Rice bacterial endophytes: isolation of a collection, identification of beneficial strains and microbiome analysis

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.

Changes in Endophyte Communities across the Different Plant Compartments in Response to the Rice Blast Infection

The rice blast disease, caused by the fungal pathogen, Magnaporthe oryzae (syn. Pyricularia oryzae), poses a significant threat to the global rice production. Understanding how this disease impacts the plant's microbial communities is crucial for gaining insights into hostpathogen interactions. In this study, we investigated the changes in communities of bacterial and fungal endophytes inhabiting different compartments in healthy and diseased plants. We found that both alpha and beta diversities of endophytic communities do not change significantly by the pathogen infection. Rather, the type of plant compartment appeared to be the main driver of endophytic community structures. Although the overall structure seemed to be consistent between healthy and diseased plants, our analysis of differentially abundant taxa revealed the specific bacterial and fungal operational taxonomic units that exhibited enrichment in the root and leaf compartments of infected plants. These findings suggest that endophyte communities are robust to the changes at the early stage of pathogen infection, and that some of endophytes enriched in infected plants might have roles in the defense against the pathogen.

Identification of synthetic consortia from a set of plant-beneficial bacteria

The use of microbial inoculants in agriculture as biofertilisers and/or biopesticides is an appealing alternative to replace or reduce the practice of agrochemicals. Plant microbiota studies are revealing the different bacterial groups which are populating plant microbiomes re-energising the plant probiotic bacteria (PPB) translational research sector. Some single-microbial strain bioinoculants have proven valid in agriculture (e.g., based on Trichoderma, mycorrhiza or rhizobia); however, it is now recommended to consider multistrain consortia since plant-beneficial effects are often a result of community-level interactions in plant microbiomes. A limiting step is the selection of a fitting combination of microbial strains in order to accomplish the best beneficial effect upon plant inoculation. In this study, we have used a subset of 23 previously identified and characterised rice-beneficial bacterial colonisers to design and test a series of associated experiments aimed to identify potential PPB consortia which are able to co-colonise and induce plant growth promotion. Bacterial strains were co-inoculated in vitro and in planta using several different methods and their co-colonisation and co-persistence monitored. Results include the identification of two 5-strain and one 2-strain consortia which displayed plant growth-promoting features. Future practical applications of microbiome research must include experiments aimed at identifying consortia of bacteria which can be most effective as crop amendments.

Seed bacterial microbiota in post-submergence tolerant and sensitive barley genotypes

Flooding is a predominant abiotic stress for cultivated plants, including barley. This cereal crop shows a large adaptability to different environmental conditions, suggesting the presence of key traits to tolerate adverse conditions. During germination, genetic variations account for dissimilarities in flooding tolerance. However, differences in the seed microbiota may also contribute to tolerance/sensitivity during seedling establishment. This work investigated differences in microbiome among the grains of barley accessions. Two barley phenotypes were compared, each either tolerant or sensitive to a short submergence period followed by a recovery. The study used a metataxonomic analysis based on 16S ribosomal RNA gene sequencing and subsequent functional prediction. Our results support the hypothesis that bacterial microbiota inhabiting the barley seeds are different between sensitive and tolerant barley accessions, which harbour specific bacterial phyla and families. Finally, bacteria detected in tolerant barley accessions show a peculiar functional enrichment that suggests a possible connection with successful germination and seedling establishment.

Diversity and plant growth promoting ability of rice root-associated bacteria in Burkina-Faso and cross-comparison with metabarcoding data

Plant-associated bacteria are essential partners in plant health and development. In addition to taking advantage of the rapid advances recently achieved in high-throughput sequencing approaches, studies on plant-microbiome interactions require experiments with culturable bacteria. A study on the rice root microbiome was recently initiated in Burkina Faso. As a follow up, the aim of the present study was to develop a collection of corresponding rice root-associated bacteria covering maximum diversity, to assess the diversity of the obtained isolates based on the culture medium used, and to describe the taxonomy, phenotype and abundance of selected isolates in the rice microbiome. More than 3,000 isolates were obtained using five culture media (TSA, NGN, NFb, PCAT, Baz). The 16S rRNA fragment sequencing of 1,013 selected isolates showed that our working collection covered four bacterial phyla (Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes) and represented 33% of the previously described diversity of the rice root microbiome at the order level. Phenotypic in vitro analysis of the plant growth promoting capacity of the isolates revealed an overall ammonium production and auxin biosynthesis capacity, while siderophore production and phosphate solubilisation were enriched in Burkholderia, Ralstonia, Acinetobacter and Pseudomonas species. Of 45 representative isolates screened for growth promotion on seedlings of two rice cultivars, five showed an ability to improve the growth of both cultivars, while five others were effective on only one cultivar. The best results were obtained with Pseudomonas taiwanensis ABIP 2315 and Azorhizobium caulinodans ABIP 1219, which increased seedling growth by 158% and 47%, respectively. Among the 14 best performing isolates, eight appeared to be abundant in the rice root microbiome dataset from previous study. The findings of this research contribute to the in vitro and in planta PGP capacities description of rice root-associated bacteria and their potential importance for plants by providing, for the first time, insight into their prevalence in the rice root microbiome.

Screening, Identification, and Growth Promotion of Antagonistic Endophytes Associated with Chenopodium quinoa Against Quinoa Pathogens

Fungal disease is one of the important reasons for crop yield reduction. Isolation of important endophytes with biocontrol and growth-promoting effects is of great significance for the exploitation of beneficial microbial resources and the biological control of crop fungal diseases. In this study, endophytes from roots, stems, and leaves of quinoa at different growth and development stages were isolated and purified; then the antagonistic activity and growth-promoting characteristics of antagonistic endophytes were determined. Finally, the antagonistic endophytes were identified by morphological characteristics and ITS/16S rRNA sequence analysis. Our results showed that 122 endophytic fungi and 371 endophytic bacteria were isolated from quinoa, of which three endophytic fungi and seven endophytic bacteria were screened that had inhibitory activity against quinoa pathogenic fungi. Most of the antagonistic strains could produce indole-3 acetic acid and had the ability to dissolve organic phosphorus. In addition, the bacterial suspension of endophytic bacteria had the ability to promote the seed germination and plant growth of quinoa. The endophytic fungi with antagonistic activity were identified as Penicillium raperi and P. pulvillorum; the endophytic bacteria were identified as Bacillus paralicheniformis, B. tequilensis, and B. velezensis, respectively. The strains of quinoa endophytes in this study can provide rich microbial resources and a theoretical basis for biological control of plant fungal diseases and agricultural production.

A Nucleolar Protein, MoRRP8 Is Required for Development and Pathogenicity in the Rice Blast Fungus

The nucleolus is the largest, membrane-less organelle within the nucleus of eukaryotic cell that plays a critical role in rRNA transcription and assembly of ribosomes. Recently, the nucleolus has been shown to be implicated in an array of processes including the formation of signal recognition particles and response to cellular stress. Such diverse functions of nucleolus are mediated by nucleolar proteins. In this study, we characterized a gene coding a putative protein containing a nucleolar localization sequence (NoLS) in the rice blast fungus, Magnaporthe oryzae. Phylogenetic and domain analysis suggested that the protein is orthologous to Rrp8 in Saccharomyces cerevisiae. MoRRP8-GFP (translational fusion of MoRRP8 with green fluorescence protein) co-localizes with a nucleolar marker protein, MoNOP1 fused to red fluorescence protein (RFP), indicating that MoRRP8 is a nucleolar protein. Deletion of the MoRRP8 gene caused a reduction in vegetative growth and impinged largely on asexual sporulation. Although the asexual spores of ΔMorrp8 were morphologically indistinguishable from those of wild-type, they showed delay in germination and reduction in appressorium formation. Our pathogenicity assay revealed that the MoRRP8 is required for full virulence and growth within host plants. Taken together, these results suggest that nucleolar processes mediated by MoRRP8 is pivotal for fungal development and pathogenesis.

Core Microbiome and Microbial Community Structure in Coralloid Roots of Cycas in Ex Situ Collection of Kunming Botanical Garden in China

Endophytes are essential in plant succession and evolution, and essential for stress resistance. Coralloid root is a unique root structure found in cycads that has played a role in resisting adverse environments, yet the core taxa and microbial community of different Cycas species have not been thoroughly investigated. Using amplicon sequencing, we successfully elucidated the microbiomes present in coralloid roots of 10 Cycas species, representing all four sections of Cycas in China. We found that the endophytic bacteria in coralloid roots, i.e., Cyanobacteria, were mainly composed of Desmonostoc_PCC-7422, Nostoc_PCC-73102 and unclassified_f__Nostocaceae. Additionally, the Ascomycota fungi of Exophiala, Paraboeremia, Leptobacillium, Fusarium, Alternaria, and Diaporthe were identified as the core fungi taxa. The Ascomycota fungi of Nectriaceae, Herpotrichiellaceae, Cordycipitaceae, Helotiaceae, Diaporthaceae, Didymellaceae, Clavicipitaceae and Pleosporaceae were identified as the core family taxa in coralloid roots of four sections. High abundance but low diversity of bacterial community was detected in the coralloid roots, but no significant difference among species. The fungal community exhibited much higher complexity compared to bacteria, and diversity was noted among different species or sections. These core taxa, which were a subset of the microbiome that frequently occurred in all, or most, individuals of Cycas species, represent targets for the development of Cycas conservation.

Rhizosphere microbiomes of resurrection plants Ramonda serbica and R. nathaliae: comparative analysis and search for bacteria mitigating drought stress in wheat (Triticum aestivum L.)

Rhizosphere microbial communities play an important role in maintaining the health and productivity of the plant host. The rhizobacteria Pseudomonas putida P2 of Ramonda serbica and Bacillus cereus P5 of R. nathaliae were selected for treatment of the Belija wheat cultivar because of their plant growth-promoting (PGP) properties. Compared to the non-treated drought-stressed plants, the plants treated with rhizobacteria showed increased activity of the two major antioxidant enzymes, superoxide dismutase, and ascorbate peroxidase. Plants treated with the B. cereus P5 strain exhibited higher proline content under drought stress, suggesting that proline accumulation depends on the relative water content (RWC) status of the plants studied. Inoculation of wheat seeds with the P. putida P2 strain improved water status by increasing RWC and alleviating oxidative stress by reducing H2O2 and malondialdehyde concentrations in plants exposed to severe drought, possibly also helping plants to overcome drought through its 1-aminocyclopropane-1-carboxylic acid deaminase activity. Analysis of data from Next Generation sequencing (NGS) revealed that the dominant bacterial taxa in the rhizosphere of resurrection plants R. serbica and R. nathaliae were extremophilic, thermotolerant, Vicinamibacter silvestris, Chthoniobacter flavus, and Gaiella occulta. From the fungi detected Penicillium was the most abundant in both samples, while Fusarium and Mucor were present only in the rhizosphere of R. serbica and the entomopathogenic fungi Metarhizium, and Tolypocladiumu only in the rhizosphere of R. nathaliae. The fungal communities varied among plants, suggesting a stronger environmental influence than plant species. Our study demonstrates the importance of in vivo experiments to confirm the properties of PGP bacteria and indicates that the rhizosphere of resurrection plants is a valuable source of unique microorganisms that can be used to improve the drought stress tolerance of crops.

Co-Inoculation of Endophytes Bacillus siamensis TUR07-02b and Priestia megaterium SMBH14-02 Promotes Growth in Rice with Low Doses of Nitrogen Fertilizer

Multiple biotic and abiotic factors influence rice cultivation. These factors limit productivity and yield, as well as an irrational use of agrochemicals in rice cultivation. A sustainable alternative is using selected growth-promoting microorganisms to increase nutritional efficiency. In the present study, the direct mechanisms of growth promotion in two strains of Bacillus, three strains of Priestia, and two strains of Burkholderia endophytes of rice were characterized. Bacillus siamensis TUR07-02b and Priestia megaterium SMBH14-02 were selected to promote Oryza sativa var's growth. "Bellavista" was used at different doses (50, 75, and 100%) of mineral nitrogen (N) using a randomized block design by quintuplicate. Both strains, SMBH14-02 and TUR07-02b, presented outstanding promoter characteristics, including auxin production (123.17 and 335.65 μg mL^-1, respectively) and biological nitrogen fixation capacity. Similarly, B. siamensis TUR07-02b could solubilize phosphate-Ca (20.94 μg mL^-1), cellulases, and pectinases. Under greenhouse conditions, co-inoculated plants receiving 75% of the total dose of mineral nitrogen showed increased agronomic parameters in relation to panicle length, grains per panicle, grain yield, and harvest index by 25.0, 30.7, 39.5, and 12.5%, respectively, compared to the 75% fertilized treatment without inoculation. The strains of B. siamensis TUR07-02b and P. megaterium SMBH14-02 are potential microbial resources in the formulation of new inoculants to reduce the use of nitrogenous fertilizers. Thus, agronomic validation of the inoculant consortium at the field level will be an essential step in providing an alternative for the sustainable management of rice cultivation and increased productivity of rice farmers in the San Martín region.

Microbiomes in agroecosystem: Diversity, function and assembly mechanisms

Soils are a main repository of biodiversity harbouring immense diversity of microbial species that plays a central role in fundamental ecological processes and acts as the seed bank for emergence of the plant microbiome in cropland ecosystems. Crop-associated microbiomes play an important role in shaping plant performance, which includes but not limited to nutrient uptake, disease resistance, and abiotic stress tolerance. Although our understanding of structure and function of soil and plant microbiomes has been rapidly advancing, most of our knowledge comes from ecosystems in natural environment. In this review, we present an overview of the current knowledge of diversity and function of microbial communities along the soil-plant continuum in agroecosystems. To characterize the ecological mechanisms for community assembly of soil and crop microbiomes, we explore how crop host and environmental factors such as plant species and developmental stage, pathogen invasion, and land management shape microbiome structure, microbial co-occurrence patterns, and crop-microbiome interactions. Particularly, the relative importance of deterministic and stochastic processes in microbial community assembly is illustrated under different environmental conditions, and potential sources and keystone taxa of the crop microbiome are described. Finally, we highlight a few important questions and perspectives in future crop microbiome research.

Genotype and organ effect on the occupancy of phyllosphere prokaryotes in different rice landraces

Bacteria community provides essential ecological services to rice plants. The bacterial diversity of rice varies across host plant genotype and organs. This study employed 16S rDNA amplicon sequencing to characterise the bacterial community associated with three rice landraces using leaf blade and stem samples. The prokaryotic community found in these rice landraces comprised of two kingdoms, 12 phyla, 25 classes, 40 orders, 80 families, and 118 genera. Proteobacteria (53.9%) was the most abundant phylum. The most abundant genus was an undefined genus under Cyanobacteria (33.0%). Homogeneity of prokaryotic community was observed across the three rice landraces, which may suggest a high similarity in biological and genetical properties of the rice landraces. The difference in prokaryotic composition between leaf blade and stem was depicted based on principal coordinate analysis. This study observed that the prokaryotic inhabitants in rice plants is predominantly determined by rice plant organs.

Microbiome and pathobiome analyses reveal changes in community structure by foliar pathogen infection in rice

Increasing evidence suggests that the plant rhizosphere may recruit beneficial microbes to suppress soil-borne pathogens, but microbiome assembly due to foliar pathogen infection and ecological mechanisms that govern microbiome assembly and functions in the diseased host are not fully understood. To provide a comprehensive view of the rice-associated microbiome, we compared bacterial and fungal communities of healthy rice and those infected with Magnaporthe oryzae, the causal agent of blast disease. We found that the soil had a greater diversity of bacterial and fungal communities than plant endospheric communities. There was no significant dysbiosis of bacterial and fungal microbiome diversity due to disease, but it caused a substantial alteration of bacterial community structure in the root and rhizosphere compartments. The pathobiome analysis showed that the microbiome community structure of leaf and grain tissues was changed markedly at the pathogen infection site, although the alpha diversity did not change. Correspondingly, the relative abundances of some bacteria and fungi were clearly altered in symptomatic tissues. We noted an increase in Rhizobium bacteria and a decline of Tylospora, Clohesyomyces, and Penicillium fungi in the symptomatic leaf and grain tissues from both locations. According to the inferred microbial network, several direct interactions between M. oryzae and other microbes were identified. The majority of edges in the interaction network were positive in diseased samples; contrastingly, the number of edges was much lower in the healthy samples. With source tracking analysis, we observed a sharp contrast in the source of root endosphere bacteria due to Magnaporthe infection. Whereas the majority (71%) of healthy root bacteria could be tracked from the soil, only a very small portion (17%) could be tracked from the soil for diseased samples. These results advanced our understanding and provided potential ideas and a theoretical basis for studying pathobiome and exploiting the microbiome for sustainable agriculture.

In vitro Screening of Sunflower Associated Endophytic Bacteria With Plant Growth-Promoting Traits

Harnessing endophytic microbes as bioinoculants promises to solve agricultural problems and improve crop yield. Out of fifty endophytic bacteria of sunflowers, 20 were selected based on plant growth-promoting. These plant growth-promoting bacteria were identified as Bacillus, Pseudomonas, and Stenotrophomonas. The qualitative screening showed bacterial ability to produce hydrogen cyanide, ammonia, siderophore, indole-3-acetic acid (IAA), exopolysaccharide, and solubilize phosphate. The high quantity of siderophore produced by B. cereus T4S was 87.73%. No significant difference was observed in the Bacillus sp. CAL14 (33.83%), S. indicatrix BOVIS40 (32.81%), S. maltophilia JVB5 (32.20%), S. maltophilia PK60 (33.48%), B. subtilis VS52 (33.43%), and P. saponiphilia J4R (33.24%), exhibiting high phosphate-solubilizing potential. S. indicatrix BOVIS40, B. thuringiensis SFL02, B. cereus SFR35, B. cereus BLBS20, and B. albus TSN29 showed high potential for the screened enzymes. Varied IAA production was recorded under optimized conditions. The medium amended with yeast extract yielded high IAA production of 46.43 μg/ml by S. indicatrix BOVIS40. Optimum IAA production of 23.36 and 20.72 μg/ml at 5% sucrose and 3% glucose by S. maltophilia JVB5 and B. cereus T4S were recorded. At pH 7, maximum IAA production of 25.36 μg/ml was obtained by S. indicatrix BOVIS40. All the isolates exhibited high IAA production at temperatures 25, 30, and 37°C. The in vitro seed inoculation enhanced sunflower seedlings compared to the control. Therefore, exploration of copious endophytic bacteria as bioinoculants can best be promising to boost sunflower cultivation.

Bacterial Endophytes Contribute to Rice Seedling Establishment Under Submergence

Flooding events caused by severe rains and poor soil drainage can interfere with plant germination and seedling establishment. Rice is one of the cereal crops that has unique germination strategies under flooding. One of these strategies is based on the fast coleoptile elongation in order to reach the water surface and re-establish the contact with the air. Microorganisms can contribute to plant health via plant growth promoters and provide protection from abiotic stresses. To characterise the community composition of the microbiome in rice germination under submergence, a 16S rRNA gene profiling metagenomic analysis was performed of temperate japonica rice varieties Arborio and Lamone seedlings, which showed contrasting responses in terms of coleoptile length when submerged. This analysis showed a distinct microbiota composition of Arborio seeds under submergence, which are characterised by the development of a long coleoptile. To examine the potential function of microbial communities under submergence, culturable bacteria were isolated, identified and tested for plant growth-promoting activities. A subgroup of isolated bacteria showed the capacity to hydrolyse starch and produce indole-related compounds under hypoxia. Selected bacteria were inoculated in seeds to evaluate their effect on rice under submergence, showing a response that is dependent on the rice genotype. Our findings suggest that endophytic bacteria possess plant growth-promoting activities that can substantially contribute to rice seedling establishment under submergence.

Endophytic Microbiota of Rice and Their Collective Impact on Host Fitness

Endophytic microbiota mainly includes positive modulator of plant growth, productivity, stress tolerance and ability to control the phytopathogens. Rice endophytes colonize in different parts like roots, shoots, leaves, seeds, flowers, ovules, etc. The diversity and colonization of endophytes depend on several factors like host specificity, environment specificity, chemotaxis, motility, etc. A mutualistic relationship between rice plant and their endophytes improves the host health. Several crucial activities of rice plants are influenced by the presence of endophytes as they endorse plant growth by producing different phytohormones, solubilized minerals, or mitigating various environmental adverse conditions. Endophytes also protect rice plants from various phytopathogen by the production of secondary metabolites, lytic enzymes, antibiotics and induced systemic acquired resistance. Furthermore, the endophytes from rice and major crops are recently been shown useful in environmental waste management and also for the synthesis of green nanoparticles. This study highlights the beneficial interaction between rice plants and their endophytic microbiota with special emphasis on highlighting their application for sustainable agricultural and environmental practices in order to enhance the agro-economy in an eco-friendly manner.

Integrated Metabarcoding and Culturomic-Based Microbiome Profiling of Rice Phyllosphere Reveal Diverse and Functional Bacterial Communities for Blast Disease Suppression

Phyllosphere-the harsh foliar plant part exposed to vagaries of environmental and climatic variables is a unique habitat for microbial communities. In the present work, we profiled the phyllosphere microbiome of the rice plants using 16S rRNA gene amplicon sequencing (hereafter termed metabarcoding) and the conventional microbiological methods (culturomics) to decipher the microbiome assemblage, composition, and their functions such as antibiosis and defense induction against rice blast disease. The blast susceptible rice genotype (PRR78) harbored far more diverse bacterial species (294 species) than the resistant genotype (Pusa1602) that showed 193 species. Our metabarcoding of bacterial communities in phyllomicrobiome revealed the predominance of the phylum, Proteobacteria, and its members Pantoea, Enterobacter, Pseudomonas, and Erwinia on the phyllosphere of both rice genotypes. The microbiological culturomic validation of metabarcoding-taxonomic annotation further confirmed the prevalence of 31 bacterial isolates representing 11 genera and 16 species with the maximum abundance of Pantoea. The phyllomicrobiome-associated bacterial members displayed antifungal activity on rice blast fungus, Magnaporthe oryzae, by volatile and non-volatile metabolites. Upon phyllobacterization of rice cultivar PB1, the bacterial species such as Enterobacter sacchari, Microbacterium testaceum, Pantoea ananatis, Pantoea dispersa, Pantoea vagans, Pseudomonas oryzihabitans, Rhizobium sp., and Sphingomonas sp. elicited a defense response and contributed to the suppression of blast disease. qRT-PCR-based gene expression analysis indicated over expression of defense-associated genes such as OsCEBiP, OsCERK1, and phytohormone-associated genes such as OsPAD4, OsEDS1, OsPR1.1, OsNPR1, OsPDF2.2, and OsFMO in phyllobacterized rice seedlings. The phyllosphere bacterial species showing blast suppressive activity on rice were found non-plant pathogenic in tobacco infiltration assay. Our comparative microbiome interrogation of the rice phyllosphere culminated in the isolation and identification of agriculturally significant bacterial communities for blast disease management in rice farming through phyllomicrobiome engineering in the future.

Retrotransposons and multilocus sequence analysis reveals diversity and genetic variability in endophytic fungi-associated with Serjania laruotteana Cambess

The composition of endophytic communities is dynamic and demonstrates host specificity; besides, they have great intra- and interspecific genetic variability. In this work, we isolated leaf endophytic fungi from Serjania laruotteana, identify them using multilocus analysis, and evaluate the genetic variability using IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microssatellite amplified polymorphism). A total of 261 fungi were isolated and 58 were identified. Multilocus phylogenetic analysis using the partial sequences from the ITS1-5.8S-ITS2 regions, elongation factor 1-alpha, β-tubulin, actin, glyceraldehyde-3-phosphate dehydrogenase, and calmodulin genes identify that most strains belonged to the Colletotrichum and Diaporthe genera, other isolated genera were Xylaria, Phyllosticta, Muyocopron, Fusarium, Nemania, Plectosphaerella, Corynespora, Bipolaris, and Curvularia. The IRAP and REMAP analyzes were performed with Colletotrichum and Diaporthe genera and showed 100% of polymorphism and high intra- and interspecific variability. This is the first report of the diversity of endophytic fungi from S. laruotteana. In addition, it demonstrated that the IRAP and REMAP can be used to distinguish morphologically similar lineages, revealing differences even strains of the same species.

Endophytes from African Rice (Oryza glaberrima L.) Efficiently Colonize Asian Rice (Oryza sativa L.) Stimulating the Activity of Its Antioxidant Enzymes and Increasing the Content of Nitrogen, Carbon, and Chlorophyll

Bacterial endophytes support the adaptation of host plants to harsh environments. In this study, culturable bacterial endophytes were isolated from the African rice Oryza glaberrima L., which is well-adapted to grow with poor external inputs in the tropical region of Mali. Among these, six N-fixer strains were used to inoculate O. glaberrima RAM133 and the Asian rice O. sativa L. cv. Baldo, selected for growth in temperate climates. The colonization efficiency and the N-fixing activity were evaluated and compared for the two rice varieties. Oryza sativa-inoculated plants showed a fairly good colonization efficiency and nitrogenase activity. The inoculation of Oryza sativa with the strains Klebsiella pasteurii BDA134-6 and Phytobacter diazotrophicus BDA59-3 led to the highest nitrogenase activity. In addition, the inoculation of ‘Baldo’ plants with the strain P. diazotrophicus BDA59-3 led to a significant increase in nitrogen, carbon and chlorophyll content. Finally, ‘Baldo’ plants inoculated with Kl. pasteurii BDA134-6 showed the induction of antioxidant enzymes activity and the maintenance of nitrogen-fixation under salt stress as compared to the unstressed controls. As these endophytes efficiently colonize high-yielding crop varieties grown in cold temperate climates, they become good candidates to promote their growth under unfavorable conditions.

Survival of the fittest: how the rice microbial community forces Sarocladium oryzae into pathogenicity

The fungus Sarocladium oryzae (Sawada) causes rice sheath rot and produces the phytotoxins cerulenin and helvolic acid. Both toxins show antimicrobial activity but only helvolic acid production in the rice sheath correlates with virulence. Sarocladium oryzae isolates that differ in their toxin production were used to study their interaction with the rice culturable bacterial endophyte community. The diversity and community structure was defined in the edge of sheath rot lesions, followed by a null model-based co-occurrence analysis to discover pairwise interactions. Non-random pairs were co-cultured to study the nature of the interactions and the role of the toxins herein. Compared to healthy sheaths, endophyte diversity strongly increased when infected with the least virulent S. oryzae isolates producing low amounts of toxins. Virulent S. oryzae isolates did not affect diversity but caused strong shifts in species composition. The endophyte community of healthy rice plants was dominated by B. cereus. This bacterium was enriched in lesions produced by low-virulent S. oryzae isolates and caused hyphal lysis. Contrarily, helvolic acid producers eliminated this bacterium from the sheath endosphere. We conclude that S. oryzae needs to produce antibiotics to defend itself against antagonistic rice endophytes to successfully colonize and infect the rice sheath.

Sequence and evolutionary analysis of bacterial ribosomal S1 proteins

The multi-domain bacterial S1 protein is the largest and most functionally important ribosomal protein of the 30S subunit, which interacts with both mRNA and proteins. The family of ribosomal S1 proteins differs in the classical sense from a protein with tandem repeats and has a "bead-on-string" organization, where each repeat is folded into a globular domain. Based on our recent data, the study of evolutionary relationships for the bacterial phyla will provide evidence for one of the proposed theories of the evolutionary development of proteins with structural repeats: from multiple repeats of assembles to single repeats, or vice versa. In this comparative analysis of 1333 S1 sequences that were identified in 24 different phyla, we demonstrate how such phyla can form independently/dependently during evolution. To the best of our knowledge, this work is the first study of the evolutionary history of bacterial ribosomal S1 proteins. The collected and structured data can be useful to computer biologists as a resource for determining percent identity, amino acid composition and logo motifs, as well as dN/dS ratio in bacterial S1 protein. The obtained research data indicate that the evolutionary development of bacterial ribosomal S1 proteins evolved from multiple assemblies to single repeat. The presented data are integrated into the server, which can be accessed at http://oka.protres.ru:4200.

LuxR Solos from Environmental Fluorescent Pseudomonads

LuxR solos are related to quorum sensing (QS) LuxR family regulators; however, they lack a cognate LuxI family protein. LuxR solos are widespread and almost exclusively found in proteobacteria. In this study, we investigated the distribution and conservation of LuxR solos in the fluorescent pseudomonads group. Our analysis of more than 600 genomes revealed that the majority of fluorescent Pseudomonas spp. carry one or more LuxR solos, occurring considerably more frequently than complete LuxI/LuxR archetypical QS systems. Based on the adjacent gene context and conservation of the primary structure, nine subgroups of LuxR solos have been identified that are likely to be involved in the establishment of communication networks. Modeling analysis revealed that the majority of subgroups shows some substitutions at the invariant amino acids of the ligand-binding pocket of QS LuxRs, raising the possibility of binding to non-acyl-homoserine lactone (AHL) ligands. Several mutants and gene expression studies on some LuxR solos belonging to different subgroups were performed in order to shed light on their response. The commonality of LuxR solos among fluorescent pseudomonads is an indication of their important role in cell-cell signaling.

IMPORTANCE Cell-cell communication in bacteria is being extensively studied in simple settings and uses chemical signals and cognate regulators/receptors. Many Gram-negative proteobacteria use acyl-homoserine lactones (AHLs) synthesized by LuxI family proteins and cognate LuxR-type receptors to regulate their quorum sensing (QS) target loci. AHL-QS circuits are the best studied QS systems; however, many proteobacterial genomes also contain one or more LuxR solos, which are QS-related LuxR proteins which are unpaired to a cognate LuxI. A few LuxR solos have been implicated in intraspecies, interspecies, and interkingdom signaling. Here, we report that LuxR solo homologs occur considerably more frequently than complete LuxI/LuxR QS systems within the Pseudomonas fluorescens group of species and that they are characterized by different genomic organizations and primary structures and can be subdivided into several subgroups. The P. fluorescens group consists of more than 50 species, many of which are found in plant-associated environments. The role of LuxR solos in cell-cell signaling in fluorescent pseudomonads is discussed.

Bacterial community dynamics across developmental stages of fungal fruiting bodies

Increasing evidence suggest that bacteria form diverse communities in various eukaryotic hosts, including fungi. However, little is known about their succession and the functional potential at different host development stages. Here we examined the effect of fruiting body parts and developmental stages on the structure and potential function of fungus-associated bacterial communities. Using high-throughput sequencing, we characterized bacterial communities and their associated potential functions in fruiting bodies from ten genera belonging to four major mushroom-forming orders and three different developmental stages of a model host species Cantharellus cibarius. Our results demonstrate that bacterial community structure differs between internal and external parts of the fruiting body but not between inner tissues. The structure of the bacterial communities showed significant variation across fruiting body developmental stages. We provide evidence that certain functional groups, such as those related to nitrogen fixation, persist in fruiting bodies during the maturation, but are replaced by putative parasites/pathogens afterwards. These data suggest that bacterial communities inhabiting fungal fruiting bodies may play important roles in their growth and development.

Metagenomics of two gnotobiotically grown aromatic rice cultivars reveals genotype-dependent and tissue-specific colonization of endophytic bacterial communities attributing multiple plant growth promoting traits

Exploration of community structures, habitations, and potential plant growth promoting (PGP) attributes of endophytic bacteria through next generation sequencing (NGS) is a prerequisite to culturing PGP endophytic bacteria for their application in sustainable agriculture. The present study unravels the taxonomic abundance and diversity of endophytic bacteria inhabiting in vitro grown root, shoot and callus tissues of two aromatic rice cultivars through 16S rRNA gene-based Illumina NGS. Wide variability in the number of bacterial operational taxonomic units (OTUs) and genera was observed between the two samples of the root (55, 14 vs. 310, 76) and shoot (26, 12 vs. 276, 73) but not between the two callus samples (251, 61 vs. 259, 51), indicating tissue-specific and genotype-dependent bacterial community distribution in rice plant, even under similar gnotobiotic growth conditions. Sizes of core bacteriomes of the selected two rice genotypes varied from 1 to 15 genera, with Sphingomonas being the only genus detected in all six samples. Functional annotation, based upon the abundance of bacterial OTUs, revealed the presence of several PGP trait-related genes having variable relative abundance in tissue-specific and genotype-dependent manners. In silico study also documented a higher abundance of certain genes in the same biochemical pathway, such as nitrogen fixation, phosphate solubilization and indole acetic acid production; implying their crucial roles in the biosynthesis of metabolites leading to PGP. New insights on utilizing callus cultures for isolation of PGP endophytes aiming to improve rice crop productivity are presented, owing to constancy in bacterial OTUs and genera in callus tissues of both the rice genotypes.

Multiple endogenous seed-born bacteria recovered rice growth disruption caused by Burkholderia glumae

Burkholderia glumae is a causal agent of bacterial grain and seedling rot in rice, and is a threat to stable global food supply. The virulence of B. glumae was suppressed when it was inoculated on budding seed rather than on non-budding seed. To clarify the phenomena, pathogen titer inside the rice plant was measured by serial dilution plating of lysates from budding rice seedlings. Surprisingly, morphologically different types of colonies were observed on the plates. These 'contaminated' rice seed-born bacteria (RSB) were identified by sequencing 16S rRNA genes as three strains of Pseudomonas putida (RSB1, RSB10, RSB15) and Stenotrophomonas maltophilia (RSB2). All bacteria and B. glumae were simultaneously inoculated onto rice seeds, and all three P. putida RSBs suppressed the growth disruption caused by B. glumae, whereas RSB2 had no effect. Thus, the virulence was synergistically suppressed when co-treated with RSBs. The effect could be dependent on the high biofilm formation ability of RSB2. By comprehensive microbiota analysis, endogenous rice flora were changed by RSBs treatment. These results suggest the possibility of novel pathogen control through pre-treatment with endogenous beneficial microorganisms. The method would contribute substantially to the implementation of sustainable agriculture stated in Sustainable Development Goals of United Nations.

Bacterial communities associated with sugarcane under different agricultural management exhibit a diversity of plant growth-promoting traits and evidence of synergistic effect

Plant-associated microbiomes have been a target of interest for the prospection of microorganisms, which may be acting as effectors to increase agricultural productivity. For years, the search for beneficial microorganisms has been carried out from the characterization of functional traits of growth-promotion using tests with a few isolates. However, eventually, the expectations with positive results may not be realized when the evaluation is performed in association with plants. In our study, we accessed the cultivable sugarcane microbiome under two conditions of agronomic management: organic and conventional. From the use of a new customized culture medium, we recovered 944 endophytic and epiphytic bacterial communities derived from plant roots, stalks, leaves, and rhizospheric soil. This could be accomplished by using a large-scale approach, initially performing an in planta (Cynodon dactylon) screening process of inoculation to avoid early incompatibility. The inoculation was performed using the bacterial communities, considering that in this way, they could act synergistically. This process resulted in 38 candidate communities, 17 of which had higher Indole-3-acetic acid (IAA) production and phosphate solubilization activity and, were submitted to a new in planta test using Brachiaria ruziziensis and quantification of functional traits for growth-promotion and physiological tests. Enrichment analysis of selected communities has shown that they derived mainly from epiphytic populations of sugarcane stalks under conventional management. The sequencing of the V3-V4 region of the 16S rRNA gene revealed 34 genera and 24 species distributed among the phylum Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. We also observed a network of genera in these communities where the genus Chryseobacterium stands out with a greater degree of interaction, indicating a possible direct or indirect role as a keystone taxon in communities with plant-growth promotion capacities. From the results achieved, we can conclude that the approach is useful in the recovery of a set of sugarcane bacterial communities and that there is, evidence of synergistic action providing benefits to plants, and that they are compatible with plants of the same family (Poaceae). Thus, we are reporting the beneficial bacterial communities identified as suitable candidates with rated potential to be exploited as bioinoculants for crops.

Deciphering core-microbiome of rice leaf endosphere: Revelation by metagenomic and microbiological analysis of aromatic and non-aromatic genotypes grown in three geographical zones

We have deciphered the leaf endophytic-microbiome of aromatic (cv. Pusa Basmati-1) and non-aromatic (cv. BPT-5204) rice-genotypes grown in the mountain and plateau-zones of India by both metagenomic NGS (mNGS) and conventional microbiological methods. Microbiome analysis by sequencing V3-V4 region of ribosomal gene revealed marginally more bacterial operational taxonomic units (OTU) in the mountain zone at Palampur and Almora than plateau zone at Hazaribagh. Interestingly, the rice leaf endophytic microbiomes in mountain zone were found clustered separately from that of plateau-zone. The Bray-Curtis dissimilarity indices indicated influence of geographical location as compared to genotype per se for shaping rice endophytic microbiome composition. Bacterial phyla, Proteobacteria followed by Bacteroidetes, Firmicutes, and Actinobacteria were found abundant in all three locations. The core-microbiome analysis devulged association of Acidovorax; Acinetobacter; Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium; Aureimonas; Bradyrhizobium; Burkholderia-Caballeronia-Paraburkholderia; Enterobacter; Pantoea; Pseudomonas; Sphingomonas; and Stenotrophomonas with the leaf endosphere. The phyllosphere and spermosphere microbiota appears to have contributed to endophytic microbiota of rice leaf. SparCC network analysis of the endophytic-microbiome showed complex cooperative and competitive intra-microbial interactions among the microbial communities. Microbiological validation of mNGS data further confirmed the presence of core and transient genera such as Acidovorax, Alcaligenes, Bacillus, Chryseobacterium, Comamonas, Curtobacterium, Delftia, Microbacterium, Ochrobactrum, Pantoea, Pseudomonas, Rhizobium, Rhodococcus, Sphingobacterium, Staphylococcus, Stenotrophomonas, and Xanthomonas in the rice genotypes. We isolated, characterized and identified core-endophytic microbial communities of rice leaf for developing microbiome assisted crop management by microbiome reengineering in future.

Genotypic Variation of Endophytic Nitrogen-Fixing Activity and Bacterial Flora in Rice Stem Based on Sugar Content

Enhancement of the nitrogen-fixing ability of endophytic bacteria in rice is expected to result in improved nitrogen use under low-nitrogen conditions. Endophytic nitrogen-fixing bacteria require a large amount of energy to fix atmospheric nitrogen. However, it is unknown which carbon source and bacteria would affect nitrogen-fixing activity in rice. Therefore, this study examined genotypic variations in the nitrogen-fixing ability of rice plant stem as affected by non-structural carbohydrates and endophytic bacterial flora in field-grown rice. In the field experiments, six varieties and 10 genotypes of rice were grown in 2017 and 2018 to compare the acetylene reduction activity (nitrogen-fixing activity) and non-structural carbohydrates (glucose, sucrose, and starch) concentration in their stems at the heading stage. For the bacterial flora analysis, two genes were amplified using a primer set of 16S rRNA and nitrogenase (NifH) gene-specific primers. Next, acetylene reduction activity was correlated with sugar concentration among genotypes in both years, suggesting that the levels of soluble sugars influenced stem nitrogen-fixing activity. Bacterial flora analysis also suggested the presence of common and genotype-specific bacterial flora in both 16S rRNA and nifH genes. Similarly, bacteria classified as rhizobia, such as Bradyrhizobium sp. (Alphaproteobacteria) and Paraburkholderia sp. (Betaproteobacteria), were highly abundant in all rice genotypes, suggesting that these bacteria make major contributions to the nitrogen fixation process in rice stems. Gammaproteobacteria were more abundant in CG14 as well, which showed the highest acetylene reduction activity and sugar concentration among genotypes and is also proposed to contribute to the higher amount of nitrogen-fixing activity.

Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From Seeds

Microbes form close associations with host plants including rice as both surface (epiphytes) and internal (endophytes) inhabitants. Yet despite rice being one of the most important cereal crops agriculturally and economically, knowledge of its microbiome, particularly core inhabitants and any functional properties bestowed is limited. In this study, the microbiome in rice seedlings derived directly from seeds was identified, characterized and compared to the microbiome of the seed. Rice seeds were sourced from two different locations in Arkansas, USA of two different rice genotypes (Katy, M202) from two different harvest years (2013, 2014). Seeds were planted in sterile media and bacterial as well as fungal communities were identified through 16S and ITS sequencing, respectively, for four seedling compartments (root surface, root endosphere, shoot surface, shoot endosphere). Overall, 966 bacterial and 280 fungal ASVs were found in seedlings. Greater abundance and diversity were detected for the microbiome associated with roots compared to shoots and with more epiphytes than endophytes. The seedling compartments were the driving factor for microbial community composition rather than other factors such as rice genotype, location and harvest year. Comparison with datasets from seeds revealed that 91 (out of 296) bacterial and 11 (out of 341) fungal ASVs were shared with seedlings with the majority being retained within root tissues. Core bacterial and fungal microbiome shared across seedling samples were identified. Core bacteria genera identified in this study such as Rhizobium, Pantoea, Sphingomonas, and Paenibacillus have been reported as plant growth promoting bacteria while core fungi such as Pleosporales, Alternaria and Occultifur have potential as biocontrol agents.

Deciphering the Omics of Plant-Microbe Interaction: Perspectives and New Insights

Introduction

Plants do not grow in isolation, rather they are hosts to a variety of microbes in their natural environments. While, few thrive in the plants for their own benefit, others may have a direct impact on plants in a symbiotic manner. Unraveling plant-microbe interactions is a critical component in recognizing the positive and negative impacts of microbes on plants. Also, by affecting the environment around plants, microbes may indirectly influence plants. The progress in sequencing technologies in the genomics era and several omics tools has accelerated in biological science. Studying the complex nature of plant-microbe interactions can offer several strategies to increase the productivity of plants in an environmentally friendly manner by providing better insights. This review brings forward the recent works performed in building omics strategies that decipher the interactions between plant-microbiome. At the same time, it further explores other associated mutually beneficial aspects of plant-microbe interactions such as plant growth promotion, nitrogen fixation, stress suppressions in crops and bioremediation; as well as provides better insights on metabolic interactions between microbes and plants through omics approaches. It also aims to explore advances in the study of Arabidopsis as an important avenue to serve as a baseline tool to create models that help in scrutinizing various factors that contribute to the elaborate relationship between plants and microbes. Causal relationships between plants and microbes can be established through systematic gnotobiotic experimental studies to test hypotheses on biologically derived interactions.

Conclusion

This review will cover recent advances in the study of plant-microbe interactions keeping in view the advantages of these interactions in improving nutrient uptake and plant health.

The endosphere microbial communities, a great promise in agriculture

Agricultural food production and sustainability need intensification to address the current global food supply to meet human demand. The continuous human population increase and other anthropogenic activities threaten food security. Agrochemical inputs have long been used in conventional agricultural systems to boost crop productivity, but they are disadvantageous to a safe environment. Towards developing environmentally friendly agriculture, efforts are being directed in exploring biological resources from soil and plant microbes. The survival of the rhizosphere and endosphere microbiota is influenced by biotic and abiotic factors. Plant microbiota live interdependently with the host plants. Endophytes are regarded as colonizer microbes inhabiting and establishing microbial communities within the plant tissue. Their activities are varied and include fixing atmospheric nitrogen, solubilizing phosphate, synthesis of siderophores, secretion of metabolite-like compounds containing active biocontrol agents in the control of phytopathogens, and induced systemic resistance that stimulates plant response to withstand stress. Exploring beneficial endophyte resources in the formulation of bio-inoculants, such as biofertilizers, as an alternative to agrochemicals (fertilizers and pesticides) in developing environmentally friendly agriculture and for incorporation into crop breeding and disease control program is promising. Therefore, in this review, endosphere microbial ecology, associating environmental factors, and their roles that contribute to their effectiveness in promoting plant growth for maximum agricultural crop productivity were highlighted.

Water management and phenology influence the root-associated rice field microbiota

Microbial communities associated with plants are greatly influenced by water availability in soil. In flooded crops, such as rice, the impact of water management on microbial dynamics is not fully understood. Here, we present a comprehensive study of the rice microbiota investigated in an experimental field located in one of the most productive areas of northern Italy. The microbiota associated with paddy soil and root was investigated using 454 pyrosequencing of 16S, ITS and 18S rRNA gene amplicons under two different water managements, upland (non-flooded, aerobic) and lowland (traditional flooding, anaerobic), at three plant development stages. Results highlighted a major role of the soil water status in shaping microbial communities, while phenological stage had low impacts. Compositional shifts in prokaryotic and fungal communities upon water management consisted in significant abundance changes of Firmicutes, Methanobacteria, Chloroflexi, Sordariomycetes, Dothideomycetes and Glomeromycotina. A vicariance in plant beneficial microbes and between saprotrophs and pathotrophs was observed between lowland and upland. Moreover, through network analysis, we demonstrated different co-abundance dynamics between lowland and upland conditions with a major impact on microbial hubs (strongly interconnected microbes) that fully shifted to aerobic microbes in the absence of flooding.

LuxR Solos in the Plant Endophyte Kosakonia sp. Strain KO348

Cell-cell signaling in bacteria allows a synchronized and coordinated behavior of a microbial community. LuxR solos represent a subfamily of proteins in proteobacteria which most commonly detect and respond to signals produced exogenously by other microbes or eukaryotic hosts. Here, we report that a plant-beneficial bacterial endophyte belonging to the novel genus of Kosakonia possesses two LuxR solos; one is involved in the detection of exogenous N-acyl homoserine lactone quorum sensing signals and the other in detecting a compound(s) produced by the host plant. These two Kosakonia LuxR solos are therefore most likely involved in interspecies and interkingdom signaling.

Endophytes are microorganisms that live inside plants and are often beneficial for the host. Kosakonia is a novel bacterial genus that includes several species that are diazotrophic and plant associated. This study revealed two quorum sensing-related LuxR solos, designated LoxR and PsrR, in the plant endophyte Kosakonia sp. strain KO348. LoxR modeling and biochemical studies demonstrated that LoxR binds N-acyl homoserine lactones (AHLs) in a promiscuous way. PsrR, on the other hand, belongs to the subfamily of plant-associated-bacterium (PAB) LuxR solos that respond to plant compounds. Target promoter studies as well as modeling and phylogenetic comparisons suggest that PAB LuxR solos are likely to respond to different plant compounds. Finally, LoxR is involved in the regulation of T6SS and PsrR plays a role in root endosphere colonization.

IMPORTANCE Cell-cell signaling in bacteria allows a synchronized and coordinated behavior of a microbial community. LuxR solos represent a subfamily of proteins in proteobacteria which most commonly detect and respond to signals produced exogenously by other microbes or eukaryotic hosts. Here, we report that a plant-beneficial bacterial endophyte belonging to the novel genus of Kosakonia possesses two LuxR solos; one is involved in the detection of exogenous N-acyl homoserine lactone quorum sensing signals and the other in detecting a compound(s) produced by the host plant. These two Kosakonia LuxR solos are therefore most likely involved in interspecies and interkingdom signaling.

Tissue-Specific Dynamics in the Endophytic Bacterial Communities in Arctic Pioneer Plant Oxyria digyna

The rapid developments in the next-generation sequencing methods in the recent years have provided a wealth of information on the community structures and functions of endophytic bacteria. However, the assembly processes of these communities in different plant tissues are still currently poorly understood, especially in wild plants in natural settings. The aim of this study was to compare the composition of endophytic bacterial communities in leaves and roots of arcto-alpine pioneer plant Oxyria digyna, and investigate, how plant tissue (leaf or root) or plant origin affect the community assembly. To address this, we planted micropropagated O. digyna plants with low bacterial load (bait plants) in experimental site with native O. digyna population, in the Low Arctic. The endophytic bacterial community structures in the leaves and roots of the bait plants were analyzed after one growing season and one year in the field, and compared to those of the wild plants growing at the same site. 16S rRNA gene targeted sequencing revealed that endophytic communities in the roots were more diverse than in the leaves, and the diversity in the bait plants increased in the field, and was highest in the wild plants. Both tissue type and plant group had strong impact on the endophytic bacterial community structures. Firmicutes were highly abundant in the leaf communities of both plant types. Proteobacteria and Bacteroidetes were more abundant in the roots, albeit with different relative abundances in different plant groups. The community structures in the bait plants changed in the field over time, and increasingly resembled the wild plant endophytic communities. This was due to the changes in the relative abundances of several bacterial taxa, as well as species acquisition in the field, but with no species turnover. Several OTUs that were acquired by the bait plants in the field and represent phosphate solubilizing and diazotrophic bacterial taxa, suggesting major role in nutrient acquisition of these bacteria for this nonmycorrhizal plant, thriving in the nutrient poor arctic soils.

[Genetic characterization of rice endophytic bacteria (Oryza sativa L.) with antimicrobial activity against Burkholderia glumae]

The aim of the present study was to isolate, select and characterize endophytic bacteria in rice inhibiting Burkholderia glumae THT as well as to characterize the genetic diversity and virulence factors in strains of B. glumae and Burkholderia gladioli of rice. Rice plants were collected in 4 departments from the northern region of Peru, isolating endophytic bacteria, after tissue sterilization, at 30°C (48h) in Trypticase Soy Agar (TSA), evaluating the antimicrobial activity against B. glumae THT, production of siderophores, resistance of toxoflavine and partial sequencing of the 16S rRNA gene. Furthermore, B. glumae and B. gladioli were isolated in selective medium (pH 4.5) at 41°C/72h. Molecular identification was performed using BOX-PCR and sequencing of the 16S rRNA gene, in addition to the production of extracellular enzymes, motility tests and sensitivity/resistance to bactericides. One hundred and eighty nine (189) endophytic bacteria were isolated, and only 9 strains showed antimicrobial activity against B. glumae THT, highlighting Burkholderia vietnamiensis TUR04-01, B. vietnamiensis TUR04-03 and Bacillus aryabhattai AMH12-02. The strains produced siderophores and at least 55.5% were resistant to toxoflavin. Additionally, 17 strains were grouped into 9 BOX-PCR profiles, where 16 had similarity with B. glumae LMG2196^T (100%) and 1 with B. gladioli NBRC 13700^T (99.86%). High diversity was found according to geographical origin and virulence factors. In conclusion, strains of the genus Bacillus and Burkholderia are potential biocontrol agents against B. glumae.

Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed

BACKGROUND

Plant-associated microbiomes, which are shaped by host and environmental factors, support their hosts by providing nutrients and attenuating abiotic and biotic stresses. Although host genetic factors involved in plant growth and immunity are known to shape compositions of microbial communities, the effects of host evolution on microbial communities are not well understood.

RESULTS

We show evidence that both host speciation and domestication shape seed bacterial and fungal community structures. Genome types of rice contributed to compositional variations of both communities, showing a significant phylosymbiosis with microbial composition. Following the domestication, abundance inequality of bacterial and fungal communities also commonly increased. However, composition of bacterial community was relatively conserved, whereas fungal membership was dramatically changed. These domestication effects were further corroborated when analyzed by a random forest model. With these changes, hub taxa of inter-kingdom networks were also shifted from fungi to bacteria by domestication. Furthermore, maternal inheritance of microbiota was revealed as a major path of microbial transmission across generations.

CONCLUSIONS

Our findings show that evolutionary processes stochastically affect overall composition of microbial communities, whereas dramatic changes in environments during domestication contribute to assembly of microbiotas in deterministic ways in rice seed. This study further provides new insights on host evolution and microbiome, the starting point of the holobiome of plants, microbial communities, and surrounding environments.

In Planta Colonization and Role of T6SS in Two Rice Kosakonia Endophytes

Endophytes live inside plants and are often beneficial. Kosakonia is a novel bacterial genus that includes many diazotrophic plant-associated isolates. Plant-bacteria studies on two rice endophytic Kosakonia beneficial strains were performed, including comparative genomics, secretome profiling, in planta tests, and a field release trial. The strains are efficient rhizoplane and root endosphere colonizers and localized in the root cortex. Secretomics revealed 144 putative secreted proteins, including type VI secretory system (T6SS) proteins. A Kosakonia T6SS genomic knock-out mutant showed a significant decrease in rhizoplane and endosphere colonization ability. A field trial using rice seed inoculated with Kosakonia spp. showed no effect on plant growth promotion upon nitrogen stress and microbiome studies revealed that Kosakonia spp. were significantly more present in the inoculated rice. Comparative genomics indicated that several protein domains were enriched in plant-associated Kosakonia spp. This study highlights that Kosakonia is an important, recently classified genus involved in plant-bacteria interaction.

Alterations in the Endophyte-Enriched Root-Associated Microbiome of Rice Receiving Growth-Promoting Treatments of Urea Fertilizer and Rhizobium Biofertilizer

We examined the bacterial endophyte-enriched root-associated microbiome within rice (Oryza sativa) 55 days after growth in soil with and without urea fertilizer and/or biofertilization with a growth-promotive bacterial strain (Rhizobium leguminosarum bv. trifolii E11). After treatment to deplete rhizosphere/rhizoplane communities, washed roots were macerated and their endophyte-enriched communities were analyzed by 16S ribosomal DNA 454 amplicon pyrosequencing. This analysis clustered 99,990 valid sequence reads into 1105 operational taxonomic units (OTUs) with 97% sequence identity, 133 of which represented a consolidated core assemblage representing 12.04% of the fully detected OTU richness. Taxonomic affiliations indicated Proteobacteria as the most abundant phylum (especially α- and γ-Proteobacteria classes), followed by Firmicutes, Bacteroidetes, Verrucomicrobia, Actinobacteria, and several other phyla. Dominant genera included Rheinheimera, unclassified Rhodospirillaceae, Pseudomonas, Asticcacaulis, Sphingomonas, and Rhizobium. Several OTUs had close taxonomic affiliation to genera of diazotrophic rhizobacteria, including Rhizobium, unclassified Rhizobiales, Azospirillum, Azoarcus, unclassified Rhizobiaceae, Bradyrhizobium, Azonexus, Mesorhizobium, Devosia, Azovibrio, Azospira, Azomonas, and Azotobacter. The endophyte-enriched microbiome was restructured within roots receiving growth-promoting treatments. Compared to the untreated control, endophyte-enriched communities receiving urea and/or biofertilizer treatments were significantly reduced in OTU richness and relative read abundances. Several unique OTUs were enriched in each of the treatment communities. These alterations in structure of root-associated communities suggest dynamic interactions in the host plant microbiome, some of which may influence the well-documented positive synergistic impact of rhizobial biofertilizer inoculation plus low doses of urea-N fertilizer on growth promotion of rice, considered as one of the world's most important food crops.

The Role of Secretion Systems, Effectors, and Secondary Metabolites of Beneficial Rhizobacteria in Interactions With Plants and Microbes

Beneficial rhizobacteria dwell in plant roots and promote plant growth, development, and resistance to various stress types. In recent years there have been large-scale efforts to culture root-associated bacteria and sequence their genomes to uncover novel beneficial microbes. However, only a few strains of rhizobacteria from the large pool of soil microbes have been studied at the molecular level. This review focuses on the molecular basis underlying the phenotypes of three beneficial microbe groups; (1) plant-growth promoting rhizobacteria (PGPR), (2) root nodulating bacteria (RNB), and (3) biocontrol agents (BCAs). We focus on bacterial proteins and secondary metabolites that mediate known phenotypes within and around plants, and the mechanisms used to secrete these. We highlight the necessity for a better understanding of bacterial genes responsible for beneficial plant traits, which can be used for targeted gene-centered and molecule-centered discovery and deployment of novel beneficial rhizobacteria.

Culturable endophytic bacteria of Camellia species endowed with plant growth promoting characteristics

AIM

Tea (Camellia sinensis (L.) O. Kuntze) is an economically important caffeine-containing beverage crop with massive plantation in the Northeast corner of the agroclimatic belt of India. The main aim of the work was to isolate, identify and characterize the native plant growth promoting endophytes associated with tea for future microbe based bioformulation.

METHODS AND RESULTS

A total of 129 endophytic bacteria were isolated and characterized for plant growth promoting traits such as indole-3-acetic acid (IAA), phosphate solubilization, ammonia production, biocontrol traits like siderophore and extracellular enzyme production. BOX-PCR fingerprinting was used to differentiate the various bacterial isolates obtained from six different tea species. 16S rRNA sequencing and blast analysis showed that these isolates belonged to different genera, that is, Bacillus, Brevibacterium, Paenibacillus and Lysinibacillus. Lysinibacillus sp. S24 showed the highest phosphate solubilization and IAA acid production efficiency of 268·4 ± 14·3 and 13·5 ± 0·5 µg ml^-1 , respectively. Brevibacterium sp. S91 showed the highest ammonia production of 6·2 ± 0·5 µmol ml^-1 . Chitinase, cellulase, protease and pectinase activities were shown by 4·6, 34·1, 27·13 and 13·14% of the total isolates, respectively. Similarly, 41% of the total isolates were positive for 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity. Further, the potent PGP isolates, S24 and S91 were able to enhance the vegetative parameters such as dry/fresh weight of root and shoot of tea plants in nursery conditions.

CONCLUSION

Our findings corroborate that tea endophytic bacteria possess the potential to demonstrate multiple PGP traits both, in vivo and in vitro and have the potential for further large-scale trials.

SIGNIFICANCE AND IMPACT OF THE STUDY

The exploration of tea endophytic bacterial community is suitable for the development of bioformulations for an integrated nutrient management and thus sustainable crop production and decreasing the hazardous effects of chemical fertilizers on the environment and human health.

Bacterial Microbiota of Rice Roots: 16S-Based Taxonomic Profiling of Endophytic and Rhizospheric Diversity, Endophytes Isolation and Simplified Endophytic Community

Rice is currently the most important food crop in the world and we are only just beginning to study the bacterial associated microbiome. It is of importance to perform screenings of the core rice microbiota and also to develop new plant-microbe models and simplified communities for increasing our understanding about the formation and function of its microbiome. In order to begin to address this aspect, we have performed a 16S rDNA taxonomic bacterial profiling of the rhizosphere and endorhizosphere of two high-yield rice cultivars—Pionero 2010 FL and DANAC SD20A—extensively grown in Venezuela in 2014. Fifteen putative bacterial endophytes were then isolated from surface-sterilized roots and further studied in vitro and in planta. We have then performed inoculation of rice seedlings with a simplified community composed by 10 of the isolates and we have tracked them in the course of 30 days in greenhouse cultivation. The results obtained suggest that a set was able to significantly colonize together the rice endorhizospheres, indicating possible cooperation and the ability to form a stable multispecies community. This approach can be useful in the development of microbial solutions for a more sustainable rice production.

Understanding and exploiting plant beneficial microbes

After a century of incremental research, technological advances, coupled with a need for sustainable crop yield increases, have reinvigorated the study of beneficial plant-microbe interactions with attention focused on how microbiomes alter plant phenotypes. We review recent advances in plant microbiome research, and describe potential applications for increasing crop productivity. The phylogenetic diversity of plant microbiomes is increasingly well characterized, and their functional diversity is becoming more accessible. Large culture collections are available for controlled experimentation, with more to come. Genetic resources are being brought to bear on questions of microbiome function. We expect that microbial amendments of varying complexities will expose rules governing beneficial plant-microbe interactions contributing to plant growth promotion and disease resistance, enabling more sustainable agriculture.

Taxonomy and systematics of plant probiotic bacteria in the genomic era

Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics.

Essential Genes for In Vitro Growth of the Endophyte Herbaspirillum seropedicae SmR1 as Revealed by Transposon Insertion Site Sequencing

The interior of plants contains microorganisms (referred to as endophytes) that are distinct from those present at the root surface or in the surrounding soil. Herbaspirillum seropedicae strain SmR1, belonging to the betaproteobacteria, is an endophyte that colonizes crops, including rice, maize, sugarcane, and sorghum. Different approaches have revealed genes and pathways regulated during the interactions of H. seropedicae with its plant hosts. However, functional genomic analysis of transposon (Tn) mutants has been hampered by the lack of genetic tools. Here we successfully employed a combination of in vivo high-density mariner Tn mutagenesis and targeted Tn insertion site sequencing (Tn-seq) in H. seropedicae SmR1. The analysis of multiple gene-saturating Tn libraries revealed that 395 genes are essential for the growth of H. seropedicae SmR1 in tryptone-yeast extract medium. A comparative analysis with the Database of Essential Genes (DEG) showed that 25 genes are uniquely essential in H. seropedicae SmR1. The Tn mutagenesis protocol developed and the gene-saturating Tn libraries generated will facilitate elucidation of the genetic mechanisms of the H. seropedicae endophytic lifestyle.

IMPORTANCE

A focal point in the study of endophytes is the development of effective biofertilizers that could help to reduce the input of agrochemicals in croplands. Besides the ability to promote plant growth, a good biofertilizer should be successful in colonizing its host and competing against the native microbiota. By using a systematic Tn-based gene-inactivation strategy and massively parallel sequencing of Tn insertion sites (Tn-seq), it is possible to study the fitness of thousands of Tn mutants in a single experiment. We have applied the combination of these techniques to the plant-growth-promoting endophyte Herbaspirillum seropedicae SmR1. The Tn mutant libraries generated will enable studies into the genetic mechanisms of H. seropedicae-plant interactions. The approach that we have taken is applicable to other plant-interacting bacteria.