Endophyte microbiome diversity in micropropagated Atriplex canescens and Atriplex torreyi var griffithsii

Endophytes from Halotolerant Plants Aimed to Overcome Salinity and Draught

The aim of our research was to study the endosphere of four halophytic plants: Salicornia europaea L., Salsola australis (R.Br.), Bassia sedoides (Pall.) and Kochia prostrata (L.) Schrad. from arid and saline areas of the Stavropol Territory, Russia. In total, 28 endophyte strains were isolated from the roots and stems of these halophytic plants. Most of the isolates (23 out of 28) were identified as Bacillus sp. while others belonged to the genera Oceanobacillus, Paenibacillus, Pantoea, Alcaligenes and Myroides. Three strains of Bacillus sp. (Se5R, Se1-1R, and Se1-3S), isolated from the S. europaea were capable of growth at 55 °C and in 10% of NaCl. Strains Se1-4S, Kp20-2S, and Bs11-2S Bacillus sp. (isolated from the S. australis, K. prostrata and B. sedoides, respectively) demonstrated strong plant growth promoting activity: 85-265% over control lettuce plants and a high degree of growth suppression (59.1-81.2%) of pathogenic fungi Fusarium oxysporum, Bipolaris sorokiniana and Rhizoctonia solani. Selected strains can be promising candidates for the development of bioinoculants to facilitate salt soil phytoremediation and be beneficial for mitigating the salt stress to the plants growing in salt-affected habitats.

Endophytes and Halophytes to Remediate Industrial Wastewater and Saline Soils: Perspectives from Qatar

Many halophytes are considered to be salt hyperaccumulators, adopting ion extrusion and inclusion mechanisms. Such plants, with high aboveground biomass, may play crucial roles in saline habitats, including soil desalination and phytoremediation of polluted soils and waters. These plants cause significant changes in some of the soil’s physical and chemical properties; and have proven efficient in removing heavy metals and metabolizing organic compounds from oil and gas activities. Halophytes in Qatar, such as Halopeplis perfoliata, Salicornia europaea, Salsola soda, and Tetraena qatarensis, are shown here to play significant roles in the phytoremediation of polluted soils and waters. Microorganisms associated with these halophytes (such as endophytic bacteria) might boost these plants to remediate saline and polluted soils. A significant number of these bacteria, such as Bacillus spp. and Pseudomonas spp., are reported here to play important roles in many sectors of life. We explore the mechanisms adopted by the endophytic bacteria to promote and support these halophytes in the desalination of saline soils and phytoremediation of polluted soils. The possible roles played by endophytes in different parts of native plants are given to elucidate the mechanisms of cooperation between these native plants and the associated microorganisms.

An unexpected guest: a green microalga associated with the arsenic-tolerant shrub Acacia farnesiana

The best-known plant endophytes include mainly fungi and bacteria, but there are also a few records of microalgae growing endophytically in vascular land plants, some of which belong to the genus Coccomyxa. In this study, we isolated a single-celled photosynthetic microorganism from the arsenic-tolerant shrub Acacia farnesiana, thus we hypothesized that it is an endophytic arsenic-tolerant microalga. The microorganism was identified as belonging to the genus Coccomyxa, and the observation of algal cells within the root tissues strongly suggests its endophytic nature. The alga's tolerance to arsenate (AsV) and its influence on the fitness of A. farnesiana in the presence of AsV were evaluated. Coccomyxa sp. can tolerate up to 2000 µM of AsV for periods shorter than 10 days, however, AsV-tolerance decreased significantly in longer exposure periods. The association with the microalga increased the pigment content in aboveground tissues of A. farnesiana seedlings exposed to AsV for 50 days, without changes in plant growth or arsenic accumulation. This work describes the association, probably endophytic, between an angiosperm and a microalga, confirming the ability of the genus Coccomyxa to form associations with land plants and broadening the known variety of plant endophytes.

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.

Impact of seed-transmitted endophytic bacteria on intra- and inter-cultivar plant growth promotion modulated by certain sets of metabolites in rice crop

Exploring the beneficial interactions between plant and endophytes could be an effective strategy in the implementation of sustainable agricultural practices to enhance crop productivity. In this study, we aimed to evaluate holistically the plant growth promoting (PGP) abilities rendered by seed-transmitted endophytic bacteria isolated from in vitro grown calli of two rice cultivars. Nine bacterial endophytes, designated as PB001-PB009, were isolated and identified at the genus level through 16S rRNA gene sequence analysis. Biochemical investigations disclosed that they possess several PGP traits, such as phosphate solubilization, indole acetic acid biosynthesis, ammonia production, nitrogen fixation, amylase production and siderophore production. Results in gnotobiotic conditions revealed an increase in fresh weight, dry weight, root length and shoot length of seedlings germinated from endophyte-primed seeds than the control (uninoculated) set in a non-host and two host rice cultivars. In net house experiments, plants germinated from Micrococcus sp. PB001, Pseudomonas sp. PB002, Methylobacterium sp. PB005 and Methylorubrum sp. PB009 primed seeds showed an increase of upto 34.06 %, 38.77 %, 182.87 %, 16.59 % and 33.52 % in chlorophyll content, number of tillers/plant, number of grains/plant, grain size and grain weight, respectively than control plant sets in the non-host rice cultivar, further validating inter-cultivar PGP abilities of these endophytes. Metabolite profiling unfolded the abundance of few metabolites that are involved in pathways associated with PGP traits, in seedlings germinated from the endophyte-primed seeds. Together, the study documents the effect of seed-transmitted endophytic bacteria on intra- and inter-cultivar PGP by modulating certain sets of metabolites in rice plant, and is promising in developing bioinoculant formulations employing these selected endophytes for enhancement of rice productivity.

Use of Autochthonous Lactobacilli to Increase the Safety of Zgougou

Seeds of Pinus halepensis are used for preparing zgougou, a spontaneously fermented matrix giving juice and seeds debris, consumed in many Arabian countries, including Tunisia. In the same way as all the food processes based on spontaneous fermentation, zgougou hides health risks due to eventual pathogenic microorganisms and derived toxins. This study aimed at investigating the effect of the use of autochthonous Lactobacillus paraplantarum A1 and Lactobacillus plantarum A2, as fermentation starters, on the microbiological characteristics, profiles of volatile organic compounds (VOC), antibacterial and antioxidant activities of juice and seeds debris from zgougou. The starter lactobacilli inhibited undesired bacteria (e.g., Enterobacter and Aeromonas) and coccus-shaped lactic acid bacteria, as shown by culture-dependent and-independent methods. The inhibitory effect was more evident in juice than in seeds debris. Some VOC (ethanol, acetoin, phenol,2-methoxy and caryophyllene) were present at higher concentrations in juice and seeds obtained upon spontaneous fermentation, compared to the samples deriving from fermentation with lactobacilli. The latter samples were characterized by higher concentrations of acetic acid, decane, 1-nonanol, bornyl acetate and bornyl formate. In addition, they showed a wider spectrum of antibacterial activity than spontaneously fermented juice and seeds. The use of autochthonous lactobacilli did not relevantly affect the antioxidant activity of zgougou. When juice from lactobacilli-driven fermentation was used to prepare a traditional Tunisian pudding ("Assidat-Zgougou"), it improved color and odor with respect to the pudding containing juice from spontaneous fermentation. This study showed that the use, at laboratory scale, of autochthonous lactobacilli is a feasible biotechnological tool to outgrow undesired bacteria, thus improving the safety of zgougou juice. Future studies should be undertaken to confirm the observed benefits at industrial scale.

Secrets of plants: Endophytes

Endophytic fungi are an important component that colonizes in healthy tissues of living plants and can be readily isolated from any microbial or plant growth medium. They act as reservoirs of novel bioactive secondary metabolites, such as alkaloids, phenolic acids, quinones, steroids, saponins, tannins, and terpenoids that serve as a potential candidate for antimicrobial, anti-insect, anticancer and many more properties. Their huge diversity and particular habituation, they can provide a good area for research in the field of making new medicines and novel drug-like molecules. Because of the impact of endophytes on host plant by enhancing their growth or increasing their fitness, also making them tolerant to abiotic and biotic stresses and holding the secondary metabolites, endophytes are gaining attention as a subject for research. This review aims to comprehend the contribution and uses of endophytes and relationships between endophytic fungi and their host medicinal plants.

A Hypothetical Bottleneck in the Plant Microbiome

The plant microbiome may be bottlenecked at the level of endophytes of individual seeds. Strong defense of developing seeds is predicted by optimal defense theory, and we have experimentally demonstrated exclusionary interactions among endophytic microbes infecting individual seeds of Centaurea stoebe. Having found a single, PDA-culturable microbe per seed or none in an exploratory study with Centaurea stoebe, we completed a more extensive survey of an additional 98 plant species representing 39 families. We again found that individual, surface-sterilized seeds of all species hosted only one PDA-culturable bacterial or fungal endophyte per seed, or none. PDA-unculturables were not determined but we expect them to also be bottlenecked in individual seeds, as they too should be governed by exclusionary interactions. If the bottleneck were confirmed with high-throughput sequencing of individual seeds then it would make sense to further investigate the Primary Symbiont Hypothesis (PSH). This includes the prediction that primary symbionts (i.e., the winners of the exclusionary battles among seed endophytes) have strong effects on seedlings depending on symbiont identity.

High content analysis of sea buckthorn, black chokeberry, red and white currants microbiota - A pilot study

The high potential of sea buckthorn, black chokeberry, red and white currants in healthy food industry boosted interest in the plant cultivation. The present study is the first work providing comprehensive information on microbial populations of these berries. Next Generation Sequencing allowed identification of eukaryotic and prokaryotic microorganisms prevalent on specific berries, including uncultivable microorganisms. Our study revealed the broad diversity of berries-associated bacterial and fungal microorganisms. Analysis of representative microbial OTUs showed a clear separation among inhabitants of sea buckthorn, black chokeberry and both currants, indicating plant-defined differences in the composition of the bacterial and fungal microbiota. Among the microorganisms distributed on tested berries, we documented potentially beneficial fungi and bacteria along with potential phytopathogens or those harmful for humans. Thus, plant microbiota appears to be highly relevant for the evaluation of the microbiota impact on food quality and human health.

Endophytic bacterial microbiome associated with leaves of genetically modified (AtAREB1) and conventional (BR 16) soybean plants

Plant leaves (phyllosphere) have a great potential for colonization and microbial growth, consisting of a dynamic environment in which several factors can interfere with the microbial population structure. The use of genetically modified (GM) plants has introduced several traits in agriculture, such as the improvement of plant drought tolerance, as observed in the AtAREB1 transcription factor overexpression in soybean (Glycine max L. Merrill). The present study aimed at investigating the taxonomic and functional profile of the leaf microbial community of bacteria found in GM (drought-tolerant event 1Ea2939) and conventional (BR 16) soybean plants. Bacterial DNA was extracted from leaf samples collected from each genotype and used for microbial diversity and richness analysis through the MiSeq Illumina platform. Functional prediction was performed using the PICRUSt tool and the STAMP v 2.1.3 software. The obtainment of the GM event 1Ea2939 showed minimum effects on the microbial community and in the potential for chemical-genetic communication, i.e. in the potential for symbiotic and/or mutualistic interaction between plants and their natural microbiota.

Mining Halophytes for Plant Growth-Promoting Halotolerant Bacteria to Enhance the Salinity Tolerance of Non-halophytic Crops

Salinity stress is one of the major abiotic stresses limiting crop production in arid and semi-arid regions. Interest is increasing in the application of PGPRs (plant growth promoting rhizobacteria) to ameliorate stresses such as salinity stress in crop production. The identification of salt-tolerant, or halophilic, PGPRs has the potential to promote saline soil-based agriculture. Halophytes are a useful reservoir of halotolerant bacteria with plant growth-promoting capabilities. Here, we review recent studies on the use of halophilic PGPRs to stimulate plant growth and increase the tolerance of non-halophytic crops to salinity. These studies illustrate that halophilic PGPRs from the rhizosphere of halophytic species can be effective bio-inoculants for promoting the production of non-halophytic species in saline soils. These studies support the viability of bioinoculation with halophilic PGPRs as a strategy for the sustainable enhancement of non-halophytic crop growth. The potential of this strategy is discussed within the context of ensuring sustainable food production for a world with an increasing population and continuing climate change. We also explore future research needs for using halotolerant PGPRs under salinity stress.

What Is There in Seeds? Vertically Transmitted Endophytic Resources for Sustainable Improvement in Plant Growth

Phytobeneficial microbes, particularly endophytes, such as fungi and bacteria, are concomitant partners of plants throughout its developmental stages, including seed germination, root and stem growth, and fruiting. Endophytic microbes have been identified in plants that grow in a wide array of habitats; however, seed-borne endophytic microbes have not been fully explored yet. Seed-borne endophytes are of great interest because of their vertical transmission; their potential to produce various phytohormones, enzymes, antimicrobial compounds, and other secondary metabolites; and improve plant biomass and yield under biotic and abiotic stresses. This review addresses the current knowledge on endophytes, their ability to produce metabolites, and their influence on plant growth and stress mitigation.

Bacterial Endophytes in Plant Tissue Culture: Mode of Action, Detection, and Control

Endophytic bacteria have been increasingly in the focus of research projects during the last decade. This has changed the view on bacteria in plant tissue culture and led to the differentiation between artificially introduced contaminations and naturally occurring endophytes with neutral, negative, or positive impact on the plant propagation process. This review chapter gives an overview on recent findings about the impact that bacteria have on the plant physiology in general and during micropropagation. Additionally, methods for the detection and identification of bacteria in plant tissue are described and, finally, suggestions of how to deal with bacterial endophytes in in vitro culture are given.

Host Specificity of Endophytic Mycobiota of Wild Nicotiana Plants from Arid Regions of Northern Australia

In arid regions of northern Australia, plants survive under water deficit, high temperatures, intense solar radiation and nutrient-impoverished soils. They employ various morpho-physiological and biochemical adaptations including interaction with microbial symbionts. We evaluated identity, host and tissue association with geographical distribution of fungal endophytes isolated from above- and below-ground tissues of plants of three indigenous Australian Nicotiana species. Isolation frequency and α-diversity were significantly higher for root endophyte assemblages than those of stem and leaf tissues. We recorded no differences in endophyte species richness or diversity as a function of sampling location, but did detect differences among different host genotypes and plant tissues. There was a significant pattern of community similarity associated with host genotypes but no consistent pattern of fungal community structuring associated with sampling location and tissue type, regardless of the community similarity measurements used.

Diverse Plant-Associated Pleosporalean Fungi from Saline Areas: Ecological Tolerance and Nitrogen-Status Dependent Effects on Plant Growth

Similar to mycorrhizal mutualists, the rhizospheric and endophytic fungi are also considered to act as active regulators of host fitness (e.g., nutrition and stress tolerance). Despite considerable work in selected model systems, it is generally poorly understood how plant-associated fungi are structured in habitats with extreme conditions and to what extent they contribute to improved plant performance. Here, we investigate the community composition of root and seed-associated fungi from six halophytes growing in saline areas of China, and found that the pleosporalean taxa (Ascomycota) were most frequently isolated across samples. A total of twenty-seven representative isolates were selected for construction of the phylogeny based on the multi-locus data (partial 18S rDNA, 28S rDNA, and transcription elongation factor 1-α), which classified them into seven families, one clade potentially representing a novel lineage. Fungal isolates were subjected to growth response assays by imposing temperature, pH, ionic and osmotic conditions. The fungi had a wide pH tolerance, while most isolates showed a variable degree of sensitivity to increasing concentration of either salt or sorbitol. Subsequent plant-fungal co-culture assays indicated that most isolates had only neutral or even adverse effects on plant growth in the presence of inorganic nitrogen. Interestingly, when provided with organic nitrogen sources the majority of the isolates enhanced plant growth especially aboveground biomass. Most of the fungi preferred organic nitrogen over its inorganic counterpart, suggesting that these fungi can readily mineralize organic nitrogen into inorganic nitrogen. Microscopy revealed that several isolates can successfully colonize roots and form melanized hyphae and/or microsclerotia-like structures within cortical cells suggesting a phylogenetic assignment as dark septate endophytes. This work provides a better understanding of the symbiotic relationship between plants and pleosporalean fungi, and initial evidence for the use of this fungal group in benefiting plant production.

Specialized Microbiome of a Halophyte and its Role in Helping Non-Host Plants to Withstand Salinity

Root microbiota is a crucial determinant of plant productivity and stress tolerance. Here, we hypothesize that the superior halo-tolerance of seepweed Suaeda salsa is tightly linked to a specialized belowground microbiome. To test this hypothesis, we performed a phylogenetic trait-based framework analysis based on bacterial 16S rRNA gene and fungal nuclear rRNA internal transcribed spacer profiling. Data showed that the dominant α-proteobacteria and γ-proteobacteria communities in bulk soil and root endosphere tend to be phylogenetically clustered and at the same time exhibit phylogenetic over-dispersion in rhizosphere. Likewise, the dominant fungal genera occurred at high phylogenetic redundancy. Interestingly, we found the genomes of rhizospheric and endophytic bacteria associated with S. salsa to be enriched in genes contributing to salt stress acclimatization, nutrient solubilization and competitive root colonization. A wide diversity of rhizobacteria with similarity to known halotolerant taxa further supported this interpretation. These findings suggest that an ecological patterned root-microbial interaction strategy has been adopted in S. salsa system to confront soil salinity. We also demonstrated that the potential core microbiome members improve non-host plants growth and salt tolerance. This work provides a platform to improve plant fitness with halophytes-microbial associates and novel insights into the functions of plant microbiome under salinity.

Effects of growth stage and fulvic acid on the diversity and dynamics of endophytic bacterial community in Stevia rebaudiana Bertoni leaves

The aim of this study was to learn the interactions among the endophytic bacteria, the plant growth, the foliar spray of fulvic acid, and the accumulation of steviol glycosides in the leaves of Stevia rebaudiana. Metagenomic DNA was extracted from the Stevia leaves at different growth stages with or without the fulvic acid treatment; and the diversity of endophytic bacteria in Stevia leaves was estimated by pyrosequencing of 16S rRNA genes. As results, Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were found to be the dominant phyla despite the growth stages and fulvic acid application. Stevia growth stages strongly regulated composition of endophytic community. The genera Agrobacterium (12.3%) and Erwinia (7.2%) dominated in seedling stage were apparently declined in the vegetable and initial flowering stages, while Sphingomonas and Methylobacterium increased in mature leaves at harvest time, which showed that the mature leaves of Stevia preferred to accumulate some certain endophytic bacteria. Sphingomonas and Methylobacterium constituted an important part of the core endophytic community and were positively correlated with the stevioside content and UGT74G1 gene expression, respectively; while Erwinia, Agrobacterium, and Bacillus were negatively correlated with the stevioside accumulation. Fulvic acid treatment accelerated the variation of endophytes along the growth stages and increased the steviol glycosides content. This is the first study to reveal the community composition of endophytic bacteria in the Stevia leaves, to evidence the strong effects of growth stage and fulvic acid application on the endophytes of Stevia, and to demonstrate the correlation between the endophytic bacteria and the steviol glycosides accumulation.

Fungal endophytes in aboveground tissues of desert plants: infrequent in culture, but highly diverse and distinctive symbionts

In hot deserts, plants cope with aridity, high temperatures, and nutrient-poor soils with morphological and biochemical adaptations that encompass intimate microbial symbioses. Whereas the root microbiomes of arid-land plants have received increasing attention, factors influencing assemblages of symbionts in aboveground tissues have not been evaluated for many woody plants that flourish in desert environments. We evaluated the diversity, host affiliations, and distributions of endophytic fungi associated with photosynthetic tissues of desert trees and shrubs, focusing on nonsucculent woody plants in the species-rich Sonoran Desert. To inform our strength of inference, we evaluated the effects of two different nutrient media, incubation temperatures, and collection seasons on the apparent structure of endophyte assemblages. Analysis of >22,000 tissue segments revealed that endophytes were isolated four times more frequently from photosynthetic stems than leaves. Isolation frequency was lower than expected given the latitude of the study region and varied among species a function of sampling site and abiotic factors. However, endophytes were very species-rich and phylogenetically diverse, consistent with less arid sites of a similar latitudinal position. Community composition differed among host species, but not as a function of tissue type, sampling site, sampling month, or exposure. Estimates of abundance, diversity, and composition were not influenced by isolation medium or incubation temperature. Phylogenetic analyses of the most commonly isolated genus (Preussia) revealed multiple evolutionary origins of desert-plant endophytism and little phylogenetic structure with regard to seasonality, tissue preference, or optimal temperatures and nutrients for growth in vitro. Together, these results provide insight into endophytic symbioses in desert-plant communities and can be used to optimize strategies for capturing endophyte biodiversity at regional scales.

Seasonal variation of bacterial endophytes in urban trees

Bacterial endophytes, non-pathogenic bacteria residing within plants, contribute to the growth and development of plants and their ability to adapt to adverse conditions. In order to fully exploit the capabilities of these bacteria, it is necessary to understand the extent to which endophytic communities vary between species and over time. The endophytes of Acer negundo, Ulmus pumila, and Ulmus parvifolia were sampled over three seasons and analyzed using culture dependent and independent methods (culture on two media, terminal restriction fragment length polymorphism, and tagged pyrosequencing of 16S ribosomal amplicons). The majority of culturable endophytes isolated were Actinobacteria, and all the samples harbored Bacillus, Curtobacterium, Frigoribacterium, Methylobacterium, Paenibacilllus, and Sphingomonas species. Regardless of culture medium used, only the culturable communities obtained in the winter for A. negundo could be distinguished from those of Ulmus spp. In contrast, the nonculturable communities were dominated by Proteobacteria and Actinobacteria, particularly Erwinia, Ralstonia, and Sanguibacter spp. The presence and abundance of various bacterial classes and phyla changed with the changing seasons. Multivariate analysis on the culture independent data revealed significant community differences between the endophytic communities of A. negundo and Ulmus spp., but overall season was the main determinant of endophytic community structure. This study suggests studies on endophytic populations of urban trees should expect to find significant seasonal and species-specific community differences and sampling should proceed accordingly.

Soil-foraging animals alter the composition and co-occurrence of microbial communities in a desert shrubland

Animals that modify their physical environment by foraging in the soil can have dramatic effects on ecosystem functions and processes. We compared bacterial and fungal communities in the foraging pits created by bilbies and burrowing bettongs with undisturbed surface soils dominated by biocrusts. Bacterial communities were characterized by Actinobacteria and Alphaproteobacteria, and fungal communities by Lecanoromycetes and Archaeosporomycetes. The composition of bacterial or fungal communities was not observed to vary between loamy or sandy soils. There were no differences in richness of either bacterial or fungal operational taxonomic units (OTUs) in the soil of young or old foraging pits, or undisturbed soils. Although the bacterial assemblage did not vary among the three microsites, the composition of fungi in undisturbed soils was significantly different from that in old or young foraging pits. Network analysis indicated that a greater number of correlations between bacterial OTUs occurred in undisturbed soils and old pits, whereas a greater number of correlations between fungal OTUs occurred in undisturbed soils. Our study suggests that digging by soil-disturbing animals is likely to create successional shifts in soil microbial and fungal communities, leading to functional shifts associated with the decomposition of organic matter and the fixation of nitrogen. Given the primacy of organic matter decomposition in arid and semi-arid environments, the loss of native soil-foraging animals is likely to impair the ability of these systems to maintain key ecosystem processes such as the mineralization of nitrogen and the breakdown of organic matter, and to recover from disturbance.

Spatial structuring of arbuscular mycorrhizal communities in benchmark and modified temperate eucalypt woodlands

Arbuscular mycorrhizal fungi (AMF) are crucial to the functioning of the plant-soil system, but little is known about the spatial structuring of AMF communities across landscapes modified by agriculture. AMF community composition was characterized across four sites in the highly cleared south-western Australian wheatbelt that were originally dominated by forb-rich eucalypt woodlands. Environmentally induced spatial structuring in AMF composition was examined at four scales: the regional scale associated with location, the site scale associated with past management (benchmark woodlands with no agricultural management history, livestock grazing, recent revegetation), the patch scale associated with trees and canopy gaps, and the fine scale associated with the herbaceous plant species beneath which soils were sourced. Field-collected soils were cultured in trap pots; then, AMF composition was determined by identifying spores and through ITS1 sequencing. Structuring was strongest at site scales, where composition was strongly related to prior management and associated changes in soil phosphorus. The two fields were dominated by the genera Funneliformis and Paraglomus, with little convergence back to woodland composition after revegetation. The two benchmark woodlands were characterized by Ambispora gerdemannii and taxa from Gigasporaceae. Their AMF communities were strongly structured at patch scales associated with trees and gaps, in turn most strongly related to soil N. By contrast, there were few patterns at fine scales related to different herbaceous plant species, or at regional scales associated with the 175 km distance between benchmark woodlands. Important areas for future investigation are to identify the circumstances in which recolonization by woodland AMF may be limited by fungal propagule availability, reduced plant diversity and/or altered chemistry in agricultural soils.

Linking Bacterial Endophytic Communities to Essential Oils: Clues from Lavandula angustifolia Mill

Endophytic bacteria play a crucial role in plant life and are also drawing much attention for their capacity to produce bioactive compounds of relevant biotechnological interest. Here we present the characterisation of the cultivable endophytic bacteria of Lavandula angustifolia Mill.—a species used since antiquity for its therapeutic properties—since the production of bioactive metabolites from medical plants may reside also in the activity of bacterial endophytes through their direct production, PGPR activity on host, and/or elicitation of plant metabolism. Lavender tissues are inhabited by a tissue specific endophytic community dominated by Proteobacteria, highlighting also their difference from the rhizosphere environment where Actinobacteria and Firmicutes are also found. Leaves' endophytic community resulted as the most diverse from the other ecological niches. Overall, the findings reported here suggest: (i) the existence of different entry points for the endophytic community, (ii) its differentiation on the basis of the ecological niche variability, and (iii) a two-step colonization process for roots endophytes. Lastly, many isolates showed a strong inhibition potential against human pathogens and the molecular characterization demonstrated also the presence of not previously described isolates that may constitute a reservoir of bioactive compounds relevant in the field of pathogen control, phytoremediation, and human health.

Novel symbiotic protoplasts formed by endophytic fungi explain their hidden existence, lifestyle switching, and diversity within the plant kingdom

Diverse fungi live all or part of their life cycle inside plants as asymptomatic endophytes. While endophytic fungi are increasingly recognized as significant components of plant fitness, it is unclear how they interact with plant cells; why they occur throughout the fungal kingdom; and why they are associated with most fungal lifestyles. Here we evaluate the diversity of endophytic fungi that are able to form novel protoplasts called mycosomes. We found that mycosomes cultured from plants and phylogenetically diverse endophytic fungi have common morphological characteristics, express similar developmental patterns, and can revert back to the free-living walled state. Observed with electron microscopy, mycosome ontogeny within Aureobasidium pullulans may involve two organelles: double membrane-bounded promycosome organelles (PMOs) that form mycosomes, and multivesicular bodies that may form plastid-infecting vesicles. Cultured mycosomes also contain a double membrane-bounded organelle, which may be homologous to the A. pullulans PMO. The mycosome PMO is often expressed as a vacuole-like organelle, which alternatively may contain a lipoid body or a starch grain. Mycosome reversion to walled cells occurs within the PMO, and by budding from lipid or starch-containing mycosomes. Mycosomes discovered in chicken egg yolk provided a plant-independent source for analysis: they formed typical protoplast stages, contained fungal ITS sequences and reverted to walled cells, suggesting mycosome symbiosis with animals as well as plants. Our results suggest that diverse endophytic fungi express a novel protoplast phase that can explain their hidden existence, lifestyle switching, and diversity within the plant kingdom. Importantly, our findings outline "what, where, when and how", opening the way for cell and organelle-specific tests using in situ DNA hybridization and fluorescent labels. We discuss developmental, ecological and evolutionary contexts that provide a robust framework for continued tests of the mycosome phase hypothesis.

Analysis of plant-bacteria interactions in their native habitat: bacterial communities associated with wild tobacco are independent of endogenous jasmonic acid levels and developmental stages

Jasmonic acid (JA) mediates defense responses against herbivores and necrotrophic pathogens but does it influence the recruitment of bacterial communities in the field? We conducted field and laboratory experiments with transformed Nicotiana attenuata plants deficient in jasmonate biosynthesis (irAOC) and empty vector controls (EV) to answer this question. Using both culture-dependent and independent techniques, we characterized root and leaf-associated bacterial communities over five developmental stages, from rosette through flowering of plants grown in their natural habitat. Based on the pyrosequencing results, alpha and beta diversity did not differ among EV and irAOC plants or over ontogeny, but some genera were more abundant in one of the genotypes. Furthermore, bacterial communities were significantly different among leaves and roots. Taxa isolated only from one or both plant genotypes and hence classified as 'specialists' and 'generalists' were used in laboratory tests to further evaluate the patterns observed from the field. The putative specialist taxa did not preferentially colonize the jasmonate-deficient genotype, or alter the plant's elicited phytohormone signaling. We conclude that in N. attenuata, JA signaling does not have a major effect on structuring the bacterial communities and infer that colonization of plant tissues is mainly shaped by the local soil community in which the plant grows.

Simultaneous profiling of seed-associated bacteria and fungi reveals antagonistic interactions between microorganisms within a shared epiphytic microbiome on Triticum and Brassica seeds

In order to address the hypothesis that seeds from ecologically and geographically diverse plants harbor characteristic epiphytic microbiota, we characterized the bacterial and fungal microbiota associated with Triticum and Brassica seed surfaces. The total microbial complement was determined by amplification and sequencing of a fragment of chaperonin 60 (cpn60). Specific microorganisms were quantified by qPCR. Bacteria and fungi corresponding to operational taxonomic units (OTU) that were identified in the sequencing study were isolated and their interactions examined. A total of 5477 OTU were observed from seed washes. Neither total epiphytic bacterial load nor community richness/evenness was significantly different between the seed types; 578 OTU were shared among all samples at a variety of abundances. Hierarchical clustering revealed that 203 were significantly different in abundance on Triticum seeds compared with Brassica. Microorganisms isolated from seeds showed 99-100% identity between the cpn60 sequences of the isolates and the OTU sequences from this shared microbiome. Bacterial strains identified as Pantoea agglomerans had antagonistic properties toward one of the fungal isolates (Alternaria sp.), providing a possible explanation for their reciprocal abundances on both Triticum and Brassica seeds. cpn60 enabled the simultaneous profiling of bacterial and fungal microbiota and revealed a core seed-associated microbiota shared between diverse plant genera.

Live cell imaging reveals extensive intracellular cytoplasmic colonization of banana by normally non-cultivable endophytic bacteria

It is generally believed that endophytic microorganisms are intercellular inhabitants present in either cultivable or non-cultivable form primarily as root colonizers. The objective of this study was to determine whether the actively mobile micro-particles observed in the intracellular matrix of fresh tissue sections of banana included endophytic bacteria. Tissue sections (50-100 µm) from apical leaf sheaths of surface-disinfected suckers (cv. Grand Naine) displayed 'Brownian motion'-reminiscent abundant motile micro-particles under bright-field and phase-contrast (×1000), which appeared similar in size and motility to the pure cultures of endophytes previously isolated from banana. Observations on callus, embryonic cells and protoplasts with intact cell wall/plasma membrane confirmed their cytoplasmic nature. The motility of these entities reduced or ceased upon tissue fixation or staining with safranin/crystal violet (0.5 % w/v), but continued uninterrupted following treatment with actin-disrupting drugs, ruling out the possibility of micro-organelles like peroxisomes. Staining with 2,3,5-triphenyl tetrazolium chloride (TTC) confirmed them to be live bacteria with similar observations after dilute safranin (0.005 %) treatment. Tissue staining with SYTO-9 coupled with epi-fluorescence or confocal laser scanning microscopy showed bacterial colonization along the peri-space between cell wall and plasma membrane initially. SYTO-9 counterstaining on TTC- or safranin-treated tissue and those subjected to enzymatic permeabilization revealed the cytoplasmic bacteria. These included organisms moving freely in the cytoplasm and those adhering to the nuclear envelope or vacuoles and the intravacuolar colonizers. The observations appeared ubiquitous to different genomes and genotypes of banana. Plating the tissue homogenate on nutrient media seldom yielded colony growth. This study, supported largely by live cell video-imaging, demonstrates enormous intracellular colonization in bananas by normally non-cultivable endophytic bacteria in two niches, namely cytoplasmic and periplasmic, designated as 'Cytobacts' and 'Peribacts', respectively. The integral intracellular association with their clonal perpetuation suggests a mutualistic relationship between endophytes and the host.

Fungal diversity in adult date palm (Phoenix dactylifera L.) revealed by culture-dependent and culture-independent approaches

Endophytic flora plays a vital role in the colonization and survival of host plants, especially in harsh environments, such as arid regions. This flora may, however, contain pathogenic species responsible for various troublesome host diseases. The present study is aimed at investigating the diversity of both cultivable and non-cultivable endophytic fungal floras in the internal tissues (roots and leaves) of Tunisian date palm trees (Phoenix dactylifera). Accordingly, 13 isolates from both root and leaf samples, exhibiting distinct colony morphology, were selected from potato dextrose agar (PDA) medium and identified by a sequence match search wherein their 18S-28S internal transcribed spacer (ITS) sequences were compared to those available in public databases. These findings revealed that the cultivable root and leaf isolates fell into two groups, namely Nectriaceae and Pleosporaceae. Additionally, total DNA from palm roots and leaves was further extracted and ITS fragments were amplified. Restriction fragment length polymorphism (RFLP) analysis of the ITS from 200 fungal clones (leaves: 100; roots: 100) using HaeIII restriction enzyme revealed 13 distinct patterns that were further sequenced and led to the identification of Alternaria, Cladosporium, Davidiella (Cladosporium teleomorph), Pythium, Curvularia, and uncharacterized fungal endophytes. Both approaches confirmed that while the roots were predominantly colonized by Fusaria (members of the Nectriaceae family), the leaves were essentially colonized by Alternaria (members of the Pleosporaceae family). Overall, the findings of the present study constitute, to the authors' knowledge, the first extensive report on the diversity of endophytic fungal flora associated with date palm trees (P. dactylifera).

Characterization of the fungal microbiome (mycobiome) in fecal samples from dogs

The prevalence and phylogenetic description of fungal organisms and their role as part of the intestinal ecosystem have not yet been studied extensively in dogs. This study evaluated the fungal microbiome of 19 dogs (12 healthy dogs and 7 dogs with acute diarrhea) using fungal tag-encoded FLX-Titanium amplicon pyrosequencing. Five distinct fungal phyla were identified, with Ascomycota (medians: 97.9% of obtained sequences in healthy dogs and 98.2% in diseased dogs) and Basidiomycota (median 1.0% in healthy dogs and median 0.5% in diseased dogs) being the most abundant fungal phyla. A total of 219 fungal genera were identified across all 19 dogs with a median (range) of 28 (4–69) genera per sample. Candida was the most abundant genus found in both the diseased dogs (median: 1.9%, range: 0.2%–38.5% of sequences) and healthy dogs (median: 5.2%, range: 0.0%–63.1% of sequences). Candida natalensis was the most frequently identified species. No significant differences were observed in the relative proportions of fungal communities between healthy and diseased dogs. In conclusion, fecal samples of healthy dogs and dogs with acute diarrhea harbor various fungal genera, and their role in gastrointestinal health and disease warrants further studies.

Microscopic elucidation of abundant endophytic bacteria colonizing the cell wall–plasma membrane peri-space in the shoot-tip tissue of banana

Plants are known to harbor endophytic bacteria, the organisms residing internally without imparting any apparent adverse effects on the host. Endophytes are generally known to be present in few numbers colonizing the intercellular spaces, primarily in roots. This study adopting SYTO 9 staining and live confocal imaging of fresh tissue sections from the shoot-tip region of banana, supported by transmission electron microscopy, brings out, possibly for the first time, extensive bacterial colonization in the confined cell wall – plasma membrane peri-space. The integral host-association and their abundance suggest a prominent role of endophytes in the biology of the host.

This study was aimed at generating microscopic evidence of intra-tissue colonization in banana in support of the previous findings on widespread association of endophytic bacteria with the shoot tips of field-grown plants and micropropagated cultures, and to understand the extent of tissue colonization. Leaf-sheath tissue sections (∼50–100 µm) from aseptically gathered shoot tips of cv. Grand Naine were treated with Live/Dead bacterial viability kit components SYTO 9 (S9) and propidium iodide (PI) followed by epifluorescence or confocal laser scanning microscopy (CLSM). The S9, which targets live bacteria, showed abundant green-fluorescing particles along the host cell periphery in CLSM, apparently in between the plasma membrane and the cell wall. These included non-motile and occasional actively motile single bacterial cells seen in different x–y planes and z-stacks over several cell layers, with the fluorescence signal similar to that of pure cultures of banana endophytes. Propidium iodide, which stains dead bacteria, did not detect any, but post-ethanol treatment, both PI and 4′,6-diamidino-2-phenylindole detected abundant bacteria. Propidium iodide showed clear nuclear staining, as did S9 to some extent, and the fluorophores appeared to detect bacteria at the exclusion of DNA-containing plant organelles as gathered from bright-field and phase-contrast microscopy. The S9–PI staining did not work satisfactorily with formalin- or paraformaldehyde-fixed tissue. The extensive bacterial colonization in fresh tissue was further confirmed with the suckers of different cultivars, and was supported by transmission electron microscopy. This study thus provides clear microscopic evidence of the extensive endophytic bacterial inhabitation in the confined cell wall–plasma membrane peri-space in shoot tissue of banana with the organisms sharing an integral association with the host. The abundant tissue colonization suggests a possible involvement of endophytes in the biology of the host besides recognizing cell wall–plasma membrane peri-space as a major niche for plant-associated bacteria.

CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota

BACKGROUND

Besides the development of comprehensive tools for high-throughput 16S ribosomal RNA amplicon sequence analysis, there exists a growing need for protocols emphasizing alternative phylogenetic markers such as those representing eukaryotic organisms.

RESULTS

Here we introduce CloVR-ITS, an automated pipeline for comparative analysis of internal transcribed spacer (ITS) pyrosequences amplified from metagenomic DNA isolates and representing fungal species. This pipeline performs a variety of steps similar to those commonly used for 16S rRNA amplicon sequence analysis, including preprocessing for quality, chimera detection, clustering of sequences into operational taxonomic units (OTUs), taxonomic assignment (at class, order, family, genus, and species levels) and statistical analysis of sample groups of interest based on user-provided information. Using ITS amplicon pyrosequencing data from a previous human gastric fluid study, we demonstrate the utility of CloVR-ITS for fungal microbiota analysis and provide runtime and cost examples, including analysis of extremely large datasets on the cloud. We show that the largest fractions of reads from the stomach fluid samples were assigned to Dothideomycetes, Saccharomycetes, Agaricomycetes and Sordariomycetes but that all samples were dominated by sequences that could not be taxonomically classified. Representatives of the Candida genus were identified in all samples, most notably C. quercitrusa, while sequence reads assigned to the Aspergillus genus were only identified in a subset of samples. CloVR-ITS is made available as a pre-installed, automated, and portable software pipeline for cloud-friendly execution as part of the CloVR virtual machine package (http://clovr.org).

CONCLUSION

The CloVR-ITS pipeline provides fungal microbiota analysis that can be complementary to bacterial 16S rRNA and total metagenome sequence analysis allowing for more comprehensive studies of environmental and host-associated microbial communities.

Dynamics of seed-borne rice endophytes on early plant growth stages

Bacterial endophytes are ubiquitous to virtually all terrestrial plants. With the increasing appreciation of studies that unravel the mutualistic interactions between plant and microbes, we increasingly value the beneficial functions of endophytes that improve plant growth and development. However, still little is known on the source of established endophytes as well as on how plants select specific microbial communities to establish associations. Here, we used cultivation-dependent and -independent approaches to assess the endophytic bacterrial community of surface-sterilized rice seeds, encompassing two consecutive rice generations. We isolated members of nine bacterial genera. In particular, organisms affiliated with Stenotrophomonas maltophilia and Ochrobactrum spp. were isolated from both seed generations. PCR-based denaturing gradient gel electrophoresis (PCR-DGGE) of seed-extracted DNA revealed that approximately 45% of the bacterial community from the first seed generation was found in the second generation as well. In addition, we set up a greenhouse experiment to investigate abiotic and biotic factors influencing the endophytic bacterial community structure. PCR-DGGE profiles performed with DNA extracted from different plant parts showed that soil type is a major effector of the bacterial endophytes. Rice plants cultivated in neutral-pH soil favoured the growth of seed-borne Pseudomonas oryzihabitans and Rhizobium radiobacter, whereas Enterobacter-like and Dyella ginsengisoli were dominant in plants cultivated in low-pH soil. The seed-borne Stenotrophomonas maltophilia was the only conspicuous bacterial endophyte found in plants cultivated in both soils. Several members of the endophytic community originating from seeds were observed in the rhizosphere and surrounding soils. Their impact on the soil community is further discussed.