Seed and Root Endophytic Fungi in a Range Expanding and a Related Plant Species

Novel report of Acinetobacter johnsonii as an indole-producing seed endophyte in Tamarindus indica L

Plant-microbe associations have been regarded as an exciting topic of research due to their potential as environment friendly alternatives for stimulating crop growth and development. Seeds of Tamarindus indica L. have been chosen for the present study as seed endophytes prefer larger or nutritive cotyledon and hard seed coats for their colonization. The main objectives of our study were to isolate and identify the seed endophytes, their bioefficacy, and responsible chemical compounds. In a dose-dependent experiment, tamarind seed exudates (TSE) showed plant growth-promoting properties on Oryza sativa (53-81%), Daucus carota (10-31%), and Raphanus sativa (21-42%). Identification of the bacterial load in TSE through 16S rRNA sequencing revealed the existence of two bacterial species, Acinetobacter johnsonii and Niallia nealsonii. This is the first report of these two bacteria as seed endophytes of Tamarindus indica L. HRLC-MS analysis of TSE confirmed the presence of indole derivatives, primarily indole-3-lactic acid (ILA). The quantitative phytochemical estimation of bacterial culture filtrates revealed that indole-like substances were present in the extracts only in A. johnsonii at a concentration of 0.005 mg/ml of indole acetic acid equivalent. Experimental results suggested that the stimulatory activity of TSE was caused by the presence of A. johnsonii, a potential plant growth-promoting bacteria that produced indole-like compounds. This study suggests tamarind seed exudates with its endophytic microbiota as a potent plant growth-promoting agent that may find use as a cheap and sustainable source of metabolites useful in the agro-industries.

Diversity and Biological Characteristics of Seed-Borne Bacteria of Achnatherum splendens

As a high-quality plant resource for ecological restoration, Achnatherum splendens has strong adaptability and wide distribution. It is a constructive species of alkaline grassland in Northwest China. The close relationship between seed-borne bacteria and seeds causes a specific co-evolutionary effect which can enhance the tolerance of plants under various stresses. In this study, 272 bacterial isolates were isolated from the seeds of Achnatherum splendens in 6 different provinces of China. In total, 41 dominant strains were identified, and their motility, biofilm formation ability and antibiotic resistance were analyzed. The results showed that the bacteria of Achnatherum splendens belonged to 3 phyla and 14 genera, of which Firmicutes was the dominant phylum and Bacillus was the dominant genus. The motility and biofilm formation ability of the isolated strains were studied. It was found that there were six strains with a moving diameter greater than 8 cm. There were 16 strains with strong biofilm formation ability, among which Bacillus with biofilm formation ability was the most common, accounting for 37.5%. The analysis of antibiotic resistance showed that sulfonamides had stronger antibacterial ability to strains. Correlation analysis showed that the resistance of strains to aminoglycosides (kanamycin, amikacin, and gentamicin) was significantly positively correlated with their biofilm formation ability. This study provides fungal resources for improving the tolerance of plants under different stresses. In addition, this is the first report on the biological characteristics of bacteria in Achnatherum splendens.

Why Are There So Few Basidiomycota and Basal Fungi as Endophytes? A Review

A review of selected studies on fungal endophytes confirms the paucity of Basidiomycota and basal fungi, with almost 90% attributed to Ascomycota. Reasons for the low number of Basidiomycota and basal fungi, including the Chytridiomycota, Mucoromycota, and Mortierellomycota, are advanced, including isolation procedure and media, incubation period and the slow growth of basidiomycetes, the identification of non-sporulating isolates, endophyte competition, and fungus-host interactions. We compare the detection of endophytes through culture-dependent methods and culture-independent methods, the role of fungi on senescence of the host plant, and next-generation studies.

Native plants change the endophyte assembly and growth of an invasive plant in response to climatic factors

Climate change, microbial endophytes, and local plants can affect the establishment and expansion of invasive species, yet no study has been performed to assess these interactions. Using a growth chamber, we integrated the belowground (rhizosphere soils) and aboveground (mixture of mature leaf and leaf litter) microbiota into an experimental framework to evaluate the impacts of four native plants acting as microbial inoculation sources on endophyte assembly and growth of the invasive plant Ageratina adenophora in response to drought stress and temperature change. We found that fungal and bacterial enrichment in the leaves and roots of A. adenophora exhibited distinct patterns in response to climatic factors. Many fungi were enriched in roots in response to high temperature and drought stress; in contrast, many bacteria were enriched in leaves in response to low temperature and drought stress. Inoculation of microbiota from phylogenetically close native plant species (i.e., Asteraceae Artemisia atrovirens) causes the recipient plant A. adenophora (Asteraceae) to enrich dominant microbial species from inoculation sources, which commonly results in a lower dissimilar endophytic microbiota and thus produces more negative growth effects when compared to non-Asteraceae inoculations. Drought, microbial inoculation source, and temperature directly impacted the growth of A. adenophora. Both drought and inoculation also indirectly impacted the growth of A. adenophora by changing the root endophytic fungal assembly. Our data indicate that native plant identity can greatly impact the endophyte assembly and host growth of invasive plants, which is regulated by drought and temperature.IMPORTANCEThere has been increasing interest in the interactions between global changes and plant invasions; however, it remains to quantify the role of microbial endophytes in plant invasion with a consideration of their variation in the root vs leaf of hosts, as well as the linkages between microbial inoculations, such as native plant species, and climatic factors, such as temperature and drought. Our study found that local plants acting as microbial inoculants can impact fungal and bacterial enrichment in the leaves and roots of the invasive plant Ageratina adenophora and thus produce distinct growth effects in response to climatic factors; endophyte-mediated invasion of A. adenophora is expected to operate more effectively under favorable moisture. Our study is important for understanding the interactions between climate change, microbial endophytes, and local plant identity in the establishment and expansion of invasive species.

Insights into the seed microbiome and its ecological significance in plant life

In recent years, the microbiome has attracted much attention because of the multiple roles and functions that microbes play in plants, animals, and human beings. Seed-associated microbes are of particular interest in being the initial microbial inoculum that affects the critical early life stages of a plant. The seed-microbe interactions are also known to improve nutrient acquisition, resilience against pathogens, and resistance against abiotic stresses. Despite these diverse roles, the seed microbiome has received little attention in plant ecology. Thus, we review the current knowledge on seed microbial diversity, community structure, and functions obtained through culture-dependent and culture-independent approaches. Furthermore, we present a comprehensive synthesis of the ecological literature on seed-microbe interactions to better understand the impact of these interactions on plant health and productivity. We suggest that future research should focus on the role of the seed microbiome in the establishment, colonization and spread of plant species in their native and non-native ranges as it may provide new insights into conservation biology and invasion ecology.

Fallopia japonica and Impatiens glandulifera are colonized by species-poor root-associated fungal communities but have minor impacts on soil properties in riparian habitats

Fallopia japonica and Impatiens glandulifera are major plant invaders on a global scale that often become dominant in riparian areas. However, little is known about how these species affect interactions in soil–plant systems. The aim of this study was to investigate the impact of both species on abiotic and biotic soil properties, with a special focus on fungi. We investigated eight sites along small streams invaded by F. japonica and I. glandulifera, respectively, and compared each with nearby sites dominated by the native species Urtica dioica. Three different types of samples were collected: bulk soil, rhizosphere soil and roots from invasive and native stands at each site. Bulk soil samples were analysed for soil physicochemical, microbial properties (soil microbial respiration and ergosterol) and soil arthropod abundance (Acari and Collembola). Soil respiration was also evaluated in rhizosphere samples. The fungal community composition of both bulk soil and roots were analysed using a metabarcoding approach. Soil physicochemical properties as well as soil microbial activity, fungal biomass and soil fungal operational unit taxonomic unit (OTU) richness did not differ between invaded and native riparian habitats, indicating only minor belowground impacts of the two invasive plant species. Soil microbial activity, fungal biomass and soil fungal OTU richness were rather related to the soil physicochemical properties. In contrast, Acari abundance decreased by 68% in the presence of F. japonica, while Collembola abundance increased by 11% in I. glandulifera sites. Moreover, root-associated fungal communities differed between the invasive and native plants. In F. japonica roots, fungal OTU richness of all investigated ecological groups (mycorrhiza, endophytes, parasites, saprobes) were lower compared to U. dioica. However, in I. glandulifera roots only the OTU richness of mycorrhiza and saprobic fungi was lower. Overall, our findings show that F. japonica and I. glandulifera can influence the abundance of soil arthropods and are characterized by lower OTU richness of root-associated fungi.

In Vitro and In Silico Antioxidant Efficiency of Bio-Potent Secondary Metabolites From Different Taxa of Black Seed-Producing Plants and Their Derived Mycoendophytes

Oxidative stress is involved in the pathophysiology of multiple health complications, and it has become a major focus in targeted research fields. As known, black seeds are rich sources of bio-active compounds and widely used to promote human health due to their excellent medicinal and pharmaceutical properties. The present study investigated the antioxidant potency of various black seeds from plants and their derived mycoendophytes, and determined the total phenolic and flavonoid contents in different extracts, followed by characterization of major constituents by HPLC analysis. Finally, in silico docking determined their binding affinities to target myeloperoxidase enzymes. Ten dominant mycoendophytes were isolated from different black seed plants. Three isolates were then selected based on high antiradical potency and further identified by ITS ribosomal gene sequencing. Those isolated were Aspergillus niger TU 62, Chaetomium madrasense AUMC14830, and Rhizopus oryzae AUMC14823. Nigella sativa seeds and their corresponding endophyte A. niger had the highest content of phenolics in their n-butanol extracts (28.50 and 24.43 mg/g), flavonoids (15.02 and 11.45 mg/g), and antioxidant activities (90.48 and 81.48%), respectively, followed by Dodonaea viscosa and Portulaca oleracea along with their mycoendophytic R. oryzae and C. madrasense. Significant positive correlations were found between total phenolics, flavonoids, and the antioxidant activities of different tested extracts. The n-butanol extracts of both black seeds and their derived mycoendophytes showed reasonable IC50 values (0.81–1.44 mg/ml) compared to the control with significant correlations among their phytochemical contents. Overall, seventeen standard phenolics and flavonoids were used, and the compounds were detected in different degrees of existence and concentration in the examined extracts through HPLC analysis. Moreover, the investigation of the molecular simulation results of detected compounds against the myeloperoxidase enzyme revealed that, as a targeted antioxidant, rutin possessed a high affinity (−15.3184 kcal/mol) as an inhibitor. Taken together, the black seeds and their derived mycoendophytes are promising bio-prospects for the broad industrial sector of antioxidants with several valuable potential pharmaceutical and nutritional applications.

Strategies to Enhance the Use of Endophytes as Bioinoculants in Agriculture

The findings on the strategies employed by endophytic microbes have provided salient information to the researchers on the need to maximally explore them as bio-input in agricultural biotechnology. Biotic and abiotic factors are known to influence microbial recruitments from external plant environments into plant tissues. Endophytic microbes exhibit mutualism or antagonism association with host plants. The beneficial types contribute to plant growth and soil health, directly or indirectly. Strategies to enhance the use of endophytic microbes are desirable in modern agriculture, such that these microbes can be applied individually or combined as bioinoculants with bioprospecting in crop breeding systems. Scant information is available on the strategies for shaping the endophytic microbiome; hence, the need to unravel microbial strategies for yield enhancement and pathogen suppressiveness have become imperative. Therefore, this review focuses on the endophytic microbiome, mechanisms, factors influencing endophyte recruitment, and strategies for possible exploration as bioinoculants.

Site and Organ-Specific Culture-Dependent Endophytic Diversity of Crocus sativus L. (Saffron) in Kashmir Himalaya, India

The endophytic diversity of a host plant has been shown to vary across various spatio-temporal scales and between different organs of a plant, but no such study has been carried out on the economically important plant Crocus sativus (saffron). To fill this knowledge gap, the present study was undertaken to document the diversity of culturable bacterial, actinomycete and fungal endophytes at multiple sites from vegetative and reproductive organs of C. sativus. A total of 1170 culturable endophytic isolates were recovered from 6480 tissue segments of C. sativus collected from six different study sites in Pampore region of Kashmir valley in India. These isolates were identified using 16S and ITS (internal transcribed spacer) rDNA barcode sequence analysis and were classified into 84 operational taxonomic units (OTUs), including 52 bacterial OTUs, 7 actinomycete OTUs and 25 fungal OTUs. The phylogenetic analysis of sequences separated them into four phyla, namely, Firmicutes (46%), Ascomycota (30%), Proteobacteria (16%) and Actinobacteria (8%). Significant differences were observed in the diversity of endophytic assemblages across various study sites and different plant organs (P ≤ 0.001). Species richness was highest at the Baroosa site and lowest at the Chandhar site while the Shannon index was highest at the Baroosa site and lowest at the Letpur site. Among organs, species richness was highest in stigma and lowest in leaf. Similarly, Shannon index was highest for root and lowest for leaf. Further, 15 culturable endophytic OTUs showed organ specificity. The present study is the first comprehensive report that not only brings out differences in the diversity of endophytes associated with different organs and at different sites but also highlights the complexity of host-endophyte interaction at multiple scales.

Grass species identity shapes communities of root and leaf fungi more than elevation

Fungal symbionts can buffer plants from environmental extremes and may affect host capacities to acclimate, adapt, or redistribute under environmental change; however, the distributions of fungal symbionts along abiotic gradients are poorly described. Fungal mutualists should be the most beneficial in abiotically stressful environments, and the structure of networks of plant-fungal interactions likely shift along gradients, even when fungal community composition does not track environmental stress. We sampled 634 unique combinations of fungal endophytes and mycorrhizal fungi, grass species identities, and sampling locations from 66 sites across six replicate altitudinal gradients in the western Colorado Rocky Mountains. The diversity and composition of leaf endophytic, root endophytic, and arbuscular mycorrhizal (AM) fungal guilds and the overall abundance of fungal functional groups (pathogens, saprotrophs, mutualists) tracked grass host identity more closely than elevation. Network structures of root endophytes become more nested and less specialized at higher elevations, but network structures of other fungal guilds did not vary with elevation. Overall, grass species identity had overriding influence on the diversity and composition of above- and belowground fungal endophytes and AM fungi, despite large environmental variation. Therefore, in our system climate change may rarely directly affect fungal symbionts. Instead, fungal symbiont distributions will most likely track the range dynamics of host grasses.

Contrasting effects of soil microbial interactions on growth-defence relationships between early- and mid-successional plant communities

Plants allocate resources to processes related to growth and enemy defence. Simultaneously, they interact with complex soil microbiomes that also affect plant performance. While the influence of individual microbial groups on single plants is increasingly studied, effects of microbial interactions on growth, defence and growth-defence relationships remain unknown, especially at the plant community level. We investigated how three microbial groups (bacteria, fungi, protists), alone and in full-factorial combinations, affect plant performance and potential growth-defence relationships by measuring phenolics composition in early- and mid-successional grass and forb communities in a glasshouse experiment. Microbial groups did not affect plant growth and only fungi increased defence compounds in early- and mid-successional forbs, while grasses were not affected. Shoot biomass-defence relationships were negatively correlated in most microbial treatments in early-successional forbs, but positively in several microbial treatments in mid-successional forbs. The growth-defence relationship was generally negative in early-successional but not in mid-successional grasses. The presence of different microbiomes commonly removed the observed growth-defence relationships. We conclude that soil microorganisms and their interactions can shift growth-defence relationships differentially for plant functional groups and the relationships vary between successional stages. Microbial interaction-induced growth-defence shifts might therefore underlie distinct plant strategies and fitness.

Plant-Soil Feedbacks for the Restoration of Degraded Mine Lands: A Review

Much effort has been made to remediate the degraded mine lands that bring severe impacts to the natural environments. However, it remains unclear what drives the recovery of biodiversity and ecosystem functions, making the restoration of these fragile ecosystems a big challenge. The interactions among plant species, soil communities, and abiotic conditions, i.e., plant-soil feedbacks (PSFs), significantly influence vegetation development, plant community structure, and ultimately regulate the recovery of ecosystem multi-functionality. Here, we present a conceptual framework concerning PSFs patterns and potential mechanisms in degraded mine lands. Different from healthy ecosystems, mine lands are generally featured with harsh physical and chemical properties, which may have different PSFs and should be considered during the restoration. Usually, pioneer plants colonized in the mine lands can adapt to the stressful environment by forming tolerant functional traits and gathering specific soil microbial communities. Understanding the mechanisms of PSFs would enhance our ability to predict and alter both the composition of above- and below-ground communities, and improve the recovery of ecosystem functions in degraded mine lands. Finally, we put forward some challenges of the current PSFs study and discuss avenues for further research in the ecological restoration of degraded mine lands.

Reconstitution and Transmission of Gut Microbiomes and Their Genes between Generations

Microbiomes are transmitted between generations by a variety of different vertical and/or horizontal modes, including vegetative reproduction (vertical), via female germ cells (vertical), coprophagy and regurgitation (vertical and horizontal), physical contact starting at birth (vertical and horizontal), breast-feeding (vertical), and via the environment (horizontal). Analyses of vertical transmission can result in false negatives (failure to detect rare microbes) and false positives (strain variants). In humans, offspring receive most of their initial gut microbiota vertically from mothers during birth, via breast-feeding and close contact. Horizontal transmission is common in marine organisms and involves selectivity in determining which environmental microbes can colonize the organism's microbiome. The following arguments are put forth concerning accurate microbial transmission: First, the transmission may be of functions, not necessarily of species; second, horizontal transmission may be as accurate as vertical transmission; third, detection techniques may fail to detect rare microbes; lastly, microbiomes develop and reach maturity with their hosts. In spite of the great variation in means of transmission discussed in this paper, microbiomes and their functions are transferred from one generation of holobionts to the next with fidelity. This provides a strong basis for each holobiont to be considered a unique biological entity and a level of selection in evolution, largely maintaining the uniqueness of the entity and conserving the species from one generation to the next.

The 'black box' of plant demography: how do seed type, climate and seed fungal communities affect grass seed germination?

Demographic studies measure drivers of plant fecundity including seed production and survival, but few address both abiotic and biotic drivers of germination such as variation in climate among sites, population density, maternal plants, seed type and fungal pathogen abundance. We examined germination and microbial communities of seeds of Danthonia californica, which are either chasmogamous (external, wind-pollinated) or cleistogamous (internal, self-fertilized) and Festuca roemeri, which are solely chasmogamous. Seed populations were sourced across environmental gradients. We tested germination and used high-throughput sequencing to characterize seed fungal community structure. For F. roemeri, maternal plants significantly influenced germination as did climate and pathogens; germination increased from wetter, cooler sites. For D. californica, the main drivers of germination were maternal plant, seed type and pathogens; on average, more chasmogamous seeds germinated. Fungal communities depended largely on seed type, with fewer fungi associated with cleistogamous seeds, but the communities also depended on site factors such as vapor pressure deficit, plant density and whether the seeds had germinated. Putative pathogens that were negatively correlated with germination were more abundant for both D. californica and F. roemeri chasmogamous seeds than D. californica cleistogamous seeds. In D. californica, cleistogamous and chasmogamous seeds contain vastly different fungal communities.

Beneficial traits of grain-residing endophytic communities in wheat with different sensitivity to Pseudomonas syringae

Deep insight into compositional and functional features of endophytic bacterial communities residing in wheat grains opens the way to the use of their plant growth promoting and biocontrol abilities in agricultural biotechnology. The aim of this work was to compare grain-residing endophytes from winter wheat varieties with different sensitivity to Pseudomonas syringae pv. atrofaciens (McCulloch) and to examine their plant-beneficial traits and antagonistic effects. Grain-residing bacteria were isolated from surface-sterilized grains of three wheat varieties sown in Ukraine following a culture-dependent protocol, and were screened for their plant growth promotion (PGP) and antagonistic properties. Bacterial morphotypes were represented by gram-negative rods, endospore-forming bacilli and gram-positive cocci. Different resistance to phytopathogenic pseudomonads was associated with distinctive quantitative and functional features of grain-residing endophytic communities. High resistance to P. syringae was coupled with the prevalence of gram-negative rods in the endophytic community, the highest proportion of endophytic bacteria possessing three PGP activities (phosphate solubilization, nitrogen fixation and production of indolic compounds) simultaneously, and with the most potent antagonistic activity of grain-residing endospore-forming bacilli. In total, five grain-residing isolates, which were obtained from three wheat varieties (two isolates from varieties with medium and high resistance and one – from a low-resistant variety), demonstrated ability to restrain P. syringae pv. atrofaciens (McCulloch) growth. Two isolates (P6 and P10) which were obtained from the high-resistant wheat variety Podolyanka and were assigned to Paenibacillus and Brevibacillus genera according to their biochemical profiling and MS-DS identification, showed the most potent antagonistic effects as indicated by maximum inhibition zone in agar well diffusion assay. These results shed light on the association of the features of grain-residing endophytic bacteria with wheat resistance to phytopathogenic pseudomonads. Isolates from the high-resistant wheat variety can be recommended for grain dressing as plant growth promoting and biocontrol agents for P. syringae pv. atrofaciens (McCulloch).

Seed Treatment With Systemic Fungicides: Time for Review

Pre-sowing seed treatment with systemic fungicides is a firmly entrenched practice for most agricultural crops worldwide. The treatment is intended to protect the crop against seed- and soil-borne diseases. In recent years, there is increasing evidence that fungicidal applications to manage diseases might inadvertently also affect non-target organisms, such as endophytes. Endophytes are ubiquitously present in plants and contribute to plant growth and development besides offering resistance to biotic and abiotic stresses. In seeds, endophytes may play a role in seed development, seed germination, seedling establishment and crop performance. In this paper, we review the recent literature on non-target effects of fungicidal applications on endophytic fungal community and discuss the possible consequences of indiscriminate seed treatment with systemic fungicide on seed endophytes. It is now well recognized that endophytes are ubiquitously present in all parts of the plant, including the seeds. They may be transmitted vertically from seed to seed as in many grasses and/or acquired horizontally from the soil and the environment. Though the origins and evolution of these organisms in plants are a matter of conjecture, numerous studies have shown that they symbiotically aid in plant growth and development, in nutrient acquisition as well in protecting the plants from abiotic and biotic stresses. Against this background, it is reasonable to assume that the use of systemic fungicides in seed treatment may not only affect the seed endophytes but also their attendant benefits to seedling growth and establishment. While there is evidence to indicate that fungicidal applications to manage plant diseases also affect foliar endophytes, there are only few studies that have documented the effect of seed treatment on seed-borne endophytes. Some of the convincing examples of the latter come from studies on the effect of fungicide application on rye grass seed endophyte AR37. More recently, experiments have shown that removal of seed endophytes by treatment with systemic fungicides leads to significant loss of seedling vigour and that such losses could be partially restored by enriching the seedlings with the lost endophytes. Put together, these studies reinforce the importance of seed endophytes to seedling growth and establishment and draw attention on how to trade the balance between the benefits of seed treatments and the direct and indirect costs incurred due to loss of endophytes. Among several approaches, use of reduced-risk fungicides and identifying fungicide-resistant endophytes are suggested to sustain the endophyte contribution to early seedling growth.

Filtrates from cultures of endophytic fungi isolated from leaves of Copaifera oblongifolia (Fabaceae) affect germination and seedling development differently

Interactions between endophytic fungi (EFs) and their host plants range from positive to neutral to negative. The results of such interactions can vary depending on the organ of the infected host plant. EFs isolated from the leaves of some species of plants have potential for use as agents to inhibit seed germination and control invasive plants. The objectives of this study were to identify EFs present in the leaves of Copaifera oblongifolia and to evaluate the role of these fungi in seed germination and seedling development. A total of 11 species of EFs were isolated, which were identified using the internal transcribed spacers (ITS) sequence of the nuclear ribosomal DNA. The isolated species of EFs are generalists and probably are transmitted horizontally. Laboratory tests revealed that filtrates of these fungal isolates differently affect seed germination and seedling development of C. oblongifolia. The species Curvularia intermedia, Neofusicoccum parvum, Pseudofusicoccum stromaticum and Phomopsis sp. negatively affected seed germination, with N. parvum standing out for its negative effects, inhibiting seedling germination and survival in 89 and 222%, respectively. In addition, Cochliobolus intermedius negatively affected seedling development. Thus, the combined use of N. parvum and C. intermedius, or products from the metabolism of these microorganisms, in the control of invasive plants deserves attention from future studies.

Phytomicrobiome for promoting sustainable agriculture and food security: Opportunities, challenges, and solutions

Ensuring food security in an environmentally sustainable way is a global challenge. To achieve this agriculture productivity requires increasing by 70 % under increasingly harsh climatic conditions without further damaging the environmental quality (e.g. reduced use of agrochemicals). Most governmental and inter-governmental agencies have highlighted the need for alternative approaches that harness natural resource to address this. Use of beneficial phytomicrobiome, (i.e. microbes intimately associated with plant tissues) is considered as one of the viable solutions to meet the twin challenges of food security and environmental sustainability. A diverse number of important microbes are found in various parts of the plant, i.e. root, shoot, leaf, seed, and flower, which play significant roles in plant health, development and productivity, and could contribute directly to improving the quality and quantity of food production. The phytomicrobiome can also increase productivity via increased resource use efficiency and resilience to biotic and abiotic stresses. In this article, we explore the role of phytomicrobiome in plant health and how functional properties of microbiome can be harnessed to increase agricultural productivity in environmental-friendly approaches. However, significant technical and translation challenges remain such as inconsistency in efficacy of microbial products in field conditions and a lack of tools to manipulate microbiome in situ. We propose pathways that require a system-based approach to realize the potential to phytomicrobiome in contributing towards food security. We suggest if these technical and translation constraints could be systematically addressed, phytomicrobiome can significantly contribute towards the sustainable increase in agriculture productivity and food security.

Diversity and Spatiotemporal Distribution of Fungal Endophytes Associated with Salvia multicaulis

Salvia multicaulis has been an important medicinal plant in Iran and several East Asian countries for hundreds of years. Because of growing demand, overharvesting of wild S. multicaulis has endangered its wild populations. Endophytes are well known for protecting wild plant populations against biotic and abiotic stresses, especially under harsh situations, as well as for their plant growth enhancement activities. Since no information was on endophyte biology in S. multicaulis, here we aimed at analyzing diversity and spatiotemporal distribution of fungal endophytes associating S. multicaulis in their main wild habitats in Iran, i.e., Qazvin, Alborz and Mazandaran provinces. A total of 153 fungal endophytes were isolated and identified according to their morphology and ribosomal ITS rDNA sequences. As results indicated Ascomycota dominated in colonizing S. multicaulis with a relative frequency (RF) of 96.77%, comprising of Eurotiomycetes (RF: 40.5%), Sordariomycetes (RF: 33.9%) and Dothideomycetes (RF: 20.5%). Mucoromycota, comprised the rest of endophytes (RF: 5.23%). The entire fungal microbiome was classified into nine genera including Fusarium (25.5%), Penicillium (21.5%), Aspergillus (17.0%), Alternaria (15.5%), Colletotrichum (5.2%), Rhizopus (5.2%), Macrophomina (4.5%), Trichoderma (3.25%) and Nodulisporium (2.0%). Analyses of different diversity indices indicated significant correlations with tissue type, sampling locations and season of recovery. Almost 43% of fungal endophytes were recovered at Mazandaran, Kojur; 35.4% at Qazvin, Barajin Forest Park; 30.1% at Alborz, Taleqan; and 21% at Alborz, Mahdasht. The highest overall endophyte recovery was in summer (36.8%), followed by spring (31.6%), autumn (21%), and winter (10.5%). In total, the number of endophytes recovered from roots (91) was higher than those of stems (32) and leaves (30), especially during autumn and winter. Accordingly, we conclude that Ascomycota are the major endophytic fungi colonizing S. multicaulis, and that sampling location, tissue type and season can affect the fungal endophyte composition of this medicinal plant. This knowledge could be further applied in protection and health management of this endangered species.

Contrasting effects of Rhizophagus irregularis versus bacterial and fungal seed endophytes on Trifolium repens plant-soil feedback

Interactions between plants and soil affect plant-plant interactions and community composition by modifying soils conditions in plant-soil feedback, where associated microbes have the most crucial role. Both arbuscular mycorrhizal fungi (AMF) and microbial seed endophytes have been demonstrated to influence, directly or indirectly, biotic or abiotic soil properties, thus affecting subsequent plant growth, and community structure. However, little is known about how plant endophyte communities, individually or in interaction with AMF, affect plant-soil feedback processes. Here, we investigated, through a manipulative experiment, the behavior of endophyte-free and endophyte-associated Trifolium repens plants grown in soils previously conditioned by conspecific endophyte-free and endophyte-associated plants, inoculated or not by Rhizophagus intraradices. Furthermore, we identified microbial endophytes directly from the inner tissues of seeds by high-throughput sequencing, to compare seed fungal and bacterial endophyte composition. Results demonstrated that the outcome of simultaneous occurrence of seed endophytes and AMF on plant behavior depended on matching the endophytic status, i.e., either the presence or absence of seed microbial endophytes, of the conditioning and response phase. Seed fungal endophytes generated strong conspecific negative feedback, while seed bacterial endophytes proved to shift the feedback from negative to positive. Moreover, the simultaneous occurrence of both seed endophytes with AMF could either generate or expand negative plant-soil feedback effects. Our results show that seed and root symbionts can play a significant role on setting conspecific plant-soil feedback.

New Insight into the Composition of Wheat Seed Microbiota

Endophytes are associated with host plants throughout their life history from seed germination to fruit development. One of the most important plant organs colonized by endophytic microbiota is the seed. The aim of this study was to determine the structure of the seed core microbiome inhabiting the endosperms and embryos of eight wheat cultivars with the use of a culture-independent technique. The seeds of Triticum aestivum L. cv. Hondia, Wilejka, STH, Opcja, Tybalt, Euforia and Triticum spelta L. cv. Rokosz and Schwabencorn (producer: Plant Breeding Strzelce Sp. z o.o. Group IHAR) were studied. Rokosz and Hondia were cultured in vitro and in vivo to identify obligatory bacterial endophytes. A restrictive analysis of reads originating from the in vitro plants has demonstrated that the bacterial genera Paenibacillus and Propionibacterium inhabiting Rokosz and Hondia plants have a status of obligatory microorganisms. Greater biodiversity of seed-borne endophytes was found in the seed endosperms than in the embryos. The multiple comparison analysis of the OTU abundance indicated that the seed part significantly influenced the relative abundance. The seed-born microbiome is not statistically significantly dependent on the wheat cultivars; however, it cannot be claimed that every wheat seed is the same.

Effects of Cultured Root and Soil Microbial Communities on the Disease of Nicotiana tabacum Caused by Phytophthora nicotianae

BACKGROUND

Black shank, caused by the oomycete pathogen Phytophthora nicotianae, is responsible for huge economic losses worldwide. Research has focused on biocontrol to prevent disease and to minimize the use of synthetic fungicides.

METHODS

We explored and compared the efficacy of suppressive microflora cultured from soil and roots on the growth of P. nicotianae for controlling the incidence of black shank.

RESULTS

We found that 31 microfloral communities, enriched from 40 root samples but only 18 microfloral communities from soil samples, were antagonistic to P. nicotianae. In the field experiment, the root functional microflora (RFM) showed a greater suppressiveness of black shank than the soil functional microflora (SFM), while both RFM and SFM altered diversity, composition, structure, and interaction of soil bacterial communities during plant growth. Although the inoculation of RFM onto roots significantly (p < 0.05) decreased microbial diversity, molecular ecological network analysis indicated more possible interactions among soil microbes, while an opposite trend was observed with SFM inoculation. Linear regression analysis revealed that diversity indices were negatively correlated with suppression on the black shank, suggesting that specific taxa (e.g., OTU_322 and OTU_6478) could colonize and be active during plant growth at the expense of microbial diversity. In addition, 18 functional strains, isolated and screened from 3 RMF (12 strains) and 3 SMF (6 strains), were identified as bacterial genera Acinetobacter (12), Enterobacter (1), Bacillus (1), Stenotrophomonas (2), and Citrobacter (2). Spearman's ranked correlation tests revealed that relative abundances of some OTUs affiliated with genera Acinetobacter, Enterobacter, and Bacillus were significantly (p < 0.05) and positively correlated with the level of disease suppression.

CONCLUSION

Microfloral communities or key functional species isolated from plant roots might be more effective in controlling black shank than those from soil, and they may be developed for disease control.

Metagenomics methods for the study of plant-associated microbial communities: A review

Plant microbiota have different effects on the plant which can be beneficial or pathogenic. In this study, we concentrated on beneficial microbes associated with plants using endophytic microbes as a case study. Detailed knowledge of the microbial diversity, abundance, composition, functional genes patterns, and metabolic pathways at genome level could assist in understanding the contributions of microbial community towards plant growth and health. Recently, the study of microbial community has improved greatly with the discovery of next-generation sequencing and bioinformatics technologies. Analysis of next generation sequencing data and a proper computational method plays a key role in examining microbial metagenome. This review presents the general metagenomics and computational methods used in processing plant associated metagenomes with concentration on endophytes. This includes 1) introduction of plant-associated microbiota and the factors driving their diversity. 2) plant metagenome focusing on DNA extraction, verification and quality control. 3) metagenomics methods used in community analysis of endophytes focusing on maize plant and, 4) computational methods used in the study of endophytic microbiomes. Limitations and future prospects of metagenomics and computational methods for the analysis of plant-associated metagenome (endophytic metagenome) were also discussed with the aim of fostering its development. We conclude that there is need to adopt advanced genomic features such as k-mers of random size, which do not depend on annotation and can represent other sequence alternatives.

Tissue-Specific and Geographical Variation in Endophytic Fungi of Ageratina adenophora and Fungal Associations With the Environment

To understand the distribution of the cultivable fungal community in plant tissues and the associations of these fungi with their surrounding environments during the geographical expansion of an invasive plant, Ageratina adenophora, we isolated the cultivable fungi from 72 plant tissues, 12 soils, and 12 air samples collected from six areas in Yunnan Province, China. A total of 4066 isolates were investigated, including 1641 endophytic fungi, 233 withered leaf fungi, 1255 fungi from air, and 937 fungi from soil. These fungi were divided into 458 and 201 operational taxonomic units (OTUs) with unique and 97% ITS gene sequence identity, respectively. Phylogenetic analysis showed that the fungi belonged to four phyla, including Ascomycota (94.20%), Basidiomycota (2.71%), Mortierellomycota (3.03%), and Mucoromycota (0.07%). The dominant genera of cultivable endophytic fungi were Colletotrichum (34.61%), Diaporthe (17.24%), Allophoma (8.03%), and Fusarium (4.44%). Colletotrichum and Diaporthe were primarily isolated from mature leaves, Allophoma from stems, and Fusarium from roots, indicating that the enrichment of endophytic fungi is tissue-specific and fungi rarely grew systemically within A. adenophora. In the surrounding environment, Alternaria (21.46%), Allophoma (19.31%), Xylaria (18.45%), and Didymella (18.03%) were dominant in the withered leaves, Cladosporium (22.86%), Trichoderma (14.27%), and Epicoccum (9.83%) were dominant in the canopy air, and Trichoderma (27.27%) and Mortierella (20.46%) were dominant in the rhizosphere soils. Further analysis revealed that the cultivable endophytic fungi changed across geographic areas and showed a certain degree of variation in different tissues of A. adenophora. The cultivable fungi in mature and withered leaves fluctuated more than those in roots and stems. We also found that some cultivable endophytic fungi might undergo tissue-to-tissue migration and that the stem could be a transport tissue by which airborne fungi infect roots. Finally, we provided evidence that the fungal community within A. adenophora was partially shared with the contiguous environment. The data suggested a frequent interaction between fungi associated with A. adenophora and those in surrounding environments, reflecting a compromise driven by both functional requirements for plant growth and local environmental conditions.

Latitudinal variation in soil nematode communities under climate warming-related range-expanding and native plants

Current climate change has led to latitudinal and altitudinal range expansions of numerous species. During such range expansions, plant species are expected to experience changes in interactions with other organisms, especially with belowground biota that have a limited dispersal capacity. Nematodes form a key component of the belowground food web as they include bacterivores, fungivores, omnivores and root herbivores. However, their community composition under climate change-driven intracontinental range-expanding plants has been studied almost exclusively under controlled conditions, whereas little is known about actual patterns in the field. Here, we use novel molecular sequencing techniques combined with morphological quantification in order to examine nematode communities in the rhizospheres of four range-expanding and four congeneric native species along a 2,000 km latitudinal transect from South-Eastern to North-Western Europe. We tested the hypotheses that latitudinal shifts in nematode community composition are stronger in range-expanding plant species than in congeneric natives and that in their new range, range-expanding plant species accumulate fewest root-feeding nematodes. Our results show latitudinal variation in nematode community composition of both range expanders and native plant species, while operational taxonomic unit richness remained the same across ranges. Therefore, range-expanding plant species face different nematode communities at higher latitudes, but this is also the case for widespread native plant species. Only one of the four range-expanding plant species showed a stronger shift in nematode community composition than its congeneric native and accumulated fewer root-feeding nematodes in its new range. We conclude that variation in nematode community composition with increasing latitude occurs for both range-expanding and native plant species and that some range-expanding plant species may become released from root-feeding nematodes in the new range.

Seeds of native alpine plants host unique microbial communities embedded in cross-kingdom networks

BACKGROUND

The plant microbiota is crucial for plant health and growth. Recently, vertical transmission of a beneficial core microbiota was identified for crop seeds, but for native plants, complementary mechanisms are almost completely unknown.

METHODS

We studied the seeds of eight native plant species growing together for centuries under the same environmental conditions in Alpine meadows (Austria) by qPCR, FISH-CLSM, and amplicon sequencing targeting bacteria, archaea, and fungi.

RESULTS

Bacteria and fungi were determined with approx. 1010 gene copy numbers g-1 seed as abundant inhabitants. Archaea, which were newly discovered as seed endophytes, are less and represent only 1.1% of the signatures. The seed microbiome was highly diversified, and all seeds showed a species-specific, highly unique microbial signature, sharing an exceptionally small core microbiome. The plant genotype (species) was clearly identified as the main driver, while different life cycles (annual/perennial) had less impact on the microbiota composition, and fruit morphology (capsule/achene) had no significant impact. A network analysis revealed significant co-occurrence patterns for bacteria and archaea, contrasting with an independent fungal network that was dominated by mutual exclusions.

CONCLUSIONS

These novel insights into the native seed microbiome contribute to a deeper understanding of seed microbial diversity and phytopathological processes for plant health, and beyond that for ecosystem plasticity and diversification within plant-specific microbiota.

Belowground Consequences of Intracontinental Range-Expanding Plants and Related Natives in Novel Environments

Introduced exotic plant species that originate from other continents are known to alter soil microbial community composition and nutrient cycling. Plant species that expand range to higher latitudes and altitudes as a consequence of current climate warming might as well affect the composition and functioning of native soil communities in their new range. However, the functional consequences of plant origin have been poorly studied in the case of plant range shifts. Here, we determined rhizosphere bacterial communities of four intracontinental range-expanding plant species in comparison with their four congeneric natives grown in soils collected from underneath those plant species in the field and in soils that are novel to them. We show that, when controlling for both species relatedness and soil characteristics, range-expanding plant species in higher latitude ecosystems will influence soil bacterial community composition and nutrient cycling in a manner similar to congeneric related native species. Our results highlight the importance to include phylogenetically controlled comparisons to disentangle the effect of origin from the effect of contrasting plant traits in the context of exotic plant species.

Comparison of plant-soil feedback experimental approaches for testing soil biotic interactions among ecosystems

The study of interactions and feedbacks between plants and soils is a rapidly expanding research area, and a primary tool used in this field is to perform glasshouse experiments where soil biota are manipulated. Recently, there has been vigorous debate regarding the correctness of methods for carrying out these types of experiment, and specifically whether it is legitimate to mix soils from different sites or plots (mixed soil sampling, MSS) or not (independent soil sampling, ISS) to create either soil inoculum treatments or subjects. We performed the first empirical comparison of MSS vs ISS approaches by comparing growth of two boreal tree species (Picea abies and Pinus sylvestris) in soils originating from 10 sites near the boreal forest limit in northern Sweden, and 10 sites in the subarctic region where boreal forests may potentially expand as a result of climate change. We found no consistent differences in the conclusions that we reached whether we used MSS or ISS approaches. We propose that researchers should not choose a soil handling method based on arguments that one method is inherently more correct than the other, but rather that method choice should be based on correct alignment with specific research questions and goals.

Endophytes of industrial hemp (Cannabis sativa L.) cultivars: identification of culturable bacteria and fungi in leaves, petioles, and seeds

Plant endophytes are a group of microorganisms that reside asymptomatically within the healthy living tissue. The diversity and molecular and biochemical characterization of industrial hemp-associated endophytes have not been previously studied. This study explored the abundance and diversity of culturable endophytes residing in petioles, leaves, and seeds of three industrial hemp cultivars, and examined their biochemical attributes and antifungal potential. A total of 134 bacterial and 53 fungal strains were isolated from cultivars Anka, CRS-1, and Yvonne. The number of bacterial isolates was similarly distributed among the cultivars, with the majority recovered from petiole tissue. Most fungal strains originated from leaf tissue of cultivar Anka. Molecular and phylogenetic analyses grouped the endophytes into 18 bacterial and 13 fungal taxa, respectively. The most abundant bacterial genera were Pseudomonas, Pantoea, and Bacillus, and the fungal genera were Aureobasidium, Alternaria, and Cochliobolus. The presence of siderophores, cellulase production, and phosphorus solubilization were the main biochemical traits. In proof-of-concept experiments, re-inoculation of tomato roots with some endophytes confirmed their migration to aerial tissues of the plant. Taken together, this study demonstrates that industrial hemp harbours a diversity of microbial endophytes, some of which could be used in growth promotion and (or) in biological control designed experiments.

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.