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Properties of bacterial endophytes and their proposed role in plant grow
Abstract
Bacterial endophytes live inside plants for at least part of their life cycle. Studies of the interaction of endophytes with their host plants and their function within their hosts are important to address the ecological relevance of endophytes. The modulation of ethylene levels in plants by bacterially produced 1-aminocyclopropane-1-carboxylate deaminase is a key trait that enables interference with the physiology of the host plant. Endophytes with this capacity might profit from association with the plant, because colonization is enhanced. In turn, host plants benefit by stress reduction and increased root growth. This mechanism leads to the concept of competent endophytes, defined as endophytes that are equipped with genes important for maintenance of plantendophyte associations. The ecological role of these endophytes and their relevance for plant growth are discussed here
... The interactions between plants and endophytes are dynamic and can range from mutualism to parasitism to commensalism (Hardoim et al., 2008;Porras-Alfaro and Bayman, 2011). Endophytes reside in a large number of plant species as a microbiome and have proven to positively influence plant growth and responses to pathogens Frontiers in Microbiology 10 frontiersin.org ...
... The variable presence of certain endophytes from one seed generation to the next suggests that the composition of the endophytic community evolves over the genustions. However, some studies have shown that members of seed-associated microbiomes can be conserved across plant genustions (Hardoim et al., 2008;Truyens et al., 2016) and even through human evolution and selection (Johnston-Monje and Raizada, 2011). ...
... Finally, the constitution and functions of the seed microbiome are complex processes affected by multiple environmental and host genetic factors (Hardoim et al., 2008;Johnston-Monje and Raizada, 2011). Nevertheless, our results suggest that seed-dominant endophytes could provide numerous benefits covering the initial germination and establishment needs of seedlings (Truyens et al., 2015) and improve photosynthesis, nutrition, and stress alleviation (Arshad et al., 2007;Hardoim et al., 2008). ...
Microbial endophytes are microorganisms that live inside plants, and some of them play important yet understudied roles in plant health, growth, and adaptation to environmental conditions. Their diversity within plants has traditionally been underestimated due to the limitations of culture-dependent techniques. Metagenomic profiling provides a culture-independent approach to characterize entire microbial communities. The argan tree (Argania spinosa) is ecologically and economically important in Morocco, yet its seed endophyte microbiome remains unexplored. This study aimed to compare the bacterial and fungal endophyte communities associated with argan seeds collected from six sites across Morocco using Illumina MiSeq sequencing of the 16S rRNA gene and ITS regions, respectively. Bacterial DNA was extracted from surface-sterilized seeds and amplified using universal primers, while fungal DNA was isolated directly from seeds. Bioinformatics analysis of sequencing data identified taxonomic profiles at the phylum to genus levels. The results indicated that bacterial communities were dominated by the genus Rhodoligotrophos, while fungal communities exhibited varying degrees of dominance between Ascomycota and Basidiomycota depending on site, with Penicillium being the most abundant overall. Distinct site-specific profiles were observed, with Pseudomonas, Bacillus, and Aspergillus present across multiple locations. Alpha diversity indices revealed variation in endophyte richness between seed sources. In conclusion, this first exploration of the argan seed endophyte microbiome demonstrated environmental influence on community structure. While facing limitations due to small sample sizes and lack of ecological metadata, it provides a foundation for future mechanistic investigations into how specific endophyte–host interactions shape argan adaptation across Morocco’s diverse landscapes.
... Microorganisms associated with the endosphere, known as endophytes, directly influence plant metabolism and plant cells. Several studies have highlighted the benefits of endophytes in improving plant health (Harman et al., 2021) by revealing their ability to enhance nutrient uptake, disease resistance, stress tolerance, conserve water, and promote soil health, which contributes to reducing environmental impacts, increasing productivity, and long-term sustainability in agriculture (Hardoim et al., 2008;Compant et al., 2010;Hardoim et al., 2015). Therefore, harnessing these natural benefits as biocontrol agents can reduce environmental impacts of pest management, offer targeted pests and disease control, and enhance agricultural system resilience. ...
... Horizontal pathway: Horizontal transfer is mainly realized by the soil-to-root route because roots are considered the main entry point for microorganisms. Indeed, bacteria can penetrate the endodermis, the innermost layer of the root cortex, through root hair channels, cracks in the epidermis, cell-to-cell junctions, or through root cap cells that detach as the roots grow (Hardoim et al., 2008). Once bacteria reach the endodermis, they must pass through the Casparian strip, a cell wall thickening that prevents the free diffusion of molecules and ions between the root cortex and vascular tissues. ...
... In addition to this main transport route, other endophytes also colonize intercellular spaces (Hardoim et al., 2015). This pathway can be considered passive or active (Hardoim et al., 2008) depending on the penetration mode within the plant. An active penetration pathway can be mediated by the attachment of bacterial endophytes to plant cells using their flagellum and the secretion of metabolites that facilitate the penetration process (mostly exopolysaccharides [EPS] and cell wall degrading enzyme; Kandel et al., 2017;Pinski et al., 2019;Ullah et al., 2019). ...
Currently, it seems inconceivable to dispute the major role of microorganisms in human health or insects with endosymbionts. Although microbial endophytes were discovered long ago, little is known about the roles of plant-associated microorganisms. Some endophytes are horizontally transmitted, whereas others are seed-borne; together, they influence plant health. Beneficial endophytes can promote plant growth and yield by increasing plant resistance to biotic and abiotic stresses. Recently, the tools available to study the phytobiome have much improved, opening doors for a better understanding of the fascinating interactions taking place at the plant level. This review redefines the conceptual framework for “endophyte” and “endophytome,” focusing on the intricate dynamics of bacterial endophytomes. Systematically examining the formation pathways and profiling endophytes allows for a comprehensive exploration of the intricate dynamics governing plant-microbe interactions. Additionally, the assessment of how endophytomes are influenced by both biotic and abiotic factors provides essential insights into the adaptability and resilience of plant-associated microorganisms. Our comprehensive analysis integrates genomic insights with environmental considerations, offering a nuanced perspective on the functional roles of bacterial endophytomes. Therefore, a new, inclusive definition is essential to accurately represent the complexity of interactions within the plant microbiome as well as having the whole picture of associated concepts.
... Ethylene is an important compound that regulates root growth and development (Madhaiyan et al., 2006a, b, c). The concentration of ethylene production is related to the biosynthesis pathway of auxin (HarDOIm, van Overbeek, & van Elsas, 2008). A high concentration of ethylene has a negative effect on plant growth and root elongation as it imparts stress conditions in plants which accelerate abscission, aging and senescence (Glick, 1995). ...
... SAM is converted to ACC by the enzyme ACC synthase and ACC is converted to ethylene by the enzyme ACC oxidase. Various biotic and abiotic factors regulate transcriptionally both of these enzymes (Madhaiyan et al., 2006a, b, c;HarDOIm et al., 2008). The interesting finding is that the ACC activity of plants is increased when bacterial IAA production is also increased. ...
... This phenomenon indicates the similarity between these two pathways. According to researcher (HarDOIm et al., 2008), for the maintenance of endophytic bacterial plant colonization, the fundamental process is the balance between IAA and ethylene. The acdS gene, which encodes an ACC deaminase enzyme, is present in various PPFM organisms. ...
Purpose
The purpose of this article is to provide information about interactions between pink-pigmented facultative methylotroph (PPFM) organisms and plants, their molecular mechanisms of methylotrophic metabolism, application of PPFMs in agriculture, biotechnology and bioremediation and also to explore lacuna in PPFMs research and direction for future research.
Design/methodology/approach
Research findings on PPFM organisms as potent plant growth promoting organisms are discussed in the light of reports published by various workers. Unexplored field of PPFM research are detected and their application as a new group of biofertilizer that also help host plants to overcome draught stress in poorly irrigated crop field is suggested.
Findings
PPFMs are used as plant growth promoters for improved crop yield, seed germination capacity, resistance against pathogens and tolerance against drought stress. Anti-oxidant and UV resistant properties of PPFM pigments protect the host plants from strong sunshine. PPFMs have excellent draught ameliorating capacity.
Originality/value
To meet the ever increasing world population, more and more barren, less irrigated land has to be utilized for agriculture and horticulture purpose and use of PPFM group of organisms due to their draught ameliorating properties in addition to their plant growth promoting characters will be extremely useful. PPFMs are also promising candidates for the production of various industrially and medicinally important enzymes and other value-added products. Wider application of this ecofriendly group of bacteria will reduce crop production cost thus improving economy of the farmers and will be a greener alternative of hazardous chemical fertilizers and fungicides.
Graphicalabstract:
... not only soil attached microorganisms adhering to the roots and inhabit the root surface, but also the colonized microorganisms in the root interior environment [4]. Depending on the chemical signals and nutrients released by the root, microorganisms are enriched and grown in the rhizosphere soil, and then they pass through the regulation and selection by plant own metabolism to stably colonize the root tissues [5][6][7]. ...
... For instance, the rhizosphere bacterial community can promote the decomposition of mineral nutrients, defend against soilborne diseases and improve plant resilience to adverse growth conditions [10][11][12]. It is reported that the inoculated plant-growth-promoting rhizobacteria strains contributed to the increase in young apple tree growth and fruit yield [13]. Often the beneficial effects of root endophytes, without causing any evident damage to the host plants, are greater than many rhizosphere bacteria [5,14]. Plant-growth-promoting bacterial endophytes facilitate plant growth by producing phytohormones, antimicrobial metabolites, and increasing supply of nutrients [15,16]. ...
... Compared with the root endosphere, we found that the rhizosphere network had a higher scale and complexity based on the topological properties (Fig. 8, Table 1). Only bacteria that were able to pass through root cortical and endodermis can continue to colonize the endothelial layer [5,46]. Therefore, the root endosphere environment had a stronger filtering effect on microorganisms than the rhizosphere. ...
Background
Compared with aerial plant tissues (such as leaf, stem, and flower), root-associated microbiomes play an indisputable role in promoting plant health and productivity. We thus explored the similarities and differences between rhizosphere and root endosphere bacterial community in the grafted apple system.
Results
Using pot experiments, three microhabitats (bulk soil, rhizosphere and root endosphere) samples were obtained from two-year-old apple trees grafted on the four different rootstocks. We then investigated the bacterial community composition, diversity, and co-occurrence network in three microhabitats using the Illumina sequencing methods. Only 63 amplicon sequence variants (ASVs) out of a total of 24,485 were shared in the rhizosphere and root endosphere of apple grafted on the four different rootstocks (M9T337, Malus hupehensis Rehd., Malus robusta Rehd., and Malus baccata Borkh.). The core microbiome contained 8 phyla and 25 families. From the bulk soil to the rhizosphere to the root endosphere, the members of the phylum and class levels demonstrated a significant enrichment and depletion pattern. Co-occurrence network analysis showed the network complexity of the rhizosphere was higher than the root endosphere. Most of the keystone nodes in both networks were classified as Proteobacteria, Actinobacteriota and Bacteroidetes and were low abundance species.
Conclusion
The hierarchical filtration pattern existed not only in the assembly of root endosphere bacteria, but also in the core microbiome. Moreover, most of the core ASVs were high-abundance species, while the keystone ASVs of the network were low-abundance species.
... Se requiere una investigación continua que amplíe nuestro entendimiento de los mecanismos de interacción entre los HE y las plantas, así como su influencia en la salud del suelo y la productividad agrícola (Mendes et al., 2011). Además, es crucial desarrollar estrategias innovadoras para la selección, aplicación y manejo de estos microorganismos en sistemas agrícolas ecológicos, con el objetivo de maximizar su potencial para promover la salud de las plantas y la sostenibilidad agrícola (Pablo R. Hardoim, Leo S. van Overbeek, 2008) Las plantas asociadas con hongos en zonas áridas y semiáridas se encuentran entre entornos hostiles y pueden tener implicaciones para la biodiversidad como también en el funcionamiento de los ecosistemas (Noui et al., 2019). La presente revisión tiene como objetivo evaluar el impacto de los hongos endófitos en la agricultura ecológica. ...
... Los microorganismos endófitos son importantes en la salud de las plantas y la sostenibilidad agrícola en sistemas ecológicos (Pablo R. Hardoim, Leo S. van Overbeek, 2008), estos microorganismos simbióticos mejoran el crecimiento vegetal, la protección contra patógenos y el fortalecimiento de la resistencia al estrés abiótico. Además, identifican desafíos en la comprensión de los mecanismos de LATAM Revista Latinoamericana de Ciencias Sociales y Humanidades, Asunción, Paraguay. ...
Los microorganismos endófitos que colonizan los tejidos internos de las plantas de forma mutualista están emergiendo como protagonistas clave en la agricultura ecológica. Los microorganismos endófitos estimulan el crecimiento de las plantas al ayudar en la absorción de nutrientes, especialmente fósforo y nitrógeno, además de fortalecer la resistencia a factores abióticos y bióticos como sequías, salinidad y patógenos. Estos microorganismos también pueden producir compuestos bio-activos, como fitohormonas y metabolitos secundarios, que contribuyen al crecimiento y la salud de las plantas. De esta manera, poseen un potencial importante para el control biológico de plagas y enfermedades. Los microorganismos endófitos son una herramienta prometedora para la agricultura ecológica, ya que proporcionan opciones sostenibles y respetuosas con el medio ambiente para incrementar la productividad agrícola y garantizar la seguridad alimentaria. El artículo tiene como objetivo evaluar la importancia de los hongos endófitos en la agricultura ecológica
... Endophytes penetrate the plant root after becoming established on the rhizoplane either through active or passive process. The endophytes can passively penetrate the root tissue through lateral root emergence and wounds (Hallmann, 2001: Hardoim et al., 2008. For active penetration, Böhm et al. (2007) revealed that twitching motility of the bacteria influences the movement of endophytes inside the host. ...
... Ethylene-mediated plant growth inhibition decreases as ACC and ethylene levels decrease. Hence, endophytic microbes promote plant growth by reducing the ethylene-inducing stresses (Glick et al., 2007;Hardoim et al., 2008). ...
Sustainable agriculture in combination with crop improvement programme is gaining more attention in the scientific field nowadays. With abundance of resources, endophytes offer an environmentally friendly and sustainable approach to increase crop yield, improve soil fertility while protecting the plants from a number of biotic and abiotic stresses. Residing within plant, endophytes are unique group of symbionts that systematically invade the internal environment of host without causing any pathogenic symptoms. Endophytes, which include bacteria, fungi, and viruses, have been shown to have beneficial effects on their hosts, either directly or indirectly. On the other hand, Zingiberaceae is a valuable family of ginger that has a lot of economic benefits. Endophytes isolated from the Zingiberaceae plants are known to promote plant development through the production of phytohormone, 1- aminocyclopropane -1 carboxylic acid (ACC) deaminase, siderophore and also assist the host plant in phosphate solubilization activity. They are also prominent producers of several secondary metabolites with a lot of bioactivities. However, the full potential of endophytes from the Zingiberaceae plants largely remain untapped. Thus, the aim of this review is to discover various types of endophytes isolated from the Zingiberaceae plants, their phytohormone production, nutrient acquisition, biohardening application, secondary metabolites production and bioactivities. The broad knowledge of endophytes from Zingiberaceae plants will provide insight into new economic potentials and determine its future in sustainable agriculture practices.
... are found in the leafy or rhizospheric areas, or in the roots of plants in the soil. Endophytic bacteria are those that survive and grow inside their host plant , Hardoim et al., 2008. The term "endophyte" literally means "in the plant," since endo means "inside" and phyton means "plant." ...
... Plants have the ability to "choose" their microbiome in order to introduce beneficial bacteria to stimulate the growth of host plants (Hardoim et al. 2008, Marasco et al., 2012, Rashid et al. 2012. Most endophytic microbes originate in the phyllosphere or rhizosphere (Aloo et al., 2019). ...
... The Pharmaceutical and Chemical Journal, 2023, 10(1): [21][22][23][24][25][26][27][28][29][30][31][32] The Pharmaceutical and Chemical Journal 25 roots, stem, resin canals, and even meristems. The same physical characteristics of colony, vegetative hyphae, and asexual/sexual spores are utilized for identifying endophytic fungus as are used for identifying other types of fungi (conidial development, size, shape, conidia, attachment of conidia and shape of conidial head). ...
... It is interesting to note that rhizobia have also been identified invading the tissues of non-legume plants; however, the induction of nodule formation in these plants has never been recorded, with the exception of Parasponia. Endophytic rhizobia have been shown in multiple studies to stimulate the growth of plants that are not legumes; hence, the use of endophytic rhizobia as biofertilizers may be an effective technique for achieving sustainable agriculture [28][29][30][31]. ...
Endophytic bacteria are those that live inside of plants for at least some of the plant's life cycle but do not cause any outwardly apparent symptoms of the disease. In light of the fact that endophytes are a source of phytochemicals of high value, it is essential to bioprospect these microorganisms in order to find a wide variety of related phytochemicals that have some sort of therapeutic effect. Plant endophytes can stimulate plant growth in a number of different ways, including fixing atmospheric nitrogen, creating phytohormones, preventing the spread of phytopathogens, and improving mineral uptake. Endophytes possess different types of bioactivity, such as antibacterial, anticancer, antifungul and antiviral agents.
... Heavy metals are well recognized to have detrimental impacts on biomass development. Plants, algae, and microbes may experience slower growth and production due to their inhibition of several biological processes [32][33][34]. The ability of the isolate Stenotrophomonas rhizophila to improve cleanup and generate biomass was thus validated. ...
... Furthermore, it was noted that the transmittance of the peaks observed in the loaded biomass exhibited a significantly diminished value compared to the transmittance observed in the unloaded bacteria biomass. In conclusion, the formation of different spectra after the metal ions were adsorbable to bacterial biomass substantiated the role of functional groups in metal binding [34][35][36][37]. Numerous substances, particularly trace metals, bind to the functional groups on the surfaces of microbes and cling to the surfaces of cells and minerals [36]. ...
... These creatures inhabit undamaged tissues of the host plant and perform a wide range of biological interactions ranging from symbiotic to slightly pathogenic (Strobel et al., 2005). The interaction between the plant and endophytes is a symbiotic relationship based on the benefit of both the plant and the microorganism (Polesi, 2011;Hardoim et al., 2008). As a result of this wonderful relationship, the microbes inside the plant produce a group of substances (secondary metabolites) with unique structures that cannot be obtained from a chemical reaction and which are of great importance to the plant (Carroll, 1988;Schulz et al., 1998;Parker, 1999;Redman et al., 2001;Schulz et al., 2002;Strobel and Daisy, 2003;Lee et al., 2004;Dudeja et al., 2012). ...
Pulicaria crispa is a medicinal and aromatic plant that is distributed around the world. In this study, a remarkable variety of endophytic fungi and bacteria were isolated from different parts of P. crispa. Fourteen endophytic fungal species belonging to seven genera (Cladosporium, Chaetomium, Volutella, Emericella, Aspergillus, Penicillium, and Ulocladium) were recorded. The relative abundance of genus Aspergillus was 40.5% (recorded the highest count of genera). Volutella ciliata registered the highest fungal species count with a relative abundant of 16.2% and it is the first record of this fungus in Aswan region. Five bacterial species belonging to the genus Bacillus including Bacillus sianensis, B. safensis, B. subtilis, B. altitudinis, and B. vallismortis were isolated. B. sianensis which colonized roots represented the highest relative abundance percent (32 %). This is the first study of the microbes' diversity inside the tissue of the medicinal plant P. crispa.
... The opposite was observed in terms of evenness (Fig. 3c). The endophytic bacteria mostly derive from the rhizosphere (Hardoim et al. 2008;Compant et al. 2005Compant et al. , 2010 and the diversity of rhizosphere microorganisms has a direct influence on endophytic bacteria (Znoj et al. Dong et al. 2019, 2021b. ...
Deschampsia antarctica Desv. and Poa annua L. are two Poaceae plants with enough endurance to successfully establish populations in the Antarctic region. Their adaptation to the Antarctic environment is closely linked to root-associated microbial communities. In this study, we obtained 16S rRNA sequencing data of the root-associated microbial communities of these two Poaceae plants from NCBI. Meta-analysis was used to investigate the similarities and differences between the root endosphere and rhizosphere-dwelling microbial communities in these two Poaceae plants. Here we report that two Poaceae-Poaceae plants’ rhizospheric communities were found to be more species diversity than endospheric communities. The species diversity of P. annua was higher than that of D. antarctica in both endosphere and rhizosphere communities. Seven bacterial families form a core microbiome of two Antarctic Poaceae plants’ root endosphere, in which Microbacteriaceae appears to be obligatory root endophytes of the two Antarctic Poaceae plants. The core microbiome of the two Poaceae plants’ rhizosphere has six bacterial families. Chitinophagaceae, Burkholderiaceae, and Flavobacteriaceae are most likely to play a crucial role in Poaceae plants’ adaptation to cold Antarctic conditions. Sphingobacteriaceae, Caulobacteraceae, Gemmatimonadaceae, and Flavobacteriaceae have a great influence on two Antarctic Poaceae plants.
... On the other hand, the symbiosis of endophytes with their host plants could be facultative or obligate [4]. Obligate endophytes require plant tissues to complete their life cycle, whereas facultative endophytes periodically colonize internal plant tissues [5]. To some extent, plant preference for VTEs with obligate traits may imply that these endophytes have exceptional functions from which plants could derive long-term benefits. ...
Vertically transmitted endophytes (VTEs) with multi-host-supporting functions are considered plant-acquired heritable traits, which can be manipulated to develop plants with the stable inheritance of these VTEs, defined here as ‘plant endophytic modification (PEM)’. To translate this hypothetical strategy into agricultural and horticultural practice, a PEM was carried out by introducing an anti-fungal pathogenic bacterium, Bacillus cereus (strain ID: ZX-2), into grapevine cuttings and growing the cuttings into vine plants. Bacterial strain XZ-2 is highly efficient in infecting grapevine cuttings and colonizing the interior of the infected cuttings, various parts of the subsequently established vine plants, and next year’s emerging vine shoots and leaves. Profiling the endophytic microbiota by high-throughput sequencing to the grapevines revealed that the colonization with exogenous ZX-2 slightly affected endophytic diversity, while significantly altering the composition and the predicted phenotypes of endophytic microbiota in ZX-2-modified grapevines (ZX-2mg). Most importantly, leaves (from both first- and second-year grapevines) of ZX-2mg conferred significantly higher (p < 0.001) anti-fungal pathogen abilities and a reduction in naturally occurring lesion area than leaves compared to the control grapevines. For all detected vines, a significant correlation (N = 37, r = 0.418; p < 0.01) between fungal pathogen inhibition rates and B. cereus (ZX-2) isolation rates was observed. In addition, ZX-2mg showed some growth promotion and a delay (15–20 days) in leaf abscission. The work established an alternative strategy to create plant lines with functions of specific VTEs via PEM, confirming the practical value of PEM in future organic farming systems.
... Endophytes are ubiquitous and have been associated with almost all plants examined [9]. Beneficial endophytes are mostly found in the rhizosphere, but they also colonize the phyllosphere, and a few are obligate symbionts transmitted to seeds [10]. The endophytic communities and the networks that drive them are thus remarkably diverse and complex. ...
Plant growth-promoting rhizobacteria (PGPR) applications have emerged as an ideal substitute for synthetic chemicals by their ability to improve plant nutrition and resistance against pathogens. In this study, we isolated fourteen root endophytes from healthy wheat roots cultivated in Tunisia. The isolates were identified based from their 16S rRNA gene sequences. They belonged to Bacillota and Pseudomonadota taxa. Fourteen strains were tested for their growth-promoting and defense-eliciting potentials on durum wheat under greenhouse conditions, and for their in vitro biocontrol power against Fusarium culmorum, an ascomycete responsible for seedling blight, foot and root rot, and head blight diseases of wheat. We found that all the strains improved shoot and/or root biomass accumulation, with Bacillus mojavensis, Paenibacillus peoriae and Variovorax paradoxus showing the strongest promoting effects. These physiological effects were correlated with the plant growth-promoting traits of the bacterial endophytes, which produced indole-related compounds, ammonia, and hydrogen cyanide (HCN), and solubilized phosphate and zinc. Likewise, plant defense accumulations were modulated lastingly and systematically in roots and leaves by all the strains. Testing in vitro antagonism against F. culmorum revealed an inhibition activity exceeding 40% for five strains: Bacillus cereus, Paenibacillus peoriae, Paenibacillus polymyxa, Pantoae agglomerans, and Pseudomonas aeruginosa. These strains exhibited significant inhibitory effects on F. culmorum mycelia growth, sporulation, and/or macroconidia germination. P. peoriae performed best, with total inhibition of sporulation and macroconidia germination. These finding highlight the effectiveness of root bacterial endophytes in promoting plant growth and resistance, and in controlling phytopathogens such as F. culmorum. This is the first report identifying 14 bacterial candidates as potential agents for the control of F. culmorum, of which Paenibacillus peoriae and/or its intracellular metabolites have potential for development as biopesticides.
... Endophytes are ubiquitous and have been associated with almost all plants examined [9]. Beneficial endophytes are mostly found in the rhizosphere, but they also colonize the phyllosphere, and a few are obligate symbionts transmitted to seeds [10]. The endophytic communities and the networks that drive them are thus remarkably diverse and complex. ...
In recent decades, agriculture has been under strong pressure to achieve intensive levels of production. The success of this goal, largely achieved, is notably linked to the massive use of pesticides and chemical fertilizers. However, the use of these agrochemical products profoundly deteriorates the quality of soils and the environment. The challenge lies in the development of sustainable agricultural practices that harness the naturally associated microbiomes in crops, especially in cereal cultivation. This thesis aims to shed light on the complex aspects of microbial communities associated with an ancient variety of wheat, by identifying their potential beneficial effects on wheat growth and innate immunity. A total of 206 fungal isolates and 102 bacterial isolates were obtained from the rhizosphere, roots, and ears of the ancient wheat variety Florence Aurore. Among these isolates, 6 strains of Trichoderma from the rhizosphere and 14 root endophytic bacteria were selected to characterize their biofertilization potential for plant growth and their biocontrol activity against Fusarium culmorum, a predominant pathogen in Tunisia
causing economically damaging diseases. All these isolates demonstrated their
biostimulatory effectiveness in planta by increasing fresh and dry biomass as well as
chlorophyll content in wheat plants under controlled conditions. These capabilities
correlated with the ability of these strains in vitro to solubilize phosphate and zinc,
produce indolic compounds, ammonia, and hydrogen cyanide. At the same time, these strains showed biocontrol ability by eliciting systemic plant defenses in 21-day-old wheat seedlings. Similarly, the bacterial endophytes Paenibacillus polymyxa, Paenibacillus peoriae, and Pantoea agglomerans inhibited the mycelial growth, sporulation, and germination of F. culmorum macroconidia in vitro, either through direct contact or by treating the pathogen with purified intracellular fractions. These antagonistic abilities could be explained by the production of volatile organic compounds, antifungal substances, and extracellular lytic enzymes such as Amylase, Cellulase, Pectinase, Protease, and Chitinase. These observations offer promising solutions to further boost more environmentally friendly and productive cereal crops in Tunisia.
... The process behind the plant growth promotion activities that are regulated by endophytes is not fully understood (Hardoim et al., 2008). Growth and development of the host plant are promoted by endophytes either directly or indirectly. ...
Endophytes are endosymbiotic microorganisms colonizing the internal tissues of healthy host plants [1] and possess the ability to improve the quality and growth rate of theirrespective hosts [2]. Their colonization does not produce any disease symptoms or morphological changes like gall formation of plant tissues [3]. Most of the plants on earth arehost to one or more types of endophytes [4]. These endophytes can be either bacteria or fungi [5,6]. Their population density in a host plant can vary from hundreds to more than 9 x 109 bacteria per gram of plant tissue [7,8, 9]. They can be either obligate or a facultative and the obligate types cannot be cultured due to their specificity of growth conditions. On the other hand, facultative endophytes can be cultured outside the plant tissue using artificial nutrient media [10, 11]. Endophytes form an important part of the micro-ecosystem inside plant tissues [12]. The most explored endophytes are non-pathogenic fungi that provide a number of useful characteristics to their host plant. However, bacterial endophytes remain an unexplored group [13]. Any bacteria which could be isolated from a surface-sterilized plant or extracted from its tissues can be called an endophyte if it does not affect the plant negatively. Bacteria can positively promote plant growth whereas studies show that plants are able to select these beneficial bacterial members in their microbiome including those inside the plant tissues [14, 15, 16]. There is no shred of evidence suggesting that these bacteria take advantage in this relationship [17], but certainly, they get protection from pathogens in adverse times. They could also communicate much better than the rhizospheric bacteria at times of stress [18,19]
... Ethylene is produced in excess during stress and this can harm plant health. ACC deaminase will ultimately bring down ethylene concentration in stressed conditions thus aiding plants to better resist abiotic stress(Hardoim et al., 2008). ...
Endophytes are endosymbiotic microorganisms colonizing the internal tissues of healthy host plants [1] and possess the ability to improve the quality and growth rate of theirrespective hosts [2]. Their colonization does not produce any disease symptoms or morphological changes like gall formation of plant tissues [3]. Most of the plants on earth arehost to one or more types of endophytes [4]. These endophytes can be either bacteria or fungi [5,6]. Their population density in a host plant can vary from hundreds to more than 9 x 109 bacteria per gram of plant tissue [7,8, 9]. They can be either obligate or a facultative and the obligate types cannot be cultured due to their specificity of growth conditions. On the other hand, facultative endophytes can be cultured outside the plant tissue using artificial nutrient media [10, 11]. Endophytes form an important part of the micro-ecosystem inside plant tissues [12]. The most explored endophytes are non-pathogenic fungi that provide a number of useful characteristics to their host plant. However, bacterial endophytes remain an unexplored group [13]. Any bacteria which could be isolated from a surface-sterilized plant or extracted from its tissues can be called an endophyte if it does not affect the plant negatively. Bacteria can positively promote plant growth whereas studies show that plants are able to select these beneficial bacterial members in their microbiome including those inside the plant tissues [14, 15, 16]. There is no shred of evidence suggesting that these bacteria take advantage in this relationship [17], but certainly, they get protection from pathogens in adverse times. They could also communicate much better than the rhizospheric bacteria at times of stress [18,19]
... A maioria das plantas vasculares abrigam bactérias endofíticas ( XIE et al., 2020). Esses micro-organismos vivem intra ou intercelularmente sem causar danos aparentes à planta (JOO et al., 2020;GOUVEIA et al., 2020), em pelo menos uma parte do seu ciclo de vida (HARDOIM et al., 2008), e são detectados por métodos culturais ou moleculares (KHAN et al., 2020). ...
... Furthermore, various microbe-derived secondary metabolites have attracted more and more attention due to their remarkable physiological functions alone or in combination with the corresponding metabolites-producing bacteria and fungi in helping plants resist biotic and abiotic stresses. Therefore, exploring the identity and function of tissue-specific microbes and their metabolites will provide a better understanding of their role in promoting the healthy growth of plants (Hardoim et al., 2008, Weyens et al., 2009, Brader et al., 2014. Therefore, to elucidate the link between long-term cultivation and stress resilience in bayberry plants, this study examines the bacterial and fungal microbiomes present in the rhizosphere and endosphere of both ancient and cultivated bayberry varieties. ...
The ancient bayberry demonstrates superior resistance to both biotic and abiotic stresses compared to cultivated bayberry, yet the underlying mechanisms remain largely unexplored. This study investigates whether long‐term bayberry cultivation enhances stress resistance through modulation of tissue‐specific microbes and metabolites. Employing microbiome amplicon sequencing alongside untargeted mass spectrometry analysis, we scrutinize the role of endosphere and rhizosphere microbial communities and metabolites in shaping the differential resistance observed between ancient and cultivated bayberry trees. Our findings highlight the presence of core microbiome and metabolites across various bayberry tissues, suggesting that the heightened resistance of ancient bayberry may stem from alterations in rhizosphere and endosphere microbial communities and secondary metabolites. Specifically, enrichment of Bacillus in roots and stems, Pseudomonas in leaves, and Mortierella in rhizosphere soil of ancient bayberry was noted. Furthermore, correlation analysis underscores the significance of enriched microbial species in enhancing ancient bayberry's resistance to stresses, with elevated levels of resistance‐associated metabolites such as beta‐myrcene, benzothiazole, L‐glutamic acid, and gamma‐aminobutyric acid identified through GC–MS metabolomics analysis. The beneficial role of these resistance‐associated metabolites was further elucidated through assessment of their promotive and allelopathic effects, as well as their phytostatic and antioxidant functions in lettuce plants. Ultimately, our study delves into the intrinsic reasons behind the greater resistance of ancient bayberry to biotic and abiotic stresses by evaluating the impact of long‐term planting on the microbial community and metabolites in the bayberry endosphere and rhizosphere, shedding light on the complex dynamics of host‐microbial interactions.
... There have been multiple reports of endophytic bacteria up to this point due to scientists' growing interest. According to Hardoim et al. (2008), Abreu-Tarazi et al. (2010), and , they can be divided into two major groups: facultative and obligatory endophytes. In the obligatory relationship, the host plant supplies nourishment, stable development environments for the endophyte, and endophytes, in addition to producing a variety of helpful metabolites, provide biotic and abiotic stress tolerance (Fig. 1). ...
... In response to biotic or abiotic stress, plants secrete chemical factors to help them adapt to these stresses by recruiting beneficial microorganisms, which is known as the "cry for help" strategy [5,8]. Crop roots are colonized by large numbers of microorganisms, collectively known as the root-microbiome, which modulate plant growth as well as development and contribute to plant fitness under diverse environmental conditions [9,10]. Roots also secret organic acids, amino acids, and sugars, which provide microorganisms in the rhizosphere with rich nutrients, enabling microbiota to migrate into the rhizosphere and roots [11]. ...
Crop roots are colonized by large numbers of microorganisms, collectively known as the root-microbiome, which modulate plant growth, development and contribute to elemental nutrient uptake. In conditions of nitrogen limitation, the over-expressed Calcineurin B-like interacting protein kinase 2 (OsCIPK2) gene with root-specific promoter (RC) has been shown to enhance growth and nitrogen uptake in rice. Analysis of root-associated bacteria through high-throughput sequencing revealed that OsCIPK2 has a significant impact on the diversity of the root microbial community under low nitrogen stress. The quantification of nifH gene expression demonstrated a significant enhancement in nitrogen-fixing capabilities in the roots of RC transgenetic rice. Synthetic microbial communities (SynCom) consisting of six nitrogen-fixing bacterial strains were observed to be enriched in the roots of RC, leading to a substantial improvement in rice growth and nitrogen uptake in nitrogen-deficient soils. Forty and twenty-three metabolites exhibiting differential abundance were identified in the roots and rhizosphere soils of RC transgenic rice compared to wild-type (WT) rice. These findings suggest that OSCIPK2 plays a role in restructuring the microbial community in the roots through the regulation of metabolite synthesis and secretion. Further experiments involving the exogenous addition of citric acid revealed that an optimal concentration of this compound facilitated the growth of nitrogen-fixing bacteria and substantially augmented their population in the soil, highlighting the importance of citric acid in promoting nitrogen fixation under conditions of low nitrogen availability. These findings suggest that OsCIPK2 plays a role in enhancing nitrogen uptake by rice plants from the soil by influencing the assembly of root microbial communities, thereby offering valuable insights for enhancing nitrogen utilization in rice cultivation.
Supplementary Information
The online version contains supplementary material available at 10.1186/s12870-024-04982-0.
... The type of pathway used by the microorganism to synthesize IAA, whether inside or close to the plants, is determined by genetic and/or environmental factors, and can ascertain whether the microorganism is beneficial or harmful to the plants (Spaepen et al., 2007). Most beneficial endophytes use the IPA pathway while the phytopathogens produce IAA via the IAM pathway (Hardoim et al., 2008). Since most plants are sensitive to the amount of IAA available in their tissues at any given time, a beneficial IAA-producing endophyte must provide the accurate dose of IAA while accounting for endogenous IAA produced by the plants; otherwise, steep IAA concentrations can be harmful to the plants (Ali et al., 2017). ...
... In addition, we found a higher percentage of co-occurrence interactions among OTUs in root, pointing a possible enhancement of mutualistic interactions useful for survival and growth under arid conditions (Mosqueira et al., 2019). We detected a higher abundance of putative dual-role root-associated bacteria (Hardoim et al., 2008), Bacillus (biofilm) (Khan et al., 2021), Streptomyces (biocontrol) (Saeed et al., 2017) and Dongia (heat stress), whose modules (RM2 and RM3) correlated positively to irrigation water pH, indicating their versatile role in plant homeostasis and growth promotion. Similarly, we found enrichment of specific OTUs, Hyphomicrobium (denitrification) (Martineau et al., 2015), Romboutsia (acetogenesis), Novibacillus (biocontrol), Gracilibacillus (biocontrol), Pedomicrobium (iron cycle), and Gemmatimonadaceae_unclassified (nitrous oxide reduction) (Oshiki et al., 2022) and their respective modules (SM3 and SM4) to water pH in soil, which perhaps help in regulating soil health and nutrient cycling in arid soil. ...
Date palms are widely cultivated in arid agroecosystems, where knowledge of irrigation water effect on their soil and root-associated bacterial communities is limited. Using 16S rDNA metabarcoding, we studied soil and root-associated bacterial communities of date palms growing in United Arab Emirates. Overall, 12.18% of bacterial operational taxonomic units (OTUs) were unique to roots, whereas 41.55% were specific to soil. The bacterial diversity was lower in root and community patterns were distinct between compartments, wherein irrigation water pH was a key structuring factor in both compartments, while salinity (electrical conductivity) was important only in the soil. Co-occurrence network analysis revealed a decrease in complexity in the soil–root continuum, and specific taxa/modules also varied with water pH. We observed a higher abundance of endophyte–saprotroph (Bacillus, Streptomyces and Dongia) dual-role OTUs in both compartments, possibly involved in nutrient mobilisation and plant growth. Based on PICRUSt and trait-based analyses, we showed that these OTUs are putatively involved in the nitrogen cycle (nitrification, denitrification, and assimilatory nitrate reduction). Taken together, we suggest that irrigation water pH, not soil pH, transiently affects belowground bacterial communities and selects bacteria in specific pH ranges, which may be important for nutrient cycling (i.e. nitrogen cycle) in arid agroecosystems.
... Although endophytic bacteria can colonize aerial plant organs (Hardoim et al. 2008;Reinhold-Hurek and Hurek 2011), the bulk of research has centered on root endophytic bacteria (For example, Romero et al. 2014). The diversity of leaf endophytic bacteria and their network within plant hosts during different developmental stage was need more research. ...
Background and aims Endophytic bacteria of leaves play a crucial role in plant development, but how structure and co-occurrence networks within these communities respond to seed and soil microbial communities is unknown. Methods To address this, endophytic bacteria of pea (Pisum sativum L.) seedling leaves (SL) after growing 3 and flowering leaves (FL) after 6 weeks were studied using Illumina sequencing of 16S rRNA gene. Results Richness and diversity of endophytic bacteria of FL were similar to non-planted soil (NS) and were higher than SL and seeds (S), while those of SL endophytic bacteria were similar to S. PCoA analysis showed endophytic bacterial community was dynamic during the developmental stage. At the genus level, Bacteroides was enriched and dominant at SL and decreased at FL, whereas Pantoea, Helicobacter and Coriobacteriaceae_UCG_002 tended to be enriched and dominant at FL. Interestingly, the endophytic bacterial community at FL was similar to those at NS. Besides, S and SL networks both had higher modular structures than FL network. Among networks constructed by the combined dataset, the ecosystem of S – SL, S – FL and SL - FL had more microbial interaction than other ecosystems (SL – NS and FL - NS), while the SL – NS and FL - NS ecosystems showed the higher modularity indicating the more special and resistant to secondary extinction species existed. Conclusions In our present study, bacteria from seeds and soils play a critical role for endophytic bacterial community of pea leaves at its developmental stage.
... Endophytes are microorganisms that live inside plant tissues. Due to their intimate associations with their hosts, they can have powerful effects on plant physiology (Hardoim et al., 2008;Johnston-Monje and Raizada, 2011;Hardoim et al., 2012, Hardoim et al., 2015Truyens et al., 2015). Endophytes can promote plant growth by providing nutrients, increasing nutrient uptake, modulating and secreting phytohormones, and defending against pathogens of plants (Hu et al., 2003;Johnston-Monje and Raizada, 2011;Mousa et al., 2016;Shehata et al., 2017). ...
Introduction
Phytobiomes have a significant impact on plant health. The microbiome of Cannabis sativa is particularly interesting both because of renewed interest in this crop and because it is commercially propagated in two different ways (i.e. clonally and by seed). Angiosperms obtain a founding population of seed-borne endophytes from their seed-bearing parent. This study examines the influence of both seed and soil-derived bacteria on the endospheres of cannabis seedlings of both hemp- and drug-types.
Methods
A multi-factorial metagenomic study was conducted with three cannabis genotypes and two soil sources, which were tested both before and after autoclave sterilization. Seedlings were grown on soil, then rinsed and surface-sterilized, and 16S rDNA amplicons from seedling endophytes were sequenced, taxonomically classified, and used to estimate alpha- and beta-diversity in Qiime2. The statistical significance of differences in seedling microbiomes across treatments was tested, and PiCRUST2 was used to infer the functional relevance of these differences.
Results
Soil was found to have a profound effect on the alpha-diversity, beta-diversity, relative abundance, and functional genes of endophytic bacteria in germinating cannabis seedlings. Additionally, there was a significant effect of cannabis genotype on beta diversity, especially when genotypes were grown in sterilized soil. Gammaproteobacteria and Bacilli were the two most abundant taxa and were found in all genotypes and soil types, including sterilized soil.
Discussion
The results indicated that a component of cannabis seedling endosphere microbiomes is seed-derived and conserved across the environments tested. Functional prediction of seedling endophytes using piCRUST suggested a number of important functions of seed-borne endophytes in cannabis including nutrient and amino acid cycling, hormone regulation, and as precursors to antibiotics. This study suggested both seed and soil play a critical role in shaping the microbiome of germinating cannabis seedlings.
... The phyllosphere is in continual touch with the environment, serving as an essential source of bacteria that interact with the plant surface [7]. Moreover, the distribution of endophytic microbes also depends on the physiological stages of the plants [8]. ...
Endophytic microbes i.e. bacteria, fungi, and actinomycetes live inside the plant tissues without causing any harmful effect on them. Recently, research has been conducted on endophytic microbes to enhance agriculture and environmental sustainability. Endophytes stabilize a close association with their host, which leads to major changes in plant physiology. Endophytic microbes and pathogens use the same strategies for entering the host cell. This condition may create competition between the endophytes and the pathogen. Therefore, host plants develop strategies to allow the entry of specific microorganisms. Additionally, endophytic microorganisms may temper their own genetic structure to survive and avoid the host defence machinery. The plant-endophyte symbionts promote direct and indirect defences to host plants. This plays an essential role in modulating plant defences against various stresses, particularly biotic stress. In this minireview, we highlight the interaction of endophytic microbes with their host. As well as the role of endophytic microbes in the enhancement of plant defence systems.
... Frontiers in Microbiology 11 frontiersin.org rhizospheric microorganisms, where plants exhibit a stronger selectivity for endophytic microorganisms (Hardoim et al., 2008;Berendsen et al., 2012). Unlike rhizospheric microorganisms, endophytic microorganisms experience fewer biotic and abiotic stresses within plant tissues, and their abundance is less influenced by soil nutrient levels (Wang et al., 2016;Chen et al., 2020). ...
Stover mulching, as a sustainable agricultural conservation practice, has been shown to effectively increase soil organic matter and enhance crop yields. The impact of stover mulching on soil microorganisms has been extensively studied. However, less attention has been given to endophytic and rhizospheric microorganisms that have closer relationships with crops. How do the quality and frequency of stover mulching affect the composition and structure of these endosphere and rhizosphere microbial communities? And what is their influence on critical indicators of soil health such as bacterial plant pathogen and Rhizobiales? These questions remain unresolved. Therefore, we investigated the responses of the microbial functional guilds in the endosphere and rhizosphere to maize stover mulching qualities (0%, 33%, 67%, and total stover mulching every year) and frequencies (once every 3 years and twice every 3 years) under 10-year no-till management. Results showed significant correlations between Bacillales and Rhizobiales orders and soil SOC, NO3⁻N, and NH4⁺N; Hypocreales and Eurotiales orders were significantly correlated with soil NO3⁻N, with the Aspergillus genus also showing a significant correlation with soil SOC. The frequency and quality of stover mulching had a significant effect on root and rhizospheric microbial communities, with the lowest relative abundance of bacterial plant pathogens and highest relative abundance of nitrogen-fixing bacteria such as Rhizobiales and Hypocreales observed under F1/3 and F2/3 conditions. The most complex structures in endosphere and rhizospheric microbial communities were found under Q33 and Q67 conditions, respectively. This research indicates that from a soil health perspective, low-frequency high-coverage stover mulching is beneficial for the composition of endosphere and rhizosphere microbial communities, while moderate coverage levels are conducive to more complex structures within these communities. This study holds significant ecological implications for agricultural production and crop protection.
... (inoculated plants) had the longest roots and the heaviest roots in both fresh and dry weight when compared with control plants. Numerous studies have examined PGBs, notably Bacillus spp., which exhibit a variety of features that enable them to mobilize soil nutrients and synthesise phytohormones that promote plant growth [35][36][37]. Inoculated maize seeds with the PGPR Azospirillum lipoferum produced more root tips, more root branching, and longer cumulative roots [38]. ...
The production of crops depending on many factors including water, nutrient, soil types, climate and crops types, water stress and drought is in one of the important factors affecting crop productivity. The experiment was conducted in pots to evaluate the effect of biofertilizers (Bacillus simplex) with deficit irrigations on the early development and growth of maize crop under greenhouse condition. Pre sowing seed was inoculated with strain of bacteria (B+/B-) and different irrigation levels (no stress: 100% (I 1) and deficit irrigation: 75 (I 2), 50 (I 3), 25 (I 4) % of required water amount to reach pot capacity) was performed. Data was collected on different morphological characteristics and root characteristic of maize crop. Highest plant height (125 cm), stem diameter (18.02 mm), leaf area (350 cm − 2), plant weight (180.42 g in fresh, 73.58 g in dry), root length (92.83 cm) root ((91.70 g in fresh, (28.66 g in dry) weight were recorded in pots applied with 100% irrigation followed by 75%. Bacillus treated plants showed significant increase in leaf area (214.20 cm − 2), plant fresh weight (91.65 g) and dry weight (42.05 g), root length (79.20 cm), root fresh (53.52 g) and dry weight (16.70 g) compared with control (without bacteria). Likewise highest relative water content of leaf was observed with I 3 followed by I 2 and I 1 respectively. Highest water use efficiency was recorded as 0.67 g pot − 1 mm − 1 in I 1 with B + treatment. Likewise, Bacillus inoculated pots resulted in increased water use efficiency (0.44 g pot − 1 mm − 1) compared with no application (0.36 g pot − 1 mm − 1). It can be endorsed from the outcome that Bacillus inoculation increased plant biomass, root biomass of maize and water use efficiency during early growth stage of maize despite of water stress and can be used under limited water condition for crop combating during moderate to lower stress conditions.
... Beyond fundamental biocontrol strategies such as the production of siderophores, Hydrogen Cyanide (HCN), volatile and non-volatile organic compounds, as well as lytic enzymes, there exists an intriguing proposition that endophytic bacteria might even trigger plant defence mechanisms via a phenomenon termed Induced Systemic Resistance (ISR) (Amruta et al. 2018;Prasanna et al., 2021). This approach capitalizes on their unique capability to induce antagonistic effects precisely at the site of infection, facilitated by their remarkable colonization abilities (Hardoim et al., 2008). Hence, the present research is directed towards harnessing the potential of endophytic bacteria as potent biocontrol agents. ...
Rice is the global staple food, contributing over half of the world's agricultural production. Excessive fungicide use in rice farming poses environmental, fungicide resistance, and beneficial microbial disruption concerns, making biocontrol, particularly bacteria, a promising biocontrol agent due to their rapid growth, ease of handling, and robust colonization attributes. Endophytes are endosymbionts residing within host plants, playing a pivotal role in plant health without inciting any pathogenic effects. In this study, we investigated the antagonistic potential of four characterized bacterial endophytic strains, viz., Bacillus velezensis strains A6 and P42, B. pseudomycoides HP3d and Paenibacillus polymyxa PGSS-1 against major foliar rice pathogens viz., Magnaporthe oryzae and Cochliobolus miyabeanus. Against M. oryzae, all the endophytic strains exhibited significant per cent inhibition (50.00-66.67%) and the highest inhibition of 66.67% was achieved by B. pseudomycoides strain HP3d, while the lowest inhibition of 50 and 51.11% was by B. velezensis strain A6, P42, and P. polymyxa PGSS1, respectively. These endophytes outperformed the positive control, P. fluorescens which showed 44.44% inhibition. Similarly, against C. miyabeanus, 31.25-43.75% inhibition was recorded, of which B. velezensis strain A6 exhibited the highest inhibition (43.75%), while B. velezensis strain P42 showed the lowest (31.25%). Furthermore, a double Petri dish assay was conducted to evaluate the volatile compounds produced by these endophytes against the two rice pathogens. It was observed that the volatile compounds produced by B. pseudomycoides strain HP3d and P. polymyxa strain PGSS1 significantly and effectively inhibited the growth of M. oryzae by 88.89% when compared to P. fluorescens (50.00%), whereas B. velezensis strain A6 showed the lowest inhibition (33.33%). Against the brown spot pathogen, C. miyabeanus, the endophytes demonstrated inhibition ranging from 56.25-87.50%, with B. pseudomycoides strain HP3d and P. fluorescens achieving the highest inhibition (87.50%) and B. velezensis strain P42 showing the lowest (56.25%). These results highlight the significant and varied inhibitory effects of volatile compounds released by these endophytes against fungal pathogens of rice. Overall, our findings highlight the promising biocontrol potential of these endophytic strains under in vitro conditions with B. pseudomycoides strain HP3d and P. polymyxa PGSS1 showing exceptional efficacy and they can be deployed in the field for the management of foliar fungal pathogens in rice.
... Salt stress also reduces the ability of plant cells to store water, which shows effect on leaf water content, and results in a build-up of Na + ions inside plant cells (Zhao et al., 2021). The lower relative water content exhibits negative osmotic imbalance ultimately inhibiting plant growth (Hardoim et al., 2008). In this study, A. terreus CR7 inoculated plants had higher relative water content compared with un-inoculated plants. ...
Soil salinity is one of the major environmental stresses that results in reduction of cultivable land and decreased productivity. In the present study, halotolerant and plant growth-promoting endophytic fungi were isolated from Catharanthus roseus, and their effect in mitigating salt stress in Vigna radiata was evaluated. An isolate CR7, identified to be Aspergillus terreus, showing plant growth promotion activities, viz. IAA production (23.43 ± 0.79 μg/ml), phosphate solubilization (133.63 ± 6.40 μg/ml), ACC deaminase activity (86.36 ± 2.70 μmol α-ketobutyrate/h/mg protein) etc. and ability to grow at 15% NaCl was selected for further in vivo studies. Colonization of CR7 was carried out in V. radiata which was subjected to different concentrations of salt (150, 200, and 250 mM NaCl). Under salt stress, A. terreus CR7 inoculated plants showed substantially improved root and shoot length, biomass, chlorophyll content, relative water content, phenolics, protein content, and DPPH scavenging activity. Endogenous IAA level was enhanced by 5.28-fold in treated plants at maximum salt stress. Inoculation of A. terreus CR7 affected oxidative stress parameters, exhibiting an increase in catalase and superoxide dismutase and reduction in proline, electrolyte leakage, and malondialdehyde content. Fluorescent microscopic analysis of roots revealed improved cell viability and decreased levels of glutathione and hydrogen peroxide under salt stress in treated plants. The isolate A. terreus CR7 also protected against DNA damage induced by salt stress which was evaluated using comet assay. A decrease in DNA tail length, tail moment, and olive tail moment to the extent of 19.87%, 19.76%, and 24.81%, respectively, was observed in A. terreus CR7-colonized plants under salt stress. It can be concluded that A. terreus CR7 can be exploited for alleviating the impact of salt stress in crop plants.
... Among the PGPB, plant growth-promoting endophytes (PGPEs) stand out as microorganisms that colonize the internal tissues of plants without causing harm to the host [2]. This unique characteristic makes PGPEs promising alternative agents as potential biocontrol agents and plant growth promoters. ...
We performed isolation and characterization of endospore forming endophytic bacteria (EEB) from endorhizospheric region of healthy bush cowpea var. Bhagyalakshmi. All the EEB isolates were evaluated for their ability to produce plant growth promoting traits such as production of indole acetic acid (IAA), gibberellic acid, ammonia, ACC deaminase, volatile organic compounds and siderophore, and capacity for nitrogen fixation, and solubilization of phosphorus and potassium. Roll towel assay was used for assessing the seedling vigour index of cowpea after seed priming with the EEB isolates. Based on growth promotion and seedling vigour index, seven superior bacterial isolates were selected, and antagonistic activity against the fungal pathogens Fusarium oxysporum, Rhizoctonia solani, Colletotrichum sp., Phytophthora sp., and Pythium sp., was assayed. The isolates were pooled together to form a consortium and biopriming of cowpea seeds were done. Bioprimed seeds were tested for plant growth promotion and abiotic stress management in cowpea under protray condition. The seedlings of the bioprimed cowpea seeds showed better seedling vigour index and stress tolerance compared to hydro-primed seeds and the unprimed control. EEB isolated from the host plant could be developed as plant growth promoting bioagents.
... Still, these bacteria would be subject to varying osmotic fluctuations arising from ionic fluxes among compartments. The lack of statistical differences in the endosphere across our salinity gradient may in part be explained due to a colonization filter, i.e., habitats inside the plant are only able to be colonized by competent endophytes (and transient bacteria, by a minor extent) (Hardoim et al. 2008), while also showing a more homogeneous environment compared to the rhizosphere. ...
Background
Soil salinization has a major impact on crop production and it is expected to increase in area in the coming years. In this scenario, exploring the potential of halophytes and their plant-associated microbiomes as to increase phytoremediation strategies represents a suitable and sustainable strategy.
Methods
We conducted a microcosm experiment with the halophyte Atriplex nummularia, cultivating it in two contrasting soils (clay and sandy) at distinct levels of salinity (0, 10 and 20 mS/cm). After 109 days, we assessed its growth and bacteriome composition, through 16S rRNA gene sequencing of the leaf and root endospheres, as well as rhizosphere.
Results
A. nummularia showed increased growth under salinity levels of up to 20 mS/cm in both soils. Salinity and soil type had an effect in determining the rhizosphere bacterial communities of A. nummularia, with a stronger signal in the sandy soil. Most interestingly, no differences were found in endophytic bacterial communities, suggesting a strong buffering effect of the plant physiology, even though this halophyte accumulates NaCl. Last, functional prediction based on a subset of differentially abundant taxa in the rhizosphere revealed an increase in plant-growth promotion and salinity tolerance traits in higher salinity, indicating simultaneous selection by salinity and A. nummularia under stress.
Conclusion
Collectively, these results provide valuable insights into halophyte-associated bacteria, advancing our understanding of this complex system with potential application in phytoremediation strategies for saline soils.
Background Technosoils in Inowrocław, central Poland, are impacted by human activities and exhibit high salinity (ECe up to 70 dS/m) due to a soda lime repository. These saline environments pose challenges to plant growth and soil health. However, they also offer an opportunity for the evolution of microorganisms adapted to such conditions, including plant growth-promoting rhizospheric (PGPR) bacteria. The hypothesis tested here was that introducing PGPR bacteria from these environments could boost degraded soil performance, leading to better plant biomass and improved pathogen defense. Methods Azotobacter chroococcum W4ii was isolated from the rhizosphere of wheat ( Triticum aestivum L.) for its plant growth properties on wheat plants under salt stress. Results Wheat seeds co-inoculated with A. chroococcum W4ii under 200 mM salt stress showed significant improvement in various growth parameters such as seeds germination (by 130%), shoot biomass (15%), chlorophyll b content (40%) compared to un-inoculated ones. Bacterial inoculation decreased the level of malondialdehyde (MDA), whereas it elevated the antioxidative enzymatic activities of peroxidase (POD). The test isolate also enhanced the level of defense enzymes like β-1,3-glucanase, which can protect plants from infection by pathogens. The bacterium could also successfully colonize the wheat plants. Conclusions These results indicate that A. chroococcum isolated from the technosoil has the potential to promote wheat growth under salt stress and can be further used as a bioinoculant in the salt affected agricultural fields.
Rice, one of the most important crops, is inhabited by diverse groups of bacterial endophytes, many of which are still functionally unknown. This chapter summarizes information on the diversity and community structure of bacterial endophytes residing in the rice endosphere. Specifically, it presents an overview of those endophytes inhabiting the rice microniches, including the roots, shoots, and seeds. The bacterial endophyte community structure and diversity across Oryza spp., mainly those from Oryza sativa ssp. indica and ssp. japonica, are presented. A literature survey of 16S rDNA sequences from cultured and uncultured endophytic bacteria is presented. A total of 1047 screened 16S rDNA sequences were collated with complete taxonomic classification. The most abundant and commonly detected endophytic bacterial groups in the phylum level mainly include Proteobacteria (61%), followed by Actinobacteria (20%) and Firmicutes (14%). Class-level identification mostly shows that Gammaproteobacteria (32%), Actinobacteria (19%), and Alphaproteobacteria (19%) are the commonly detected groups, followed by less abundant groups. The most prominent trend observed is the occurrence of the same bacterial genera isolated or detected throughout the rice endosphere. Bacterial genera such as Bacillus, Enterobacter, Herbaspirillum, Methylobacterium, Microbacterium, Pantoea, Pseudomonas, Sphingomonas, and others are commonly detected throughout the rice endosphere. This indicates the potential importance of these groups to the rice plants and could be targeted as plant growth-promoting bacterial bioinoculants. On the other hand, there are also bacterial genera that are more specifically isolated or detected in the major microniches of rice, including Bradyrhizobium, Azospirillum, and Aeromonas (roots), Azorhizobium (leaves), and Kosakonia (seeds). In addition, this chapter encompasses bioprospecting potential bacterial endophytes of rice, focusing on target groups of interest, as classified in terms of their plant growth-promoting (PGP) mechanism or bacterial genera where they are identified. There are diverse bacterial endophytic communities, and some of these bacterial groups are present in all the major microniches of rice, indicating their high association and functional importance.
Fusarium crown rot (FCR), Fusarium head blight (FHB), and bacterial leaf streak (BLS) of wheat are important diseases worldwide. The lack of commercially resistant cultivars and the harmful effects of using chemical poisons to control these diseases prompted scientists to use biological agents as eco-friendly strategies for disease management. Plants carry a small community of microbes known as endophytes that affect plant growth regulation and protect plants against phytopathogens. The present study aimed to isolate and evaluate antagonistic plant growth-promoting endophytic bacteria in wheat. In this study, 464 endophytic bacteria were isolated from seeds, shoots, and roots of 14 Iranian wheat cultivars (Arg, Bahar, Baharan, Behrang, Chamran, Chamran 2, Dena, Falat, Heidari, Parsi, Pishgam, Sayonz, Sirvan, and Sivand) and the logarithm of population density was estimated. According to the calculations, endophytes were more abundant in roots than shoots and seeds, and Gram-positive bacteria were dominant in all tissues. The antifungal and antibacterial activity of the isolates against two main pathogens Fusarium graminearum and Xanthomonas translucens were analyzed by dual culture assays. The highest percentage of fungal growth inhibition was evaluated at 86.66% and the highest inhibition halo of bacteria was 49.33%. Among the endophytic bacteria, twelve potent antagonists capable of increasing seed germination in vitro by at least 10% more than untreated seeds and could increase shoot and root length, were selected for further characterization. All of them could produce protease, pectinase, cellulase, amylase, catalase, indole acetic acid (IAA), ammonia, siderophore, and phosphate solubilization. Two of them did not show lipase activity and none of them could produce chitinase. Growing on minimal salt medium DF test indicated that just two isolates could not produce ACC deaminase and all of them growing on nitrogen-free medium have the potential to fix atmospheric nitrogen. Biofilm formation and sensitivity to H2O2 varied among isolates. Greenhouse experiments indicated that the plant growth-promoting characteristics like length, wet and dry weight of shoots, and roots were significantly increased in plants treated with endophytes. Five isolates belonged to different morphological groups were identified by 16S rRNA sequencing and biochemical tests as Bacillus subtilis (MT258405) and two groups of Paenibacillus polymyxa (MT258403, MT258407, MT258404, and MT258406). One thousand grains weight, chlorophyll, and carotenoid content were increased in the plants treated with the endophytic bacteria. Light and scanning electron microscopy showed alternations in the F. graminearum structures in the presence of the endophytes. Isolates could decrease mycotoxin DON production and fungal spore germination. Evaluated bacteria can enter the wheat plants and this test verified the isolates’ endophytic ability. The protection rate against pathogenic bacteria was evaluated from 49.13 to 68.23 %. The percentages of FHB infection reduction were from 64.1 to 80.33 % and FCR severity reduction was evaluated from 65.41 to 78.19 %. Antimicrobial lipopeptides were isolated from the successful bacterium in this study, namely B. subtilis CB2. LC-MS analyses indicated that this bacterium could produce surfactins and iturins. Considering that the antagonistic range of the isolates is wide, these beneficial endophytes can be used as biocontrol agents to protect plants against various plant pathogens and as fertilizers to increase the growth of different plants. This is the first report that indicates the effect of these endophytic bacteria in the biocontrol of Fusarium crown rot and bacterial leaf streak diseases.
It elucidates the fundamental principles of RNAi and its specific mechanisms in plants, emphasizing its potential to selectively silence crucial genes involved in pathogen virulence. The discussion encompasses the diverse methods employed to deliver small interfering RNAs (siRNAs) and microRNAs for targeted gene suppression, showcasing the versatility of RNAi in mitigating various plant pathogens. Furthermore, the chapter outlines potential benefits, including enhanced
crop yield, reduced reliance on chemical pesticides, and improved environmental sustainability. Despite these advantages, current limitations such as off-target effects and delivery challenges are also addressed. A nuanced examination of RNAi's contributions and challenges in the context of plant disease control is presented, offering valuable insights for researchers and practitioners seeking innovative and sustainable solutions in agriculture.
Increasing evidence infers that some complex diseases are attributed to co-infection with multiple pathogens, such as shrimp white feces syndrome (WFS); however, there is a lack of experimental evidence to validate such causal link. This deficiency further impedes rational design of probiotics to elicit desired benefits to shrimp WFS resistance. Herein, we validated the causal roles of Vibrio fluvialis , V. coralliilyticus and V. tubiashii (in a ratio of 7:2:1) in shrimp WFS etiology, which fully satisfied Koch’s postulates. Correspondingly, we precisely designed four antagonistic strains: Ruegeria lacuscaerulensis , Nioella nitratireducens , Bacillus subtilis and Streptomyces euryhalinus in a ratio of 4:3:2:1, which efficiently guarded against WFS. Dietary supplementation of the probiotics stimulated beneficial gut populations, streptomycin, short chain fatty acids, taurine metabolism potentials, network stability, tight junction, and host selection, while reducing turnover rate and average variation degree of gut microbiota, thereby facilitating ecological and mechanical barriers against pathogens. Additionally, shrimp immune pathways, such as Fcγ R-mediated phagocytosis, Toll-like receptor and RIG-I-like receptor signaling pathways conferring immune barrier, were activated by probiotics supplementation. Collectively, we establish an updated framework for precisely validating co-infection with multiple pathogens and rationally designing antagonistic probiotics. Furthermore, our findings uncover the underlying beneficial mechanisms of designed probiotics from the probiotics–gut microbiome–host immunity axis.
Archaea, bacteria, and fungi in the soil are increasingly recognized as determinants of agricultural productivity and sustainability. A crucial step for exploring soil microbiomes with important ecosystem functions is to perform statistical analyses on the potential relationship between microbiome structure and functions based on comparisons of hundreds or thousands of environmental samples collected across broad geographic ranges. In this study, we integrated agricultural field metadata with microbial community analyses by targeting 2,903 bulk soil samples collected along a latitudinal gradient from cool-temperate to subtropical regions in Japan (26.1–42.8 °N). The data involving 632 archaeal, 26,868 bacterial, and 4,889 fungal operational taxonomic units detected across the fields of 19 crop plant species allowed us to conduct statistical analyses (permutational analyses of variance, generalized linear mixed models, randomization analyses, and network analyses) on the relationship among edaphic factors, microbiome compositions, and crop disease prevalence. We then examined whether the diverse microbes form species sets varying in potential ecological impacts on crop plants. A network analysis suggested that the observed prokaryotes and fungi were classified into several species sets (network modules), which differed substantially in association with crop disease prevalence. Within the network of microbe-to-microbe coexistence, ecologically diverse microbes, such as an ammonium-oxidizing archaeon, an antibiotics-producing bacterium, and a potentially mycoparasitic fungus, were inferred to play key roles in shifts between crop-disease-promotive and crop-disease-suppressive states of soil microbiomes. The bird’s-eye view of soil microbiome structure will provide a basis for designing and managing agroecosystems with high disease-suppressive functions.
IMPORTANCE
Understanding how microbiome structure and functions are organized in soil ecosystems is one of the major challenges in both basic ecology and applied microbiology. Given the ongoing worldwide degradation of agroecosystems, building frameworks for exploring structural diversity and functional profiles of soil microbiomes is an essential task. Our study provides an overview of cropland microbiome states in light of potential crop-disease-suppressive functions. The large data set allowed us to explore highly functional species sets that may be stably managed in agroecosystems. Furthermore, an analysis of network architecture highlighted species that are potentially used to cause shifts from disease-prevalent states of agroecosystems to disease-suppressive states. By extending the approach of comparative analyses toward broader geographic ranges and diverse agricultural practices, agroecosystem with maximized biological functions will be further explored.
A novel endophytic actinomycete, strain MEP2-6T, was isolated from scab tissues of potato tubers collected from Mae Fag Mai Sub-district, San Sai District, Chiang Mai Province, Thailand. Strain MEP2-6T is a gram-positive filamentous bacteria characterized by meso-diaminopimelic acid in cell wall peptidoglycan and arabinose, galactose, glucose, and ribose in whole-cell hydrolysates. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and hydroxy-phosphatidylethanolamine were the major phospholipids, of which MK-9(H6) was the predominant menaquinone, whereas iso-C16:0 and iso-C15:0 were the major cellular fatty acids. The genome of the strain was 10,277,369 bp in size with a G + C content of 71.7%. The 16S rRNA gene phylogenetic and core phylogenomic analyses revealed that strain MEP2-6T was closely related to Amycolatopsis lexingtonensis NRRL B-24131T (99.4%), A. pretoriensis DSM 44654T (99.3%), and A. eburnea GLM-1T (98.9%). Notably, strain MEP2-6T displayed 91.7%, 91.8%, and 87% ANIb and 49%, 48.8%, and 35.4% dDDH to A. lexingtonensis DSM 44653T (=NRRL B-24131T), A. eburnea GLM-1T, and A. pretoriensis DSM 44654T, respectively. Based on phenotypic, chemotaxonomic, and genomic data, strain MEP2-6T could be officially assigned to a novel species within the genus Amycolatopsis, for which the name Amycolatopsis solani sp. nov. has been proposed. The type of strain is MEP2-6T (=JCM 36309T = TBRC 17632T = NBRC 116395T). Amycolatopsis solani MEP2-6T was strongly proven to be a non-phytopathogen of potato scab disease because stunting of seedlings and necrotic lesions on potato tuber slices were not observed, and there were no core biosynthetic genes associated with the BGCs of phytotoxin-inducing scab lesions. Furthermore, comparative genomics can provide a better understanding of the genetic mechanisms that enable A. solani MEP2-6T to adapt to the plant endosphere. Importantly, the strain smBGCs accommodated 33 smBGCs encoded for several bioactive compounds, which could be beneficially applied in the fields of agriculture and medicine. Consequently, strain MEP2-6T is a promising candidate as a novel biocontrol agent and antibiotic producer.
Toxic contaminants from intense industrial operations are entering wetlands, harming human health and biodiversity. Macrophytes serve as principal producers in aquatic environments including natural wetlands, providing shelter, food, and, most crucially, intricate relationships with the surrounding microbial assemblage for support and microorganisms attachment. Wetlands have been nature's kidneys, for filtering water. Recent research has examined macrophytes' phytoremediation abilities. With recent improvements focused on engineered wetland technology, microbiological characterization, and genetic engineering, phytoremediation strategies have also benefited. However, little research has examined the role surrounding microbial population play on macrophyte efficiency in pollutant degradation, the extent and even mechanisms of these interactions, and their potential utility in wastewater treatment of diverse industrial effluents. Our bid for greener solutions implies that macrophyte-microorganisms’ interspecific interactions for in situ treatment of effluents should be optimised to remove contaminants before discharge in natural waterbodies or for recycle water usage. This review provides for the varied types of plants and microbial interspecific interactions beneficial to effective phytoremediation processes in artificial wetland design as well as considerations and modifications in constructed wetland designs necessary to improve the bioremediation processes. Additionally, the review discusses the latest advancements in genetic engineering techniques that can enhance the effectiveness of phyto-assisted wastewater treatment. We will also explore the potential utilisation of invasive species for their demonstrated ability to remove pollutants in the controlled setting of constructed wetlands.
Uncontrolled usage of chemical fertilizers, climate change due to global warming, and the ever-increasing demand for food have necessitated sustainable agricultural practices. Removal of ever-increasing environmental pollutants, treatment of life-threatening diseases, and control of drug-resistant pathogens are also the need of the present time to maintain the health and hygiene of nature, as well as human beings. Research on plant–microbe interactions is paving the way to ameliorate all these sustainably. Diverse bacterial endophytes inhabiting the internal tissues of different parts of the plants promote the growth and development of their hosts by different mechanisms, such as through nutrient acquisition, phytohormone production and modulation, protection from biotic or abiotic challenges, assisting in flowering and root development, etc. Notwithstanding, efficient exploitation of endophytes in human welfare is hindered due to scarce knowledge of the molecular aspects of their interactions, community dynamics, in-planta activities, and their actual functional potential. Modern “-omics-based” technologies and genetic manipulation tools have empowered scientists to explore the diversity, dynamics, roles, and functional potential of endophytes, ultimately empowering humans to better use them in sustainable agricultural practices, especially in future harsh environmental conditions. In this review, we have discussed the diversity of bacterial endophytes, factors (biotic as well as abiotic) affecting their diversity, and their various plant growth-promoting activities. Recent developments and technological advancements for future research, such as “-omics-based” technologies, genetic engineering, genome editing, and genome engineering tools, targeting optimal utilization of the endophytes in sustainable agricultural practices, or other purposes, have also been discussed.
Backgrounds and aims
Plant rhizosphere microbiome play crucial roles in plant growth. However, the mechanisms governing the rhizosphere microbiome assembly remain poorly understood. Here, we studied the contributions of sub-communities, referring to the recruited sub-community from bulk soil microbiome (SR) and the released sub-community from endosphere microbiome (ER), to the taxonomical and functional assembly of the rhizosphere microbiome.
Methods
We transplanted maize seedlings across different soils to identify the origin source of rhizosphere microbial communities. The profiles of rhizosphere microbial communities were acquired using 16S rRNA marker gene sequencing.
Results
The amplicon data analyses revealed that, in the reassembled rhizosphere microbial communities after transplanting, the SR and ER sub-communities were distinguished among different soils and the SR sub-communities showed higher bacterial diversity than ER sub-communities. The SR sub-communities dominated the variable selection process, while the ER sub-communities dominated the homogeneous selection process in rhizosphere microbiome assembly. Moreover, we found that specific taxa derived from endosphere play important roles in promoting nitrogen accumulation and reducing nitrogen losses in nitrogen-deficient soil, suggesting that the soil nitrogen level affects the specific taxa from endosphere to rhizosphere to maintain plant nitrogen requirement.
Conclusions
Plants could assemble compensatory functional rhizosphere microbiome to guarantee their nutrient requirement in nutrient-deficient soil. Specifically, some taxa derived from endosphere, make great contributions to the functional compensatory assembly in rhizosphere. These findings facilitate our understanding of the assembly mechanisms in rhizosphere, and further soil biological fertility improvement will benefit from isolation and application of these specific functional microbes.
This book sheds light on exciting advancements in plant protection technology that have the potential to revolutionise the way we safeguard our crops. It explores a range of topics, including pest management strategies, artificial intelligence, and biotechnological applications, to name a few. This book is a repository hub of knowledge.
This research investigated the association of consortium endophyte bacteria from different hosts to enhance the performance of Vetiveria zizanioides in treating textile wastewater using Floating Treatment Wetlands (FTWs). The endophyte bacteria were isolated from the roots of three natural plants (Oryza sativa, Colocasia esculenta, and Alternanthera philoxeroides) contaminated by textile wastewater. The selected isolated endophyte bacteria were subjected to the four FTWs reactors containing the Vetiveria sp and ran for 30 days in a semi-batch system to evaluate their performance. FTWs reactors-augmented endophyte bacteria could reduce the COD, color, and heavy metals in textile wastewater. The highest removal efficiencies of COD (74%) and color (F4) were observed in FK2 (vegetated control) and F4 reactor, respectively. The addition of endophyte bacteria increased the heavy reductions of Pb (52%) and Cd (33%) in reactors of F3 and F4, respectively. This study exhibited that the consortium endophyte bacteria isolated from the contaminated plants could improve the FTWs reactor performance. Finally, they reduce the plant stresses in the contaminated wastewater by increasing the plant biomass in roots and shoots. These findings reveal that the consortium of natural endophyte bacteria from different hosts does not inhibit their function and association with the other host plant, but they contribute positive responses to plant growth and pollutant degradation.
Engineering the plant microbiome with beneficial endophytic bacteria can improve the growth, health, and productivity of the holobiont. Here, we administered two beneficial bacterial strains, Kosakonia VR04 sp. and Rhizobium GR12 sp., to micropropagated grapevine cuttings obtained via somatic embryogenesis. While both strains colonized the plant endosphere, only Rhizobium GR12 sp. increased root biomass under nutritional-deficit conditions, as supported by the plant growth promotion traits detected in its genome. Phylogenetic and co-occurrence analyses revealed that the plant native bacterial community, originally dominated by Streptococcaceae and Micrococcaceae, dramatically changed depending on the inoculation treatments, as invading strains differently affected the relative abundance and the interactions of pre-existing taxa. After 30 days of plantlets’ growth, Pantoea became a predominant taxon, and considering untreated plantlets as references, Rhizobium sp. GR12 showed a minor impact on the endophytic bacterial community. On the other hand, Kosakonia sp. VR04 caused a major change in community composition, suggesting an opportunistic colonization pattern. Overall, the results corroborate the importance of preserving the native endophytic community structure and functions during plant microbiome engineering.
IMPORTANCE
A better comprehension of bacterial colonization processes and outcomes could benefit the use of plant probiotics in the field. In this study, we applied two different beneficial bacteria to grapevine micropropagated plantlets and described how the inoculation of these strains impacts endophytic microbiota assembly. We showed that under nutritional deficit conditions, the response of the receiving endophytic bacterial communities to the invasion of the beneficial strains related to the manifestation of plant growth promotion effects by the inoculated invading strains. Rhizobium sp. GR12 was able to preserve the native microbiome structure despite its effective colonization, highlighting the importance of the plant-endophyte associations for the holobiont performance. Moreover, our approach showed that the use of micropropagated plantlets could be a valuable strategy to study the interplay among the plant, its native microbiota, and the invader on a wider portfolio of species besides model plants, facilitating the application of new knowledge in agriculture.
Sugarcane is a very important crop that grows associated with diazotrophic and plant hormone-producing endophytic bacteria, such as Gluconacetobacter diazotrophicus, Herbaspirillum seropedicae and H. rubrisubalbicans. In this interaction, bacteria colonize the intercellular spaces and vascular tissues of most plant organs, promoting plant growth without inducing disease symptoms or nodule formation. Probably, plant genetic factors control the processes involved in plant colonization by these endophytes. The signaling pathways by which sugarcane plants can decipher bacterial signals and respond properly for a successful association are still not clearly understood. Here, we searched the sugarcane database for all expressed sequence tags (ESTs) preferentially or exclusively expressed in cDNA libraries constructed from sugarcane plants inoculated with G. diazotrophicus and H. rubrisubalbicans. Two such data sets of ESTs were generated in the infected libraries and ESTs from both data sets were functionally organized. For all categories, ESTs candidates to be involved in different processes of plant/bacteria signaling were identified, suggesting that the initial steps of colonization are actively controlled by the plant in the sugarcane/diazotrophic endophyte association.
More than 800 rhizobacterial strains were isolated from winter wheat “rhizosphere” (the soil tightly adhering to the roots), “rhizoplane” (the root surface) and “endorhiza” (the interior of the roots) at different plant growth stages (two leaves, four leaves, flowering and full maturity). The data obtained clearly show that the proportion of motile strains gradually increased from “rhizosphere”, through “rhizoplane”, to “endorhiza”. These results strongly suggest that flagellar motility is an important factor in the colonization of plant roots (especially the root interiors) by bacteria. However, high proportions of nonmotile bacteria among the bacterial isolates from the root surface at four leaves and flowering stages suggest that flagellar motility is not an absolutely necessary bacterial feature in colonization of plant roots. Pseudomonads and enterobacteria were the main motile bacteria, and Cytophaga-Flavobacterium the main nonmotile ones.The role of flagellar motility in plant root colonization is discussed in relation to other bacterial traits
Endophytic bacteria were isolated from surface-sterilized stems, seeds, and leaf sheaths of wild and traditionally cultivated rice varieties. Phylogenetic analyses based on 16S rDNA revealed a wide divergence among the isolates. However, the most frequently isolated groups were Methylobacterium sp. in the α-subdivision of Proteobacteria, and Curtobacterium sp. in the high G+ C Gram-positive group. Various phenotypic traits that are expected to be involved in the persistence and functions of the bacteria were analyzed: Most of the isolates from rice excreted pectinase, were motile, and showed an osmotic resistance to 0.6 M sucrose. These traits may be involved in endophytic characteristics in rice. About 50% of the isolates showed a cellulase activity. A few isolates fixed nitrogen, produced indole-3-acetic acid, and formed capsules. These activities were partially correlated with the phylogenetic group.
To date, there has been only limited commercial use of plant growth-promoting bacteria in agriculture, horticulture, and silviculture. However, with recent progress toward understanding the mechanisms that these organisms utilize to facilitate plant growth, the use of plant growth-promoting bacteria is expected to continue to increase worldwide. One of the key mechanisms employed by plant growth-promoting bacteria to facilitate plant growth is the lowering of plant ethylene levels by the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase. This article reviews the published work on this enzyme, with an emphasis on its biochemistry, protein structure, genes, and regulation. In addition, this article provides some initial insights into the changes in both plants and ACC deaminase-containing plant growth-promoting bacteria as a consequence of plant-microbe interactions. Finally, a brief discussion of how bacterial ACC deaminase and indoleacetic acid (IAA) together modulate plant growth and development is included.
Endophytic bacteria are ubiquitous in most plant species, residing latently or actively colonizing plant tissues locally as well as systemically. Several definitions have been proposed for endophytic bacteria; in this review endophytes will be defined as those bacteria that can be isolated from surface-disinfested plant tissue or extracted from within the plant, and that do not visibly harm the plant. While this definition does not include nonextractable endophytic bacteria, it is a practical definition based on experimental limitations and is inclusive of bacterial symbionts, as well as internal plant-colonizing nonpathogenic bacteria with no known beneficial or detrimental effects on colonized plants. Historically, endophytic bacteria have been thought to be weakly virulent plant pathogens but have recently been discovered to have several beneficial effects on host plants, such as plant growth promotion and increased resistance against plant pathogens and parasites. In general, endophytic bacteria originate from the epiphytic bacterial communities of the rhizosphere and phylloplane, as well as from endophyte-infested seeds or planting materials. Besides gaining entrance to plants through natural openings or wounds, endophytic bacteria appear to actively penetrate plant tissues using hydrolytic enzymes like cellulase and pectinase. Since these enzymes are also produced by pathogens, more knowledge on their regulation and expression is needed to distinguish endophytic bacteria from plant pathogens. In general, endophytic bacteria occur at lower population densities than pathogens, and at least some of them do not induce a hypersensitive response in the plant, indicating that they are not recognized by the plant as pathogens. Evolutionarily, endophytes appear to be intermediate between saprophytic bacteria and plant pathogens, but it can only be speculated as to whether they are saprophytes evolving toward pathogens, or are more highly evolved than plant pathogens and conserve protective shelter and nutrient supplies by not killing their host. Overall, the endophytic microfloral community is of dynamic structure and is influenced by biotic and abiotic factors, with the plant itself constituting one of the major influencing factors. Since endophytic bacteria rely on the nutritional supply offered by the plant, any parameter affecting the nutritional status of the plant could consequently affect the endophytic community. This review summarizes part of the work being done on endophytic bacteria, including their methodology, colonization, and establishment in the host plant, as well as their role in plant–microbe interactions. In addition, speculative conclusions are raised on some points to stimulate thought and research on endophytic bacteria.Key words: endophytic bacteria, methods, localization, diversity, biological control.
Root exudates represent an important source of nutrients for microorganisms in the rhizosphere and seem to participate in early colonization inducing chemotactic responses of rhizospheric bacteria. We characterized the root exudates collected from rice plantlets cultured under hydroponic conditions and assessed their effects on the chemotaxis of two strains of endophytic bacteria, Corynebacterium flavescens and Bacillus pumilus, collected from the rice rhizosphere. We compared these chemotactic effects on endophytic bacteria with those on two strains of plant-growth-promoting bacteria, Azospirillum brasilense (isolated from the corn rhizosphere) and Bacillus sp. (from the rice rhizosphere). The root exudates were collected at different time intervals. The highest concentration and diversity of amino acids and carbohydrates were found during the first 2 weeks after seeding. Histidine, proline, valine, alanine, and glycine were the main amino acid residues identified during the 4 weeks of culture. The main carbohydrates identified were glucose, arabinose, mannose, galactose, and glucuronic acid. The chemotactic responses of the analyzed endophytic bacteria to root exudates were 3.9 to 5.1 times higher than those of A. brasilense and 2.2 to 2.8 times higher than Bacillus sp. Our results indicate that rice exudates may induce a higher chemotactic response for endophytic bacteria than for other bacterial strains present in the rice rhizosphere.
Following transposon Tn5 mutagenesis of the plant growth-promoting rhizobacterium Pseudomonas putida GR12-2, mutants that were able to grow in the presence of the tryptophan analog 5-fluorotryptophan were selected. Seven of
the 50 5-fluorotryptophan-resistant mutants overproduced the phytohormone indoleacetic acid (IAA). Of these seven mutants,
the highest level of IAA was observed with strain P. putida GR12-2/aux1, which produced four times the amount of indoleacetic acid synthesized by the wild-type strain. Strain P. putida GR12-2/aux1, in contrast to the wild type, lost the ability to stimulate the elongation of the roots of canola seedlings under gnotobiotic
conditions. The growth rate, siderophore production, and 1-aminocyclopropane-1-carboxylate deaminase activity of mutant strain
P. putida GR12-2/aux1 were identical to those of the wild-type strain. The role of IAA in the mechanism of plant growth stimulation by P. putida GR12-2 and other plant growth-promoting rhizobacteria is discussed.
Several endophytic diazotrophs were isolated from cultivars of rice and screened for their diazotrophy by nitrogenase assay
and amplification of partial nifH gene. Ability of one of the diazotrophic endophytes, Serratia sp. (isolate EDA2 from cultivar ADT36) to colonize the rice seedlings grown in the presence of flavonoids and growth hormones,
under gnotobiotic condition was assessed in cultivar ADT36 using a strain marked with transposon-based egfp and Km
r
. The endophytic colonization was monitored through re-isolation from different parts of rice seedlings in LB+Km plates. Addition
of the flavonoids quercetin and diadzein to the growth medium increased the extent of endophytic colonization of the conjugant
in rice seedlings by colonizing throughout the plant. Population and in planta nitrogenase activity of Serratia in rice seedlings were significantly increased by addition of flavonoids, quercetin and diadzein, whereas growth hormones,
IAA and NAA reduced the efficiency of Serratia. The inoculation of Serratia sp. with flavonoids increased the plant biomass and biochemical constituents of rice seedlings under controlled condition.
This review focuses mainly on eudicot seeds, and on the interactions between abscisic acid (ABA), gibberellins (GA), ethylene, brassinosteroids (BR), auxin and cytokinins in regulating the interconnected molecular processes that control dormancy release and germination. Signal transduction pathways, mediated by environmental and hormonal signals, regulate gene expression in seeds. Seed dormancy release and germination of species with coat dormancy is determined by the balance of forces between the growth potential of the embryo and the constraint exerted by the covering layers, e.g. testa and endosperm. Recent progress in the field of seed biology has been greatly aided by molecular approaches utilizing mutant and transgenic seeds of Arabidopsis thaliana and the Solanaceae model systems, tomato and tobacco, which are altered in hormone biology. ABA is a positive regulator of dormancy induction and most likely also maintenance, while it is a negative regulator of germination. GA releases dormancy, promotes germination and counteracts ABA effects. Ethylene and BR promote seed germination and also counteract ABA effects. We present an integrated view of the molecular genetics, physiology and biochemistry used to unravel how hormones control seed dormancy release and germination.
It was previously shown that a number of plant growth promoting rhizobacteria contain an enzyme, 1-aminocyclopropane-1-carboxylate deaminase, that catalyses the cleavage of 1-aminocyclopropane-1-carboxylate, the immediate precursor of ethylene in plants. Moreover, experimental evidence indicated that the activity of this enzyme was the key factor in the ability of plant growth promoting rhizobacteria to stimulate the elongation of plant roots. In the model presented in this manuscript we address the question of how the bacterial enzyme 1-aminocyclopropane-1-carboxylate deaminase, with a low affinity for 1-aminocyclopropane-1-carboxylate, can effectively compete with the plant enzyme 1-aminocyclopropane-1-carboxylate oxidase, which has a high affinity for the same substrate, 1-aminocyclopropane-1-carboxylate, with the result that the plant's endogenous ethylene concentration is reduced. It is argued that the simplest explanation for the observed biological activity of plant growth promoting rhizobacteria relates to the relative amounts of 1-aminocyclopropane-1-carboxylate deaminase and 1-aminocyclopropane-1-carboxylate oxidase in the system under consideration. For plant growth promoting rhizobacteria to be able to lower plant ethylene levels, the 1-aminocyclopropane-1-carboxylate deaminase level should be at least 100- to 1000-fold greater then the 1-aminocyclopropane-1-carboxylate oxidase level. This is likely to be the case, provided that the expression of 1-aminocyclopropane-1-carboxylate oxidase has not been induced.Copyright 1998 Academic Press Limited Copyright 1998 Academic Press Limited
A colonization mutant of the efficient root-colonizing biocontrol strain Pseudomonas fluorescens WCS365 is described that is impaired in competitive root-tip colonization of gnotobiotically grown potato, radish, wheat, and tomato, indicating a broad host range mutation. The colonization of the mutant is also impaired when studied in potting soil, suggesting that the defective gene also plays a role under more natural conditions. A DNA fragment that is able to complement the mutation for colonization revealed a multicistronic transcription unit composed of at least six ORFs with similarity to lppL, lysA, dapF, orf235/233, xerC/sss, and the largely incomplete orf238. The transposon insertion in PCL1233 appeared to be present in the orf235/233 homologue, designated orf240. Introduction of a mutation in the xerC/sss homologue revealed that the xerC/sss gene homologue rather than orf240 is crucial for colonization. xerC in Escherichia coli and sss in Pseudomonas aeruginosa encode proteins that belong to the lambda integrase family of site-specific recombinases, which play a role in phase variation caused by DNA rearrangements. The function of the xerC/sss homologue in colonization is discussed in terms of genetic rearrangements involved in the generation of different phenotypes, thereby allowing a bacterial population to occupy various habitats. Mutant PCL1233 is assumed to be locked in a phenotype that is not well suited to compete for colonization in the rhizosphere. Thus we show the importance of phase variation in microbe-plant interactions.
Agrobacterium tumefaciens 1D1609, which was originally isolated from alfalfa (Medicago sativa L.), contains genes that increase competitive root colonization on that plant by reducing the accumulation of alfalfa isoflavonoids in the bacterial cells. Mutant strain I-1 was isolated by its isoflavonoid-inducible neomycin resistance following mutagenesis with the transposable promoter probe Tn5-B30. Nucleotide sequence analysis showed the transposon had inserted in the first open reading frame, ifeA, of a three-gene locus (ifeA, ifeB, and ifeR), which shows high homology to bacterial efflux pump operons. Assays on alfalfa showed that mutant strain I-1 colonized roots normally in single-strain tests but was impaired significantly (P < or = 0.01) in competition against wild-type strain 1D1609. Site-directed mutagenesis experiments, which produced strains I-4 (ifeA::gusA) and I-6 (ifeA::omega-Tc), confirmed the importance of ifeA for competitive root colonization. Exposure to the isoflavonoid coumestrol increased beta-glucuronidase activity in strain I-4 21-fold during the period when coumestrol accumulation in wild-type cells declined. In the same test, coumestrol accumulation in mutant strain I-6 did not decline. Expression of the ifeA-gusA reporter was also induced by the alfalfa root isoflavonoids formononetin and medicarpin but not by two triterpenoids present in alfalfa. These results show that an efflux pump can confer measurable ecological benefits on A. tumefaciens in an environment where the inducing molecules are known to be present.
Rhizosphere colonization is one of the first steps in the pathogenesis of soilborne microorganisms. It can also be crucial for the action of microbial inoculants used as biofertilizers, biopesticides, phytostimulators, and bioremediators. Pseudomonas, one of the best root colonizers, is therefore used as a model root colonizer. This review focuses on (a) the temporal-spatial description of root-colonizing bacteria as visualized by confocal laser scanning microscopal analysis of autofluorescent microorganisms, and (b) bacterial genes and traits involved in root colonization. The results show a strong parallel between traits used for the colonization of roots and of animal tissues, indicating the general importance of such a study. Finally, we identify several noteworthy areas for future research.
Understanding the relative abundance of species in plant communities is an unsolved problem. Mechanisms such as competition, resource partitioning, dispersal ability and predation tolerance do not adequately explain relative abundance under field conditions. Recent work suggests that interactions between plants and soil microbes is important. Here I show that such interaction explains a significant proportion of the variance in the relative abundance of species in plant communities. Rare plants exhibited a relative decrease in growth on 'home' soil in which pathogens had had a chance to accumulate, whereas invasive plants benefited from interactions with mycorrhizal fungi. Some plant species accumulate pathogens quickly and maintain low densities as a result of the accumulation of species-specific pathogens, whereas others accumulate species-specific pathogens more slowly and do not experience negative feedback until plant densities reach high levels. These results indicate that plants have different abilities to influence their abundance by changing the structure of their soil communities, and that this is an important regulator of plant community structure.
A beta-glucoronidase (GUS)-marked strain of Herbaspirillum seropedicae Z67 was inoculated onto rice seedling cvs. IR42 and IR72. Internal populations peaked at over 10(6) log CFU per gram of fresh weight by 5 to 7 days after inoculation (DAI) but declined to 10(3) to 10(4) log CFU per gram of fresh weight by 28 DAI. GUS staining was most intense on coleoptiles, lateral roots, and at the junctions of some of the main and lateral roots. Bacteria entered the roots via cracks at the points of lateral root emergence, with cv. IR72 appearing to be more aggressively infected than cv. IR42. H. seropedicae subsequently colonized the root intercellular spaces, aerenchyma, and cortical cells, with a few penetrating the stele to enter the vascular tissue. Xylem vessels in leaves and stems were extensively colonized at 2 DAI but, in later harvests (7 and 13 DAI), a host defense reaction was often observed. Dense colonies of H. seropedicae with some bacteria expressing nitrogenase Fe-protein were seen within leaf and stem epidermal cells, intercellular spaces, and substomatal cavities up until 28 DAI. Epiphytic bacteria were also seen. Both varieties showed nitrogenase activity but only with added C, and the dry weights of the inoculated plants were significantly increased. Only cv. IR42 showed a significant (approximately 30%) increase in N content above that of the uninoculated controls, and it also incorporated a significant amount of 15N2.
Citrus variegated chlorosis (CVC) is caused by Xylella fastidiosa, a phytopathogenic bacterium that can infect all Citrus sinensis cultivars. The endophytic bacterial communities of healthy, resistant, and CVC-affected citrus plants were studied by using
cultivation as well as cultivation-independent techniques. The endophytic communities were assessed in surface-disinfected
citrus branches by plating and denaturing gradient gel electrophoresis (DGGE). Dominant isolates were characterized by fatty-acid
methyl ester analysis as Bacillus pumilus, Curtobacterium flaccumfaciens, Enterobacter cloacae, Methylobacterium spp. (including Methylobacterium extorquens, M. fujisawaense, M. mesophilicum, M. radiotolerans, and M. zatmanii), Nocardia sp., Pantoea agglomerans, and Xanthomonas campestris. We observed a relationship between CVC symptoms and the frequency of isolation of species of Methylobacterium, the genus that we most frequently isolated from symptomatic plants. In contrast, we isolated C. flaccumfaciens significantly more frequently from asymptomatic plants than from those with symptoms of CVC while P. agglomerans was frequently isolated from tangerine (Citrus reticulata) and sweet-orange (C. sinensis) plants, irrespective of whether the plants were symptomatic or asymptomatic or showed symptoms of CVC. DGGE analysis of
16S rRNA gene fragments amplified from total plant DNA resulted in several bands that matched those from the bacterial isolates,
indicating that DGGE profiles can be used to detect some endophytic bacteria of citrus plants. However, some bands had no
match with any isolate, suggesting the occurrence of other, nonculturable or as yet uncultured, endophytic bacteria. A specific
band with a high G+C ratio was observed only in asymptomatic plants. The higher frequency of C. flaccumfaciens in asymptomatic plants suggests a role for this organism in the resistance of plants to CVC.
Motility is a major trait for competitive tomato root-tip colonization by Pseudomonas fluorescens. To test the hypothesis that this role of motility is based on chemotaxis toward exudate components, cheA mutants that were defective in flagella-driven chemotaxis but retained motility were constructed in four P. fluorescens strains. After inoculation of seedlings with a 1:1 mixture of wild-type and nonmotile mutants all mutants had a strongly reduced competitive root colonizing ability after 7 days of plant growth, both in a gnotobiotic sand system as well as in nonsterile potting soil. The differences were significant on all root parts and increased from root base to root tip. Significant differences at the root tip could already be detected after 2 to 3 days. These experiments show that chemotaxis is an important competitive colonization trait. The best competitive root-tip colonizer, strain WCS365, was tested for chemotaxis toward tomato root exudate and its major identified components. A chemotactic response was detected toward root exudate, some organic acids, and some amino acids from this exudate but not toward its sugars. Comparison of the minimal concentrations required for a chemotactic response with concentrations estimated for exudates suggested that malic acid and citric acid are among major chemo-attractants for P. fluorescens WCS365 cells in the tomato rhizosphere.
Several chemical changes in soil are associated with plant growth-promoting rhizobacteria (PGPR). Some bacterial strains directly regulate plant physiology by mimicking synthesis of plant hormones, whereas others increase mineral and nitrogen availability in the soil as a way to augment growth. Identification of bacterial chemical messengers that trigger growth promotion has been limited in part by the understanding of how plants respond to external stimuli. With an increasing appreciation of how volatile organic compounds signal plants and serve in plant defense, investigations into the role of volatile components in plant-bacterial systems now can follow. Here, we present chemical and plant-growth data showing that some PGPR release a blend of volatile components that promote growth of Arabidopsis thaliana. In particular, the volatile components 2,3-butanediol and acetoin were released exclusively from two bacterial strains that trigger the greatest level of growth promotion. Furthermore, pharmacological applications of 2,3-butanediol enhanced plant growth whereas bacterial mutants blocked in 2,3-butanediol and acetoin synthesis were devoid in this growth-promotion capacity. The demonstration that PGPR strains release different volatile blends and that plant growth is stimulated by differences in these volatile blends establishes an additional function for volatile organic compounds as signaling molecules mediating plant-microbe interactions.
Plant-growth-promoting rhizobacteria colonize the root systems of plants and can modulate plant growth by enhancing the availability of nutrients, inducing metabolic activities by phytohormones and analogs, by shifting the phytohormonal balance, by inducing defense programs such as systemic acquired resistance (SAR) and induced systemic resistance (ISR), or by reducing phytotoxic microbial communities. A recently discovered novel mode of growth promotion and induction of ISR is based on airborne volatiles (butanediol, acetoin) released from certain microorganisms. According to studies with mutants of Arabidopsis thaliana, the growth-promotion response appears to be controlled by cytokinins and ethylene.
The presence of human-pathogenic, enteric bacteria on the surface and in the interior of raw produce is a significant health
concern. Several aspects of the biology of the interaction between these bacteria and alfalfa (Medicago sativa) seedlings are addressed here. A collection of enteric bacteria associated with alfalfa sprout contaminations, along with
Escherichia coli K-12, Salmonella enterica serotype Typhimurium strain ATCC 14028, and an endophyte of maize, Klebsiella pneumoniae 342, were labeled with green fluorescent protein, and their abilities to colonize the rhizosphere and the interior of the
plant were compared. These strains differed widely in their endophytic colonization abilities, with K. pneumoniae 342 and E. coli K-12 being the best and worst colonizers, respectively. The abilities of the pathogens were between those of K. pneumoniae 342 and E. coli K-12. All Salmonella bacteria colonized the interiors of the seedlings in high numbers with an inoculum of 102 CFU, although infection characteristics were different for each strain. For most strains, a strong correlation between endophytic
colonization and rhizosphere colonization was observed. These results show significant strain specificity for plant entry
by these strains. Significant colonization of lateral root cracks was observed, suggesting that this may be the site of entry
into the plant for these bacteria. At low inoculum levels, a symbiosis mutant of Medicago truncatula, dmi1, was colonized in higher numbers on the rhizosphere and in the interior by a Salmonella endophyte than was the wild-type host. Endophytic entry of M. truncatula appears to occur by a mechanism independent of the symbiotic infections by Sinorhizobium meliloti or mycorrhizal fungi.
Bacterial endophytes reside within the interior of plants without causing disease or forming symbiotic structures. Some endophytes, such as Klebsiella pneumoniae 342 (Kp342), enhance plant growth and nutrition. Others, such as Salmonella enterica serovar Typhimurium (S. typhimurium), are human pathogens that contaminate raw produce. Several lines of evidence are presented here to support the hypothesis that plant defense response pathways regulate colonization by endophytic bacteria. An ethylene-insensitive mutant of Medicago truncatula is hypercolonized by Kp342 compared to the parent genotype. Addition of ethylene, a signal molecule for induced systemic resistance in plants, decreased endophytic colonization in Medicago spp. This ethylene-mediated inhibition of endophytic colonization was reversed by addition of the ethylene action inhibitor, 1-methylcyclopropene. Colonization of Medicago spp. by S. typhimurium also was affected by exogenous ethylene. Mutants lacking flagella or a component of the type III secretion system of Salmonella pathogenicity island 1 (TTSS-SPI1) colonize the interior of Medicago spp. in higher numbers than the wild type. Arabidopsis defense response-related genotypes indicated that only salicylic acid (SA)-independent defense responses contribute to restricting colonization by Kp342. In contrast, colonization by S. typhimurium is affected by both SA-dependent and -independent responses. S. typhimurium mutants further delineated these responses, suggesting that both flagella and TTSS-SPI1 effectors can be recognized. Flagella act primarily through SA-independent responses (compromising SA accumulation still affected colonization in the absence of flagella). Removal of a TTSS-SPI1 effector resulted in hypercolonization regardless of whether the genotype was affected in either SA-dependent or SA-independent responses. Consistent with these results, S. typhimurium activates the promoter of PR1, a SA-dependent pathogenesis-related gene, while S. typhimurium mutants lacking the TTSS-SPI1 failed to activate this promoter. These observations suggest approaches to reduce contamination of raw produce by human enteric pathogens and to increase the number of growth-promoting bacteria in plants.
The phytohormone ethylene is a key regulator of plant growth and development. Components of the pathway for ethylene signal transduction were identified by genetic approaches in Arabidopsis and have now been shown to function in agronomically important plants as well.
This review focuses on recent advances in our knowledge on ethylene signal transduction, in particular on recently proposed components of the pathway, on the interaction between the pathway components and on the roles of transcriptional and post-transcriptional regulation in ethylene signalling.
Data indicate that the site of ethylene perception is at the endoplasmic reticulum and point to the importance of protein complexes in mediating the initial steps in ethylene signal transduction. The expression level of pathway components is regulated by both transcriptional and post-transcriptional mechanisms, degradation of the transcription factor EIN3 being a primary means by which the sensitivity of plants to ethylene is regulated. EIN3 also represents a control point for cross-talk with other signalling pathways, as exemplified by the effects of glucose upon its expression level. Amplification of the initial ethylene signal is likely to play a significant role in signal transduction and several mechanisms exist by which this may occur based on properties of known pathway components. Signal output from the pathway is mediated in part by carefully orchestrated changes in gene expression, the breadth of these changes now becoming clear through expression analysis using microarrays.
In recent years, an increased awareness of the harmful effects of environ- mental pollutants-including agricultural fertilizer by-products, pesticides, herbicides and fungicides-has promoted research into alternative means of facilitating plant growth. The ideal replacement for these chemicals should not only enhance plant growth, but, unlike fertilizers, also inhibit those organisms that impede plant growth. Chapter 19 already discussed the development and use of biopesticides (biocontrol agents or BCA) in agriculture. In addition to these biocontrol agents, the use of organisms known as plant growth- promoting bacteria may be highly advantageous to plants. In Chapter 8, we examined the intricacies of the rhizosphere environment as a habitat for bacteria, including plant growth promoters and BCA. Next to binding to roots (rhizosphere bacteria), bacteria also localize on leaves (phyllosphere bacteria) and thrive on the nutrients released by roots and/or leaves [1,2]. In both settings, but primarily at the roots, the plant-associated bacteria can stimulate plant growth as a result of their plant-driven activities [3].
Plant roots harbor a large diversity of microorganisms that have an essential role in ecosystem functioning. To better understand the level of intimacy of root-inhabiting microbes such as arbuscular mycorrhizal fungi and bacteria, we provided 13CO2 to plants at atmospheric concentration during a 5-h pulse. We expected microbes dependent on a carbon flux from their host plant to become rapidly labeled. We showed that a wide variety of microbes occurred in roots, mostly previously unknown. Strikingly, the greatest part of this unsuspected diversity corresponded to active primary consumers. We found 17 bacterial phylotypes co-occurring within roots of a single plant, including five potentially new phylotypes. Fourteen phylotypes were heavily labeled with the 13C. Eight were phylogenetically close to Burkholderiales, which encompass known symbionts; the others were potentially new bacterial root symbionts. By analyzing unlabeled and 13C-enriched RNAs, we demonstrated differential activity in C consumption among these root-inhabiting microbes. Arbuscular mycorrhizal fungal RNAs were heavily labeled, confirming the high carbon flux from the plant to the fungal compartment, but some of the fungi present appeared to be much more active than others. The results presented here reveal the possibility of uncharacterized root symbioses.
Endophytic nitrogen-fixing bacteria are believed to contribute substantial amounts of N to certain gramineous crops. We have been interested to find (a) a diazotroph(s) in rice which can aggressively and stably persist and fix nitrogen in interior tissues and (b) unique rice-diazotrophic endophyte combinations. To achieve these objectives, it has been essential to find an efficient method to surface sterilize rice tissues. The method described here consists of exposing tissues to 1% Chloramine T for 15 min followed by shaking with glass beads. It has proven very efficient since (a) surface bacterial populations on the root and culm were found to be reduced by more than 90%, (b) the number of the internal colonizers was found to be significantly higher than the number of surface bacteria, and (c) colonization of root but not subepidermal tissue by gusA-marked Herbaspirillum seropedicae Z67 bacteria was found to be virtually eliminated. Nitrogen-fixing putative endophytic populations (MPN g dry wt−1) in the root (7.94 × 107) and culm (2.57 × 106) on field-grown IR72 plants grown in the absence of N fertilizer was found to be significantly higher near heading stage. The corresponding total putative endophyte populations in the tissues of 25 highly diverse genotypes of rice and their relatives was found to range from 105−108and 104−109, in the roots and culms, respectively. Generally, the resident bacteria were found to be non-diazotrophic, although in isolated cases diazotrophs were found, for example in the roots and culm of IR72 rice plants, or the culm of Zizaniopsis villanensis plants. The size of populations of diazotrophic bacteria in different rice genotypes was found to be 103−107 for the roots and 104−106 for the culms, respectively. The rice genera-related plants Potamophila pariffora and Rhynchoryza subulata showed the highest levels.
Currently proposed means of entry of bacterial endophytes into roots of field-grown crop plants, as well as niches available for their successful colonization of living tissues, are evaluated from a plant biology perspective and the following conclusions drawn. (1) Opportunities for passive 'crack entry' into healthy, undisturbed roots in the field may not be as available as studies with laboratory-grown plants have suggested. Consistent entry of endophytes into living root tissues in the field probably requires bacterial capability to hydrolyse the hydrophobic incrustations of the walls of epidermal, hypodermal, endodermal and other cortical cells. (2) Xylem lumen apoplast is an unsuitable niche for endophytes, especially in the grasses, because of the reduced fitness such colonization imposes on plants subjected to field stresses. (3) The intercellular space apoplast is the most suitable niche for endophytes. More data about the environment of this apoplast are urgently needed so that plant varieties can be tailored to provide an optimal environment in these spaces for particular endophytes. It is suggested that many bacterial 'endophytes' may not have colonized living tissues, but are living in protective niches in dead surface tissues or closely adhering soil of rhizosheaths. Selection of strains of beneficial bacteria adapted for colonizing these external niches may be desirable.
Plant-growth-promoting rhizobacteria colonize the root systems of plants and can modulate plant growth by enhancing the availability of nutrients, inducing metabolic activities by phytohormones and analogs, by shifting the phytohormonal balance, by inducing defense programs such as systemic acquired resistance (SAR) and induced systemic resistance (ISR), or by reducing phytotoxic microbial communities. A recently discovered novel mode of growth promotion and induction of ISR is based on airborne volatiles (butanediol, acetoin) released from certain microorganisms. According to studies with mutants of Arabidopsis thaliana, the growth-promotion response appears to be controlled by cytokinins and ethylene.
ABSTRACT Colonization of the rhizosphere by micro-organisms results in modifications in plant growth and development. This review examines the mechanisms involved in growth promotion by plant growth-promoting rhizobacteria which are divided into indirect and direct effects. Direct effects include enhanced provision of nutrients and the production of phytohormones. Indirect effects involve aspects of biological control: the production of antibiotics and iron-chelating siderophores and the induction of plant resistance mechanisms. The study of the molecular basis of growth promotion demonstrated the important role of bacterial traits (motility, adhesion and growth rate) for colonization. New research areas emerge from the discovery that molecular signalling occurs through plant perception of eubacterial flagellins. Recent perspectives in the molecular genetics of cross-talking mechanisms governing plant–rhizobacteria interactions are also discussed.
An endophytic bacterium was isolated from Chinese medicinal plant Scutellaria baicalensis Georgi. The phylogenetic and physiological characzterization indicated that the isolate, strain ES-2, was Bacillus amyloliquefaciens, which produced two families of secondary metabolites with broad-spectrum antibacterial and antifungal activities. Culture filtrate of ES-2 displayed antagonism against some phytopathogenic, food-borne pathogenic and spoilage bacteria and fungi owing to the existence of antimicrobial compounds. A HPLC-MS analysis showed two series of ion peaks from the culture filtrate. A further electrospray ionization/collision-induced dissociation spectrum revealed that the two series ion peaks represented different fengycin homologues and surfactin homologues, respectively, which had a potential for food preservation and the control of several fungal plant diseases.
The endophytic colonization, nitrogen fixation, and plant growth-promoting abilities of Herbaspirillum sp. strain B501 gfpl, which is a diazotrophic endophyte isolated from wild rice, were studied after infection (at 101 and 10(8) cells ml(-1)) of seedlings of cultivated rice Oryza sativa cv. Nipponbare. Both doses resulted in colonization of the roots and stem (basal stein and leaf sheath). No colonization of leaves was observed. Higher bacterial populations were observed in the roots than stems. The bacteria colonized the intercellular spaces of the root epidermis and the spaces at the junctions of the lateral roots. They also colonized the epidermis and pericycle of the basal stem and the sub-epidermal tissues of the dermal tissue system of the leaf sheath at later stages. The colonizing bacteria incorporated significant amounts of N-15(2) into the infected plants. The inoculated plants also had higher dry weights and fresh weights than the control (uninoculated) plants.
The plant growth promoting rhizobacterium Pseudomonas putida GR12-2 was mutagenized with nitrosoguanidine and three separate mutants that were unable to utilize 1-aminocyclopropane-1-carboxylic acid (ACC) as a sole nitrogen source were selected. These mutants are devoid of the ACC deaminase activity that is present in wild-type P. putida GR12-2 cells. Only wild-type cells, but not any of the ACC deaminase mutants, promoted root elongation of developing canola seedlings under gnotobiotic conditions. These results are interpreted in terms of a model in which P. putida GR12-2 promotes root elongation by binding to germinating seeds and sequesters and hydrolyzes some of the unbound ACC, thereby lowering the level of ACC and hence the endogenous ethylene concentration, allowing the roots to grow longer.
The effects of inoculum density (0, 4.6 × 107, 4.2 × 108, and 8.8 × 108 cfu∙mL−1), temperature (10, 20, and 30 °C), and plant genotype (cultivars Celebrity, Blazer, Scotia, and Mountain Delight) on bacterial colonization and plant growth promotion were investigated in a gnotobiotic system. An in vitro dual culture of tomato (Lycopersicon esculentum L.) plantlets and a Pseudomonas sp., strain PsJN, were used. Epiphytic (external) and endophytic (internal) bacterial populations were determined to evaluate plantlet colonization. Shoot and root biomass of bacterized plantlets was significantly higher (p ≤ 0.05) than that of nonbacterized controls. Growth promotion was best with inoculum densities of 3 × 108 – 7 × 108 cfu∙mL−1 at 20 °C, particularly in the early maturing cultivars Blazer and Scotia. Lower inoculum densities were required to maximize root growth (approximately 1 × 108 cfu∙mL−1) than shoot growth (approximately 3 × 108 cfu∙mL−1). Shoot surface populations did not vary with inoculum density or temperature, but the bacterium colonized the shoot exterior of cultivars Celebrity, Mountain Delight, and Scotia better than cultivar Blazer. The root surface populations increased linearly with increasing inoculum density (within a range of 107–108 cfu∙mL−1), decreased with increasing temperatures (from 10 to 30 °C), and were higher for the main season cultivar Celebrity than for cultivars Blazer, Scotia, and Mountain Delight. Populations of shoot endophytes did not vary with initial inoculum density or genotype but were affected by temperature; the highest colonization was at 10 °C. The number of root endophytes was also highest at 10 °C at the inoculum density of approximately 4 × 108 cfu∙mL−1 and did not vary with genotypes. The experiments clearly indicate that there was no relationship between root surface colonization and plant growth promotion. However, the range of inoculum levels (3 × 108 – 7 × 108 cfu∙mL−1) that promoted colonization of the inner root tissues (endophytic) also best promoted plant growth. A possible biostimulation threshold within the tissues of the inoculated plants under conditions favourable to the growth of tomato is proposed.Key words: Pseudomonas sp., tomato, colonization, growth promotion.
Bacterial contaminants of micropropagated plant cultures were isolated and characterized with standard bacteriological tests and appropriate API strips. Results obtained were analysed by the API identification software. Of 198 bacterial strains isolated from nine plant species, 90% were identified as Bacillus, Enterobacter, Micrococcus, Staphylococcus, Pseudomonas or Lactobacillus species. Possible sources of contamination are discussed.
We have studied intercellular colonization of wheat roots by Azorhizobium caulinodans and other diazotrophic bacteria, using strains marked with the lacZ reporter gene to facilitate their detection and identification. A. caulinodans was observed by light and electron microscopy to enter the roots of wheat at high frequency at the points of emergence of lateral roots (lateral root cracks). After lateral root crack colonization, bacteria moved into intercellular spaces within the cortical cell layer of roots. The flavonoid naringenin at 10 and 100 mmol m–3 significantly stimulated root colonization. The roles of the structural nodABC genes and the regulatory nodD gene were also studied; lateral root crack colonization of wheat was shown to be Nod factor- and NodD-independent. Similar frequencies of lateral root crack colonization were observed following inoculation of wheat with Azospirillum brasilense. Colonization by A. brasilense was stimulated by naringenin and also by other flavonoid molecules.
In conclusion, of the plants thus far studied, the spectrum and diversity of endophytic bacteria in the roots varies greatly.
What about the endophytic bacterial spectrum of plants growing under extreme climatic conditions, such as halophytes and xerophytes?
Survival mechanisms developed by those bacteria may have some interesting industrial or pharmaceutical applications. Newly
developed cultivation-independent methods have made clear that there is much more diversity among endophytic bacteria than
at first expected. The major factors influencing bacterial diversity and colonisation have been discussed and their potential
to manage endophytic communities towards increased benefits for plants and human health have been outlined. However, the potential
risks of endophytic bacteria, especially of those strains known also to be potential human pathogens, need further exploration.
Endophytic nitrogen-fixing bacteria are believed to contribute substantial amounts of N to certain gramineous crops. We have been interested to find (a) a diazotroph(s) in rice which can aggressively and stably persist and fix nitrogen in interior tissues and (b) unique rice-diazotrophic endophyte combinations. To achieve these objectives, it has been essential to find an efficient method to surface sterilize rice tissues. The method described here consists of exposing tissues to 1% Chloramine T for 15 min followed by shaking with glass beads. It has proven very efficient since (a) surface bacterial populations on the root and culm were found to be reduced by more than 90%, (b) the number of the internal colonizers was found to be significantly higher than the number of surface bacteria, and (c) colonization of root but not subepidermal tissue by gusA-marked Herbaspirillum seropedicae Z67 bacteria was found to be virtually eliminated. Nitrogen-fixing putative endophytic populations (MPN g dry wt) in the root (7.94 10) and culm (2.57 10) on field-grown IR72 plants grown in the absence of N fertilizer was found to be significantly higher near heading stage. The corresponding total putative endophyte populations in the tissues of 25 highly diverse genotypes of rice and their relatives was found to range from 10–10and 10–10, in the roots and culms, respectively. Generally, the resident bacteria were found to be non-diazotrophic, although in isolated cases diazotrophs were found, for example in the roots and culm of IR72 rice plants, or the culm of Zizaniopsis villanensis plants. The size of populations of diazotrophic bacteria in different rice genotypes was found to be 10–10 for the roots and 10–10 for the culms, respectively. The rice genera-related plants Potamophila pariffora and Rhynchoryza subulata showed the highest levels.
ABSTRACT The physiology and virulence of Ralstonia solanacearum biovar 2 strain 1609, kept in water at 4 and 20 degrees C, were studied. At 20 degrees C, total cell and plate count (colony forming units; CFU) numbers were similar, between log 5.03 and log 5.55 CFU, and log 5.03 and log 5.51 cells per ml, at days 0 and 132, respectively. However, CFU in the cultures kept at 4 degrees C dropped from log 6.78 CFU/ml at day 0 to below detection after 84 days. The presence of catalase in the agar resulted in higher CFU, and at day 84, log 1.95 CFU/ml still was detectable. No colonies were observed at day 125. The presence of viable-but-nonculturable (VBNC) cells in the 4 degrees C cultures was confirmed using SYTO9 viability staining. Viable cell numbers were log 1.77 higher than CFU on plates with catalase. At day 84 and after 125 days, log 3.70 viable cells per ml still were present. Shifts in subpopulations differing in viability were found by flow cytometric sorting of 4 degrees C-treated cells stained with SYTO9 (healthy) and propidium iodide (PI; compromised). The SYTO9-stained cell fractions dropped from 99 to 39%, and the PI-stained fractions increased from 0.7 to 33.3% between days 0 and 125. At 20 degrees C, the SYTO9-stained fraction remained stable at 99% until day 132. SYTO9-stained cells sorted from 4 degrees C cultures at day 100 were injected into tomato plants. Upon incubation for 30 days, these plants did not show wilting. However, more than log 4.19 CFU and log 8.17 cells were recovered from these plants. Cells from colonies isolated from the nonwilted plants did not regain their virulence as demonstrated by subsequent injection into several new sets of tomato plants. Cells from 4 degrees C cultures injected at day 125 were not able to cause wilting of, or proliferate in, tomato plants. The threat posed by VBNC R. solanacearum cells upon incubation at 4 degrees C was thus ephemeral because cells lost their capacity to cause disease after 125 days.
Adherence of bacteria to eukaryotic cells is essential for the initiation of infection in many animal and human pathogens, e.g. Neisseria gonorrhoeae and Pseudomonas aeruginosa. Adhesion-mediating type IV pili, filamentous surface appendages formed by pilin subunits, are crucial virulence factors. Here, we report that type IV pilus-dependent adhesion is also involved in plant-bacteria and fungus-bacteria interactions. Nitrogen-fixing, endophytic bacteria, Azoarcus sp., can infect the roots of rice and spread systemically into the shoot without causing symptoms of plant disease. Formation of pili on solid media was dependent on the pilAB locus. PilA encodes an unusually short (6.4 kDa) putative pilin precursor showing 100% homology to the conserved N-terminus of the Pseudomonas aeruginosa type IV pilin. PilB encodes for a 14.2 kDa polypeptide showing similarity to FimF, a component of type I fimbriae of Escherichia coli. It was found to be extruded beyond the cell surface by immunofluorescence studies, and it may, therefore, be part of a pilus assembly complex or the pilus itself. Both genes are involved in the establishment of bacteria on the root surface of rice seedlings, as detected by fluorescence microscopy. Moreover, both genes are necessary for bacterial adhesion to the mycelium of an ascomycete, which was isolated from the same rhizosphere as the bacteria. In co-culture with the fungus, Azoarcus sp. forms complex intracytoplasmic membranes, diazosomes, which are related to efficient nitrogen fixation. Adhesion to the mycelium appears to be crucial for this process, as diazosomes were absent and nitrogen fixation rates were decreased in pilAB mutants in co-culture.
The rhizosphere is a densely populated area in which plant roots must compete with invading root systems of neighboring plants for space, water, and mineral nutrients, and with other soil-borne organisms, including bacteria and fungi. Root-root and root-microbe communications are continuous occurrences in this biologically active soil zone. How do roots manage to simultaneously communicate with neighboring plants, and with symbiotic and pathogenic organisms within this crowded rhizosphere? Increasing evidence suggests that root exudates might initiate and manipulate biological and physical interactions between roots and soil organisms, and thus play an active role in root-root and root-microbe communication.
Plant growth-promoting rhizobacteria, in association with plant roots, can trigger induced systemic resistance (ISR). Considering that low-molecular weight volatile hormone analogues such as methyl jasmonate and methyl salicylate can trigger defense responses in plants, we examined whether volatile organic compounds (VOCs) associated with rhizobacteria can initiate ISR. In Arabidopsis seedlings exposed to bacterial volatile blends from Bacillus subtilis GB03 and Bacillus amyloliquefaciens IN937a, disease severity by the bacterial pathogen Erwinia carotovora subsp. carotovora was significantly reduced compared with seedlings not exposed to bacterial volatiles before pathogen inoculation. Exposure to VOCs from rhizobacteria for as little as 4 d was sufficient to activate ISR in Arabidopsis seedlings. Chemical analysis of the bacterial volatile emissions revealed the release of a series of low-molecular weight hydrocarbons including the growth promoting VOC (2R,3R)-(-)-butanediol. Exogenous application of racemic mixture of (RR) and (SS) isomers of 2,3-butanediol was found to trigger ISR and transgenic lines of B. subtilis that emitted reduced levels of 2,3-butanediol and acetoin conferred reduced Arabidopsis protection to pathogen infection compared with seedlings exposed to VOCs from wild-type bacterial lines. Using transgenic and mutant lines of Arabidopsis, we provide evidence that the signaling pathway activated by volatiles from GB03 is dependent on ethylene, albeit independent of the salicylic acid or jasmonic acid signaling pathways. This study provides new insight into the role of bacteria VOCs as initiators of defense responses in plants.
Strains of rhizobia within a single species can have three different genetically determined strategies. Mutualistic rhizobia provide their legume hosts with nitrogen. Parasitic rhizobia infect legumes, but fix little or no nitrogen. Nonsymbiotic strains are unable to infect legumes at all. Why have rhizobium strains with one of these three strategies not displaced the others? A symbiotic (mutualistic or parasitic) rhizobium that succeeds in founding a nodule may produce many millions of descendants. The chances of success can be so low, however, that nonsymbiotic rhizobia can have greater reproductive success. Legume sanctions against nodules that fix little or no nitrogen favor more mutualistic strains, but parasitic strains that use plant resources only for their own reproduction may do well when they share nodules with mutualistic strains.