Insights into the early stages of plant-endophytic bacteria interaction

Bioinoculant substitution enhances rhizosphere soil quality and maize growth by modulating microbial communities and host gene expression in alkaline soils

The application of plant growth-promoting bacteria (PGPB) as bioinoculants is widely recognized for improving crop yields and soil fertility. However, the precise mechanisms underlying their impact on rhizosphere soil quality and crop productivity remain insufficiently understood. This study elucidates how a solid bioinoculant, comprising Bacillus velezensis FZB42 and attapulgite clay, enhances rhizosphere soil quality and maize (Zea mays) growth in nutrient-deficient alkaline calcareous soils. Pot experiments reveal that bioinoculant application promotes extensive root colonization under nitrogen-deficient conditions, with significantly higher colonization rates observed in the half-nitrogen (HN) and zero-nitrogen (ZN) treatments compared to full-nitrogen conditions. Notably, bioinoculant application in ZN and HN significantly increases phosphorus availability and soil quality in the rhizosphere. Furthermore, maize growth parameters, including plant height, stem diameter, and kernel yield, are markedly enhanced, with optimal biomass accumulation achieved under HN conditions. High-throughput sequencing of rhizosphere microbiomes uncovers significant shifts in microbial community composition, with enrichment of key taxa involved in nutrient cycling and plant-microbe interactions. Transcriptomic analysis of maize tissues demonstrates the upregulation of genes associated with nutrient transport, photosynthesis, fatty acid biosynthesis, and kernel development, with a pronounced enrichment in metabolic pathways linked to growth and productivity. Structural equation modeling indicates that increased microbial diversity and gene expression collectively account for 69 % of the variance in the soil quality index and 45 % of the variance in maize yield. These findings provide critical mechanistic insights into the role of solid bioinoculant in enhancing soil fertility and crop performance, highlighting their potential as a sustainable agricultural strategy for improving productivity in low-fertility alkaline soils.

Biochar-induced microbial and metabolic reprogramming enhances bioactive compound accumulation in Panax quinquefolius L

Panax quinquefolius L., with a history of over 300 years in traditional Chinese medicine, is notably rich in ginsenosides-its primary bioactive components. Although our previous study found that biochar application could enhance the content of ginsenoside Re, Rg and other contents in P. quinquefolius, its effect on the overall secondary metabolism of P. quinquefolius and its mechanism are still unclear. In this paper, the correlation between plant microbiome and secondary metabolites was studied from the perspective of plant rhizosphere microorganisms and endophytes, and the mechanism of biochar-induced metabolic reprogramming of P. quinquefolius was revealed. The results showed that biochar treatment significantly increased the accumulation of various substances in P. quinquefolius, including nucleosides, glycerophosphocholines, fatty acyls, steroidal glycosides, triterpenoids, and other bioactive compounds. Additionally, biochar treatment significantly enriched beneficial rhizosphere microorganisms such as Bacillus, Flavobacterium, and Devosia, while reducing the relative abundance of harmful fungi like Fusarium. Furthermore, it promoted endophytic Flavobacterium, Acaulospora, and Glomus, and suppressed pathogenic genera such as Plectosphaerella, Cladosporium, and Phaeosphaeria. These shifts in rhizosphere microbial community and endophytes structure and function were closely linked to the accumulation of secondary metabolites (e.g. ginsenosides Rg3, F2) in P. quinquefolius. Overall, our findings suggest that biochar may influence key endophytes and rhizosphere microorganisms to regulate the accumulation of secondary metabolites in P. quinquefolius. Therefore, this study provides valuable insights into the potential application of biochar in Chinese medicine agriculture.

Biopriming of Maize with their endophyte Aspergillus fumigatus reinforces their resistance to salinity stress and improves their physiological traits

Zea mays L. (Maize) is one of the most crucial world's crops, for their nutritional values, however, the water scarcity and consequent soil salinization are the major challenges that limit the growth and productivity of this plant, particularly in the semi-arid regions in Egypt. Recently, biopriming has been recognized as one of the most efficient natural-ecofriendly approaches to mitigate the abiotic salt stress on plants. The haploid (128) and triploid (368) seeds of maize were selected as model verities for assessing their resistance to salt stress and mitigating their effect by fungal-biopriming. Overall, the haploid and triploid plants viabilities were drastically affected by salt concentration, at 500 mM of NaCl. At 500 mM NaCl, the fresh weights of the triploid and haploid seedlings were reduced by ~ 5 and 6.1 folds, compared to the controls, ensuring slightly higher salt resistance of the triploid than haploid ones. The pattern of the endophytic fugal isolates was plausibly changed with the salt concentration for both plant types, Aspergillus fumigatus isolate was emerged with the higher NaCl concentration (400-500 mM), and their morphological identity was molecularly confirmed and deposited into Genbank with accession # PQ200673. The fungal bioprimed seeds of the haploid and triploid plants were irrigated with 400 mM NaCl. The fungal-bioprimed plants displayed a significant improvement on the shoot density, fibrous roots, root length, shoot length, and leaves numbers and areas of the stressed-plants by ~ 1.7 folds, compared to control, ensures the triggering of different salt resistance machineries in plants upon fungal biopriming. The total antioxidant enzymes activities "catalase, peroxidase, superoxide dismutase" of the salt-stressed bioprimed maize plants were increased by ~ 4.7-5.3%, compared to control, confirming the mitigating effect of the salinity stress on plants upon fungal biopriming. The chlorophyll and carotenoids contents were significantly increased of the salt stressed maize upon biopriming with A. fumigatus. The expression of the sod, apx2, nhx11, hkt1, H + -PPase, nced of the plant salt stressed was strongly increased in response to A. fumigatus biopriming, normalized to β-actin gene. The expression of apx2 was dramatically increased by about 30 and 43 folds, in response to fungal biopriming. The nhx1 was significantly up-regulated by 18.9 fold in response to fungal biopriming, compared to control.

Effects of endophytes on early growth and ascorbate metabolism in Brassica napus

Understanding the early interactions between plants and endophytes will contribute to a more systematic approach to enhancing endophyte-mediated effects on plant growth and environmental stress resistance. This study examined very early growth and ascorbate metabolism after seed treatment of Brassica napus with three different endophytes. The three endophytes used were Bacillus amyloliquefaciens pb1(Bapb1), Micrococcus luteus (Ml) and Pseudomonas fluorescens SLB4 (SLB4). Seeds of Brassica napus cv. trophy were surface sterilized and plated on 1/2 MS Basal salts (pH 5.7 -5.8) + 0.8% agarose. Under sterile conditions, endophyte suspensions or sterile distilled water (controls) were applied to plated seeds. After two days, all plates were scanned to produce digital images for subsequent growth analysis. Then, seedlings were gently removed from the plates and placed in sterile microfuge tubes. For biochemical analyses, extracts were prepared from samples and assayed spectrophotometrically. We detected slight changes in seedling root tip and/or primary root growth with Bapb1 and Ml. Seedlings treated with SLB4 exhibited significantly increased primary root and root tip length after two days of growth. Ascorbate oxidation, however, was the primary significant change common to all endophyte-treated seedlings. In relation to ascorbate oxidation, soluble ascorbate oxidase (AO) was slightly reduced in Bapb1 and Ml-treated seedlings, whereas ionically-bound AO was reduced in Bapb1 and SLB4-treated seedlings. Total AO activity was significantly reduced in Bapb1-treated seedlings. There were no differences in cytosolic APX activity or glutathione levels between endophyte-treated seedlings and controls. Like pathogens, endophytes can trigger an oxidative burst in the plant. A level of ascorbate oxidation seems required to propagate ROS as signaling molecules as part of the plant immune response. The slight to moderate reductions in plant AO activity that we found mimic the inhibitory effects of pathogens on AO activity, but there was still a level of AO activity that may have been sufficient for the apoplastic ascorbate oxidation required for subsequent ROS signaling. Other studies have suggested that endophytes may elicit a more moderate plant immune response relative to pathogens to facilitate colonization. The AO, APX, and glutathione results would be consistent with a moderate plant immune response to endophytes.

Global insights into endophytic bacterial communities of terrestrial plants: Exploring the potential applications of endophytic microbiota in sustainable agriculture

Endophytic microorganisms are indispensable symbionts during plant growth and development and often serve functions such as growth promotion and stress resistance in plants. Therefore, an increasing number of researchers have applied endophytes for multifaceted phytoremediation (e.g., organic pollutants and heavy metals) in recent years. With the availability of next-generation sequencing technologies, an increasing number of studies have shifted the focus from culturable bacteria to total communities. However, information on the composition, structure, and function of bacterial endophytic communities is still not widely synthesized. To explore the general patterns of variation in bacterial communities between plant niches, we reanalyzed data from 1499 samples in 30 individual studies from different continents and provided comprehensive insights. A group of bacterial genera were commonly found in most plant roots and shoots. Our analysis revealed distinct variations in the diversity, composition, structure, and function of endophytic bacterial communities between plant roots and shoots. These variations underscore the sophisticated mechanisms by which plants engage with their endophytic microbiota, optimizing these interactions to bolster growth, health, and resilience against stress. Highlighting the strategic role of endophytic bacteria in promoting sustainable agricultural practices and environmental stewardship, our study not only offers global insights into the endophytic bacterial communities of terrestrial plants but also underscores the untapped potential of these communities as invaluable resources for future research.

Juvenile Plant-Microbe Interactions Modulate the Adaptation and Response of Forest Seedlings to Rapid Climate Change

The negative impacts of climate change on native forest ecosystems have created challenging conditions for the sustainability of natural forest regeneration. These challenges arise primarily from abiotic stresses that affect the early stages of forest tree development. While there is extensive evidence on the diversity of juvenile microbial symbioses in agricultural and fruit crops, there is a notable lack of reports on native forest plants. This review aims to summarize the critical studies conducted on the diversity of juvenile plant-microbe interactions in forest plants and to highlight the main benefits of beneficial microorganisms in overcoming environmental stresses such as drought, high and low temperatures, metal(loid) toxicity, nutrient deficiency, and salinity. The reviewed studies have consistently demonstrated the positive effects of juvenile plant-microbiota interactions and have highlighted the potential beneficial attributes to improve plantlet development. In addition, this review discusses the beneficial attributes of managing juvenile plant-microbiota symbiosis in the context of native forest restoration, including its impact on plant responses to phytopathogens, promotion of nutrient uptake, facilitation of seedling adaptation, resource exchange through shared hyphal networks, stimulation of native soil microbial communities, and modulation of gene and protein expression to enhance adaptation to adverse environmental conditions.

Endophytic Seed-Associated Bacteria as Plant Growth Promoters of Cuban Rice (Oryza sativa L.)

Cuban rice cultivars INCA LP-5 and INCA LP-7 are widely distributed in Cuba and Caribbean countries. Although there are studies about rhizospheric bacteria associated with these cultivars, there are no reports about their seed-associated bacteria. This study aimed to isolate endophytic bacteria from rice seeds and select those with the greatest plant growth-promoting traits. A total of nineteen bacterial strains from the genera Pantoea, Bacillus, Paenibacillus, and Pseudomonas were isolated from the husk and endosperm of rice seeds. The strains Pantoea sp. S5-1, Pseudomonas sp. S5-38, and Pseudomonas sp. S7-1 were classified as the most promissory to increase rice growth as they demonstrated the presence of multiple plant growth-promoting traits such as the production of auxins, phosphate, and potassium solubilization, the production of siderophores, and the inhibition of the phytopathogen Pyricularia oryzae. The inoculation of strains of Pantoea sp. and Pseudomonas spp. in rice improves the height, root length, fresh weight, and dry weight of the shoot and root after 21 days post-inoculation in hydroponic assays. This study constitutes the first report on Cuban rice cultivars about the presence of endophytes in seeds and their potential to promote seedling growth. Pantoea sp. S5-1, Pseudomonas sp. S5-38, and Pseudomonas sp. S7-1 were selected as the more promising strains for the development of bio-stimulators or bio-inoculants for Cuban rice crops.

Endophytic bacteria isolated from Urtica dioica L.- preliminary screening for enzyme and polyphenols production

Endophytes, especially those isolated from herbal plants, may act as a reservoir of a variety of secondary metabolites exhibiting biological activity. Some endophytes express the ability to produce the same bioactive compounds as their plant hosts, making them a more sustainable industrial supply of these substances. Urtica dioica L. (common stinging nettle) is a synanthropic plant that is widely used in herbal medicine due to the diversity of bioactive chemicals it contains, e.g., polyphenols, which demonstrate anti-inflammatory, antioxidant, and anti-cancerous capabilities. This study aimed at isolating endophytic bacteria from stinging nettles for their bioactive compounds. The endophytic isolates were identified by both biochemical and molecular methods (16S rRNA) and investigated for enzymes, biosurfactants, and polyphenols production. Each of the isolated bacterial strains was capable of producing biosurfactants and polyphenols. However, three of the isolated endophytes, identified as two strains of Bacillus cereus and one strain of Bacillus mycoides, possessed the greatest capacity to produce biosurfactants and polyphenols. The derivatized extracts from culture liquid showed the 1.633 mol l-1 (9.691 mg l-1) concentration of polyphenol compounds. Therefore, the present study signifies that endophytic B. cereus and B. mycoides isolated from Urtica dioica L. could be a potential source of biosurfactants and polyphenols. However, further study is required to understand the mechanism of the process and achieve efficient polyphenol production by endophytic bacteria.

Characterization of the endophytic bacterial community of Bituminaria bituminosa plant grown in vitro and its interaction with the plant extract

INTRODUCTION

Bituminaria bituminosa is a medicinal plant recognized for its phytochemicals, such as furanocoumarins, pterocarpans, and flavonoids. Since the secondary metabolism is influenced by the plant-endophyte interactions, the endophytic bacterial community of B. bituminosa was explored and the possible interactions with the plant were described.

MATERIALS AND METHODS

Different bacterial strains were isolated from different organs of in vitro plants as shoots, roots, and seeds. The bacterial strains were identified and phenotypically characterized for different traits; strains were also exposed to different concentrations of B. bituminosa plant extract showing different susceptibility, probably determined by different secondary metabolites produced by the plant in the different organs (i.e. aerial parts and roots).

RESULTS AND DISCUSSION

Bacterial strains showed different phenotypic characteristics; the 6 detected haplotypes were dominated by a single species related to Stenotrophomonas rhizophila. Endophytes isolated from the aerial parts produced a higher indole-3-acetic acid (IAA) amount than those of the roots, while all strains were unable to produce biosurfactants and antagonistic activity toward the other strains. The research opens new perspectives for future analysis addressed to test the susceptibility of the endophytic bacterial community of B. bituminosa toward the pure compounds extracted from the plants, and to investigate the role of these compounds on the distribution of endophytes within the different plant tissues.

Endophytic Bacteria Associated with Origanum heracleoticum L. (Lamiaceae) Seeds

Seed-associated microbiota are believed to play a crucial role in seed germination, seedling establishment, and plant growth and fitness stimulation, due to the vertical transmission of a core microbiota from seeds to the next generations. It might be hypothesized that medicinal and aromatic plants could use the seeds as vectors to vertically transfer beneficial endophytes, providing plants with metabolic pathways that could influence phytochemicals production. Here, we investigated the localization, the structure and the composition of the bacterial endophytic population that resides in Origanum heracleoticum L. seeds. Endocellular bacteria, surrounded by a wall, were localized close to the aleurone layer when using light and transmission electron microscopy. From surface-sterilized seeds, cultivable endophytes were isolated and characterized through RAPD analysis and 16S RNA gene sequencing, which revealed the existence of a high degree of biodiversity at the strain level and the predominance of the genus Pseudomonas. Most of the isolates grew in the presence of six selected antibiotics and were able to inhibit the growth of clinical and environmental strains that belong to the Burkholderia cepacia complex. The endophytes production of antimicrobial compounds could suggest their involvement in plant secondary metabolites production and might pave the way to endophytes exploitation in the pharmaceutical field.

Mixed growth of Salix species can promote phosphate-solubilizing bacteria in the roots and rhizosphere

Phosphorus (P) is an essential plant nutrient that can limit plant growth due to low availability in the soil. P-solubilizing bacteria in the roots and rhizosphere increase the P use efficiency of plants. This study addressed the impact of plant species, the level of plant association with bacteria (rhizosphere or root endophyte) and environmental factors (e.g., seasons, soil properties) on the abundance and diversity of P-solubilizing bacteria in short-rotation coppices (SRC) of willows (Salix spp.) for biomass production. Two willow species (S. dasycladoscv. Loden and S. schwerinii × S. viminalis cv. Tora) grown in mono-and mixed culture plots were examined for the abundance and diversity of bacteria in the root endosphere and rhizosphere during two seasons (fall and spring) in central Sweden and northern Germany. Soil properties, such as pH and available P and N, had a significant effect on the structure of the bacterial community. Microbiome analysis and culture-based methods revealed a higher diversity of rhizospheric bacteria than endophytic bacteria. The P-solubilizing bacterial isolates belonged mainly to Proteobacteria (85%), Actinobacteria (6%) and Firmicutes (9%). Pseudomonas was the most frequently isolated cultivable bacterial genus from both the root endosphere and the rhizosphere. The remaining cultivable bacterial isolates belonged to the phyla Actinobacteria and Firmicutes. In conclusion, site-specific soil conditions and the level of plant association with bacteria were the main factors shaping the bacterial communities in the willow SRCs. In particular, the concentration of available P along with the total nitrogen in the soil controlled the total bacterial diversity in willow SRCs. A lower number of endophytic and rhizospheric bacteria was observed in Loden willow species compared to that of Tora and the mix of the two, indicating that mixed growth of Salix species promotes P-solubilizing bacterial diversity and abundance. Therefore, a mixed plant design was presented as a management option to increase the P availability for Salix in SRCs. This design should be tested for further species mixtures.

Effects of Seed Endophytic Bacteria on Life History and Reproductive Traits in a Cosmopolitan Weed, Capsella bursa-pastoris

Diverse bacteria inhabit plant seeds, and at least some of them can enhance plant performance at the early developmental stage. However, it is still inconclusive whether seed bacteria can influence post-germination traits and their contribution to plant fitness. To explore the evolutionary and ecological consequences of seed endophytic bacteria, we isolated four bacterial strains from the seeds of an annual weedy plant species, Capsella bursa-pastoris, and conducted a common garden experiment using seeds inoculated by isolated bacteria. Seeds infected by bacteria tended to germinate in spring rather than in autumn. Bacterial treatment also altered the expression of plant life history and reproductive traits, including flowering dates, rosette diameter at bolting, number of inflorescences, and fruit production. The results of the path analyses suggested that such effects of bacterial treatments were due to bacterial inoculation as well as germination delayed until spring. Spring germinants with bacterial infection showed a weaker association between post-germination traits and relative fitness than those without bacterial infection. These results suggest that seed bacteria likely affect the expression of post-germination traits directly or indirectly by delaying the germination season. An altered contribution of plant traits to relative fitness implies the influence of seed bacteria on the strength of natural selection.

Characterization of the Cultivable Endophytic Bacterial Community of Seeds and Sprouts of Cannabis sativa L. and Perspectives for the Application as Biostimulants

Endophytes are beneficial microorganisms exerting growth-promoting activities in plants; they are most often located within the plant intercellular spaces and can be found in all plant tissues, including roots, leaves, stems, flowers, and seeds. In this work, we investigated the cultivable bacterial community of the seeds and the two-week sprouts of the Cannabis sativa L. cultivar “Futura 75”. Endophytes were genotypically and phenotypically characterized and were exposed to different concentrations of seed extracts to verify their susceptibility. A bacterial strain among all the isolates was selected for germination tests of C. sativa in different experimental conditions. The results revealed the dominance of Firmicutes (Staphylococcus sp.) among the isolated strains. Two strains were different from the others for indole-3-acetic acid (IAA) production and for their resistance patterns towards abiotic and biotic stresses. The Sphingomonas sp. strain Can_S11 (Alphaproteobacteria) showed a potential ability to increase the nutraceutical features of its sprouts, particularly an increase in the polyphenol content and antioxidant activity. None of the isolated strains were susceptible to the seed extracts, which were previously tested as antimicrobial and antibiofilm agents against human pathogenic bacteria. The results open new perspectives for the study of the endophytes of C. sativa as possible biostimulants.

Chickpea (Cicer arietinum L.) Seeds as a Reservoir of Endophytic Plant Growth-Promoting Bacteria

The seed microbiome, the primary source of inoculum for plants, may play an important role in plant growth, health and productivity. However, the structure and function of chickpea seed endophytes are poorly characterized. Bacteria with beneficial characteristics can be selected by the plant and transmitted vertically via the seed to benefit the next generation. Studying the diversity and multifunctionality of seed microbial communities can provide innovative opportunities in the field of plant-microbe interaction. This study aimed to isolate, identify and characterize culturable endophytic bacteria from chickpea (Cicer arietinum L.) seeds. Phylogenetic analysis based on 16S rDNA showed that the endophytic bacteria belong to the genera Mesorhizobium, Burkholderia, Bacillus, Priestia, Paenibacillus, Alcaligenes, Acinetobacter, Rahnella, Enterobacter, Tsukamurella, and Microbacterium. The most frequently observed genus was Bacillus; however, rhizobia typically associated with chickpea roots were also found, which is a novel finding of this study. Siderophore production and phosphorus solubilization were the most widespread plant growth-promoting features, while hydrogen cyanide production was relatively rare among the isolates. Most of the isolates possess two or more plant growth-promoting features; however, only Bacillus thuringiensis Y2B, a well-known entomopathogenic bacteria, exhibited the presence of all plant growth-promoting traits evaluated. Results suggest that endophytic bacteria such as Bacillus, Mesorhizobium, and Burkholderia may be vertically transferred from inoculated plants to seeds to benefit the next generation.

The bacterial world inside the plant

Sustainable agriculture requires the recruitment of bacterial agents to reduce the demand for mineral fertilizers and pesticides such as bacterial endophytes. Bacterial endophytes represent a potential alternative to the widespread use of synthetic fertilizers and pesticides in conventional agriculture practices. Endophytes are formed by complex microbial communities and microorganisms that colonize the plant interior for at least part of their life. Their functions range from mutualism to pathogenicity. Bacterial endophytes colonize plant tissues, and their composition and diversity depend on many factors, including the plant organ, physiological conditions, plant growth stage, and environmental conditions. The presence of endophytes influences several vital activities of the host plant. They can promote plant growth, elicit a defense response against pathogen attack, and lessen abiotic stress. Despite their potential, especially with regard to crop production and environmental sustainability, research remains sparse. This review provides an overview of the current research, including the concept of endophytes, endophytes in plant organs, endophyte colonization, nutrient efficiency use, endophytes and crop nutrition, inoculation with synergistic bacteria, the effect of inoculum concentration on plant root microbiota and synthetic communities. It also examines the practical opportunities and challenges when utilizing endophytes in the field of sustainable agriculture. Finally, it explores the importance of these associations with regard to the future of agriculture and the environment.

Microbial Metabolites Beneficial to Plant Hosts Across Ecosystems

Plants are intimately connected with their associated microorganisms. Chemical interactions via natural products between plants and their microbial symbionts form an important aspect in host health and development, both in aquatic and terrestrial ecosystems. These interactions range from negative to beneficial for microbial symbionts as well as their hosts. Symbiotic microbes synchronize their metabolism with their hosts, thus suggesting a possible coevolution among them. Metabolites, synthesized from plants and microbes due to their association and coaction, supplement the already present metabolites, thus promoting plant growth, maintaining physiological status, and countering various biotic and abiotic stress factors. However, environmental changes, such as pollution and temperature variations, as well as anthropogenic-induced monoculture settings, have a significant influence on plant-associated microbial community and its interaction with the host. In this review, we put the prominent microbial metabolites participating in plant-microbe interactions in the natural terrestrial and aquatic ecosystems in a single perspective and have discussed commonalities and differences in these interactions for adaptation to surrounding environment and how environmental changes can alter the same. We also present the status and further possibilities of employing chemical interactions for environment remediation. Our review thus underlines the importance of ecosystem-driven functional adaptations of plant-microbe interactions in natural and anthropogenically influenced ecosystems and their possible applications.

Salicylic Acid in Plant Symbioses: Beyond Plant Pathogen Interactions

Plants form beneficial symbioses with a wide variety of microorganisms. Among these, endophytes, arbuscular mycorrhizal fungi (AMF), and nitrogen-fixing rhizobia are some of the most studied and well understood symbiotic interactions. These symbiotic microorganisms promote plant nutrition and growth. In exchange, they receive the carbon and metabolites necessary for their development and multiplication. In addition to their role in plant growth and development, these microorganisms enhance host plant tolerance to a wide range of environmental stress. Multiple studies have shown that these microorganisms modulate the phytohormone metabolism in the host plant. Among the phytohormones involved in the plant defense response against biotic environment, salicylic acid (SA) plays an important role in activating plant defense. However, in addition to being a major actor in plant defense signaling against pathogens, SA has also been shown to be involved in plant-microbe symbiotic interactions. In this review, we summarize the impact of SA on the symbiotic interactions. In addition, we give an overview of the impact of the endophytes, AMF, and rhizobacteria on SA-mediated defense response against pathogens.

Bacterial Community Structure and Potential Microbial Coexistence Mechanism Associated with Three Halophytes Adapting to the Extremely Hypersaline Environment

Halophytes play a crucial ecological role in drought and saline-alkali environments. However, there is limited knowledge about the structure of bacterial communities and the potential microbial coexistence mechanism associated with halophytes. This study investigated the diversity and community structure of endophytic and rhizospheric bacteria associated with three halophytes by applying high-throughput sequencing and geochemistry analyses on the studied soils. We collected 18 plant and 21 soil samples, and sequenced the V3 and V4 hypervariable regions of the 16S rRNA gene using next-generation sequencing (NGS). We also assessed geochemistry of the studied soils. The research suggested that rhizospheric bacterial richness and diversity associated with three halophytes were all significantly higher than for endophytic bacteria. The microbial community analysis indicated that Actinobacteria, Firmicutes, Bacteroidetes and Proteobacteria were the dominating bacterial phyla. Most unassigned operational taxonomic units (OTUs) implied that the microbes associated with halophytes contained abundant potential novel taxa, which are significant microbial resources. The high-abundance OTU phylogenetic tree supported the above views as well. Additionally, network analysis indicated that some conditional rare taxa (CRT) also might be keystone taxa during halophyte microbial community construction. The results of non-metric multidimensional scaling (NMDS) ordination analysis indicated significant dissimilarities in the microbial community among different sample groups. Sixty-two biomarkers were detected from seven different sample groups by linear discriminant analysis effect size (LEFSe) analysis. Microbial functions predicted based on phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) demonstrated that the abundances of nitrogen metabolism genes of endophytic bacteria were significantly higher than in rhizobacteria. Environmental factor analysis confirmed that different soil properties have different degrees of influence on the abundance and composition of the microbiota. To better adapt to the extreme hypersaline environment, halophytes could specifically recruit some plant beneficial bacterial taxa, such as nitrogen-fixing bacteria and extremely halophilic or halotolerant bacteria, to help them robustly grow and proliferate. All our preliminary results highlight microbial diversity and community related to halophytes grown on saline-alkali land of arid areas. Simultaneously, this work also advanced our further understanding of the halophyte microbiome associated with plants, and their role in plant adaptation to the extremely hypersaline environment.

A Meta-Analysis Approach to Defining the Culturable Core of Plant Endophytic Bacterial Communities

Endophytic bacteria are key members of the plant microbiome, which phylogenetic diversity has been widely described through next-generation sequencing technologies in the last decades. On the other side, a synopsis of culturable plant endophytic bacteria is still lacking in the literature. However, culturability is necessary for biotechnology innovations related to sustainable agriculture, such as biofertilizer and biostimulant agents' development. In this review, 148 scientific papers were analyzed to establish a large data set of cultured endophytic bacteria, reported at the genus level, inhabiting different compartments of wild and farmed plants, sampled around the world from different soil types and isolated using various growth media. To the best of our knowledge, this work provides the first overview of the current repertoire of cultured plant endophytic bacteria. Results indicate the presence of a recurrent set of culturable bacterial genera regardless of factors known to influence the plant bacterial community composition and the growth media used for the bacterial isolation. Moreover, a wide variety of bacterial genera that are currently rarely isolated from the plant endosphere was identified, demonstrating that culturomics can catch previously uncultured bacteria from the plant microbiome, widening the panorama of strains exploitable to support plant holobiont health and production.

Diversity of endophytic bacteria in hybrid maize seeds and Bacillus mojavensis J2416-7 may be capable of vertical transmission

The diversity of endophytic bacteria in the progeny is related to the parental lines. In this study, the traditional separation method was used to study the dominant endophytic bacteria of the shared paternal line and its pollen, different maternal lines and their F1 progeny. And the results showed that the dominant endophytic bacteria in maize seeds and the pollen were Bacillus and Pantoea. The Bacillus diversity of the progeny JMC121 and JN728 were the same as both the paternal line and the maternal line, including Bacillus subtilis, Bacillus velezensis, Bacillus mojavensis, and Bacillus licheniformis. The Bacillus subtilis and Bacillus velezensis in JN828 were the same as both the paternal line and the maternal line, while Bacillus licheniformis was only the same as the paternal line. Through the RAPD molecular typing, there was the same strain of Bacillus mojavensis existed in the paternal line J2416, the pollen and the progeny JN728; this meant that the paternal line passed its dominant endophytic bacteria to the progeny through pollen in vertical transmission. This study showed that the dominant endophytic bacteria in maize seeds and the pollen were Bacillus, and the diversity of F1 progeny was related to both the paternal line and the maternal line.

Modulation of the Wheat Seed-Borne Bacterial Community by Herbaspirillum seropedicae RAM10 and Its Potential Effects for Tryptophan Metabolism in the Root Endosphere

Plants and their associated microbiota share ecological and evolutionary traits that are considered to be inseparably woven. Their coexistence foresees the use of similar metabolic pathways, leading to the generation of molecules that can cross-regulate each other’s metabolism and ultimately influence plant phenotype. However, the extent to which the microbiota contributes to the overall plant metabolic landscape remains largely unexplored. Due to their early presence in the seed, seed-borne endophytic bacteria can intimately colonize the plant’s endosphere while conferring a series of phytobeneficial services to their host. Understanding the dynamics of these endophytic communities is a crucial step toward the formulation of microbial inoculants that can modulate the functionality of the plant-associated microbiota for improved plant fitness. In this work, wheat (Triticum aestivum) roots non-inoculated and inoculated with the bacterium Herbaspirillum seropedicae strain RAM10 were analyzed to explore the impact of inoculant–endophyte–wheat interrelationships on the regulation of tryptophan (Trp) metabolism in the endosphere environment. Root inoculation with H. seropedicae led to phylum-specific changes in the cultivable seed-borne endophytic community. This modulation shifted the metabolic potential of the community in light of its capacity to modulate the levels of key Trp-related metabolites involved in both indole-3-acetic acid (IAA) biosynthesis and in the kynurenine pathway. Our results support a mode of action of H. seropedicae relying on a shift in both the composition and functionality of the seed-borne endophytic community, which may govern important processes such as root growth. We finally provide a conceptual framework illustrating that interactions among roots, inoculants, and seed-borne endophytes are critical to fine-tuning the levels of IAA in the endosphere. Understanding the outcomes of these interactions is a crucial step toward the formulation of microbial inoculants based on their joint action with seed-borne endophytic communities to promote crop growth and health in a sustainable manner.

Reconstitution and Transmission of Gut Microbiomes and Their Genes between Generations

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

Seed inhabiting bacterial endophytes of maize promote seedling establishment and provide protection against fungal disease

Bacteria from different crops and plant varieties have been shown to possess enormous growth promotional attributes. The study aimed to investigate the role of the endophytic microbiome of seeds of corn in improving the growth of seedlings of two different varieties of maize crops (K-25 and baby corn). Furthermore, the study also assessed the role of these bacteria in the protection of seedlings from fungal pathogens. Total twenty-three endophytic bacterial strains were isolated from maize seeds and identified using 16S rDNA sequencing. Most of the isolates had the ability to synthesize auxin (70 %) and solubilize phosphate (74 %), while all the isolates showed nitrogen fixation ability. Some isolates also showed antagonistic activity against phytopathogenic fungi including Rhizoctonia solani and Fusarium sp. suggesting their biocontrol potential. The presence of different lipopeptide genes including bacillomycin D, fengycin, iturin A and surfactin was confirmed in some of the isolates. We observed that treating seeds with an antibiotic compromised the seedlings' growth; however, re-inoculation with endophytic isolates (ZM1/Lysinibacillus sp. and ZM2/Paenibacillus dendritiformis) restored the growth of the seedlings in terms of improved root and shoot development in comparison to non-inoculated controls. The colonization of inoculated bacteria on the root surface was visualized using fluorescent microscopy. Seedling protection assay showed that treated seeds (with ZMW8/ Bacillus velezensis) were protected from fungal infestation (Fusarium verticillioides) even after 12 days of inoculation in comparison to the uninoculated control. The study concludes that indigenous seed-associated bacteria of maize play a major role during seed germination, seedling formation and protect them from phytopathogens.

Humic Substances in Combination With Plant Growth-Promoting Bacteria as an Alternative for Sustainable Agriculture

Plant growth-promoting bacteria (PGPB) and humic substances (HSs) are promising options for reducing the use of pesticides and mineral fertilizers. Although many studies have shown the effects of PGPB and HSs separately, little information is available on plant responses to the combined application of these biostimulants despite the great potential for the simultaneous action of these biological inputs. Thus, the objective of this review is to present an overview of scientific studies that addressed the application of PGPB and HSs to different crops. First, we discuss the effect of these biostimulants on biological nitrogen fixation, the various effects of the inoculation of beneficial bacteria combined with the application of HSs on promoting the growth of nonleguminous plants and how this combination can increase bacterial colonization of plant hosts. We also address the effect of PGPB and HSs on plant responses to abiotic stresses, in addition to discussing the role of HSs in protecting plants against pathogens. There is a lack of studies that address the role of PGPB + HSs in biocontrol. Understanding the factors involved in the promotion of plant growth through the application of PGPB and HSs can assist in the development of efficient biostimulants for agricultural management. This approach has the potential to accelerate the transition from conventional cultivation to sustainable agrosystems.

Ecological strategies of biological and chemical control agents on wildfire disease of tobacco (Nicotiana tabacum L.)

BACKGROUND

To investigate the ecological effects of chemical and biological control methods on tobacco wildfire disease, a plot field experiment was conducted to compare the control efficiency and mechanisms of a chemical pesticide (kasugamycin wettable powder, KWP) and a biological control agent (BCA) through high-throughput sequencing of bacterial 16S rRNA genes.

RESULTS

The results showed that the BCA displayed better performance in decreasing the disease index and morbidity of tobacco than the chemical pesticide. By monitoring the endophytic community within tobacco leaves, it was found that the control effects of these two methods might be mediated by different changes in the endophytic bacterial communities and community assembly patterns. The application of either method decreased the taxonomic diversity of the leaf endophytic community. Compared to the BCA, KWP showed a more significant effect on the endophytic community structure, while the endophytic community treated with the BCA was able to return to the original state, which presented much lower disease infection. The disease control efficiency of KWP and BCA treatments might be achieved by increasing the abundance of Sphingomonas and Streptophyta, respectively. Furthermore, an analysis of the ecological processes in community assembly indicated that the BCA strengthened the homogeneous and variable selection, while KWP enhanced ecological drift.

CONCLUSIONS

The results suggested different control mechanisms between KWP and BCA treatments, which will help in developing diverse ecological strategies for plant disease control.

Herbaspirillum seropedicae strain HRC54 expression profile in response to sugarcane apoplastic fluid

Bacterial transcriptome profiling in the presence of plant fluids or extracts during microbial growth may provide relevant information on plant-bacteria interactions. Here, RNA sequencing (RNA-Seq) was used to determine the transcriptomic profile of Herbaspirillum seropedicae strain HRC54 at the early stages of response to sugarcane apoplastic fluid. Differentially expressed gene (DEG) analysis was performed using the DESeq2 and edgeR packages, followed by functional annotation using Blast2GO and gene ontology enrichment analysis using the COG and KEGG databases. After 2 h of sugarcane apoplastic fluid addition to the H. seropedicae HRC54 culture, respectively, 44 and 45 genes were upregulated and downregulated. These genes were enriched in bacterial metabolism (e.g., oxidoreductase and transferase), ABC transporters, motility, secretion systems, and signal transduction. RNA-Seq expression profiles of 12 genes identified in data analyses were verified by RT-qPCR. The results suggested that H. seropedicae HRC54 recognized sugarcane apoplastic fluid as the host signal, and some DEGs were closely involved at the early stages of the establishment of plant-bacteria interactions.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02848-y.

Bacteriophage-Mediated Control of Phytopathogenic Xanthomonads: A Promising Green Solution for the Future

Xanthomonads, members of the family Xanthomonadaceae, are economically important plant pathogenic bacteria responsible for infections of over 400 plant species. Bacteriophage-based biopesticides can provide an environmentally friendly, effective solution to control these bacteria. Bacteriophage-based biocontrol has important advantages over chemical pesticides, and treatment with these biopesticides is a minor intervention into the microflora. However, bacteriophages’ agricultural application has limitations rooted in these viruses’ biological properties as active substances. These disadvantageous features, together with the complicated registration process of bacteriophage-based biopesticides, means that there are few products available on the market. This review summarizes our knowledge of the Xanthomonas-host plant and bacteriophage-host bacterium interaction’s possible influence on bacteriophage-based biocontrol strategies and provides examples of greenhouse and field trials and products readily available in the EU and the USA. It also details the most important advantages and limitations of the agricultural application of bacteriophages. This paper also investigates the legal background and industrial property right issues of bacteriophage-based biopesticides. When appropriately applied, bacteriophages can provide a promising tool against xanthomonads, a possibility that is untapped. Information presented in this review aims to explore the potential of bacteriophage-based biopesticides in the control of xanthomonads in the future.