Seed germination critically determines successful plant establishment and agricultural productivity. In the plant holobiont's life cycle, seeds are hubs for microbial communities’ assembly, but what exactly shapes the holobiont during germination remains unknown. Here, 16S rRNA gene amplicon sequencing characterized the bacterial communities in embryonic compartments (cotyledons and axes) and on seed coats pre- and post-germination of four soybean ( Glycine max) cultivars, in the presence or absence of exogenous abscisic acid (ABA), which prevented germination and associated metabolism of seeds that had imbibed. Embryonic compartments were metabolically profiled during germination to design minimal media mimicking the seed endosphere for bacterial growth assays. The distinction between embryonic and seed coat bacterial microbiomes of dry seeds weakened during germination, resulting in the plumule, radicle, cotyledon, and seed coat all hosting the same most abundant and structurally influential genera in germinated seeds of every cultivar. Treatment with ABA prevented the increase of bacterial microbiomes’ richness, but not taxonomic homogenization across seed compartments. Growth assays on minimal media containing the most abundant metabolites that accumulated in germinated seeds revealed that seed reserve mobilization promoted enrichment of copiotrophic bacteria. Our data show that seed imbibition enabled distribution of seed-coat-derived epiphytes into embryos irrespective of germination, while germinative metabolism promoted proliferation of copiotrophic taxa, which predominated in germinated seeds. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

The association of the plant microbiota is a successional process that starts with the seed and its intrinsic microbiota. The recently reported relevance of seeds as carriers of microbiota has encouraged investigations of the assembly of these communities in different tissues. Here, we address the contributions of both seed and soil bacterial microbiota in the assembly of communities within endospheres of adult plants by 16S ribosomal RNA gene-based Illumina sequencing. Surface-sterilized seeds of the model plant Setaria viridis were sown in sterile conditions and seedlings were transferred onto either their native soil or a foreign soil. Soil-derived bacterial colonizers contributed to the highest portion of endophytic microbiota, with varying community composition depending on the cultivation soil. In contrast, the contribution of seed microbiota in those of adult plants was less evident. Moreover, seedlings grown in their native soils resulted in plants with consistent endophytic assemblages, whereas a dramatic increase in variability was observed for rhizosphere and endophytic root communities of plants grown in foreign soils.

Soil microbiota plays a significant role in plant development and health and appears to be a major component of certain forms of grapevine decline. A greenhouse experiment was conducted to study the impact of the microbiological quality of the soil and grapevine rootstock genotype on the root microbial community and development of young plants. Two rootstocks heterografted with the same scion were grown in two vineyard soils differing in microbial composition and activities. After 4 months, culture-dependent approaches and amplicon sequencing of bacterial 16S rRNA gene and fungal ITS were performed on roots, rhizosphere and bulk soil samples. The root mycorrhizal colonization and number of cultivable microorganisms in the rhizosphere compartment of both genotypes were clearly influenced by the soil status. The fungal diversity and richness were dependent on the soil status and the rootstock, whereas bacterial richness was affected by the genotype only. Fungal genera associated with grapevine diseases were more abundant in declining soil and related root samples. The rootstock affected the compartmentalization of microbial communities, underscoring its influence on microorganism selection. Fluorescence in situ hybridization (FISH) confirmed the presence of predominant root-associated bacteria. These results emphasized the importance of rootstock genotype and soil composition in shaping the microbiome of young vines.

Increasing knowledge of the microbiome has led to significant advancements in the agrifood system. Case studies based on microbiome applications have been reported worldwide and, in this review, we have selected 14 success stories that showcase the importance of microbiome research in advancing the agrifood system. The selected case studies describe products, methodologies, applications, tools, and processes that created an economic and societal impact. Additionally, they cover a broad range of fields within the agrifood chain: the management of diseases and putative pathogens; the use of microorganism as soil fertilizers and plant strengtheners; the investigation of the microbial dynamics occurring during food fermentation; the presence of microorganisms and/or genes associated with hazards for animal and human health (e.g., mycotoxins, spoilage agents, or pathogens) in feeds, foods, and their processing environments; applications to improve HACCP systems; and the identification of novel probiotics and prebiotics to improve the animal gut microbiome or to prevent chronic non-communicable diseases in humans (e.g., obesity complications). The microbiomes of soil, plants, and animals are pivotal for ensuring human and environmental health and this review highlights the impact that microbiome applications have with this regard.

Seeds offer an internal microbial niche, termed the endosphere, colonized by communities of endophytic bacteria. To elucidate the functions of seed endophytes during germination and early plant growth, studies with culturable isolates are essential. Conventional growth media favor few fast-growing taxa, while micro organisms with restricted nutrient requirements are usually outcompeted prior to isolation. Consequently, current knowledge of the interaction between seeds and their endophytes remains limited to only few bacterial taxa, despite a "black box" of unculturable isolates colonizing the endosphere. Here, we designed various solid media to mimic the endosphere of germinating soybean (Glycine max L.) seeds and assessed their effect on the diversity of culturable endophytic bacteria. The embryonic axis (i.e., the future plant) possessed higher richness and harbored more unique genera (i.e., Brevundimonas, Methylobacterium, Microbacterium, Pseudoclavibacter, and Rathayibacter) than cotyledons (i.e., seed storage organs). Overall, media containing germinating and ground seeds enabled culturing and isolation of the broadest diversity of endophytic bacteria, viewed through the molecular identification of 246 isolates. The use of multiple tailored media helped uncover trophic adaptation of the core taxa. Furthermore, comparison of seeds from four lots of distinct cultivars and origin revealed few overlapping taxa, indicating that the parental environment, including soil and fertilization regime, influenced seed endophytic diversity. Extended diversity of native seed endophytic bacteria revealed the functional relevance of unique Arthrobacter, Bacillus, and Curtobacterium strains to seed germination under salt stress, exemplifying the importance of enhanced culturing approaches to elucidate the role of microbiota in seed germination. IMPORTANCE Plant growth-promoting endophytic isolates that appear to advance seed germination are often obtained from plant niches other than the seed endosphere. Isolating pure cultures of native endophytes from seeds during germination is crucial to investigate their function during early plant growth. Here, the diversity of endophytic bacteria isolated from seeds during soybean germination was enhanced by combining media tailored to the nutritional composition of the seed endosphere, including pregerminated seeds themselves. Our results show that isolation from distinct soybean seed compartments affected such diversity, with the embryonic axis harboring more unique taxa while displaying higher endophytic richness. Furthermore, using pools of seeds from separate lots, each corresponding to a certain cultivar and field site, supported isolation of further unique strains that often unveiled substantial effects on germination performance. Such findings are relevant to assist studies on the interactions between seeds and their native endophytic bacteria.

Increasing knowledge of the microbiome has led to significant advancements in the agrifood system. Case studies based on microbiome applications have been reported worldwide and, in this review, we have selected 14 success stories that showcase the importance of microbiome research in advancing the agrifood system. The selected case studies describe products, methodologies, applications, tools, and processes that created an economic and societal impact. Additionally, they cover a broad range of fields within the agrifood chain: the management of diseases and putative pathogens; the use of microorganism as soil fertilizers and plant strengtheners; the investigation of the microbial dynamics occurring during food fermentation; the presence of microorganisms and/or genes associated with hazards for animal and human health (e.g., mycotoxins, spoilage agents, or pathogens) in feeds, foods, and their processing environments; applications to improve HACCP systems; and the identification of novel probiotics and prebiotics to improve the animal gut microbiome or to prevent chronic non-communicable diseases in humans (e.g., obesity complications). The microbiomes of soil, plants, and animals are pivotal for ensuring human and environmental health and this review highlights the impact that microbiome applications have with this regard.

Bacterial communities in the phyllosphere are shaped by host genotype and phenotype and spatio-temporal variation of the environment. In turn, bacteria have the potential for altering the plant phenotype. Field experiments can help to estimate bacterial effects on plant functional traits under natural conditions. We used a transplantation approach of culturable bacterial communities to explore how manipulation of leaf-associated microbial communities in two different successional stages within a glacier foreland can influence microbial composition and functional plant traits. Our study documents successional stage-specific variations in the composition of foliar bacterial communities and shifts therein throughout a season and between years. We show that cultured bacteria transferred between plant communities can alter diversity and composition of the microbiome on plant community level as well as species-specific functional plant traits of two selected plant species within one growing season. Furthermore, our results demonstrate a strong resilience of plant-associated bacterial communities and of plants in response to bacterial invaders. Our study illustrates that inoculation experiments in the field with naturally occurring microbial communities of wild plants are suited to investigate complex interactions between microbial communities, the environment, and plant traits.

In the past, the potato plant microbiota and rhizosphere have been studied in detail to improve plant growth and fitness. However, less is known about the postharvest potato tuber microbiome and its role in storage stability. The storage stability of potatoes depends on genotype and storage conditions, but the soil in which tubers were grown could also play a role. To understand the ecology and functional role of the postharvest potato microbiota, we planted four potato varieties in five soil types and monitored them until the tubers started sprouting. During storage, the bacterial community of tubers was analysed by next-generation sequencing of the 16S rRNA gene amplicons. The potato tubers exhibited soil-dependent differences in sprouting behaviour. The statistical analysis revealed a strong shift of the tuber-associated bacterial community from harvest to dormancy break. By combining indicator species analysis and a correlation matrix, we predicted associations between members of the bacterial community and tuber sprouting behaviour. Based on this, we identified Flavobacterium sp. isolates, which were able to influence sprouting behaviour by inhibiting potato bud outgrowth.

The modes of interactions between plants and plant-associated microbiota are manifold, and secondary metabolites often play a central role in plant-microbe interactions. Abiotic and biotic (including both plant pathogens and endophytes) stress can affect the composition and concentration of secondary plant metabolites, and thus have an influence on chemical compounds that make up for the taste and aroma of fruit. While the role of microbiota in growth and health of plants is widely acknowledged, relatively little is known about the possible effect of microorganisms on the quality of fruit of plants they are colonizing. In this work, tomato (Solanum lycopersicum L.) plants of five different cultivars were grown in soil and in hydroponics to investigate the impact of the cultivation method on the flavor of fruit, and to assess whether variations in their chemical composition are attributable to shifts in bacterial microbiota. Ripe fruit were harvested and used for bacterial community analysis and for the analysis of tomato volatiles, sugars and acids, all contributing to flavor. Fruit grown in soil showed significantly higher sugar content, whereas tomatoes from plants under hydroponic conditions had significantly higher levels of organic acids. In contrast, aroma profiles of fruit were shaped by the tomato cultivars, rather than the cultivation method. In terms of bacterial communities, the cultivation method significantly defined the community composition in all cultivars, with the bacterial communities in hydroponic tomatoes being more variable that those in tomatoes grown in soil. Bacterial indicator species in soil-grown tomatoes correlated with higher concentrations of volatiles described to be perceived as "green" or "pungent." A soil-grown specific reproducibly occurring ASV (amplicon sequence variants) classified as Bacillus detected solely in "Solarino" tomatoes, which were the sweetest among all cultivars, correlated with the amount of aroma-relevant volatiles as well as of fructose and glucose in the fruit. In contrast, indicator bacterial species in hydroponic-derived tomatoes correlated with aroma compounds with "sweet" and "floral" notes and showed negative correlations with glucose concentrations in fruit. Overall, our results point toward a microbiota-related accumulation of flavor and aroma compounds in tomato fruit, which is strongly dependent on the cultivation substrate and approach.

In endophytes, the abundance of genes coding for enzymes processing reactive oxygen species (ROS), including hydrogen peroxide (H2O2), argues for a crucial role of ROS metabolism in plant-microbe interaction for plant colonization. Here, we studied H2O2 metabolism of bread wheat (Triticum aestivum L.) seeds and their microbiota during germination and early seedling growth, the most vulnerable stages in the plant life cycle. Treatment with hot steam diminished the seed microbiota, and these seeds produced less extracellular H2O2 than untreated seeds. Using a culture-dependent approach, Pantoea and Pseudomonas genera were the most abundant epiphytes of dry untreated seeds. Incubating intact seedlings from hot steam-treated seeds with Pantoea strains triggered H2O2 production, whereas Pseudomonas strains dampened H2O2 levels, attributable to higher catalase activities. The genus Pantoea was much less represented among seedling endophytes than genus Pseudomonas, with other endophytic genera, including Bacillus and Paenibacillus, also possessing high catalase activities. Overall, our results show that certain bacteria of the seed microbiota are able to modulate the extracellular redox environment during germination and early seedling growth, and high catalase activity is proposed as a key trait of seed endophytes.

The plant endosphere is colonized by complex microbial communities and microorganisms, which colonize the plant interior at least part of their lifetime and are termed endophytes. Their functions range from mutualism to pathogenicity. All plant organs and tissues are generally colonized by bacterial endophytes and their diversity and composition depend on the plant, the plant organ and its physiological conditions, the plant growth stage as well as on the environment. Plant-associated microorganisms, and in particular endophytes, have lately received high attention, because of the increasing awareness of the importance of host-associated microbiota for the functioning and performance of their host. Some endophyte functions are known from mostly lab assays, genome prediction and few metagenome analyses; however, we have limited understanding on in planta activities, particularly considering the diversity of micro-environments and the dynamics of conditions. In our review, we present recent findings on endosphere environments, their physiological conditions and endophyte colonization. Furthermore, we discuss microbial functions, the interaction between endophytes and plants as well as methodological limitations of endophyte research. We also provide an outlook on needs of future research to improve our understanding on the role of microbiota colonizing the endosphere on plant traits and ecosystem functioning.

An amendment to this paper has been published and can be accessed via the original article.

Plant microbiota are the subject of new product developments, primarily aimed at improving plant health, nutrition, and stress resilience. However, current application of microbials in the field faces multiple challenges and we propose that multiple aspects need to be considered, for example, understanding the complexity and ecological behaviour of natural microbiota.

Seed-associated bacteria represent an important reservoir of microorganisms passed onto progeny plants and have been postulated to be important for early plant development and early plant vigor. According to a few reports, some bacterial taxa seem to be transferred from seed to seed and some seed-associated microorganisms may derive from insect visits during flowering; however, the origin of seed endophytes is poorly understood. To better understand the origin, ecology, and functional role of seed bacterial endophytes, we planted Setaria viridis seeds over several generations in a sterile growth substrate. Seed microbiota of each generation were analyzed by next generation sequencing of 16S rRNA genes and seeds were characterized regarding to their germination and plant growth. Growing plants in a sterile (or highly depleted) substrate resulted in seed microbiota, which were largely less diverse and which had altered community composition, particularly at later generations, indicating that soil is an important reservoir of seed microbiota. Some taxa were inherited to the next generations seeds; however, different subsets of taxa were inherited in different seeds/seed batches and across different generations. This suggests that other factors than the host control the establishment of most seed endophytes and only few, e.g., obligate endophytes, might be consistently inherited. Furthermore, we observed a drastic decline in seed vigor and later generations were particularly affected. Overall, our results demonstrated that the supply of endophytes from external sources such as the soil/rhizosphere environment is highly important for the build-up of a healthy seed microbiome warranting early plant establishment and vigor of next generation plants.

Plants are associated with highly diverse microbiota, which are crucial partners for their host carrying out important functions. Essentially, they are involved in nutrient supply, pathogen antagonism and protection of their host against different types of stress. The potential of microbial inoculants has been demonstrated in numerous studies, primarily under greenhouse conditions. However, field application, for example, as biofertilizer or biocontrol agent, is still a challenge as the applied microorganisms often are not provided in sufficiently high cell numbers, are rapidly outcompeted and cannot establish or require specific conditions to mediate the desired effects. We still have limited understanding on the fate of inoculants and on holobiont interactions, that is, interactions between plants, micro-biota and macro-biota and the environment, under field conditions. A better understanding will provide the basis for establishing models predicting the behaviour of strains or consortia and will help identifying microbiome members being able to establish and to mediate desired effects under certain conditions. Such models may also inform about the best management practices modulating microbiota in a desired way. Also, smart delivery approaches of microbial inoculants as well as the selection or breeding of plant genotypes better able to interact with microbiota may represent promising avenues.

Strong efforts have been made to understand the bacterial communities in potato plants and the rhizosphere. Research has focused on the effect of the environment and plant genotype on bacterial community structures and dynamics, while little is known about the origin and assembly of the bacterial community, especially in potato tubers. The tuber microbiota, however, may be of special interest as it could play an important role in crop quality, such as storage stability. Here, we used 16S rRNA gene amplicon sequencing to study the bacterial communities that colonize tubers of different potato cultivars commonly used in Austrian potato production over three generations and grown in different soils. Statistical analysis of sequencing data showed that the bacterial community of potato tubers has changed over generations and has become more similar to the soil bacterial community, while the impact of the potato cultivar on the bacterial assemblage has lost significance over time. The communities in different tuber parts did not differ significantly, while the soil bacterial community showed significant differences to the tuber microbiota composition. Additionally, the presence of OTUs in subsequent tuber generation points to vertical transmission of a subset of the tuber microbiota. Four OTUs were common to all tuber generations and all potato varieties. In summary, we conclude that the microbiota of potato tubers is recruited from the soil largely independent from the plant variety. Furthermore, the bacterial assemblage in potato tubers consists of bacteria transmitted from one tuber generation to the next and bacteria recruited from the soil.

Plants develop in a microbe-rich environment and must interact with a plethora of microorganisms, both pathogenic and beneficial. Indeed, such is the case of Pseudomonas, and its model organisms P. fluorescens and P. syringae, a bacterial genus that has received particular attention because of its beneficial effect on plants and its pathogenic strains. The present study aims to compare plant-beneficial and pathogenic strains belonging to the P. syringae species to get new insights into the distinction between the two types of plant-microbe interactions. In assays carried out under greenhouse conditions, P. syringae pv. syringae strain 260-02 was shown to promote plant-growth and to exert biocontrol of P. syringae pv. tomato strain DC3000, against the Botrytis cinerea fungus and the Cymbidium Ringspot Virus. This P. syringae strain also had a distinct volatile emission profile, as well as a different plant-colonization pattern, visualized by confocal microscopy and gfp labeled strains, compared to strain DC3000. Despite the different behavior, the P. syringae strain 260-02 showed great similarity to pathogenic strains at a genomic level. However, genome analyses highlighted a few differences that form the basis for the following hypotheses regarding strain 260-02. P. syringae strain 260-02: (i) possesses nonfunctional virulence genes, like the mangotoxin-producing operon Mbo; (ii) has different regulation pathways, suggested by the difference in the autoinducer system and the lack of a virulence activator gene; (iii) has genes encoding DNA methylases different from those found in other P. syringae strains, suggested by the presence of horizontal-gene-transfer-obtained methylases that could affect gene expression.

Introduction Despite the long-held belief that reproductive and disseminative organs of plants are sterile, it is now well established that seeds host diverse microbial assemblages (Hardoim et al. 2015; Truyens et al. 2015). Some of these associated microorganisms contribute to plant health, plant growth, and seed survival while others are detrimental (Barret et al. 2016; Saikkonen et al. 2016). Seeds can facilitate the dispersal of microorganisms, providing for early colonization of a new plant generation. Although seeds are an important means of supporting microbial growth and dispersal, relatively little is known about the ecology of seed-associated microorganisms (Saikkonen et al. 1998; Compant et al. 2010; Truyens et al. 2015; Brader et al. 2017) in comparison with root- and leaf-associated microorganisms (Mercado-Blanco and Lugtenberg 2014; Mercado-Blanco 2015; Vacher et al. 2016; Compant et al. 2016). In many instances, the composition and structure of the seed microbiota of various plants species have yet to be characterized. This includes the microorganisms living on the surface as well as the inner tissues of the seeds. Furthermore, a thorough understanding of the specific routes of seed transmission of microorganisms needs to be developed. Whereas seed transmission has been thought to occur through three main routes: the internal, floral and external pathways (Maude 1996), the relative importance of these pathways in determining the composition of the seed microbiota remains to be explored. Moreover, the impact of vertical (derived from the mother plant) and horizontal transmission (derived from air-borne or soil-borne microorganisms) in the assembly of seed microbial communities is unclear for some taxa. As much needs to be understood about seed-associated microbes, perhaps among the most important are resolving the relative roles of horizontal and vertical transmission in establishing the seed microbiota, which could lead to a better understanding of the plant holobiont, its microbiome and functioning, and the potential use of seed-associated microbes for improving agricultural productivity. This understanding could like lead to insights into the evolution of specific microbial taxa within seeds and the relative contributions of various selective forces in shaping the seed microbiota. The unraveling of these processes could provide important knowledge about how beneficial, commensal, and pathogenic fungal and bacterial microorganisms establish and maintain intimate associations with their seeds and contribute to the health of the next plant generation, improving our abilities to develop successful application strategies for microbial inoculants and their integration into sustainable crop production and protection. Since the nineteenth century, advances have been made in our understanding of plant-associated microorganisms. However, for seeds and their microbiota, there remain large gaps in our knowledge. Seed transmission of some microorganisms like Epichloids in grasses (Kauppinen et al. 2016; Saikkonen et al. 2016) or phytopathogenic fungi and bacteria (Li et al. 2017; Brader et al. 2017) have been relatively well studied. However, seed transmission of many plant-associated microorganisms remains unknown. The contributions in this Special Issue have served to greatly improve our understanding of the mechanisms of seed-microbe-soil interactions, the nature of the microbiota and functioning of the microbiome present within various seeds, the evolution of the seed microbiota, and the routes of microbial colonization. The studies include different beneficial and detrimental microorganisms as fungi and bacteria thriving as endophytes in different kinds of plants. They further describe ways in which specific native or non-native seed microorganisms may be utilized for improving seed and seedling survival and plant health and productivity

Plant microbiota has been explored in the last decades, particularly those colonizing the rhizosphere, but the awareness of their diversity and relevance has exploded in the last few years. Based on the recent discoveries made with the human microbiome, it has been recognized that also plants host highly diverse microorganisms, which have been suggested to provide an accessory genome and reservoir of important functions to that of the host plant itself contributing to important plant traits. At the same time, agricultural production has to face severe challenges due to the demographic development and climate change with extreme weather events and emerging pathogens. Furthermore, our society demands more sustainable production systems, a number of chemicals (e.g. pesticides) will be taken from the market in the coming years and several countries do not support the use of genetic modification to improve crop traits. All these factors have led to an increasing awareness of the functions mediated by plant microbiota by academia as well as by the industry. Nevertheless, there are still a number of obstacles to face in the application of plant microbiota, and we are just at the beginning to realize their full potential contributing to economic growth and sustainable development. The global population is constantly rising and expected to reach 9.8 billion in 2050 and 11.2 in 2100 (https://www.un.org/development/desa/en/news/population/world-population-prospects-2017.html). At the same time, less land will be available for crop production implying that agricultural management and technologies have to be applied allowing intensification of production. This will be particularly essential for regions with high population densities such as in East and South-east Asia or regions facing extreme environmental conditions such as in sub-Saharan Africa. However, global food security is greatly challenged by emerging pathogens and climate change facing rising temperatures, extreme weather events and long periods of drought. There are a number of technologies available or under development such as precision agriculture or also genetically engineered plants being able to cope with various stresses. Nevertheless, the latter are not well accepted in many parts of the world. Currently, there are great expectations in the application of microbial inoculants as promising results have been reported and so far this approach has been hardly applied in crop production with the exception of N2-fixing rhizobial inoculants for legume production. In many parts of the world, a number of start-up companies have emerged exploring microbial inoculants and sophisticated ways to make use of the plant beneficial activities of microorganisms. The major drivers for economic development of this sector are the global demographic development and the increasing yield loss due to abiotic stress (e.g. drought), the lack of chemistry and active ingredients with new modes of action, resistance development of pathogens and pests against chemical treatments, the pressure from society and regulators for reduced pesticides on food and the environment, the adoption of integrated pest management in Europe and other countries as well as arising opportunities in the organic food sector (Biopesticides 2016, Agrow Market Report; Biostimulants 2017, Agrow Market Report). The global microbial biopesticide market accounted in 2014 more than 800 million $ (Biopesticides 2016, Agrow Market Report), a more recent analysis reported a global biocontrol market of 2.8 billion $ today to over 11 billion $ in 2025 with about 60% microbial products (Dunham Trimmer 2017). A CAGR (compound annual growth rate) of 17% is expected for the years 2015–2020 (Dunham Trimmer 2017). Similarly, the biostimulants market is constantly increasing with an expected CAGR of 10.9% until 2022 (Biostimulants 2017, Agrow Market Report). Dunham Trimmer (2017) reported outside of India and China currently more than 200 biocontrol and more than 100 biostimulant companies. About 75% of the biocontrol companies have less than 10 million $ annual return while about five biocontrol companies have an annual return of more than 100 million. Generally, all major global seed companies have invested in the field of plant microbiome research and chemical companies increasingly explore new commercial opportunities with developing microbial alternatives to agrochemicals (Fig. 1). The exploration of plant microbiota can be particularly relevant for small and medium enterprises and those acting in less developed regions. Since 2000, global efforts to combat hunger and malnutrition have advanced significantly. However, some regions such as in Asia and Africa still suffer tremendously from hunger, food insecurity and malnutrition and technologies to increase agricultural productivity are urgently required. There, microbial inoculants can be well produced locally by small companies and applied in small-scale farms and have the capacity to ameliorate poor soils frequently occurring in such countries. Great progress has been made in South America and best practice example is Azospirillum. Members of this genus are well known for their capacity to promote plant growth by providing phytohormones and nutrients. Based on major national funding programs, in which promising Azospirillum strains were selected, a flourishing inoculant business has arisen. Microbiologists, agronomists and local industries have meanwhile rigorously tested various inoculants in the field and suitable formulations have been developed. Nowadays, in South America, there are more than 100 commercial products available containing Azospirillum strains, most of them are produced in Argentina and Brazil. These products are produced by more than 50 companies and aim at yield increase in maize, wheat and soybean (reviewed by Cassán and Díaz-Zorita, 2016). Securing and improving sanity of soil and water is a central challenge in face of climate change and all its consequences and is an explicit UN development goal. Considering the importance of plant-associated microbiota for host and ecosystem functioning the exploitation of microbial activity could provide means to achieve this goal on different levels. The application of microbials with plant growth-promoting or biocontrol activity could at least partly substitute agrochemicals, thereby reducing their release into soil and water and consequently the negative effects on the environment. A proposed management strategy to increase soil health is to apply rhizobacteria to fill vacant niches and thereby prevent pathogen invasion (Chaparro et al., 2012). Furthermore, making use of the plant stress resilience effect of many plant-associated microorganisms could help to save water and natural soils by increasing yield per acre farmland. Apart from preventing contamination, plant microbiota can also be employed in decontamination of polluted soils. Many plant species take up metals from the surrounding soil and store them in their tissues. In a process called phytoextraction such accumulator plants are planted on contaminated sites and the metal-containing biomass is harvested and the soil recovers and is made available for agricultural use (Moosavi and Seghatoleslami, 2013; Kidd et al., 2015). The activity of plant microbiota can further enhance the efficiency of phytoextraction, as many bacteria mobilize metals in soil and so facilitate the uptake by plants. Others promote leave growth, which in turn allows incorporation of higher amounts of metals per plant (Kidd et al., 2015). These microbe-assisted processes could also be employed as gentle and less-invasive alternative to conventional mining, by extraction of valuable metals accumulated in plant tissue (Ghasemi et al., 2018). Furthermore, plant microbiota partnerships enable clean-up of soils and groundwater from different organic pollutants (Afzal et al., 2014). Many plant-associated bacteria possess enzymes for the mineralization of different organic compounds, thereby reducing organic compound accumulation and transpiration in plant tissue and allowing for better plant growth (Afzal et al., 2014). The role of plant microbiota in plant health, productivity and ecosystem functioning is well acknowledged (Berg and Smalla, 2009); however, the activities of plant-associated microorganisms can also affect human health and well-being. The microbial-based management strategies for reduced use of agrochemicals or soil and water sanitation mentioned above certainly will have positive effects on human health by reducing the exposure to potentially harmful chemicals and metals. However, the plant microbiota also directly affects humans, as it consists not only of plant beneficial, neutral and plant pathogenic bacteria but comprises also potential human pathogens (Mendes et al., 2013), which are taken up by the human body through consumption of raw plants such as vegetables and fruits (van Overbeek et al., 2014). Furthermore, it was assumed that plant microbiota is interconnected with those of humans also via air, soil, animals and indoor environments (Berg et al., 2014). Consequently, strategies to ensure healthy and balanced plant microbiota, such as prebiotics for plants, could play an important role in preventing disease outbreaks in humans (Berg et al., 2014). Microbial enzymes and metabolites have been long essential products for a number of industrial processes. More than half of the commercial enzymes are fungal or bacterial origin, while a smaller part is derived from animals or plants (Borrelli and Trono, 2015). The market for industrial enzymes is projected to reach more than 6 Billion USD by 2022 with a projected annual growth rate of close to 6%. The rising demand for alternatives to energy-intensive chemical technologies led to expectations for further increasing interests in enzymes and biocatalysis (Prakash et al., 2013; Markets and Markets 2018). In addition, microbial (secondary) metabolites have been a rich source of natural products commercialized in animal and human medicine and health, food and chemical industry and in plant crop protection. In 2013, app. 40% of the new chemical entities approved by the US Food and Drug Administration are either natural products, mimics or derivatives, and approximately 75% of antitumor and anti-infective agents are derived from natural products, largely of bacterial origin (Katz and Baltz, 2016). The total microbial products (diagnosis and treatment) market is expected to reach more than 250 billion USD in 2023, with a 40% fraction in the pharmaceutical industry and an annual growth rate of more than 8% from 2017 on (Market Research Future, 2018). In agriculture, metabolites of microbial origin are less prominent in use, but different metabolites such as the insecticide spinosyn from Saccharopolyspora (Dayan et al., 2009) and biosurfactants from various Bacillus and Pseudomonas species already provide or are expected to provide products with high potential in application in agriculture (Sachdev and Cameotra, 2017). Despite this already large contribution of microbial products to different industries, the overall potential of microorganisms is far from exhaustively exploited as the majority of bacteria (> 90%) are uncultivable with conventional techniques and only a small sub-fraction of metabolic clusters are active in most cultivated microorganisms. This ‘biosynthetic dark matter’ can now be accessed by high throughput sequencing techniques and have high potential to provide a number of novel lead structures and compounds (Katz and Baltz, 2016). Due to adaptation to different host niches, differences in the chemical composition of plant hosts and the intense interaction with other microorganisms on and in plants, the plant microbiome provides a hotspot of specific and diverse metabolic and enzymatic potential of microorganisms (Aleti et al., 2017; Hassani et al., 2018). Indeed, sequence comparison within Firmicutes has revealed an enrichment of genomic clusters responsible for secondary metabolite production particularly in those strains, which have been found in association with plants (Aleti et al., 2015). As the high number of different very specific functions (including utilization of diverse metabolic products, degradation of toxins and signalling compounds of microorganisms and plants, adaptation to abiotic stress conditions) are needed to allow survival of microorganisms in plant associations, these adaptations are expected to be reflected in high diversity of metabolites and enzymes produced by plant-associated organisms (Brader et al., 2017). It is widely recognized that maintaining the genetic diversity of plants and animals is crucial for agriculture and food production. In 2016, 4.7 million samples of seeds and other plant genetic material for food and agriculture have been preserved in 602 gene banks throughout 82 countries and 14 regional and international centers (https://sustainabledevelopment.un.org/sdg2). It is similarly important to increase awareness on the importance of microorganisms being tremendously important for our life and well-being as well as for maintaining environmental functions. Soils are central components of healthy and functional ecosystems and in particular soil organisms play a key role for soil functioning. Considering the importance of mostly soil-derived microorganisms and microbial communities for plant growth, health and stress resilience, the commercial impact of soil-borne and plant-associated microbiota is immense. Recently, Manter et al. (2017) claimed that the establishment of Living Soil Repositories is needed and that such repositories represent an investment in our future. Living Soil Repositories could preserve genetic diversity and could serve as a baseline and future tool to monitor changes in community structure and functioning. Such a repository would also open commercial opportunities to make use of microbiota for agricultural needs (Manter et al., 2017). Furthermore, Berg and Raaijmakers (2018) pointed out that the centralized seed production and the global trade of seeds can lead to more homogenous plant microbiomes, potentially loosing important microbial players. The authors propose that international seed banks should also consider and maintain seed-associated microbial diversity to save microorganisms, which are important for securing global food production as well as economic viability. In the last decade, the importance of plant microbiota has gained increasing awareness, which is evident from the number of publications and ongoing projects in this field. Also, the industry sector is extremely interested in microbial applications to improve crop production. Nowadays more than 300 companies comprising big international players in this sector as well as small and medium enterprises participate in the Annual Biocontrol Industry Meeting (http://www.abim.ch/home.html) organized every year by the International Organization of Biocontrol Manufacturers in Switzerland. This international meeting has been in place for many years but participant numbers have started to explode recently demonstrating the tremendous interest by the industry. This interest is driven by major challenges such as the demographic development or climate change we nowadays face in crop production. Due to the high application potential, major investments in this sector are made and expectations are high. It will be important to manage these expectations appropriately to avoid disappointments and the premature termination of promising R&D strategies. Apart from applications in the crop production sector plant microbiota host an extremely diversity of microorganisms and functional activities, which might be equally relevant for applications in other fields such as soil sanitation or medical treatments. Overall, the public and policy sector has to be aware that plant microbiota is essential for the health and growth and plants as well as for the functioning of terrestrial ecosystems. Plant microbiota is not only an important component of biodiversity, but also have the potential to further contribute to the economic development in developed as well as less developed parts of the world. None declared.