The distribution of some fungal and bacterial endophytes in maize (Zea mays L.)

Revealing the seed microbiome: Navigating sequencing tools, microbial assembly, and functions to amplify plant fitness

Microbial communities within seeds play a vital role in transmitting themselves to the next generation of plants. These microorganisms significantly impact seed vigor and early seedling growth, for successful crop establishment. Previous studies reported on seed-associated microbial communities and their influence on processes like dormancy release, germination, and disease protection. Modern sequencing and conventional methods reveal microbial community structures and environmental impacts, these information helps in microbial selection and manipulation. These studies form the foundation for using seed microbiomes to enhance crop resilience and productivity. While existing research has primarily focused on characterizing microbiota in dried mature seeds, a significant gap exists in understanding how these microbial communities assemble during seed development. The review also discusses applying seed-associated microorganisms to improve crops in the context of climate change. However, limited knowledge is available about the microbial assembly pattern on seeds, and their impact on plant growth. The review provides insight into microbial composition, functions, and significance for plant health, particularly regarding growth promotion and pest control.

Maize pollen carry bacteria that suppress a fungal pathogen that enters through the male gamete fertilization route

In flowering plants, after being released from pollen grains, the male gametes use the style channel to migrate towards the ovary where they fertilize awaiting eggs. Environmental pathogens exploit the style passage, resulting in diseased progeny seed. The belief is that pollen also transmits pathogens into the style. By contrast, we hypothesized that pollen carries beneficial microbes that suppress environmental pathogens on the style passage. No prior studies have reported pollen-associated bacterial functions in any plant species. Here, bacteria were cultured from maize (corn) pollen encompassing wild ancestors and farmer-selected landraces from across the Americas, grown in a common field in Canada for one season. In total, 298 bacterial isolates were cultured, spanning 45 genera, 103 species, and 88 OTUs, dominated by Pantoea, Bacillus, Pseudomonas, Erwinia, and Microbacterium. Full-length 16S DNA-based taxonomic profiling showed that 78% of bacterial taxa from the major wild ancestor of maize (Parviglumis teosinte) were present in at least one cultivated landrace. The species names of the bacterial isolates were used to search the pathogen literature systematically; this preliminary evidence predicted that the vast majority of the pollen-associated bacteria analyzed are not maize pathogens. The pollen-associated bacteria were tested in vitro against a style-invading Fusarium pathogen shown to cause Gibberella ear rot (GER): 14 isolates inhibited this pathogen. Genome mining showed that all the anti-Fusarium bacterial species encode phzF, associated with biosynthesis of the natural fungicide, phenazine. To mimic the male gamete migration route, three pollen-associated bacterial strains were sprayed onto styles (silks), followed by Fusarium inoculation; these bacteria reduced GER symptoms and mycotoxin accumulation in progeny seed. Confocal microscopy was used to search for direct evidence that pollen-associated bacteria can defend living silks against Fusarium graminearum (Fg); bacterial strain AS541 (Kluyvera intermedia), isolated from pollen of ancestral Parviglumis, was observed to colonize the susceptible style/silk entry points of Fg (silk epidermis, trichomes, wounds). Furthermore, on style/silk tissue, AS541 colonized/aggregated on Fg hyphae, and was associated with Fg hyphal breaks. These results suggest that pollen has the potential to carry bacteria that can defend the style/silk passage against an environmental pathogen - a novel observation.

Maize seed endophytes

Maize is a vital global crop, and each seed (kernel) hosts an ecosystem of microbes living inside it. However, we know very little about these endophytes and what their role is in plant production and physiology. In this Microreview, I summarize the major questions around maize seed endophytes, including what organisms are present, how they get there, whether and how they transmit across generations, and how they and the plant affect each other. Although several studies touch on each of these areas, ultimately there are far more questions than answers. Future priorities for research on maize seed endophytes should include understanding what adaptations allow microbes to be seed endophytes, how the host genetics and the environment affect these communities, and how maize seed endophytes ultimately contribute to the next generation of plants.

Protective effect of Bacillus species associated with Rumex dentatus against postharvest soil borne disease in potato tubers and GC-MS metabolite profile

Potato is constantly exposed to various kinds of phytopathogens which cause diseases during the developmental stage and post-harvest storage. This investigation was designed to assay the anti-phytopathogen activity of bacterial endophytes and their suppressive effects on rot disease in potato. The study also aimed to screen isolates for their plant growth-promoting traits and establish GC-MS-based metabolite profile of the potent isolate. Endophytes were isolated from Rumex dentatus and identified based on 16S rRNA gene. They were screened in dual culture assay against fungal phytopathogens and the potent isolate was tested for its capability to suppress Fusarium rot disease in potato tubers. The mechanism of action of endophytes on the phytopathogens was assessed using scanning electron microcopy. Isolates were also screened in vitro to assay their capability to produce phytohormones, hydrolytic enzymes, and to solubilize phosphates. Endophytic isolates produced proteases with a diameter of halo zone ranging from 7 to 32 mm. Bacillus sp. KL5 exhibited the highest production of indole acetic acid (IAA) with the amount of 104.28 µg/mL and was the most potent antagonist of Fusarium oxysporum and Verticillium dahliae with an inhibitory percentage of 61.53 and 100%, respectively. It showed a reduction of potato rot disease severity by more than 50%. GC-MS of active fractions of KL5 showed the presence of dibutylphthalate and 2,4-di-tert-butylphenol as major metabolites. From this study, it is evident that endophytic Bacillus species from R. dentatus are potent antagonists of F. oxysporum and V. dahliae. Bacillus sp. KL5 is a potent inhibitor of pathogenic F. oxysporum in potato tubers and can be developed as a biocontrol agent.

Can nitrogen supersede host identity in shaping the community composition of foliar endophytic fungi in an alpine meadow ecosystem?

The availability of limiting nutrients plays a crucial role in shaping communities of endophytes. Moreover, whether fungal endophytes are host-specific remains controversial. We hypothesized that in a harsh and nitrogen (N)-deficient area, diversity and community composition of foliar endophytic fungi (FEFs) varied substantially among plots with experimentally elevated levels of macronutrients, and thus, N availability, instead of host species identity, would have a greater influence in structuring fungal communities at different scales. We also expected an important subset of taxa shared among numerous host species and N gradients to form a community-wide core microbiome. We measured the leaf functional traits and community structures of FEFs of three commonly seen species in an alpine meadow nested with a long-term N fertilization experiment. We found that host plant identity was a powerful factor driving the endophytic fungal community in leaves, even in habitats where productivity was strongly limited by nitrogen (p < 0.001). We also found that within the same host, nitrogen was an important driving force for the composition of the endophytic fungi community (p < 0.05). In addition, the leaf carbon content was the most important functional trait that limited the diversity of endophytic fungi (p < 0.001). Finally, we documented a distinct core microbiome shared among our three focal species and N gradients.

Identification of Genetic Diversity, Pyrrocidine-Producing Strains and Transmission Modes of Endophytic Sarocladium zeae Fungi from Zea Crops

Genotyping by sequencing (GBS) was used to reveal the inherent genetic variation within the haploid fungi Sarocladium zeae isolated from diverse Zea germplasm, including modern Zea mays and its wild progenitors—the teosintes. In accordance with broad host relationship parameters, GBS analysis revealed significant host lineages of S. zeae genetic diversity, indicating that S. zeae genetic variation may associate with different evolutionary histories of host species or varieties. Based on a recently identified PKS-NRPS gene responsible for pyrrocidine biosynthesis in S. zeae fungi, a novel PCR assay was developed to discriminate pyrrocidine-producing S. zeae strains. This molecular method for screening bioactive strains of S. zeae is complementary to other approaches, such as chemical analyses. An eGFP-labelled S. zeae strain was also developed to investigate the endophytic transmission of S. zeae in Z. mays seedlings, which has further improved our understanding of the transmission modes of S. zeae endophytes in maize tissues.

Bacillus toyonensis SAU-19 and SAU-20 Isolated From Ageratina adenophora Alleviates the Intestinal Structure and Integrity Damage Associated With Gut Dysbiosis in Mice Fed High Fat Diet

This study was performed to identify potential probiotic endophytes from Ageratina adenophora and evaluate their ameliorating effects on gut injury and integrity damage associated with microbiota dysbiosis in mice fed high fat diet. Using morphological and biochemical tests, and 16S rRNA gene sequencing technique, two bacteria endophytes were identified as strains of Bacillus toyonensis and were named Bacillus toyonensis SAU-19 (GenBank No. MW287198) and Bacillus toyonensis SAU-20 (GenBank No. MW287199). Sixty (60) mice were divided into five groups, group 1 was the negative control fed normal diet (NS), group 2 was fed High fat diet (HF), Group 3 was fed High fat diet + 106 Lactobacillus rhamnosus (LGG), group 4 was fed High fat + 106 Bacillus toyonensis SAU-19 and group 5 fed High fat diet + 106 Bacillus toyonensis SAU-20. After 35 days, histological and immunohistochemistry examination were performed in the ileum tissues. Furthermore, DAO and antioxidants activities were measured in serum, mRNA expressions of tight junction proteins (occludin and ZO-1) and inflammation related cytokines (IL-1β, TFN-α, IL-2, IL-4, and IL-10) in the ileum tissues as well as sIgA levels and total bacteria (Escherichia coli, Salmonella, Staphylococcus, and Lactobacillus) in the small intestine and cecum content. The results showed an increase in the DAO activity, oxidative stress parameter (MDA), pro-inflammation cytokines (IL-1β, TFN-α, IL-2), reduce immunity (sIgA), and destroyed intestinal structure and integrity (reduce tight junction proteins) in the high fat diet group and this was associated with destruction of the gut microbiota composition (increasing pathogenic bacteria; E. coli, Salmonella, Staphylococcus and reducing beneficial bacteria, Lactobacillus spp.) in mice (P < 0.05). However, the administration of Bacillus toyonensis SAU-19 and SAU-20 reverted these effects. Our findings indicated that, Bacillus toyonensis SAU-19 and SAU-20 isolated from A. adenophora could prevent the excess weight gain from high fat diet feeding, improved antioxidant status and alleviated the intestine integrity damage as well as reduce the population of enteric bacteria such as E. coli, Salmonella, and S. aureus and increasing the population of beneficial bacteria such as Lactobacillus in the gut of mice fed high fat diet, therefore, can serve as a potential probiotics in humans and animals.

Surface sterilization for isolation of endophytes: Ensuring what (not) to grow

Endophytic microbiota opens a magnificent arena of metabolites that served as a potential source of medicines for treating a variety of ailments and having prospective uses in agriculture, food, cosmetics, and many more. There are umpteen reports of endophytes improving the growth and tolerance of plants. In addition, endophytes from lifesaving drug-producing plants such as Taxus, Nothapodytes, Catharanthus, and so forth have the ability to produce host mimicking compounds. To harness these benefits, it is imperative to isolate the true endophytes, not the surface microflora. The foremost step in endophyte isolation is the removal of epiphytic microbes from plant tissues, called as surface sterilization. The success of surface sterilization decides "what to grow" (the endophytes) and "what not to grow" (the epiphytes). It is very crucial to use an appropriate sterilant solution, concentration, and exposure time to ensure thorough surface disinfection with minimal damage to the endophytic diversity. Commonly used surface sterilants include sodium hypochlorite (2%-10%), ethanol (70%-90%), mercuric chloride (0.1%), formaldehyde (40%), and so forth. In addition, the efficiency could further be improved by pretreatment with surfactants such as Triton X-100, Tween 80, and Tween 20. This review comprehensively deals with the various sterilants and sterilization methods for the isolation of endophytic microbes. In addition, the mechanisms and rationale behind using specific surface sterilants have also been elaborated at length.

Isolation and characterization of endophytic bacteria from tomato foliage and their in vitro efficacy against root-knot nematodes

Fifteen endophytic bacteria were isolated from leaves and stems of Solanum lycopersicum and Solanum pimpinellifolium collected from different locations of the Jorhat district of Assam and characterized by morphological, cultural, biochemical and molecular approaches. An in vitro study was carried out to evaluate their potentiality as biological control agents against second stage juvenile of the root-knot nematode, Meloidogyne incognita race2. Thirty second stage juveniles (J₂) of M. incognita race 2 were exposed to cell free culture filtrates of all the 15 bacterial endophytes in a sterile cavity block at a concentration of S(100%), S/2(50%), S/4(25%), S/6(17%) and S/10(10%) for a duration of 6, 12, 24, and 48 hr. The results revealed that all the isolates had the potentiality to significantly increase the mortality of the second stage juveniles (J₂). The percent mortality was directly proportional to the duration of exposure time and the concentration of the culture filtrate. The isolate BETL2 showed the best result with 81.47% mortality of juveniles followed by isolates BETL4 (81.43%), BETLI (79.07%), BETS2 (78.87%), and BETL6 (78.17%). The 16S rRNA sequence amplification results indicated that these isolates were Bacillus marisflavi (BETL2), Bacillus altitudinis (BETL4), Microbacterium arborescens (BETL1), Exiguobacterium indicum (BETS2), and Bacillus marisflavi (BETL6). The four most efficient isolates were structurally analyzed using a scanning electron microscope and this revealed that the length and breadth of isolates—BETLI, BETL2, BETL4, and BETS2 were 701.70 nm × 348.30 nm, 954.10 nm × 303.10 nm, 984.10 nm × 332.90 nm and 1422.00 nm × 742.00 nm, respectively. The result of the present study indicated that the above four novel strains of endophytic bacterial isolates enhance the mortality of J₂ of M. incognita race2 and has the potentiality as biological control agents against M. incognita.

Nitrogen fixing cereal: A rising hero towards meeting food security

Nitrogen serves as one of the primary components of major biomolecules and thus extends a significant contribution to crop growth and yield. But the inability of plants to utilize freely available atmospheric N₂ makes the whole agricultural system dependent on chemical fertilizers, which incur significant input cost to supplement required quantities of nitrogen to crops. Only bacteria and archaea have been gifted with the power of drawing free N₂ from air to convert them into NH₃, which is one of the two utilizable forms of nitrogen taken up by plants. Legumes, the only family of crops, can engage themselves in symbiotic nitrogen fixation where they establish a mutualistic relationship with nitrogen-fixing bacteria and in turn, can waive off the necessity of adding nitrogen fertilizers. Sincere effort, therefore, has been undertaken to incorporate this capability of nitrogen-fixation into non-legume crops, especially cereals which make up a vital portion in the food basket. Biotechnological interventions have also played important role in providing nitrogen fixing trait to non-legumes. This review takes up an effort to look into and accumulate all the important updates to date regarding nitrogen-fixing non-legumes with a special focus on cereals, which is one of the most important future goals in the field of science in the present era.

Fungal Community Analyses of Endophytic Fungi from Two Oak Species, Quercus mongolica and Quercus serrata, in Korea

Fungal endophytes have been recorded in various plant species with a richness of diversity, and their presence plays an essential role in host plant protection against biotic and abiotic stresses. This study applied the Illumina MiSeq sequencing platform based on the amplification of fungal ribosomal ITS2 region to analyze fungal endophytic communities of two oak species (Quercus mongolica and Q. serrata) with different oak wilt disease susceptibilities in Korea. The results showed a total of 230,768 sequencing reads were obtained and clustered at a 97% similarity threshold into 709 operational taxonomic units (OTUs). The OTUs of Q. serrata were higher than that of Q. mongolica with the number of 617 OTUs and 512 OTUs, respectively. Shannon index also showed that Q. serrata had a significantly higher level of fungal diversity than Q. mongolica. Total of OTUs were assigned into 5 fungal phyla, 17 classes, 60 orders, 133 families, 195 genera, and 280 species. Ascomycota was the dominant phylum with 75.11% relative abundance, followed by Basidiomycota with 5.28%. Leptosillia, Aureobasidium and Acanthostigma were the most abundant genera detected in Q. serrata with the average relative abundance of 2.85, 2.76, and 2.19%, respectively. On the other hand, Peltaster, Cladosporium and Monochaetia were the most common genera detected in Q. mongolica with the average relative abundance of 4.83, 3.03, and 2.87%, respectively. Our results indicated that fungal endophytic communities were significantly different between two oak species and these differences could influence responses of host trees to oak wilt disease caused by Raffaelea quercus-mongolicae.

The Tripartite Rhizobacteria-AM Fungal-Host Plant Relationship in Winter Wheat: Impact of Multi-Species Inoculation, Tillage Regime and Naturally Occurring Rhizobacteria Species

Soils and plant root rhizospheres have diverse microorganism profiles. Components of this naturally occurring microbiome, arbuscular mycorrhizal (AM) fungi and plant growth promoting rhizobacteria (PGPR), may be beneficial to plant growth. Supplementary application to host plants of AM fungi and PGPR either as single species or multiple species inoculants has the potential to enhance this symbiotic relationship further. Single species interactions have been described; the nature of multi-species tripartite relationships between AM fungi, PGPR and the host plant require further scrutiny. The impact of select Bacilli spp. rhizobacteria and the AM fungus Rhizophagus intraradices as both single and combined inoculations (PGPR[i] and AMF[i]) within field extracted arable soils of two tillage treatments, conventional soil inversion (CT) and zero tillage (ZT) at winter wheat growth stages GS30 and GS39 have been conducted. The naturally occurring soil borne species (PGPR[s] and AMF[s]) have been determined by qPCR analysis. Significant differences (p < 0.05) were evident between inocula treatments and the method of seedbed preparation. A positive impact on wheat plant growth was noted for B. amyloliquefaciens applied as both a single inoculant (PGPR[i]) and in combination with R. intraradices (PGPR[i] + AMF[i]); however, the two treatments did not differ significantly from each other. The findings are discussed in the context of the inocula applied and the naturally occurring soil borne PGPR[s] present in the field extracted soil under each method of tillage.

Evaluation of Pantoea eucalypti FBS135 for pine (Pinus massoniana) growth promotion and its genome analysis

AIMS

Pinus massoniana is one of the most widely distributed forest plants in China. In this study, we isolated a bacterial endophyte (designated FBS135) from apical buds and needles of P. massoniana. Investigations were performed to understand the effects of the strain on pine growth, its genomic features and the functions of the plasmids it carries.

METHODS AND RESULTS

Based on its morphological features and 16S rRNA sequence, strain FBS135 was primarily identified as Pantoea eucalypti. We found that FBS135 not only promoted the growth of P. massoniana seedlings, but also significantly increased the survival rate of pine seedlings. The whole genome of FBS135 was sequenced, which revealed that the bacterium carries one chromosome and four plasmids. Its chromosome is 4 023 751 bp in size and contains dozens of genes involved in plant symbiosis. Curing one of the four plasmids, pPant1, resulted in a decrease in the size of the FBS135 colonies and the loss of the ability to synthesize yellow pigment, indicating that this plasmid may be very important for FBS135.

CONCLUSIONS

Pantoea eucalypti FBS135 has a genomic basis to be implicated in plant-associated lifestyle and was established to have the capability to promote pine growth.

SIGNIFICANCE AND IMPACT OF THE STUDY

To the best of our knowledge, this is the first report that such a bacterial species, P. eucalypti, was isolated from pine trees and evidenced to have pine beneficial activities. Our results elucidate the ecological effects of endophytes on forest plants as well as endophyte-plant interaction mechanisms.

Core endophyte communities of different citrus varieties from citrus growing regions in China

The native microbiomes of citrus trees play important roles in plant health, with good communication between the native microbiome and the host plant. Here, we report on the native endophytes in 24 citrus varieties in nine citrus growing regions in China; some of the trees were healthy and others had asymptomatic or symptomatic huanglongbing, which is caused by the pathogen Candidatus Liberibacter asiaticus (CLas). We used culture-dependent analysis and characterized the isolates by partial 16S rRNA gene sequencing. The endophytes were compared between different citrus varieties, regions, and disease states (healthy, asymptomatic, and symptomatic). The total number of endophytes isolated from most of the citrus varieties was 104-106 CFU/g of leaves, but it differed significantly by disease state, with the highest numbers in the healthy leaves and the lowest in the symptomatic leaves (p < 0.05). Among the citrus varieties, the Valencia variety had the maximum number of endophyte species (22). The most dominant endophytes were Bacillus subtilis, B. velezensis, Curtobacterium luteum, and Microbacterium testaceum. The higher frequency of B. subtilis in the healthy/asymptomatic plants compared to the symptomatic plants suggests that it has a role in huanglongbing resistance. Native endophyte communities in various citrus varieties could be used to improve citrus growth and combat CLas.

Seed Biopriming with Microbial Inoculant Triggers Local and Systemic Defense Responses against Rhizoctonia solani Causing Banded Leaf and Sheath Blight in Maize (Zea mays L.)

Plant growth promoting rhizobacteria Pseudomonas aeruginosa strain MF-30 isolated from maize rhizosphere was characterized for several plant growth stimulating attributes. The strain MF-30 was also evaluated for antifungal properties against Rhizoctonia solani causing banded leaf and sheath blight in maize (Zea mays L.) under in vitro conditions and was found to have higher mycelial growth suppression in the culture suspension (67.41%) followed by volatile organic compounds (62.66%) and crude extract (51.20%) in a dual plate assay. The endophytic and epiphytic colonization ability was tested using Green Fluorescent Protein (GFP)-tagging. Visualization through confocal scanning laser microscope clearly indicated that strain MF-30 colonizes the root and foliar parts of the plants. Further, the effects of seed bio-priming with P. aeruginosa MF-30 was evaluated in the induction and bioaccumulation of defense-related biomolecules, enzymes, natural antioxidants, and other changes in maize under pot trial. This not only provided protection from R. solani but also ensured growth promotion under pathogenic stress conditions in maize. The maximum concentration of hydrogen peroxide (H2O2) was reported in the root and shoot of the plants treated with R. solani alone (8.47 and 17.50 mmol mg-1 protein, respectively) compared to bioagent, P. aeruginosa MF-30 bio-primed plants (3.49 and 7.50 mmol mg-1 protein, respectively). Effects on total soluble sugar content, total protein, and total proline were also found to enhanced significantly due to inoculation of P. aeruginosa MF-30. The activities of anti-oxidative defense enzymes phenylalanine ammonia lyase (PAL), ascorbate peroxidase, peroxidase, superoxide dismutase, and catalase increased significantly in the plants bio-primed with P. aeruginosa MF-30 and subsequent foliar spray of culture suspension of MF-30 compared to pathogen alone inoculated plants. qRT-PCR analysis revealed that seed bio-priming and foliar application of P. aeruginosa MF-30 significantly increased the expression of PR-1 and PR-10 genes with the simultaneous decrease in the disease severity and lesion length in the maize plants under pathogenic stress conditions. A significant enhancement of shoot and root biomass was recorded in MF-30 bio-primed plants as compared to untreated control (p < 0.05). Significant increase in plant growth and antioxidant content, as well as decreased disease severity in the P. aeruginosa MF-30 bio-primed plants, suggested the possibility of an eco-friendly and economical means of achieving antioxidants-rich, healthier maize plants.

Phytostabilization of Polluted Military Soil Supported by Bioaugmentation with PGP-Trace Element Tolerant Bacteria Isolated from Helianthus petiolaris

Lead (Pb) and cadmium (Cd) are major environmental pollutants, and the accumulation of these elements in soils and plants is of great concern in agricultural production due to their toxic effects on crop growth. Also, these elements can enter into the food chain and severely affect human and animal health. Bioaugmentation with plant growth-promoting bacteria (PGPB) can contribute to an environmentally friendly and effective remediation approach by improving plant survival and promoting element phytostabilization or extraction under such harsh conditions. We isolated and characterised Pb and Cd-tolerant root-associated bacteria from Helianthus petiolaris growing on a Pb/Cd polluted soil in order to compose inoculants that can promote plant growth and also ameliorate the phytostabilization or phytoextraction efficiency. One hundred and five trace element-tolerant rhizospheric and endophytic bacterial strains belonging to eight different genera were isolated from the aromatic plant species Helianthus petiolaris. Most of the strains showed multiple PGP-capabilities, ability to immobilise trace elements on their cell wall, and promotion of seed germination. Bacillus paramycoides ST9, Bacillus wiedmannii ST29, Bacillus proteolyticus ST89, Brevibacterium frigoritolerans ST30, Cellulosimicrobium cellulans ST54 and Methylobacterium sp. ST85 were selected to perform bioaugmentation assays in greenhouse microcosms. After 2 months, seedlings of sunflower (H. annuus) grown on polluted soil and inoculated with B. proteolyticus ST89 produced 40% more biomass compared to the non-inoculated control plants and accumulated 20 % less Pb and 40% less Cd in the aboveground plant parts. In contrast, B. paramycoides ST9 increased the bioaccumulation factor (BAF) of Pb three times and of Cd six times without inhibiting plant growth. Our results indicate that, depending on the strain, bioaugmentation with specific beneficial bacteria can improve plant growth and either reduce trace element mobility or enhance plant trace element uptake.

Antagonism and antibiotic resistance drive a species-specific plant microbiota differentiation in Echinacea spp

A key factor in the study of plant-microbes interactions is the composition of plant microbiota, but little is known about the factors determining its functional and taxonomic organization. Here we investigated the possible forces driving the assemblage of bacterial endophytic and rhizospheric communities, isolated from two congeneric medicinal plants, Echinacea purpurea (L.) Moench and Echinacea angustifolia (DC) Heller, grown in the same soil, by analysing bacterial strains (isolated from three different compartments, i.e. rhizospheric soil, roots and stem/leaves) for phenotypic features such as antibiotic resistance, extracellular enzymatic activity, siderophore and indole 3-acetic acid production, as well as cross-antagonistic activities. Data obtained highlighted that bacteria from different plant compartments were characterized by specific antibiotic resistance phenotypes and antibiotic production, suggesting that the bacterial communities themselves could be responsible for structuring their own communities by the production of antimicrobial molecules selecting bacterial-adaptive phenotypes for plant tissue colonization.

Utilization of Grape Seed Flour for Antimicrobial Lipopeptide Production by Bacillus amyloliquefaciens C5 Strain

An endophytic Bacillus amyloliquefaciens strain called C5, able to produce biosurfactant lipopeptides with a broad antibacterial activity spectrum, has been isolated from the roots of olive tree. Optimization of antibacterial activity was undertaken using grape seed flour (GSF) substrate at 0.02, 0.2, and 2% (w/v) in M9 medium. Strain C5 exhibited optimal growth and antimicrobial activity (MIC value of 60 μg/ml) when incubated in the presence of 0.2% GSF while lipopeptide production culminated at 2% GSF. Thin layer chromatography analysis of lipopeptide extract revealed the presence of at least three active spots at Rf 0.35, 0.59, and 0.72 at 0.2% GSF. Data were similar to those obtained in LB-rich medium. MALDI-TOF/MS analysis of lipopeptide extract obtained from 0.2% GSF substrate revealed the presence of surfactin and bacillomycin D. These results show that GSF could be used as a low-cost culture medium supplement for optimizing the production of biosurfactants by strain C5.

Growth stage and tissue specific colonization of endophytic bacteria having plant growth promoting traits in hybrid and composite maize (Zea mays L.)

Maize, a crop cultivated worldwide, was investigated for plant tissue and crop stage specific colonization of endophytic bacteria. Such bacterial interactions have high potential to enhance maize grain yield by means of biological nitrogen fixation and/or plant growth promoting activities. In this study endophytic bacteria were isolated from a hybrid PEEHM-5 and composite PC-4 maize varieties using root, stem and leaf tissues of plants at vegetative, flowering and maturity stages of growth. PEEHM-5 harbored higher endophytic bacterial population than PC-4 at all growth stages, with highest in roots and at flowering stage. Morphologically 188 different endophytic isolates (82 from PEEHM-5, 106 from PC-4) were screened for plant growth promoting attributes viz. P, K, Zn solubilization, production of hormones, siderophore, ACC deaminase, HCN, biological nitrogen fixation and biocontrol of two maize fungal pathogens. Thirty one potential PGP isolates on RFLP analysis of their amplified 16S rRNA gene, were clustered in 13 phylogenetic groups. On sequencing and blasting of amplified 16S rRNA gene of representative isolates from each group identified PC-4 endophytic bacterial isolates as Bacillus aryabhattai, Pantoea cypripedii, Bacillus licheniformis, Klebsiella sp., Pantoea dispersa, Klebsiella variicola, Pantoea sp., Agrobacterium larrymoorei and PEEHM-5 endophytic bacterial isolates as Bacillus sp., Bacillus amyloliquefaciens, Lactococcus lactis, Bacillus cereus and Staphylococcus hominis. In planta evaluation of potential isolates at variable chemical fertilizer input indicated their potential in compensating nearly 25% of the fertilizer input as observed on their improvement of shoot and root parameters. Lactococcus lactis inoculation influenced maximum followed by Pantoea and Klebsiella isolates.

Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria

One of the most exciting scientific advances in recent decades has been the realization that the diverse and immensely active microbial communities are not only 'passengers' with plants, but instead play an important role in plant growth, development and resistance to biotic and abiotic stresses. A picture is emerging where plant roots act as 'gatekeepers' to screen soil bacteria from the rhizosphere and rhizoplane. This typically results in root endophytic microbiome dominated by Proteobacteria, Actinobacteria and to a lesser extent Bacteroidetes and Firmicutes, but Acidobacteria and Gemmatimonadetes being almost depleted. A synthesis of available data suggest that motility, plant cell-wall degradation ability and reactive oxygen species scavenging seem to be crucial traits for successful endophytic colonization and establishment of bacteria. Recent studies provide solid evidence that these bacteria serve host functions such as improving of plant nutrients through acquisition of nutrients from soil and nitrogen fixation in leaves. Additionally, some endophytes can engage 'priming' plants which elicit a faster and stronger plant defense once pathogens attack. Due to these plant growth-promoting effects, endophytic bacteria are being widely explored for their use in the improvement of crop performance. Updating the insights into the mechanism of endophytic bacterial colonization and interactions with plants is an important step in potentially manipulating endophytic bacteria/microbiome for viable strategies to improve agricultural production.

Bacterial Endophyte Colonization and Distribution within Plants

The plant endosphere contains a diverse group of microbial communities. There is general consensus that these microbial communities make significant contributions to plant health. Both recently adopted genomic approaches and classical microbiology techniques continue to develop the science of plant-microbe interactions. Endophytes are microbial symbionts residing within the plant for the majority of their life cycle without any detrimental impact to the host plant. The use of these natural symbionts offers an opportunity to maximize crop productivity while reducing the environmental impacts of agriculture. Endophytes promote plant growth through nitrogen fixation, phytohormone production, nutrient acquisition, and by conferring tolerance to abiotic and biotic stresses. Colonization by endophytes is crucial for providing these benefits to the host plant. Endophytic colonization refers to the entry, growth and multiplication of endophyte populations within the host plant. Lately, plant microbiome research has gained considerable attention but the mechanism allowing plants to recruit endophytes is largely unknown. This review summarizes currently available knowledge about endophytic colonization by bacteria in various plant species, and specifically discusses the colonization of maize plants by Populus endophytes.

Previous crop and rotation history effects on maize seedling health and associated rhizosphere microbiome

To evaluate crop rotation effects on maize seedling performance and its associated microbiome, maize plants were grown in the greenhouse in soils preceded by either maize, pea, soybean or sunflower. Soils originated from a replicated field experiment evaluating different four-year rotation combinations. In the greenhouse, a stressor was introduced by soil infestation with western corn rootworm (WCR) or Fusarium graminearum. Under non-infested conditions, maize seedlings grown in soils preceded by sunflower or pea had greater vigor. Stress with WCR or F. graminearum resulted in significant root damage. WCR root damage was equivalent for seedlings regardless of soil provenance; whereas F. graminearum root damage was significantly lower in maize grown in soils preceded by sunflower. Infestation with WCR affected specific microbial taxa (Acinetobacter, Smaragdicoccus, Aeromicrobium, Actinomucor). Similarly, F. graminearum affected fungal endophytes including Trichoderma and Endogone. In contrast to the biological stressors, rotation sequence had a greater effect on rhizosphere microbiome composition, with larger effects observed for fungi compared to bacteria. In particular, relative abundance of Glomeromycota was significantly higher in soils preceded by sunflower or maize. Defining the microbial players involved in crop rotational effects in maize will promote selection and adoption of favorable crop rotation sequences.

The Endophytic Symbiont-Pseudomonas aeruginosa Stimulates the Antioxidant Activity and Growth of Achyranthes aspera L

A plant growth promoting bacterial endophyte designated as AL2-14B isolated from the leaves of Achyranthes aspera L. was identified as Pseudomonas aeruginosa based on its phenotypic and physiological features, and 16S rRNA gene sequence analysis. AL2-14B had plant growth stimulating attributes including siderophore and indole acetic acid release, inorganic phosphate solubilization, along with nitrogenase, ammonification, and protease activities. It also exhibited antifungal property against Rhizoctonia solani. The plantlets grown in germ-free condition were inoculated with AL2-14B and studied for the colonization of endophyte. Significant increase in population of AL2-14B between 3rd and 5th days after inoculation was recorded. The treatment of plants with endophytic P. aeruginosa AL2-14B increased nitrogen, phosphorus, potassium (NPK) contents in plant by 3.8, 12.59, and 19.15%, respectively. Significant enhancement of shoot and root length, dry leaf, dry shoot and dry root weight, and leaf surface area as compared to control (P < 0.05) was recorded in AL2-14B inoculated plants. The antioxidant activities increased in plants grown in germ-free conditions and inoculated with AL2-14B. The present study emphasizes on the role of diazotrophic endophyte P. aeruginosa AL2-14B in stimulating growth of A. aspera L. and improvement of its medicinal properties. Significant increase in growth and antioxidant content of P. aeruginosa AL2-14B treated plants suggests the possibility of an economical and eco-friendly mean of achieving antioxidants rich, healthier A. aspera plants.

Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria

One of the most exciting scientific advances in recent decades has been the realization that the diverse and immensely active microbial communities are not only 'passengers' with plants, but instead play an important role in plant growth, development and resistance to biotic and abiotic stresses. A picture is emerging where plant roots act as 'gatekeepers' to screen soil bacteria from the rhizosphere and rhizoplane. This typically results in root endophytic microbiome dominated by Proteobacteria, Actinobacteria and to a lesser extent Bacteroidetes and Firmicutes, but Acidobacteria and Gemmatimonadetes being almost depleted. A synthesis of available data suggest that motility, plant cell-wall degradation ability and reactive oxygen species scavenging seem to be crucial traits for successful endophytic colonization and establishment of bacteria. Recent studies provide solid evidence that these bacteria serve host functions such as improving of plant nutrients through acquisition of nutrients from soil and nitrogen fixation in leaves. Additionally, some endophytes can engage 'priming' plants which elicit a faster and stronger plant defense once pathogens attack. Due to these plant growth-promoting effects, endophytic bacteria are being widely explored for their use in the improvement of crop performance. Updating the insights into the mechanism of endophytic bacterial colonization and interactions with plants is an important step in potentially manipulating endophytic bacteria/microbiome for viable strategies to improve agricultural production.

Characterization of bacterial communities associated with Brassica napus L. growing on a Zn-contaminated soil and their effects on root growth

The interaction between plant growth-promoting bacteria (PGPB) and plants can enhance biomass production and metal tolerance of the host plants. This work aimed at isolating and characterizing the cultivable bacterial community associated with Brassica napus growing on a Zn-contaminated site, for selecting cultivable PGPB that might enhance biomass production and metal tolerance of energy crops. The effects of some of these bacterial strains on root growth of B. napus exposed to increasing Zn and Cd concentrations were assessed. A total of 426 morphologically different bacterial strains were isolated from the soil, the rhizosphere, and the roots and stems of B. napus. The diversity of the isolated bacterial populations was similar in rhizosphere and roots, but lower in soil and stem compartments. Burkoholderia, Alcaligenes, Agrococcus, Polaromonas, Stenotrophomonas, Serratia, Microbacterium, and Caulobacter were found as root endophytes exclusively. The inoculation of seeds with Pseudomonas sp. strains 228 and 256, and Serratia sp. strain 246 facilitated the root development of B. napus at 1,000 µM Zn. Arthrobacter sp. strain 222, Serratia sp. strain 246, and Pseudomonas sp. 228 and 262 increased the root length at 300 µM Cd.

Endophytic fungi from selected varieties of soybean (Glycine max L. Merr.) and corn (Zea mays L.) grown in an agricultural area of Argentina

Endophytic fungi are ubiquitous and live within host plants without causing any noticeable symptoms of disease. Little is known about the diversity and function of fungal endophytes in plants, particularly in economically important species. The aim of this study was to determine the identity and diversity of endophytic fungi in leaves, stems and roots of soybean and corn plants and to determine their infection frequencies. Plants were collected in six areas of the provinces of Buenos Aires and Entre Ríos (Argentina) two areas were selected for sampling corn and four for soybean. Leaf, stem and root samples were surface-sterilized, cut into 1cm(2) pieces using a sterile scalpel and aseptically transferred to plates containing potato dextrose agar plus antibiotics. The species were identified using both morphological and molecular data. Fungal endophyte colonization in soybean plants was influenced by tissue type and varieties whereas in corn plants only by tissue type. A greater number of endophytes were isolated from stem tissues than from leaves and root tissues in both species of plants. The most frequently isolated species in all soybean cultivars was Fusarium graminearum and the least isolated one was Scopulariopsis brevicaulis. Furthermore, the most frequently isolated species in corn plants was Aspergillus terreus whereas the least isolated one was Aspergillus flavus. These results could be relevant in the search for endophytic fungi isolates that could be of interest in the control of agricultural pests.

Soil Influences Colonization of Root-Associated Fungal Endophyte Communities of Maize, Wheat, and Their Progenitors

Root-associated fungal endophytes are vital component of root microbiome as some mitigate their host’s abiotic and biotic stress. We characterized root-associated fungal endophytes in cereal grains and their progenitors grown on two different soil-types. We aimed at determining how clay and desert soil affects the colonization of root fungal community. Both culture-dependent and culture-independent methods were employed to identify endophytes that successfully colonized greenhouse-grown host plants. The Internal Transcriber Spacer region of fungal ribosomal DNA was utilized for identification purposes. This study revealed soil as a prominent factor influencing the composition of microfungal communities inhabiting the roots of maize (Zea mays subsp. mays) and its conspecific progenitor, teosinte (Zea mays subsp. parviglumis). Similar results were found in wheat (Triticum aestivum subsp. aestivum) and its progenitor (Triticum monococcum subsp. monococcum). The multidimensional comparisons of Morisita-Horn similarity values of fungal colonists of various host plant taxa indicated that soil plays a primary role in shaping the root fungal community; a secondary effect was plant host identity, even when the plant host is a conspecific. Future studies focused on characterizing root endophytes in other cereal grains, and studying the effect of edaphic factors on fungal colonization, can ultimately contribute to crop productivity.

Characterization of the cultivable bacterial populations associated with field grown Brassica napus L.: an evaluation of sampling and isolation protocols

Plant-associated bacteria are intensively investigated concerning their characteristics for plant growth promotion, biocontrol mechanisms and enhanced phytoremediation efficiency. To obtain endophytes, different sampling and isolation protocols are used although their representativeness is not always clearly demonstrated. The objective of this study was to acquire representative pictures of the cultivable bacterial root, stem and leaf communities for all Brassica napus L. individuals growing on the same field. For each plant organ, genotypic identifications of the endophytic communities were performed using three replicates. Root replicates were composed of three total root systems, whereas stem and leaf replicates needed to consist of six independent plant parts in order to be representative. Greater variations between replicates were found when considering phenotypic characteristics. Correspondence analysis revealed reliable phenotypic results for roots and even shoots, but less reliable ones for leaves. Additionally, realistic Shannon-Wiener biodiversity indices were calculated for all three organs and showed similar Evenness factors. Furthermore, it was striking that all replicates and thus the whole plant contained Pseudomonas and Bacillus strains although aboveground and belowground plant tissues differed in most dominant bacterial genera and characteristics.

Insecticide-degrading Burkholderia symbionts of the stinkbug naturally occupy various environments of sugarcane fields in a Southeast island of Japan

The stinkbug Cavelerius saccharivorus, which harbors Burkholderia species capable of degrading the organophosphorus insecticide, fenitrothion, has been identified on a Japanese island in farmers' sugarcane fields that have been exposed to fenitrothion. A clearer understanding of the ecology of the symbiotic fenitrothion degraders of Burkholderia species in a free-living environment is vital for advancing our knowledge on the establishment of degrader-stinkbug symbiosis. In the present study, we analyzed the composition and abundance of degraders in sugarcane fields on the island. Degraders were recovered from field samples without an enrichment culture procedure. Degrader densities in the furrow soil in fields varied due to differences in insecticide treatment histories. Over 99% of the 659 isolated degraders belonged to the genus Burkholderia. The strains related to the stinkbug symbiotic group predominated among the degraders, indicating a selection for this group in response to fenitrothion. Degraders were also isolated from sugarcane stems, leaves, and rhizosphere in fields that were continuously exposed to fenitrothion. Their density was lower in the plant sections than in the rhizosphere. A phylogenetic analysis of 16S rRNA gene sequences demonstrated that most of the degraders from the plants and rhizosphere clustered with the stinkbug symbiotic group, and some were identical to the midgut symbionts of C. saccharivorus collected from the same field. Our results confirmed that plants and the rhizosphere constituted environmental reservoirs for stinkbug symbiotic degraders. To the best of our knowledge, this is the first study to investigate the composition and abundance of the symbiotic fenitrothion degraders of Burkholderia species in farmers' fields.

Endophytic fungi from Lycium chinense Mill and characterization of two new Korean records of Colletotrichum

Chinese boxthorn or matrimony vine (Lycium chinense Mill) is found primarily in southeastern Europe and Asia, including Korea. The dried ripe fruits are commonly used as oriental medicinal purposes. Endophytic fungi were isolated from surface sterilized tissues and fruits of the medicinal plant in 2013 to identify the new or unreported species in Korea. Among 14 isolates, 10 morphospecies were selected for molecular identification with the internal transcribed spacer (ITS) gene. Phylogenetic analysis revealed that all isolates belonged to Ascomycota including the genera Acremonium, Colletotrichum, Cochliobolus, Fusarium, Hypocrea and Nemania. Two Colletotrichum species were identified at the species level, using three genes including internal transcribed spacer (ITS), glycerol-3-phosphate dehydrogenase (GAPDH) and Actin (ACT) for PCR and molecular data analysis along with morphological observations. The fungal isolates, CNU122031 and CNU122032 were identified as Colletotrichum fructicola and C. brevisporum, respectively. Morphological observations also well supported the molecular identification. C. brevisporum is represented unrecorded species in Korea and C. fructicola is the first record from the host plant.

Streptomycete endophytes from anti-diabetic medicinal plants of the Western Ghats inhibit alpha-amylase and promote glucose uptake

α-amylase inhibitor retards the liberation of glucose from dietary complex carbohydrates and delays the absorption of glucose. The purpose of the study was to isolate and select α-amylase inhibitor-producing endophytic actinomycetes from the leaves and stems of Leucas ciliata and Rauwolfia densiflora, two of the well-known medicinal plants used in the treatment for diabetes. Sterilized plant samples were inoculated on the actinomycete isolation agar medium containing 50 ppm cycloheximide and incubated for 4-8 weeks at room temperature. The actinomycetes were isolated on agar medium and identified on the basis of 16S rRNA sequences, the isolates exhibiting >99% similarities were submitted to NCBI, and gene accession numbers were obtained. They were inoculated to International Streptomyces Project 1 medium (ISP 1) for fermentation. The extracts obtained were tested for the anti-diabetic potential by the inhibition of alpha-amylase by colorimetric assay and glucose uptake in the porcine hemidiaphragm. Streptomyces longisporoflavus (JX965948) isolated from the stem fragments of L. ciliata exhibited alpha-amylase inhibitory activity (IC50 values = 162.3 ± 1.05 μg ml⁻¹) in comparison with the standard Acarbose™ (IC50 value = 73.1 ± 1.12 μg ml⁻¹). Extract of Streptomyces sp. (JQ926174) from R. densiflora indicated glucose uptake in the porcine hemidiaphragm. Results indicate for the first time the potential of endophytic streptomycete extracts with anti-diabetic activity.

SIGNIFICANCE AND IMPACT OF THE STUDY

Endophytic actinomycetes were isolated from two medicinal species of the Western Ghats, a biodiversity 'hotspot' in southern India and screened for the anti-diabetic potential for inhibition of α-amylase and improved glucose uptake in the porcine hemidiaphragm. Results indicate the inhibition of α-amylase by Streptomyces longisporoflavus extract with IC50 values of 162.3 ± 1.05 μg ml⁻¹ in comparison with the standard inhibitor Acarbose™ with IC50 value 73.1 ± 1.12 μg ml⁻¹. Further, extract from Streptomyces sp. showed increased glucose uptake by hemidiaphragm. The present investigation implicates the potential of endophytic actinomycetes as sources of anti-diabetic agents.

Diversity of endophytic bacteria in Malaysian plants as revealed by 16S rRNA encoding gene sequence based method of bacterial identification

Bacterial endophytes do have several potential applications in pharmacy, medicine and agricultural biotech industry. The main objective of this study was to understand types of bacterial endophytes associated with dicotyledonous (dicot) and monocotyledonous (monocot) plant species. Isolation of the endophytic bacteria was performed using surface-sterilized various tissue samples, and identification of the endophytic bacterial isolates (EBIs) was completed using 16S rRNA encoding gene sequence similarity based method. In total, 996 EBIs were isolated and identified from 1055 samples of 31 monocot and 65 dicot plant species from Peninsular Malaysia. The 996 EBIs represented 71 different types of bacterial species. Twelve (12) out of 71 species are reported as endophytes for the first time. We conclude that diverse types of bacterial endophytes are associated with dicot and monocot plants, and could be useful in pharmacy, medicine and agricultural biotechnology for various potential applications.

Bacterial communities associated with Brassica napus L. grown on trace element-contaminated and non-contaminated fields: a genotypic and phenotypic comparison

Cultivable bacterial strains associated with field-grown Brassica napus L. (soil, rhizosphere and roots) from a trace elements (Cd, Zn and Pb) contaminated field and a non-contaminated control field were characterized genotypically and phenotypically. Correspondence analysis of the genotypic data revealed a correlation between soil and rhizosphere communities isolated from the same field, indicating that local conditions play a more important role in influencing the composition of (rhizosphere) soil bacterial communities than root exudates. In contrast, endophytic communities of roots showed a correlation between fields, suggesting that plants on the two fields contain similar obligate endophytes derived from a common seed endophytic community and/or can select bacteria from the rhizosphere. The latter seemed not very likely since, despite the presence of several potential endophytic taxa in the rhizosphere, no significant correlation was found between root and rhizosphere communities. The majority of Cd/Zn tolerant strains capable of phosphorus solubilization, nitrogen fixation, indole-3-acetic acid production and showing 1-aminocyclopropane-1-carboxylate deaminase capacity were found in the rhizosphere and roots of plants growing on the contaminated field.

Fungal endophyte diversity in soybean

AIM

To determine the identity and diversity of endophytes in soybean plants using culture-dependent (CD) and culture-independent (CI) methods.

METHODS AND RESULTS

Stem samples were collected from three field-grown soybean cultivars grown to a reproductive stage in Minnesota, USA. Samples were surface disinfested, and CD and CI methods were used to assess the endophytes. For the CD method, fungi were isolated and grouped based on colony morphology, and the rDNA ITS region was sequenced to identify the cultures. The most frequently isolated genera were Cladosporium (36%), Alternaria (13%), Diaporthe (9%) and Epicoccum (9%). For the CI method, DNA was extracted from the stems, and the ITS region was amplified, cloned and sequenced for identification. The most prevalent genus detected using CI method was Cladosporium (85%).

CONCLUSIONS

Soybean contains a diverse array of endophytic fungi that were identified in this study. The CD method detected greater endophyte diversity (H' = 2·12) than the CI method (H' = 0·66).

SIGNIFICANCE AND IMPACT OF THE STUDY

The results improve our understanding of the identity and diversity of endophytic fungi that likely have different kinds of interactions with soybean plants. The results suggest that CD and CI methods should be used to study endophytes in soybean and perhaps other annual crop plants.

The endophytic lifestyle of Escherichia coli O157:H7: quantification and internal localization in roots

The foodborne pathogen Escherichia coli O157:H7 is increasingly associated with fresh produce (fruit and vegetables). Bacterial colonization of fresh produce plants can occur to high levels on the external tissue but bacteria have also been detected within plant tissue. However, questions remain about the extent of internalization, its molecular basis, and internal location of the bacteria. We have determined the extent of internalization of E. coli O157:H7 in live spinach and lettuce plants and used high-resolution microscopy to examine colony formation in roots and pathways to internalization. E. coli O157:H7 was found within internal tissue of both produce species. Colonization occurred within the apoplast between plant cells. Furthermore, colonies were detected inside the cell wall of epidermal and cortical cells of spinach and Nicotiana benthamiana roots. Internal colonization of epidermal cells resembled that of the phytopathogen Pectobacterium atrosepticum on potato. In contrast, only sporadic cells of the laboratory strain of E. coli K-12 were found on spinach, with no internal bacteria evident. The data extend previous findings that internal colonization of plants appears to be limited to a specific group of plant-interacting bacteria, including E. coli O157:H7, and demonstrates its ability to invade the cells of living plants.

Novel and highly diverse fungal endophytes in soybean revealed by the consortium of two different techniques

Fungal endophytes were isolated from the leaves of soybean cultivars in Brazil using two different isolation techniques - fragment plating and the innovative dilution-to-extinction culturing - to increase the species richness, frequency of isolates and diversity. A total of 241 morphospecies were obtained corresponding to 62 taxa that were identified by analysis of the internal transcribed spacer (ITS) of the ribosomal DNA (rDNA). The Phylum Ascomycota predominated, representing 99% and 95.2% of isolates in the Monsoy and Conquista cultivars, respectively, whereas the Phylum Basidiomycota represented 1% and 4.8% of isolates, respectively. The genera Ampelomyces, Annulohypoxylon, Guignardia, Leptospora, Magnaporthe, Ophiognomonia, Paraconiothyrium, Phaeosphaeriopsis, Rhodotorula, Sporobolomyces, and Xylaria for the first time were isolated from soybean; this suggests that soybean harbours novel and highly diverse fungi. The yeasts genera Rhodotorula and Sporobolomyces (subphylum Pucciniomycotina) represent the Phylum Basidiomycota. The species richness was greater when both isolation techniques were used. The diversity of fungal endophytes was similar in both cultivars when the same isolation technique was used except for Hill's index, N1. The use of ITS region sequences allowed the isolates to be grouped according to Order, Class and Phylum. Ampelomyces, Chaetomium, and Phoma glomerata are endophytic species that may play potential roles in the biological control of soybean pathogens. This study is one of the first to apply extinction-culturing to isolate fungal endophytes in plant leaves, thus contributing to the development and improvement of this technique for future studies.

Endophytic bacteria in the rice plant

Endophytic bacteria are defined as bacteria detected inside surface-sterilized plants or extracted from inside plants and having no visibly harmful effects on the plants. Various kinds of endophytic bacteria, such as Pantoea, Methylobacterium, Azospirillum, Herbaspirillum, Burkholderia and Rhizobium etc., have been found inside rice plants. This minireview summarizes and discusses recent studies of endophytic bacteria residing in rice plants, focusing on flora, origin, movement, and interaction with plants/other microbes and referring to endophytes in other plants. The findings concerning bacterial flora obtained by cultural and non-cultural methods are also compared and discussed. Some attempts to apply endophytes to the rice plant and the resultant effects are introduced. The future perspective to deepen the study of endophytes in terms of both application and basic science is considered.