahasarakhamensis sp. nov., an Endophytic Actinobacterium Isolated from Jasmine Rice and its Potential as plant Growth Promoter.

Two endophytic actinobacteria, strains MK5T and MK7, were isolated from the surface-sterilized root of Jasmine rice (Oryza sativa KDML 105). These strains were aerobic actinobacteria with a well-developed substrate and aerial mycelia that formed spiral spore chains. The type strains that shared the high 16S rRNA gene sequence similarity with both strains were Streptomyces naganishii NBRC 12892T (99.4%), "Streptomyces griseicoloratus" TRM S81-3T (99.2%), and Streptomyces spiralis NBRC 14215T (98.9%). Strains MK5T and MK7 are the same species sharing a digital DNA-DNA hybridization (dDDH) value of 95.3% and a 16S rRNA gene sequence similarity of 100%. Chemotaxonomic data confirmed the affiliation of strains MK5T and MK7 to the genus Streptomyces. Strains MK5T and MK7 contained MK-9(H4) as a major menaquinone; the whole-cell sugar of both strains was galactose and glucose. The strain MK5T shared 93.4% average nucleotide identity (ANI)-Blast, 95.5% ANI-MUMmer, 93% average amino acid identity, and 61.3% dDDH with S. spiralis NBRC 14215T. The polyphasic approach confirmed that strain MK5T represents a novel species, and the name Streptomyces mahasarakhamensis sp. nov. is proposed. The type strain is MK5T (= TBRC 17754 = NRRL B-65683). Genome mining, using an in silico approach and searching biosynthesis gene clusters of strains MK5T and MK7, revealed that the genomes contained genes encoding proteins relating to plant growth promotion, bioactive compounds, and beneficial enzymes. Strains MK5T and MK7 could produce indole acetic acid and solubilize phosphate in vitro.

Assessment of Plant Growth Promotion Potential of Endophytic Bacterium B. subtilis KU21 Isolated from Rosmarinus officinalis.

The current study aimed to evaluate the plant growth-promoting (PGP) potential of endophytic strain Bacillus subtilis KU21 isolated from the roots of Rosmarinus officinalis. The strain exhibited multiple traits of plant growth promotion viz., phosphate (P) solubilization, nitrogen fixation, indole-3-acetic acid (IAA), siderophore, hydrogen cyanide (HCN), lytic enzymes production, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. The isolate also exhibited antagonistic activity against phytopathogenic fungi, i.e., Fusarium oxysporum, Fusarium graminiarum, and Rhizoctonia solani. The P-solubilization activity of B. subtilis KU21 was further elucidated via detection of glucose dehydrogenase (gdh) gene involved in the production of gluconic acid which is responsible for P-solubilization. Further, B. subtilis KU21 was evaluated for in vivo growth promotion studies of tomato (test crop) under net house conditions. A remarkable increase in seed germination, plant growth parameters, nutrient acquisition, and soil quality parameters (NPK) was observed in B. subtilis KU21-treated plants over untreated control. Hence, the proposed module could be recommended for sustainable tomato production in the Northwest Himalayan region without compromising soil health and fertility.

Endophytic diazotrophic communities from rice roots are diverse and weakly associated with soil diazotrophic community composition and soil properties.

AIM: Bacteria that promote plant growth, such as diazotrophs, are valuable tools for achieving a more sustainable production of important non-legume crops like rice. Different strategies have been used to discover new bacteria capable of promoting plant growth. This work evaluated the contribution of soil diazotrophs to the endophytic communities established in the roots of rice seedlings cultivated on seven representative soils from Uruguay. METHODS AND RESULTS: The soils were classified into two groups according to the C and clay content. qPCR, terminal restriction fragment length polymorphism (T-RFLP), and 454-pyrosequencing of the nifH gene were used for analyzing diazotrophs in soil and plantlets' roots grown from seeds of the same genotype for 25 days under controlled conditions. A similar nifH abundance was found among the seven soils, roots, or leaves. The distribution of diazotrophs was more uneven in roots than in soils, with dominance indices significantly higher than in soils (nifH T-RFLP). Dominant soils' diazotrophs were mainly affiliated to Alphaproteobacteria and Planctomycetota. Conversely, Alpha, Beta, Gammaproteobacteria, and Bacillota were predominant in different roots, though undetectable in soils. Almost no nifH sequences were shared between soils and roots. CONCLUSIONS: Root endophytic diazotrophs comprised a broader taxonomic range of microorganisms than diazotrophs found in soils from which the plantlets were grown and showed strong colonization patterns.

Root nodules of red alder (Alnus rubra) and sitka alder (Alnus viridis ssp. sinuata) are inhabited by taxonomically diverse cultivable microbial endophytes.

The root nodules of actinorhizal plants are home to nitrogen-fixing bacterial symbionts, known as Frankia, along with a small percentage of other microorganisms. These include fungal endophytes and non-Frankia bacteria. The taxonomic and functional diversity of the microbial consortia within these root nodules is not well understood. In this study, we surveyed and analyzed the cultivable, non-Frankia fungal and bacterial endophytes of root nodules from red and Sitka alder trees that grow together. We examined their taxonomic diversity, co-occurrence, differences between hosts, and potential functional roles. For the first time, we are reporting numerous fungal endophytes of alder root nodules. These include Sporothrix guttuliformis, Fontanospora sp., Cadophora melinii, an unclassified Cadophora, Ilyonectria destructans, an unclassified Gibberella, Nectria ramulariae, an unclassified Trichoderma, Mycosphaerella tassiana, an unclassified Talaromyces, Coniochaeta sp., and Sistotrema brinkmanii. We are also reporting several bacterial genera for the first time: Collimonas, Psychrobacillus, and Phyllobacterium. Additionally, we are reporting the genus Serratia for the second time, with the first report having been recently published in 2023. Pseudomonas was the most frequently isolated bacterial genus and was found to co-inhabit individual nodules with both fungi and bacteria. We found that the communities of fungal endophytes differed by host species, while the communities of bacterial endophytes did not.

Assessing the biodiversity of rhizosphere and endophytic fungi in Knoxia valerianoides under continuous cropping conditions.

BACKGROUND: Rhizosphere and endophytic fungi play important roles in plant health and crop productivity. However, their community dynamics during the continuous cropping of Knoxia valerianoides have rarely been reported. K. valerianoides is a perennial herb of the family Rubiaceae and has been used in herbal medicines for ages. Here, we used high-throughput sequencing technology Illumina MiSeq to study the structural and functional dynamics of the rhizosphere and endophytic fungi of K. valerianoides. RESULTS: The findings indicate that continuous planting has led to an increase in the richness and diversity of rhizosphere fungi, while concomitantly resulting in a decrease in the richness and diversity of root fungi. The diversity of endophytic fungal communities in roots was lower than that of the rhizosphere fungi. Ascomycota and Basidiomycota were the dominant phyla detected during the continuous cropping of K. valerianoides. In addition, we found that root rot directly affected the structure and diversity of fungal communities in the rhizosphere and the roots of K. valerianoides. Consequently, both the rhizosphere and endophyte fungal communities of root rot-infected plants showed higher richness than the healthy plants. The relative abundance of Fusarium in two and three years old root rot-infected plants was significantly higher than the control, indicating that continuous planting negatively affected the health of K. valerianoides plants. Decision Curve Analysis showed that soil pH, organic matter (OM), available K, total K, soil sucrase (S_SC), soil catalase (S_CAT), and soil cellulase (S_CL) were significantly related (p < 0.05) to the fungal community dynamics. CONCLUSIONS: The diversity of fungal species in the rhizosphere and root of K. valerianoides was reported for the first time. The fungal diversity of rhizosphere soil was higher than that of root endophytic fungi. The fungal diversity of root rot plants was higher than that of healthy plants. Soil pH, OM, available K, total K, S_CAT, S_SC, and S_CL were significantly related to the fungal diversity. The occurrence of root rot had an effect on the community structure and diversity of rhizosphere and root endophytic fungi.

Transcriptome Analysis Reveals the Biocontrol Mechanism of Endophytic Bacterium AM201, Rhodococcus sp., against Root Rot Disease of Atractylodes macrocephala.

Atractylodes macrocephala Koidz (AMK) is a perennial herb from the plant family Asteraceae (formerly Compositae). This herb is mainly distributed in mountainous wetlands in Zhejiang, Sichuan, Yunnan, and Hunan provinces of China. Its medicinal production and quality, however, are severely impacted by root rot disease. In our previous study, endophytic bacterium designated AM201 exerted a high biocontrol effect on the root rot disease of AMK. However, the molecular mechanisms underlying this effect remain unclear. In this study, the identity of strain AM201 as Rhodococcus sp. was determined through analysis of its morphology, physiological and biochemical characteristics, as well as 16S rDNA sequencing. Subsequently, we performed transcriptome sequencing and bioinformatics analysis to compare and analyze the transcriptome profiles of root tissues from two groups: AM201 (AMK seedlings inoculated with Fusarium solani [FS] and AM201) and FS (AMK seedlings inoculated with FS alone). We also conducted morphological, physiological, biochemical, and molecular identification analyses for the AM201 strain. We obtained 1,560 differentially expressed genes, including 187 upregulated genes and 1,373 downregulated genes. We screened six key genes (GOLS2, CIPK25, ABI2, egID, PG1, and pgxB) involved in the resistance of AM201 against AMK root rot disease. These genes play a critical role in reactive oxygen species (ROS) clearance, Ca2+ signal transduction, abscisic acid signal inhibition, plant root growth, and plant cell wall defense. The strain AM201 was identified as Rhodococcus sp. based on its morphological characteristics, physiological and biochemical properties, and 16S rDNA sequencing results. The findings of this study could enable to prevent and control root rot disease in AMK and could offer theoretical guidance for the agricultural production of other medicinal herbs.

Exploring endophytic bacteria communities of Vanilla planifolia.

BACKGROUND: Rhizosphere bacterial community and endophytes are now known to influence plant health and response to environmental stress. Very few studies have reported the diversity of endophytic bacterial communities of Vanilla planifolia and their potential roles in promoting plant growth or contributing to aromatic quality. RESULTS: In this study, the composition and diversity of the Vanilla rhizosphere bacterial community were explored by analyzing rhizosphere soil and root tissue samples as well as green pods of three accessions of Vanilla planifolia grown on different types of substrates (compost and leaf litter). In addition, the endophytic bacterial diversity of roots and green pods as well as the evolution of endophytic bacteria after the curing process of vanilla green pods were analyzed based on a metabarcoding approach. The results showed that bacterial species richness and diversity were higher in the compost. The analysis of the soil bacterial composition displayed that Halomonas, Pseudoalteromonas, Enterobacter and Bradyrhizobium were the most abundant genera. Moreover, the results indicated that the soil bacterial community structure was linked to the host plant genotype. Regarding the roots endophytic bacteria composition, the genera Halomonas, Pseudoalteromonas, Bacillus and Carboxydocella genera were present in all samples, independently from the substrate nature. Several genera including Bacillus, Bradyrhizobium, Burkholderia and Halomonas were transmitted internally from the roots to the green pods. The curing process reduced the bacterial richness and bacterial diversity associated with the green pods. Halomonas, Pseudoalteromonas, Bacillus, and Carboxydocella are the dominant genera in the pods after the curing process. CONCLUSIONS: This study provides an overview of changes of the bacterial communities dynamics especially endophytic in the roots and the green pods. It highlighted bacterial genera (Halomonas, Pseudoalteromonas, Bacillus, and Carboxydocella) potentially implicated in the formation of aroma compounds of vanilla beans.

Endophytic species of Nigrospora from grasses and shrubs of Shadegan International Wetland, with new species and records from Iran.

The "Shadegan International Wetland" (SIW) is one of the wetlands internationally recognized in the Ramsar convention. The vegetation of this wetland ecosystem consists of mostly grasses and shrubs that host a large number of fungi including endophytes. In this study, Nigrospora isolates were obtained from healthy plants of this wetland and its surrounding salt marshes and identified based on morphological features and multilocus phylogenetic analyses based on three DNA loci, namely the internal transcribed spacer regions 1 and 2 including the intervening 5.8S nuclear ribosomal DNA (ITS), ß-tubulin (tub2), and elongation factor 1-α (tef1-α). Accordingly, the following Nigrospora species were identified: N. lacticolonia, N. oryzae, N. osmanthi, N. pernambucoensis and a novel taxon N. shadeganensis sp. nov., which is described and illustrated. To the best of our knowledge, 10 new hosts for Nigrospora species are here reported, namely Aeluropus lagopoides, Allenrolfea occidentalis, Anthoxanthum monticola, Arthrocnemum macrostachyum, Cressa cretica, Halocnemum strobilaceum, Seidlitzia rosmarinus, Suaeda vermiculata, Tamarix passerinoides, and Typha latifolia. Moreover, the species N. lacticolonia and N. pernambucoensis are new records for the mycobiota of Iran.

Withanolides production by the endophytic fungus Penicillium oxalicum associated with Withania somnifera (L.) Dunal.

Withanolides are steroidal lactones with diverse bioactive potential and their production from plant sources varies with genotype, age, culture conditions, and geographical region. Endophytic fungi serve as an alternative source to produce withanolides, like their host plant, Withania somnifera (L.) Dunal. The present study aimed to isolate endophytic fungi capable of producing withanolides, characterization and investigation of biological activities of these molecules. The methanolic fungal crude extract of one of the fungal isolates WSE16 showed maximum withanolide production (219 mg/L). The fungal isolate WSE16 was identified as Penicillium oxalicum based on its morphological and internal transcribed spacer (ITS) sequence analysis and submitted in NCBI (accession number OR888725). The methanolic crude extract of P. oxalicum was further purified by column chromatography, and collected fractions were assessed for the presence of withanolides. Fractions F3 and F4 showed a higher content of withanolides (51.8 and 59.1 mg/L, respectively) than other fractions. Fractions F3 and F4 exhibited antibacterial activity against Staphylococcus aureus with an IC50 of 23.52 and 17.39 µg/ml, respectively. These fractions also showed antioxidant activity (DPPH assay with IC50 of 39.42 and 38.71 µg/ml, superoxide anion scavenging assay with IC50 of 41.10 and 38.84 µg/ml, and reducing power assay with IC50 of 42.61 and 41.40 µg/ml, respectively) and acetylcholinesterase inhibitory activity (IC50 of 30.34 and 22.05 µg/ml, respectively). The withanolides present in fraction 3 and fraction 4 were identified as (20S, 22R)-1a-Acetoxy-27-hydroxywitha-5, 24-dienolide-3b-(O-b-D-glucopyranoside) and withanamide A, respectively, using UV, FTIR, HRMS, and NMR analysis. These results suggest that P. oxalicum, an endophytic fungus isolated from W. somnifera, is a potential source for producing bioactive withanolides.

Antarctica's hidden mycoviral treasures in fungi isolated from mosses: A first genomic approach.

This study investigates the presence of mycoviruses in Antarctic fungi and elucidates their evolutionary relationships. To achieve this, we aligned mycoviral gene sequences with genomes of previously sequenced Antarctic endophytic fungi, made available by our research group and accessible via Joint Genome Institute. Our findings reveal that the most prevalent genetic regions in all endophytic fungi are homologous to Partitiviruses, Baculoviridae, and Phycodnaviridae. These regions display evidence of positive selection pressure, suggesting genetic diversity and the accumulation of nonsynonymous mutations. This phenomenon implies a crucial role for these regions in the adaptation and survival of these fungi in the challenging Antarctic ecosystems. The presence of mycoviruses in Antarctic endophytic fungi may indicate shared survival strategies between the virus and its host, shedding light on their evolutionary dynamics. This study underscores the significance of exploring mycoviruses within endophytic fungi and their contributions to genetic diversity. Future research avenues could delve into the functional implications of these conserved mycoviral genetic regions in Antarctic endophytic fungi, providing a comprehensive understanding of this intriguing association and genomic retention of viral region in fungi.

Luteibacter mycovicinus sp. nov., a yellow-pigmented gammaproteobacterium found as an endohyphal symbiont of endophytic Ascomycota.

We isolated and described a yellow-pigmented strain of bacteria (strain 9143T), originally characterized as an endohyphal inhabitant of an endophytic fungus in the Ascomycota. Although the full-length sequence of its 16S rRNA gene displays 99 % similarity to Luteibacter pinisoli, genomic hybridization demonstrated <30 % genomic similarity between 9143T and its closest named relatives, further supported by average nucleotide identity results. This and related endohyphal strains form a well-supported clade separate from L. pinisoli and other validly named species including the most closely related Luteibacter rhizovicinus. The name Luteibacter mycovicinus sp. nov. is proposed, with type strain 9143T (isolate DBL433), for which a genome has been sequenced and is publicly available from the American Type Culture Collection (ATCC TSD-257T) and from the Leibniz Institute DSMZ (DSM 112764T). The type strain reliably forms yellow colonies across diverse media and growth conditions (lysogeny broth agar, King's Medium B, potato dextrose agar, trypticase soy agar and Reasoner's 2A (R2A) agar). It forms colonies readily at 27 °C on agar with a pH of 6-8, and on salt (NaCl) concentrations up to 2 %. It lacks the ability to utilize sulphate as a sulphur source and thus only forms colonies on minimal media if supplemented with alternative sulphur sources. It is catalase-positive and oxidase-negative. Although it exhibits a single polar flagellum, motility was only clearly visible on R2A agar. Its host range and close relatives, which share the endohyphal lifestyle, are discussed.

Kitasatospora cathayae sp. nov., a novel endophytic actinomycete isolated from the leaves of Cathaya argyrophylla.

Strain HUAS 3-15T was isolated from the leaves of Cathaya argyrophylla collected from Chenzhou, Hunan Province, PR China. The main fatty acids (>5.0 %) of the strain were anteiso-C15 : 0, C16 : 0, C18 : 1 ω9c, iso-C16 : 0, summed feature 5 (C18 : 2 ω6,9c/C18 : 0 ante), iso-C15 : 0 and anteiso-C17 : 0. MK-9(H6), MK-9(H8) and MK-9(H4) were detected as respiratory quinones. The diagnostic cell-wall diamino acid was meso-diaminopimelic acid. Galactose, glucose and ribose were also present in the cell wall. The major polar lipids consisted of diphosphatidylglycerol, phosphatidyl ethanolamine, phosphatidylinositol mannosides and unidentified phospholipids. The DNA G+C content of the genome sequence, consisting of 8 860 963 bp, is 72.4 mol%. blast analysis based on 16S rRNA gene sequences revealed that the strain belongs to the genus Kitasatospora, with 99.37, 99.03, 98.95, 98.68 and 98.67 % sequence similarity to Kitasatospora aureofaciens ATCC 10762T, Kitasatospora viridis DSM 44826T, Kitasatospora xanthocidica NBRC 13469T, Kitasatospora aburaviensis NRRL B-2218T and Kitasatospora kifunensis IFO 15206T, respectively. Phylogenetic trees based on 16S rRNA gene and whole-genome sequences demonstrated that strain HUAS 3-15T formed a well-supported cluster with K. aureofaciens ATCC 10762T. Further genomic characterization through average nucleotide identity (ANIb/m) and digital DNA-DNA hybridization analysis between strain HUAS 3-15T and K. aureofaciens ATCC 10762T showed values of 90.62/92.55 % and 45.3 %, respectively, lower than the 95-96 % ANI threshold and 70.0 % cutoff used as guideline values for species delineation in bacteria. Furthermore, the differences between the strain and its phylogenomic neighbour in terms of physiological (e.g. sole carbon source growth) and chemotaxonomic (e.g. cellular fatty composition) characteristics further supported this conclusion. Consequently, we concluded that strain HUAS 3-15T represents a novel species of the genus Kitasatospora, for which the name Kitasatospora cathayae sp. nov. is proposed. The type strain is HUAS 3-15T (=MCCC 1K08542T=JCM 36274T).

Endophytic species of Colletotrichum associated with cashew tree in northeastern Brazil.

Anthracnose caused by Colletotrichum is the most severe and widely occurring cashew disease in Brazil. Colletotrichum species are commonly found as pathogens, endophytes and occasionally as saprophytes in a wide range of hosts. The endophytic species associated with cashew trees are poorly studied. In this study, we report the Colletotrichum endophytic species associated with cashew trees in two locations in the state of Pernambuco, their prevalence in different plant organs (leaves, veins, branches and inflorescences), and compare the species in terms of pathogenicity and aggressiveness using different inoculation methods (wounded × unwounded). Six species of Colletotrichum were identified according to multilocus phylogenetic analyses, including Colletotrichum asianum, Colletotrichum chrysophilum, Colletotrichum karsti, Colletotrichum siamense, Colletotrichum theobromicola, and Colletotrichum tropicale. There were differences in the percentage of isolation in relation to the prevalence of colonized tissues and collection locations. C. tropicale was the prevalent species in both geographic areas and plant tissues collected, with no pattern of distribution of species between areas and plant tissues. All isolates were pathogenic in injured tissues of cashew plants. The best method to test the pathogenicity of Colletotrichum species was utilizing the combination of leaves + presence of wounds + conidial suspension, as it better represents the natural infection process. C. siamense was the most aggressive species.

Bacterial endophytic community composition varies by hemp cultivar in commercially sourced seed.

The seed-endophytic bacterial community is a potentially beneficial and heritable fraction of the plant microbiome. Its utilization as a sustainable crop improvement strategy could be especially valuable for species such as hemp, where production is being scaled up and new challenges will be faced in managing crop productivity and health. However, little is known about the makeup and variation of the hemp seed microbiome. This study profiled the endophytic bacterial communities harboured by 16 hemp cultivars sourced from commercial suppliers in Europe. A 16S rDNA amplicon sequencing approach identified 917 amplicon sequence variants across samples. Taxonomic classification of sequences revealed 4 phyla and 87 genera to be represented in the dataset. Several genera were widespread while some were specific to one or a few cultivars. Flavobacterium, Pseudomonas, and Pantoea were notable in their high overall abundance and prevalence, but community composition was variable and no one taxon was universally abundant, suggesting a high degree of flexibility in community assembly. Taxonomic composition and alpha diversity differed among cultivars, though further work is required to understand the relative influence of hemp genetic factors on community structure. The taxonomic profiles presented here can be used to inform further work investigating the functional characteristics and potential plant-growth-promoting traits of seed-borne bacteria in hemp.

Co-inoculation with novel nodule-inhabiting bacteria reduces the benefits of legume-rhizobium symbiosis.

The ecologically and economically vital symbiosis between nitrogen-fixing rhizobia and leguminous plants is often thought of as a bi-partite interaction, yet studies increasingly show the prevalence of non-rhizobial endophytes (NREs) that occupy nodules alongside rhizobia. Yet, what impact these NREs have on plant or rhizobium fitness remains unclear. Here, we investigated four NRE strains found to naturally co-occupy nodules of the legume Medicago truncatula alongside Sinorhizobium meliloti in native soils. Our objectives were to (1) examine the direct and indirect effects of NREs on M. truncatula and S. meliloti fitness, and (2) determine whether NREs can re-colonize root and nodule tissues upon reinoculation. We identified one NRE strain (522) as a novel Paenibacillus species, another strain (717A) as a novel Bacillus species, and the other two (702A and 733B) as novel Pseudomonas species. Additionally, we found that two NREs (Bacillus 717A and Pseudomonas 733B) reduced the fitness benefits obtained from symbiosis for both partners, while the other two (522, 702A) had little effect. Lastly, we found that NREs were able to co-infect host tissues alongside S. meliloti. This study demonstrates that variation of NREs present in natural populations must be considered to better understand legume-rhizobium dynamics in soil communities.