Synthesis of phytohormones by plant-associated bacteria

Indole-3-acetic acid (IAA) protects Azospirillum brasilense from indole-induced stress

Azospirillum brasilense is plant-growth promoting rhizobacteria that produces the phytohormone indole-3-acetic acid (IAA) to induce changes in plant root architecture. The major pathway for IAA biosynthesis in A. brasilense converts tryptophan into indole-3-pyruvic acid (I3P) and then, through the rate-limiting enzyme, indole-3-pyruvate decarboxylase (IpdC), into IAA. Here, we characterize the potential role for IAA biosynthesis in the physiology of these bacteria by characterizing the expression pattern of the ipdC promoter, analyzing an A. brasilense ipdC mutant using multiple physiological assays and characterizing the effect of I3P, which likely accumulates in the absence of ipdC and affects bacterial physiology. We found that the ipdC mutant derivative has a reduced growth rate and an altered physiology, including reduced translation activity as well as a more depolarized membrane potential compared to the parent strain. Similar effects could be recapitulated in the parent strain by exposing these cells to increasing concentrations of I3P, as well as other indole intermediates of IAA biosynthesis. Our results also indicate a protective role for IAA against the harmful effects of indole derivatives, with exogenous IAA restoring the membrane potential of cells exposed to indole derivatives for prolonged periods. These protective effects appeared to restore cell physiology, including in the wheat rhizosphere. Together, our data suggest that the IAA biosynthesis pathway plays a major role in A. brasilense physiology by maintaining membrane potential homeostasis and regulating translation, likely to mitigate the potential membrane-damaging effects of indoles that accumulate during growth under stressful conditions.IMPORTANCEIAA is widely synthesized in bacteria, particularly in soil and rhizosphere bacteria, where it functions as a phytohormone to modulate plant root architecture. IAA as a secondary metabolite has been shown to serve as a signaling molecule in several bacterial species, but the role of IAA biosynthesis in the physiology of the producing bacterium remains seldom explored. Results obtained here suggest that IAA serves to protect A. brasilense from the toxic effect of indoles, including metabolite biosynthetic precursors of IAA, on membrane potential homeostasis. Given the widespread production of IAA in soil bacteria, this protective effect of IAA may be conserved in diverse soil bacteria.

Culture-dependent and -independent analyses reveal unique community structure and function in the external mycelial cortices of Ophiocordyceps sinensis

Ophiocordyceps sinensis, also known as DongChong XiaCao (DCXC) in China, is a complex of the parasitic fungus Hirsutella sinensis and its caterpillars host living in extreme alpine environments on the Qinghai-Tibetan Plateau. Wild resources of O. sinensis are threatened by over-harvesting due to its perceived high medicinal value. In recent years, numerous studies have pointed out that endofungal bacteria play an important role in fungal spore germination and zygote formation. In this sense, studying the endofungal bacteria of O. sinensis is of great interest regarding the conservation of this species. In this study, we investigated the community structure (abundance and rare sub-communities) and function of the soil-mycelial-sclerotia-stromata continuum endofungal bacteria in O. sinensis from the Qilian Mountain region of the Tibetan Plateau by using amplicon and macro-genome sequencing technologies. Based on the results, rare taxa exhibited more differences among the components, and enrichment and co-occurrence network analyses revealed that abundant taxa played a more important role. We further found that endofungal bacteria in external mycelial cortices have unique community structures and functions. In particular, they play an important role in material cycling, potentially providing essential nutrients during the lifecycle of O. sinensis. We successfully isolated 52 endofungal bacterial strains using high-throughput isolation techniques, some of them were undetected by high-throughput sequencing. We systematically investigated the structure and function of endofungal bacteria of the O. sinensis, providing a solid foundation for the cultivation and conservation of wild resources of this species at an industrial scale.

Standardizing experimental approaches to investigate interactions between bacteria and ectomycorrhizal fungi

Bacteria and ectomycorrhizal fungi (EcMF) represent two of the most dominant plant root-associated microbial groups on Earth, and their interactions continue to gain recognition as significant factors that shape forest health and resilience. Yet, we currently lack a focused review that explains the state of bacteria-EcMF interaction research in the context of experimental approaches and technological advancements. To these ends, we illustrate the utility of studying bacteria-EcMF interactions, detail outstanding questions, outline research priorities in the field, and provide a suite of approaches that can be used to promote experimental reproducibility, field advancement, and collaboration. Though this review centers on the ecology of bacteria, EcMF, and trees, it by default offers experimental and conceptual insights that can be adapted to various subfields of microbiology and microbial ecology.

Modulation of fungal phosphate homeostasis by the plant hormone strigolactone

Inter-kingdom communication through small molecules is essential to the coexistence of organisms in an ecosystem. In soil communities, the plant root is a nexus of interactions for a remarkable number of fungi and is a source of small-molecule plant hormones that shape fungal compositions. Although hormone signaling pathways are established in plants, how fungi perceive and respond to molecules is unclear because many plant-associated fungi are recalcitrant to experimentation. Here, we develop an approach using the model fungus, Saccharomyces cerevisiae, to elucidate mechanisms of fungal response to plant hormones. Two plant hormones, strigolactone and methyl jasmonate, produce unique transcript profiles in yeast, affecting phosphate and sugar metabolism, respectively. Genetic analysis in combination with structural studies suggests that SLs require the high-affinity transporter Pho84 to modulate phosphate homeostasis. The ability to study small-molecule plant hormones in a tractable genetic system should have utility in understanding fungal-plant interactions.

Mechanisms of ROS-mediated interactions between Bacillus aryabhattai LAD and maize roots to promote plant growth

BACKGROUND

Plant growth-promoting rhizobacteria (PGPR), as a group of environmentally friendly bacteria growing in the rhizosphere of plants, play an important role in plant growth and development and resistance to environmental stresses. However, their limited understanding has led to the fact that their large-scale use in agriculture is still scarce, and the mechanisms by which beneficial bacteria are selected by plants and how they interact with them are still unclear.

METHOD

In this study, we investigated the interaction between the auxin-producing strain Bacillus aryabhattai LAD and maize roots, and performed transcriptomic and metabolomic analyses of Bacillus aryabhattai LAD after treatment with maize root secretions(RS).

RESULTS

Our results show that there is a feedback effect between the plant immune system and bacterial auxin. Bacteria activate the immune response of plant roots to produce reactive oxygen species(ROS), which in turn stimulates bacteria to synthesize IAA, and the synthesized IAA further promotes plant growth. Under the condition of co-culture with LAD, the main root length, seedling length, root surface area and root volume of maize increased by 197%, 107%, 89% and 75%, respectively. In addition, the results of transcriptome metabolome analysis showed that LAD was significantly enriched in amino acid metabolism, carbohydrate metabolism and lipid metabolism pathways after RS treatment, including 93 differentially expressed genes and 45 differentially accumulated metabolites.

CONCLUSION

Our findings not only provide a relevant model for exploring the effects of plant-soil microbial interactions on plant defense functions and thereby promoting plant growth, but also lay a solid foundation for the future large-scale use of PGPR in agriculture for sustainable agricultural development.

Plant growth-promoting rhizobacterial secondary metabolites in augmenting heavy metal(loid) phytoremediation: An integrated green in situ ecorestorative technology

In recent times, increased geogenic and human-centric activities have caused significant heavy metal(loid) (HM) contamination of soil, adversely impacting environmental, plant, and human health. Phytoremediation is an evolving, cost-effective, environment-friendly, in situ technology that employs indigenous/exotic plant species as natural purifiers to remove toxic HM(s) from deteriorated ambient soil. Interestingly, the plant's rhizomicrobiome is pivotal in promoting overall plant nutrition, health, and phytoremediation. Certain secondary metabolites produced by plant growth-promoting rhizobacteria (PGPR) directly participate in HM bioremediation through chelation/mobilization/sequestration/bioadsorption/bioaccumulation, thus altering metal(loid) bioavailability for their uptake, accumulation, and translocation by plants. Moreover, the metallotolerance of the PGPR and the host plant is another critical factor for the successful phytoremediation of metal(loid)-polluted soil. Among the phytotechniques available for HM remediation, phytoextraction/phytoaccumulation (HM mobilization, uptake, and accumulation within the different plant tissues) and phytosequestration/phytostabilization (HM immobilization within the soil) have gained momentum in recent years. Natural metal(loid)-hyperaccumulating plants have the potential to assimilate increased levels of metal(loid)s, and several such species have already been identified as potential candidates for HM phytoremediation. Furthermore, the development of transgenic rhizobacterial and/or plant strains with enhanced environmental adaptability and metal(loid) uptake ability using genetic engineering might open new avenues in PGPR-assisted phytoremediation technologies. With the use of the Geographic Information System (GIS) for identifying metal(loid)-impacted lands and an appropriate combination of normal/transgenic (hyper)accumulator plant(s) and rhizobacterial inoculant(s), it is possible to develop efficient integrated phytobial remediation strategies in boosting the clean-up process over vast regions of HM-contaminated sites and eventually restore ecosystem health.

Isolation of bacteria with plant growth-promoting properties from microalgae-bacterial flocs produced in high-rate oxidation ponds

Exploring plant growth-promoting (PGP) bacterial activity of microbial components aggregated by wastewater treatment can reduce dependence on fossil fuel-derived fertilisers. This study describes the isolation and identification of bacteria from microalgae-bacteria flocs (MaB-flocs) generated in high-rate algal oxidation ponds (HRAOP) of an integrated algal pond system (IAPS) remediating municipal wastewater. Amplified 16S rRNA gene sequence analysis determined the molecular identity of the individual strains. Genetic relatedness to known PGP rhizobacteria in the NCBI GenBank database was by metagenomics. Isolated strains were screened for the production of indoles (measured as indole-3-acetic acid; IAA) and an ability to mineralise NH 4 + , PO 4 3 - , and K + . Of the twelve bacterial strains isolated from HRAOP MaB-flocs, four produced indoles, nine mineralised NH 4 + , seven solubilised P, and one K. Potential of isolated strains for PGP activity according to one-way ANOVA on ranks was: ECCN 7b > ECCN 4b > ECCN 6b > ECCN 3b = ECCN 10b > ECCN 1b = ECCN 5b > ECCN 8b > ECCN 2b > ECCN 12b > ECCN 9b = ECCN 11b. Further study revealed that cell-free filtrate from indole-producing cultures of Aeromonas strain ECCN 4b, Enterobacter strain ECCN 7b, and Arthrobacter strain ECCN 6b promoted mung bean adventitious root formation suggestive of the presence of auxin-like biological activity.

Expanding the Pseudomonas diversity of the wheat rhizosphere: four novel species antagonizing fungal phytopathogens and with plant-beneficial properties

Plant-beneficial Pseudomonas bacteria hold the potential to be used as inoculants in agriculture to promote plant growth and health through various mechanisms. The discovery of new strains tailored to specific agricultural needs remains an open area of research. In this study, we report the isolation and characterization of four novel Pseudomonas species associated with the wheat rhizosphere. Comparative genomic analysis with all available Pseudomonas type strains revealed species-level differences, substantiated by both digital DNA-DNA hybridization and average nucleotide identity, underscoring their status as novel species. This was further validated by the phenotypic differences observed when compared to their closest relatives. Three of the novel species belong to the P. fluorescens species complex, with two representing a novel lineage in the Pseudomonas phylogeny. Functional genome annotation revealed the presence of specific features contributing to rhizosphere colonization, including flagella and components for biofilm formation. The novel species have the genetic potential to solubilize nutrients by acidifying the environment, releasing alkaline phosphatases and their metabolism of nitrogen species, indicating potential as biofertilizers. Additionally, the novel species possess traits that may facilitate direct promotion of plant growth through the modulation of the plant hormone balance, including the ACC deaminase enzyme and auxin metabolism. The presence of biosynthetic clusters for toxins such as hydrogen cyanide and non-ribosomal peptides suggests their ability to compete with other microorganisms, including plant pathogens. Direct inoculation of wheat roots significantly enhanced plant growth, with two strains doubling shoot biomass. Three of the strains effectively antagonized fungal phytopathogens (Thielaviopsis basicola, Fusarium oxysporum, and Botrytis cinerea), demonstrating their potential as biocontrol agents. Based on the observed genetic and phenotypic differences from closely related species, we propose the following names for the four novel species: Pseudomonas grandcourensis sp. nov., type strain DGS24T ( = DSM 117501T = CECT 31011T), Pseudomonas purpurea sp. nov., type strain DGS26T ( = DSM 117502T = CECT 31012T), Pseudomonas helvetica sp. nov., type strain DGS28T ( = DSM 117503T = CECT 31013T) and Pseudomonas aestiva sp. nov., type strain DGS32T ( = DSM 117504T = CECT 31014T).

The underground world of plant disease: Rhizosphere dysbiosis reduces above-ground plant resistance to bacterial leaf spot and alters plant transcriptome

Just as the human gut microbiome is colonized by a variety of microbes, so too is the rhizosphere of plants. An imbalance in this microbial community, known as dysbiosis, can have a negative impact on plant health. This study sought to explore the effect of rhizosphere dysbiosis on the health of tomato plants (Solanum lycopersicum L.), using them and the foliar bacterial spot pathogen Xanthomonas perforans as model organisms. The rhizospheres of 3-week-old tomato plants were treated with either streptomycin or water as a control, and then spray-inoculated with X. perforans after 24 h. Half of the plants that were treated with both streptomycin and X. perforans received soil microbiome transplants from uninfected plant donors 48 h after the streptomycin was applied. The plants treated with streptomycin showed a 26% increase in disease severity compared to those that did not receive the antibiotic. However, the plants that received the soil microbiome transplant exhibited an intermediate level of disease severity. The antibiotic-treated plants demonstrated a reduced abundance of rhizobacterial taxa such as Cyanobacteria from the genus Cylindrospermum. They also showed a down-regulation of genes related to plant primary and secondary metabolism, and an up-regulation of plant defence genes associated with induced systemic resistance. This study highlights the vital role that beneficial rhizosphere microbes play in disease resistance, even against foliar pathogens.

The Plant-Associated Flavobacterium: A Hidden Helper for Improving Plant Health

Flavobacterium is a genus within the phylum Bacteroidota that remains relatively unexplored. Recent analyses of plant microbiota have identified the phylum Bacteroidota as a major bacterial group in the plant rhizosphere. While Flavobacterium species within the phylum Bacteroidota have been recognized as pathogens in the aquatic habitats, microbiome analysis and the characterization of novel Flavobacterium species have indicated the great diversity and potential of their presence in various environments. Many Flavobacterium species have positively contribute to plant health and development, including growth promotion, disease control, and tolerance to abiotic stress. Despite the well-described beneficial interactions of the Flavobacterium species with plants, the molecular mechanisms and bacterial determinants underlying these interactions remain unclear. To broaden our understanding of the genus Flavobacterium's role in plant health, we review the recent studies focusing on their ecological niche, functional roles, and determinants in plant-beneficial interactions. Additionally, this review discusses putative mechanisms explaining the interactions between plants and Flavobacterium. We have also introduced the importance of future research on Flavobacterium spp. and its potential applications in agriculture.

Bacteria from the skin of amphibians promote growth of Arabidopsis thaliana and Solanum lycopersicum by modifying hormone-related transcriptome response

Plants and microorganisms establish beneficial associations that can improve their development and growth. Recently, it has been demonstrated that bacteria isolated from the skin of amphibians can contribute to plant growth and defense. However, the molecular mechanisms involved in the beneficial effect for the host are still unclear. In this work, we explored whether bacteria isolated from three tropical frogs species can contribute to plant growth. After a wide screening, we identified three bacterial strains with high biostimulant potential, capable of modifying the root structure of Arabidopsis thaliana plants. In addition, applying individual bacterial cultures to Solanum lycopersicum plants induced an increase in their growth. To understand the effect that these microorganisms have over the host plant, we analysed the transcriptomic profile of A. thaliana during the interaction with the C32I bacterium, demonstrating that the presence of the bacteria elicits a transcriptional response associated to plant hormone biosynthesis. Our results show that amphibian skin bacteria can function as biostimulants to improve agricultural crops growth and development by modifying the plant transcriptomic responses.

The plant growth promoting rhizobacterium Achromobacter sp. 5B1, rescues Arabidopsis seedlings from alkaline stress by enhancing root organogenesis and hormonal responses

Soil alkalinity is a critical environmental factor for plant growth and distribution in ecosystems. An alkaline condition (pH > 7) is imposed by the rising concentration of hydroxides and cations, and prevails in semiarid and arid environments, which represent more than 25% of the total arable land of the world. Despite the great pressure exerted by alkalinity for root viability and plant survival, scarce information is available to understand how root microbes contribute to alkaline pH adaptation. Here, we assessed the effects of alkalinity on shoot and root biomass production, chlorophyll content, root growth and branching, lateral root primordia formation, and the expression of CYCB1, TOR kinase, and auxin and cytokinin-inducible trangenes in shoots and roots of Arabidopsis seedlings grown in Petri plates with agar-nutrient medium at pH values of 7.0, 7.5, 8.0, 8.5, and 9.0. The results showed an inverse correlation between the rise of pH and most growth, hormonal and genetic traits analyzed. Noteworthy, root inoculation with Achromobacter sp. 5B1, a beneficial rhizospheric bacterium, with plant growth promoting and salt tolerance features, increased biomass production, restored root growth and branching and enhanced auxin responses in WT seedlings and auxin-related mutants aux1-7 and eir1, indicating that stress adaptation operates independently of canonical auxin transporter proteins. Sequencing of the Achromobacter sp. 5B1 genome unveiled 5244 protein-coding genes, including genes possibly involved in auxin biosynthesis, quorum-sensing regulation and stress adaptation, which may account for its plant growth promotion attributes. These data highlight the critical role of rhizobacteria to increase plant resilience under high soil pH conditions potentially through genes for adaptation to an extreme environment and bacteria-plant communication.

Comparative Genome Analyses Provide Insight into the Antimicrobial Activity of Endophytic Burkholderia

Endophytic bacteria are endosymbionts that colonize a portion of plants without harming the plant for at least a part of its life cycle. Bacterial endophytes play an essential role in promoting plant growth using multiple mechanisms. The genus Burkholderia is an important member among endophytes and encompasses bacterial species with high genetic versatility and adaptability. In this study, the endophytic characteristics of Burkholderia species are investigated via comparative genomic analyses of several endophytic Burkholderia strains with pathogenic Burkholderia strains. A group of bacterial genes was identified and predicted as the putative endophytic behavior genes of Burkholderia. Multiple antimicrobial biosynthesis genes were observed in these endophytic bacteria; however, certain important pathogenic and virulence genes were absent. The majority of resistome genes were distributed relatively evenly among the endophytic and pathogenic bacteria. All known types of secretion systems were found in the studied bacteria. This includes T3SS and T4SS, which were previously thought to be disproportionately represented in endophytes. Additionally, questionable CRISPR-Cas systems with an orphan CRISPR array were prevalent, suggesting that intact CRISPR-Cas systems may not exist in symbiotes of Burkholderia. This research not only sheds light on the antimicrobial activities that contribute to biocontrol but also expands our understanding of genomic variations in Burkholderia's endophytic and pathogenic bacteria.

The effect of plant compartment and geographical location on shaping microbiome of Pulsatilla chinensis

The plant-associated microbiome has an effect on plant growth. Pulsatilla chinensis (Bge.) Regel is an important Chinese medicinal plant. Currently, there is little understanding of the P. chinensis-associated microbiome and its diversity and composition. Here, the core microbiome associated with the root, leaf, and rhizospheric soil compartments of P. chinensis from five geographical locations was analyzed by the metagenomics approach. The alpha and beta diversity analysis showed that the microbiome associated with P. chinensis was shaped by the compartment, especially in the bacterial community. The geographical location had little influence on microbial community diversity associated with root and leaf. Hierarchical clustering distinguished the microbial communities of rhizospheric soil based on their geographical location and among the soil properties, pH was showed the more stronger effect on the diversity of rhizospheric soil microbial communities. Proteobacteria was the most dominant bacterial phylum in the root, leaf, and rhizospheric soil. Ascomycota and Basidiomycota were the most dominant fungal phyla in different compartments. Rhizobacter, Anoxybacillus, and IMCC26256 were the most important marker bacterial species for root, leaf, and rhizospheric soil screened by random forest, respectively. The fungal marker species for root, leaf, and rhizospheric soil were not only different across the compartments but also the geographical locations. Functional analysis showed that P. chinensis-associated microbiome had the similar function which had no obvious relationship with geographical location and compartment. The associated microbiome indicated in this study can be used for identifying microorganisms related to the quality and growth of P. chinensis. KEY POINTS: • Microbiome associated with P. chinensis was shaped by the compartment • Microbiome composition and abundance associated with rhizospheric soil were affected by the geographical location • Compared with fungi, bacterial associated with P. chinensis composition and diversity were more stable in different geographical locations and compartments.

How to build a lichen: from metabolite release to symbiotic interplay

Exposing their vegetative bodies to the light, lichens are outstanding amongst other fungal symbioses. Not requiring a pre-established host, 'lichenized fungi' build an entirely new structure together with microbial photosynthetic partners that neither can form alone. The signals involved in the transition of a fungus and a compatible photosynthetic partner from a free-living to a symbiotic state culminating in thallus formation, termed 'lichenization', and in the maintenance of the symbiosis, are poorly understood. Here, we synthesise the puzzle pieces of the scarce knowledge available into an updated concept of signalling involved in lichenization, comprising five main stages: (1) the 'pre-contact stage', (2) the 'contact stage', (3) 'envelopment' of algal cells by the fungus, (4) their 'incorporation' into a pre-thallus and (5) 'differentiation' into a complex thallus. Considering the involvement of extracellularly released metabolites in each phase, we propose that compounds such as fungal lectins and algal cyclic peptides elicit early contact between the symbionts-to-be, whereas phytohormone signalling, antioxidant protection and carbon exchange through sugars and sugar alcohols are of continued importance throughout all stages. In the fully formed lichen thallus, secondary lichen metabolites and mineral nutrition are suggested to stabilize the functionalities of the thallus, including the associated microbiota.

Sustainable Applications of Endophytic Bacteria and Their Physiological/Biochemical Roles on Medicinal and Herbal Plants: Review

Bacterial endophytes reside within the tissues of living plant species without causing any harm or disease to their hosts. These endophytes can be isolated, identified, characterized, and used as biofertilizers. Moreover, bacterial endophytes increase the plants' resistance against diseases, pests, and parasites, and are a promising source of pharmaceutically important bioactives. For instance, the production of antibiotics, auxins, biosurfactants, cytokinin's, ethylene, enzymes, gibberellins, nitric oxide organic acids, osmolytes, and siderophores is accredited to the existence of various bacterial strains. Thus, this manuscript intends to review the sustainable applications of endophytic bacteria to promote the growth, development, and chemical integrity of medicinal and herbal plants, as well as their role in plant physiology. The study of the importance of bacterial endophytes in the suppression of diseases in medicinal and herbal plants is crucial and a promising area of future investigation.

Recent Advances in the Bacterial Phytohormone Modulation of Plant Growth

Phytohormones are regulators of plant growth and development, which under different types of stress can play a fundamental role in a plant's adaptation and survival. Some of these phytohormones such as cytokinin, gibberellin, salicylic acid, auxin, and ethylene are also produced by plant growth-promoting bacteria (PGPB). In addition, numerous volatile organic compounds are released by PGPB and, like bacterial phytohormones, modulate plant physiology and genetics. In the present work we review the basic functions of these bacterial phytohormones during their interaction with different plant species. Moreover, we discuss the most recent advances of the beneficial effects on plant growth of the phytohormones produced by PGPB. Finally, we review some aspects of the cross-link between phytohormone production and other plant growth promotion (PGP) mechanisms. This work highlights the most recent advances in the essential functions performed by bacterial phytohormones and their potential application in agricultural production.

Dominance of Bacillus species in the wheat (Triticum aestivum L.) rhizosphere and their plant growth promoting potential under salt stress conditions

Wheat (Triticum aestivum L.) is a major source of calorific intake in its various forms and is considered one of the most important staple foods. Improved wheat productivity can contribute substantially to addressing food security in the coming decades. Soil salinity is the most serious limiting factor in crop production and fertilizer use efficiency. In this study, 11 bacteria were isolated from wheat rhizosphere and examined for salt tolerance ability. WGT1, WGT2, WGT3, WGT6, WGT8, and WGT11 were able to tolerate NaCl salinity up to 4%. Bacterial isolates were characterized in vitro for plant growth-promoting properties including indole-3-acetic acid (IAA) production, phosphate solubilization, nitrogen fixation, zinc solubilization, biofilm formation, and cellulase-pectinase production. Six isolates, WGT1, WGT3, WGT4, WGT6, WGT8, and WGT9 showed IAA production ability ranging from 0.7-6 µg m/L. WGT8 displayed the highest IAA production. Five isolates, WGT1, WGT2, WGT5, WGT10, and WGT11, demonstrated phosphate solubilization ranging from 1.4-12.3 µg m/L. WGT2 showed the highest phosphate solubilization. Nitrogen fixation was shown by only two isolates, WGT1 and WGT8. Zinc solubilization was shown by WGT1 and WGT11 on minimal media. All isolates showed biofilm formation ability, where WGT4 exhibited maximum potential. Cellulase production ability was noticed in WGT1, WGT2, WGT4, and WGT5, while pectinase production was observed in WGT2 and WGT3. Phylogenetic identification of potential bacteria isolates confirmed their close relationship with various species of the genus Bacillus. WGT1, WGT2, and WGT3 showed the highest similarity with B. cereus, WGT6 with B. tianshenii, WGT8 with B. subtilis, and WGT11 with B. thuringiensis. Biofertilizer characteristics of salt-tolerant potential rhizospheric bacteria were evaluated by inoculating wheat plants under controlled conditions and field experiments. B. cereus WGT1 and B. thuringiensis WGT11 displayed the maximum potential to increase plant growth parameters and enhance grain yield by 37% and 31%, respectively. Potential bacteria of this study can tolerate salt stress, have the ability to produce plant growth promoting substances under salt stress and contribute significantly to enhance wheat grain yield. These bacterial isolates have the potential to be used as biofertilizers for improved wheat production under salinity conditions and contribute to the sustainable agriculture.

Effect of Indole-3-Acetic Acid on Tomato Plant Growth

Plant growth-promoting bacteria have several abilities to promote plant growth and development. One of these skills is the synthesis of indole-3-acetic acid (IAA), which mainly promotes root and shoot development. The bacteria Bacillus subtilis and Azospirillum brasilense have been widely used in agriculture with this function. However, little is known about whether the joint inoculation of these bacteria can reduce plant development by the excess of IAA produced as a result of the joint inoculation. The objective of the present study was to verify the effect of IAA on the inoculation of B. subtilis and A. brasilense in three tomato genotypes. The Micro-Tom genotype without mutation for IAA synthesis, Entire, has high sensitivity to IAA, and the diageotropic genotype (dgt) has low sensitivity to IAA. The results show that the plant parameter most sensitive to microbial inoculation is the number of roots. No treatment increased the shoot dry mass parameters for the Micro-Tom genotype and dgt, root dry mass for the Micro-Tom genotype, plant height for the Micro-Tom and Entire genotypes, root area and root volume for the genotype dgt. The Azm treatment reduced plant height compared to the control in the dgt, the BS + Azw and BS + Azm treatments in the Micro-Tom genotype and the Azw + Azm treatment in the dgt genotype reduced the plant diameter compared to the control. BS and BS + Azw reduced the number of roots in the Micro-Tom. The results strongly support that the mixture of B. subtilis and A. brasilense can reduce some parameters of plant development; however, this effect is possibly an interference in the mode of action of growth promotion of each isolate and is not related to an excess of IAA produced by the bacteria.

Perspectives and potential applications of endophytic microorganisms in cultivation of medicinal and aromatic plants

Ensuring food and nutritional security, it is crucial to use chemicals in agriculture to boost yields and protect the crops against biotic and abiotic perturbations. Conversely, excessive use of chemicals has led to many deleterious effects on the environment like pollution of soil, water, and air; loss of soil fertility; and development of pest resistance, and is now posing serious threats to biodiversity. Therefore, farming systems need to be upgraded towards the use of biological agents to retain agricultural and environmental sustainability. Plants exhibit a huge and varied niche for endophytic microorganisms inside the planta, resulting in a closer association between them. Endophytic microorganisms play pivotal roles in plant physiological and morphological characteristics, including growth promotion, survival, and fitness. Their mechanism of action includes both direct and indirect, such as mineral phosphate solubilization, fixating nitrogen, synthesis of auxins, production of siderophore, and various phytohormones. Medicinal and aromatic plants (MAPs) hold a crucial position worldwide for their valued essential oils and several phytopharmaceutically important bioactive compounds since ancient times; conversely, owing to the high demand for natural products, commercial cultivation of MAPs is on the upswing. Furthermore, the vulnerability to various pests and diseases enforces noteworthy production restraints that affect both crop yield and quality. Efforts have been made towards enhancing yields of plant crude drugs by improving crop varieties, cell cultures, transgenic plants, etc., but these are highly cost-demanding and time-consuming measures. Thus, it is essential to evolve efficient, eco-friendly, cost-effective simpler approaches for improvement in the yield and health of the plants. Harnessing endophytic microorganisms as biostimulants can be an effective and alternative step. This review summarizes the concept of endophytes, their multidimensional interaction inside the host plant, and the salient benefits associated with endophytic microorganisms in MAPs.

Different rhizosphere soil microbes are recruited by tomatoes with different fruit color phenotypes

Background

To explore and utilize abundant soil microbes and their beneficial functions, the bacterial and fungal compositions in rhizospheres between red- and yellow-fruited tomato varieties were analyzed using high-throughput sequencing technique.

Result

Our results indicated that different soil microbes in rhizospheres of tomatoes were exactly recruited by different color fruit tomatoes. For the reasons as not only soil bacterial community, but also soil fungal compositions were all different between red and yellow fruit tomatoes. For example, Nocardioides, norank_f_norank_o_Vicinamibacterales, norank_f_norank_o_norank_c_KD4-96, norank_f_Birii41, norank_f_norank_o_S085 and Bradyrhizobium were the specific dominant soil bacterial genera, and Lecythophora, Derxomyces and unclassified_f_Pyronemataceae were the dominant soil fungal genera in the rhizospheres of red tomato varieties. By contrast, unclassified_f__Micromonsporaceae, Acidipila, Roseisolibacter, Gaiella and norank_f_Xanthobacteraceae were the unique dominant soil bacterial genera in the rhizospheres of yellow tomato varieties. And unclassified_o__Onygenales, Trichocladium, unclassified_c__Sordariomycetes, Pseudogymnoascus, Acremonium, Oidiodendron, Phialemonium, Penicillium, Phialosimplex were the unique dominant soil fungal genera in rhizospheres of yellow tomato varieties. Moreover, a higher abundance of specific soil bacterial and fungal genera in the rhizosphere was found in rhizospheres of the yellow than those of the red tomato varieties.

Conclusion

Soil bacterial and fungal compositions in rhizospheres between red- and yellow-fruited tomato varieties were found significantly different which growing in the same environment under the identical managements. It suggested that different soil microbes in rhizospheres exactly were recruited by different phenotypes tomato varieties related to fruit color formation.

Synergistic effect of co-culture rhizosphere Streptomyces: A promising strategy to enhance antimicrobial activity and plant growth-promoting function

Rhizosphere Streptomyces is one of the important types of rhizosphere microorganisms that plays an important role in promoting plant growth and controlling plant diseases to maintain agricultural ecosystem balance and green ecological agriculture development as beneficial bacteria. Microbial co-culture simulates the complex biocommunity in nature, which has more advantages than the monoculture with a synergistic effect. As the key signal mediums of microorganisms, plants, and their interactions, microbial metabolites are of great significance in revealing their functional mechanism. In this study, two potential plant growth-promoting rhizobacteria, Streptomyces albireticuli MDJK11, and Streptomyces alboflavus MDJK44, were selected to explore the effects of co-culture and monoculture on plant growth promotion and disease prevention, and the metabolic material basis was analyzed by metabonomics. Results showed that Streptomyces MDJK11, MDJK44 monoculture, and co-culture condition all showed good growth promoting and antimicrobial effects. Moreover, as compared to the monoculture, the co-culture showed the advantage of a synergistic enhancement effect. LC-MS-based metabonomics analysis showed the metabolic material bases of Streptomyces for plant growth promotion and disease prevention were mainly plant hormone and antibiotics and the co-culture condition could significantly stimulate the production of plant hormone promoters and macrolide, cyclic peptide, and aminoglycoside antibiotics. The study proved that the co-cultures of S. albireticuli MDJK11 and S. alboflavus MDJK44 have great potential in crop growth promotion and disease prevention.

Root Exudates: Mechanistic Insight of Plant Growth Promoting Rhizobacteria for Sustainable Crop Production

The breaking silence between the plant roots and microorganisms in the rhizosphere affects plant growth and physiology by impacting biochemical, molecular, nutritional, and edaphic factors. The components of the root exudates are associated with the microbial population, notably, plant growth-promoting rhizobacteria (PGPR). The information accessible to date demonstrates that PGPR is specific to the plant's roots. However, inadequate information is accessible for developing bio-inoculation/bio-fertilizers for the crop in concern, with satisfactory results at the field level. There is a need to explore the perfect candidate PGPR to meet the need for plant growth and yield. The functions of PGPR and their chemotaxis mobility toward the plant root are triggered by the cluster of genes induced by the components of root exudates. Some reports have indicated the benefit of root exudates in plant growth and productivity, yet a methodical examination of rhizosecretion and its consequences in phytoremediation have not been made. In the light of the afore-mentioned facts, in the present review, the mechanistic insight and recent updates on the specific PGPR recruitment to improve crop production at the field level are methodically addressed.

Isolation of indole-3-acetic acid-producing Azospirillum brasilense from Vietnamese wet rice: co-immobilization of isolate and microalgae as a sustainable biorefinery

Production of indole-3-acetic acid (IAA) is well documented in various studies for the bacteria that inhabit the rhizosphere of plants, but with roots of wet rice, the outstandings have been not yet elucidated. This study began with the isolation of bacteria type strain Azospirillum sp. and developed the investigation to a screening of their ability in IAA production. This screening conducted a selection of only bacteria that was capable of the production of IAA with its content of over 25µg. mL^-1 for sequencing. Of 10 isolates only one resulted from the type strain Azospirillum brasilense (A. brasilense) with a similarity of 100%. Various factors that influence A. brasilense in biosynthesizing IAA such as temperature, pH, nitrogen presence and concentration of tryptophan in the culture medium were examined. The results indicated that the culture conditions were suitable for IAA biosynthesis at pH 6.5, 30°C, culture media with nitrogen, and 0.1% trytophan. The next survey on the role of the immobilization of this bacteria with microalgae in alginate was highlighted to its support in microalgal growth. With the co-immobilization of bacteria and microalgae, the density of Chlorella vulgaris was significantly increased during 15-day culture, inducing 2.2 times of cell content in culture batch microalgae immobilized A. brasilense higher than that free-bacteria.

Pseudomonas mediated nutritional and growth promotional activities for sustainable food security

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Fluorescent and non-fluorescent species of Pseudomonas are important for plant growth promotion, phytopathogenic control and plant disease management.

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Pseudomonas belong to Pseudomonadaceae family (10 groups on the basis of rRNA-DNA hybridization) classified into 6-subgroups of rRNA gene homology and RFLP.

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Pseudomonas species produce antagonistic mechanism such as ISR and compounds like cell wall degradation enzymes, and antibiotics to maintain a mutualistic relationship with the associated plant.

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Pseudomonas sp. synthesize auxins having properties similar to phytohormones like IAA, which act as signaling molecules for regulating plant growth.

Numerous microbial communities show synergistic and antagonistic interactions among themselves, resulting in benefit and harm to either or both the associated members. The association holds accountability for nutrients recycling and energy drift, resulting in the availability of macronutrients unavailable and insoluble forms of rhizospheric nutrients, crucial for vital processes in plants, e.g., act as co-factors of various phyto-enzyme and redox mediators. Plant growth promoting rhizobacteria are known to enhance plant growth by increasing these macronutrients availability during their plant root colonization. In comparison to any other genera, Pseudomonas is the most favored bioinoculant due to its significant properties in both plant growth and phytopathogen control during its synergistic association with the host plant. These properties include siderophore production, phosphate solubilization, nitrogen fixation, phenazines, antibiotics, and induced systemic resistance carried out by various Pseudomonas species like Pseudomonas fluorescens, Pseudomonas putida, and Pseudomonas syringae. The association of Pseudomonas with crop plants procures several secretory and electron-based feedback mechanisms in order to regulate the plant growth and phytopathogen control activities through the secretion of several phytohormones (auxins, gibberellins, Indole-3-acetic acid), secondary metabolites (flavonoids) and enzymes (aminocyclopropane-1-carboxylate, phenylalanine ammonia-lyase). Ecologically significant applications of Pseudomonas in biocontrol and bioaugmentation are crucial for maintaining food security.

Plant immune system activation is necessary for efficient root colonization by auxin-secreting beneficial bacteria

Although plant roots encounter a plethora of microorganisms in the surrounding soil, at the rhizosphere, plants exert selective forces on their bacterial colonizers. Unlike immune recognition of pathogenic bacteria, the mechanisms by which beneficial bacteria are selected and how they interact with the plant immune system are not well understood. To better understand this process, we studied the interaction of auxin-producing Bacillus velezensis FZB42 with Arabidopsis roots and found that activation of the plant immune system is necessary for efficient bacterial colonization and auxin secretion. A feedback loop is established in which bacterial colonization triggers an immune reaction and production of reactive oxygen species, which, in turn, stimulate auxin production by the bacteria. Auxin promotes bacterial survival and efficient root colonization, allowing the bacteria to inhibit fungal infection and promote plant health. Thus, a feedback loop between bacteria and the plant immune system promotes the fitness of both partners.

Growth and Characteristics of Two Different Epichloë sinensis Strains Under Different Cultures

In the present study, two Epichloë sinensis endophyte strains isolated from different Festuca sinensis ecotypes were inoculated on potato dextrose agar (PDA) and potato dextrose broth (PDB) media with or without (control) exogenous additives. After 4weeks of growth, the growth (colony diameter, hyphal diameter, and mycelial biomass) and other characteristics (pH and antioxidant capacity of culture filtrate, mycelial ion contents, and hormone contents) were measured. The results showed that the culture conditions had significant effects (p<0.05) on the hyphal diameter, mycelial biomass, and hormone content of the two strains. The mycelial biomass of the two strains in PDB was significantly higher (p<0.05) than that on PDA. Except for strain 1 with indole-3-acetic acid (IAA) treatment and strain 84F with control and VB1 treatments, the hyphal diameter of the two strains in PDB under the other treatments was significantly higher (p<0.05) than that on PDA. In most cases, the IAA, cytokinins (CTK), abscisic acid (ABA), and gibberlic acid (GA) contents in the mycelia on PDA of the two strains were significantly higher (p<0.05) than those in PDB. The two E. sinensis strains exhibited significantly different performances (p<0.05) under the five treatments. The indices, including colony diameter, mycelial biomass, scavenging ability of superoxide anion radicals and hydroxyl radicals, pH of culture filtrate, ion contents, hyphal diameter, and IAA, CTK, GA, and ABA contents were significantly different (p<0.05) between the two strains, although the performance was inconsistent. Exogenous additives had significant effects (p<0.05) on the performance of the two E. sinensis strains. Indole-3-acetic acid and VB1 treatments significantly promoted (p<0.05) the growth of the two strains on both PDA and PDB. Indole-3-acetic acid treatment also significantly increased the hyphal diameters of the two strains in PDB (p<0.05). Indole-3-acetic acid and VB1 treatments significantly reduced (p<0.05) the antioxidant ability of these two strains in PDB. NaCl and ZnCl2 treatments had significant inhibitory effects (p<0.05) on fungal growth and promotion effects on the antioxidant ability of the two strains. The treatments also had significant effects (p<0.05) on hyphal diameters and ion and hormone contents, although the effects varied with different indices.

Dissecting Metabolism of Leaf Nodules in Ardisia crenata and Psychotria punctata

Root-microbe interaction and its specialized root nodule structures and functions are well studied. In contrast, leaf nodules harboring microbial endophytes in special glandular leaf structures have only recently gained increased interest as plant-microbe phyllosphere interactions. Here, we applied a comprehensive metabolomics platform in combination with natural product isolation and characterization to dissect leaf and leaf nodule metabolism and functions in Ardisia crenata (Primulaceae) and Psychotria punctata (Rubiaceae). The results indicate that abiotic stress resilience plays an important part within the leaf nodule symbiosis of both species. Both species showed metabolic signatures of enhanced nitrogen assimilation/dissimilation pattern and increased polyamine levels in nodules compared to leaf lamina tissue potentially involved in senescence processes and photosynthesis. Multiple links to cytokinin and REDOX-active pathways were found. Our results further demonstrate that secondary metabolite production by endophytes is a key feature of this symbiotic system. Multiple anhydromuropeptides (AhMP) and their derivatives were identified as highly characteristic biomarkers for nodulation within both species. A novel epicatechin derivative was structurally elucidated with NMR and shown to be enriched within the leaf nodules of A. crenata. This enrichment within nodulated tissues was also observed for catechin and other flavonoids indicating that flavonoid metabolism may play an important role for leaf nodule symbiosis of A. crenata. In contrast, pavettamine was only detected in P. punctata and showed no nodule specific enrichment but a developmental effect. Further natural products were detected, including three putative unknown depsipeptide structures in A. crenata leaf nodules. The analysis presents a first metabolomics reference data set for the intimate interaction of microbes and plants in leaf nodules, reveals novel metabolic processes of plant-microbe interaction as well as the potential of natural product discovery in these systems.

Harnessing Bacterial Endophytes for Promotion of Plant Growth and Biotechnological Applications: An Overview

Endophytic bacteria colonize plants and live inside them for part of or throughout their life without causing any harm or disease to their hosts. The symbiotic relationship improves the physiology, fitness, and metabolite profile of the plants, while the plants provide food and shelter for the bacteria. The bacteria-induced alterations of the plants offer many possibilities for biotechnological, medicinal, and agricultural applications. The endophytes promote plant growth and fitness through the production of phytohormones or biofertilizers, or by alleviating abiotic and biotic stress tolerance. Strengthening of the plant immune system and suppression of disease are associated with the production of novel antibiotics, secondary metabolites, siderophores, and fertilizers such as nitrogenous or other industrially interesting chemical compounds. Endophytic bacteria can be used for phytoremediation of environmental pollutants or the control of fungal diseases by the production of lytic enzymes such as chitinases and cellulases, and their huge host range allows a broad spectrum of applications to agriculturally and pharmaceutically interesting plant species. More recently, endophytic bacteria have also been used to produce nanoparticles for medical and industrial applications. This review highlights the biotechnological possibilities for bacterial endophyte applications and proposes future goals for their application.

Bacterial endophytes: Molecular interactions with their hosts

Plant growth promotion has been found associated with plants on the surface (epiphytic), inside (endophytic), or close to the plant roots (rhizospheric). Endophytic bacteria mainly have been researched for their beneficial activities in terms of nutrient availability, plant growth hormones, and control of soil-borne and systemic pathogens. Molecular communications leading to these interactions between plants and endophytic bacteria are now being unrevealed using multidisciplinary approaches with advanced techniques such as metagenomics, metaproteomics, metatranscriptomics, metaproteogenomic, microRNAs, microarray, chips as well as the comparison of complete genome sequences. More than 400 genes in both the genomes of host plant and bacterial endophyte are up- or downregulated for the establishment of endophytism and plant growth-promoting activity. The involvement of more than 20 genes for endophytism, about 50 genes for direct plant growth promotion, about 25 genes for biocontrol activity, and about 10 genes for mitigation of different stresses has been identified in various bacterial endophytes. This review summarizes the progress that has been made in recent years by these modern techniques and approaches.

Molecular and physiological analysis of indole-3-acetic acid degradation in Bradyrhizobium japonicum E109

Bradyrhizobium japonicum E109 is a bacterium widely used for inoculants production in Argentina. It is known for its ability to produce several phytohormones and degrade indole-3-acetic acid (IAA). The genome sequence of B. japonicum E109 was recently analyzed and it showed the presence of genes related to the synthesis of IAA by indole-3-acetonitrile, indole-3-acetamide and tryptamine pathways. Nevertheless, B. japonicum E109 is not able to produce IAA and instead has the ability to degrade this hormone under saprophytic culture conditions. This work aimed to study the molecular and physiological features of IAA degradation and identify the genes responsible of this activity. In B. japonicum E109 we identified two sequences coding for a putative 3-phenylpropionate dioxygenase (subunits α and β) responsible for the IAA degradation that were homologous to the canonical cluster of iacC and iacD of Pseudomonas putida 1290. These genes form a separate cluster together with three additional genes with unknown functions. The degradation activity was found to be constitutively expressed in B. japonicum E109. As products of IAA degradation, we identified two compounds, 3-indoleacetic acid 2,3-oxide and 2-(2-hydroperoxy-3-hydroxyindolin-3-yl) acetic acid. Our report proposes, for the first time, a model for IAA degradation in Bradyrhizobium.

Rhizobacterial consortium mediated aroma and yield enhancement in basmati and non-basmati rice (Oryza sativa L.)

Basmati and non-basmati rice varieties are commercially important. Aromatic rice varieties are low yielding and recently depletion in aroma is observed due to the shift towards modern agriculture. Therefore, it is necessary to restore the aroma and increase the yield through sustainable agriculture. The use of microbial bioinoculants is one of the promising ways to achieve these targets. With these objectives, rhizospheric bacterial strains Enterobacter hormaechei (AM122) and Lysinibacillus xylanilyticus (DB25) having the property of synthesizing 2-acetyl-1-pyrroline (2AP) were isolated from the rhizosphere of two aromatic rice varieties, Ambemohar-157 and Dehradun Basmati respectively and their effect on plant growth, aroma and yield enhancement under mono-inoculation and consortium conditions was analyzed. The bacterial inoculum in consortium resulted in significant improvement in vegetative growth, yield and 2AP content over mono inoculation and control. The study highlights the potential of E. hormaechei and L. xylanilyticus in plant growth, yield and aroma enhancement in basmati and non-basmati rice varieties. These strains can be taken up further for developing a commercial bioformulation.

Hormones as go-betweens in plant microbiome assembly

The interaction of plants with complex microbial communities is the result of co-evolution over millions of years and contributed to plant transition and adaptation to land. The ability of plants to be an essential part of complex and highly dynamic ecosystems is dependent on their interaction with diverse microbial communities. Plant microbiota can support, and even enable, the diverse functions of plants and are crucial in sustaining plant fitness under often rapidly changing environments. The composition and diversity of microbiota differs between plant and soil compartments. It indicates that microbial communities in these compartments are not static but are adjusted by the environment as well as inter-microbial and plant-microbe communication. Hormones take a crucial role in contributing to the assembly of plant microbiomes, and plants and microbes often employ the same hormones with completely different intentions. Here, the function of hormones as go-betweens between plants and microbes to influence the shape of plant microbial communities is discussed. The versatility of plant and microbe-derived hormones essentially contributes to the creation of habitats that are the origin of diversity and, thus, multifunctionality of plants, their microbiota and ultimately ecosystems.

Effect of silver nanoparticles and Bacillus cereus LPR2 on the growth of Zea mays

The effect of Plant Growth Promoting Rhizobacteria (Bacillus sp.) and silver nanoparticles on Zea mays was evaluated. The silver nanoparticles were synthesized from Tagetes erecta (Marigold) leaf and flower extracts, whereas PGPR isolated from spinach rhizosphere. The silver nanoparticles (AgNPs) were purified using ultra centrifugation and were characterized using UV-Vis spectroscopy at gradient wavelength and also by High Resolution Transmission Electron microscopy (HRTEM). The average particles size of AgNPs was recorded approximately 60 nm. Almost all potential isolates were able to produce Indole Acetic Acid (IAA), ammonia and Hydrogen cyanide (HCN), solubilized tricalcium phosphate and inhibited the growth of Macrophomina phaseolina in vitro but the isolate LPR2 was found the best among all. On the basis of 16S rRNA gene sequence, the isolate LPR2 was characterized as Bacillus cereus LPR2. The maize seeds bacterized with LPR2 and AgNPs individually showed a significant increase in germination (87.5%) followed by LPR2 + AgNPs (75%). But the maximum growth of root and shoot of maize plant was observed in seeds coated with LPR2 followed by AgNPs and a combination of both. Bacillus cereus LPR2 and silver nanoparticles enhanced the plant growth and LPR2 strongly inhibited the growth of deleterious fungal pathogen. Therefore, LPR2 and AgNPs could be utilized as bioinoculant and growth stimulator, respectively for maize.

Phytohormone release by three isolated lichen mycobionts and the effects of indole-3-acetic acid on their compatible photobionts

Evidence is emerging that phytohormones represent key inter-kingdom signalling compounds supporting chemical communication between plants, fungi and bacteria. The roles of phytohormones for the lichen symbiosis are poorly understood, particularly in the process of lichenization, i.e. the key events which lead free-living microalgae and fungi to recognize each other, make physical contact and start developing a lichen thallus. Here, we studied cellular and extracellularly released phytohormones in three lichen mycobionts, Cladonia grayi, Xanthoria parietina and Tephromela atra, grown on solid medium, and the effects of indole-3-acetic acid (IAA) on their respective photobionts, Asterochloris glomerata, Trebouxia decolorans, Trebouxia sp. Using ultra-high-performance liquid chromatography coupled with tandem mass spectrometry (UHPLC-MS/MS) we found that mycobionts produced IAA, salicylic acid (SA) and jasmonic acid (JA). IAA represented the most abundant phytohormone produced and released by all mycobionts, whereas SA was released by X. parietina and T. atra, and JA was released by C. grayi only. With a half-life of 5.2 days, IAA degraded exponentially in solid BBM in dim light. When IAA was exogenously offered to the mycobionts' compatible photobionts at "physiological" concentrations (as released by their respective mycobionts and accumulated in the medium over seven days), the photobionts' water contents increased up to 4.4%. Treatment with IAA had no effects on the maximum quantum yield of photosystem II, dry mass, and the contents of photosynthetic pigments and α-tocopherol of the photobionts. The data presented may be useful for designing studies aimed at elucidating the roles of phytohormones in lichens.

Abundance and Extracellular Release of Phytohormones in Aero-terrestrial Microalgae (Trebouxiophyceae, Chlorophyta) As a Potential Chemical Signaling Source1

Phytohormones are pivotal signaling compounds in higher plants, in which they exert their roles intracellularly, but are also released for cell-to-cell communication. In unicellular organisms, extracellularly released phytohormones can be involved in chemical crosstalk with other organisms. However, compared to higher plants, hardly any knowledge is available on the roles of phytohormones in green algae. Here, we studied phytohormone composition and extracellular release in aero-terrestrial Trebouxiophyceae. We investigated (a) which phytohormones are produced and if they are released extracellularly, and if extracellular phytohormone levels are (b) affected by environmental stimuli, and (c) differ between lichen-forming and non-lichen-forming species. Three free-living microalgae (Apatococcus lobatus, Chloroidium ellipsoideum, and Myrmecia bisecta) and three lichen-forming microalgae (Asterochloris glomerata, Trebouxia decolorans, and Trebouxia sp.) were studied. Algae were grown on solid media and the following cellular phytohormones were identified by ultra-high-performance liquid chromatography coupled with tandem mass spectrometry (UHPLC-MS/MS): indole-3-acetic acid (IAA), indole-3-butyric acid (IBA), abscisic acid (ABA), gibberellin A4 (GA4 ), and zeatin (ZT). Furthermore, IAA, IBA, ABA, jasmonic acid (JA), gibberellin A3 (GA3 ), and GA4 were found to be released extracellularly. IAA and ABA were released by all six species, and IAA was the most concentrated. Phytohormone release was affected by light and water availability, especially IAA in A. glomerata, Trebouxia sp., and C. ellipsoideum. No clear patterns were observed between lichen-forming and non-lichen-forming species. The results are envisaged to contribute valuable baseline information for further studies into the roles of phytohormones in microalgae.

Global Trends in Phytohormone Research: Google Trends Analysis Revealed African Countries Have Higher Demand for Phytohormone Information

The lines of research conducted within a country often reflect its focus on current and future economic needs. Analyzing "search" trends on the internet can provide important insight into predicting the direction of a country in regards to agriculture, health, economy, and other areas. 'Google Trends' collects data on search terms from different countries, and this information can be used to better understand sentiments in different countries and regions. Agricultural output is responsible for feeding the world and there is a continuous quest to find ways to make agriculture more productive, safe, and reliable. The application of phytohormones has been used in agriculture world-wide for many years to improve crop production and continues to be an active area of research for the application in plants. Therefore, in the current study, we searched 'Google Trends' using the phytohormone search terms, abscisic acid, auxins, brassinosteroids, cytokinin, ethylene, gibberellins, jasmonic acid, salicylic acid, and strigolactones. The results indicated that the African country Zambia had the greatest number of queries on auxin research, and Kenya had the most queries in cytokinin and gibberellin research world-wide. For other phytohormones, India had the greatest number of queries for abscisic acid and South Korea had the greatest number of ethylene and jasmonic acid search world-wide. Queries on salicylic acid have been continuously increasing while the least number of queries were related to strigolactones. Only India and United States of America had significant numbers of queries on all nine phytohormones while queries on one or more phytohormones were absent in other countries. India is one of the top five crop-producing countries in the world for apples, millet, orange, potato, pulses, rice, sugarcane, tea, and wheat. Similarly, the United States of America is one of the top five crop-producing countries of the world for apples, grapes, maze, orange, potato, sorghum, sugarcane, and wheat. These might be the most possible factors for the search queries found for all the nine phytohormones in India and the United States of America.

Siderophore and indolic acid production by Paenibacillus triticisoli BJ-18 and their plant growth-promoting and antimicrobe abilities

Paenibacillus triticisoli BJ-18, a N2-fixing bacterium, is able to promote plant growth, but the secondary metabolites that may play a role in promoting plant growth have never been characterized. In this study, untargeted metabolomics profiling of P. triticisoli BJ-18 indicated the existence of 101 known compounds, including N2-acetyl ornithine, which is the precursor of siderophores, plant growth regulators such as trehalose 6-phosphate, betaine and trigonelline, and other bioactive molecules such as oxymatrine, diosmetin, luotonin A, (-)-caryophyllene oxide and tetrahydrocurcumin. In addition, six compounds were also isolated from P. triticisoli BJ-18 using a combination of silica gel chromatography, sephadex LH-20, octadecyl silane (ODS), and high-performance liquid chromatography (HPLC). The compound structures were further analyzed by Nuclear Magnetic Resonance (NMR), Mass Spectrometry (MS), and Electronic Circular Dichroism (ECD). The six compounds included three classical siderophore fusarinines identified as deshydroxylferritriacetylfusigen, desferritriacetylfusigen, and triacetylfusigen, and three indolic acids identified as paenibacillic acid A, 3-indoleacetic acid (IAA), and 3-indolepropionic acid (IPA). Both deshydroxylferritriacetylfusigen and paenibacillic acid A have new structures. Fusarinines, which normally occur in fungi, were isolated from bacterium for the first time in this study. Both siderophores (compounds 1 and 2) showed antimicrobial activity against Escherichia coli, Staphylococcus aureus and Bacillus subtilis, but did not show obvious inhibitory activity against yeast Candida albicans, whereas triacetylfusigen (compound 3) showed no antibiosis activity against these test microorganisms. Paenibacillic acid A, IAA, and IPA were shown to promote the growth of plant shoots and roots, and paenibacillic acid A also showed antimicrobial activity against S. aureus. Our study demonstrates that siderophores and indolic acids may play an important role in plant growth promotion by P. triticisoli BJ-18.

Treatments with native Coleus forskohlii endophytes improve fitness and secondary metabolite production of some medicinal and aromatic plants

Endophytes have been shown to play a crucial role in determining the fitness of host plant during their association, yet the cross-functional effect of endophytes of one plant on another plant remains largely uncharacterized. In this study, we attempt to analyze the effect of native endophytes of Coleus forskohlii (Phialemoniopsis cornearis (SF1), Macrophomina pseudophaseolina (SF2), and Fusarium redolens (RF1), isolated from stem and root parts) on plant growth and secondary metabolite enhancement in medicinal plant Andrographis paniculata, and aromatic plants Pelargonium graveolens and Artemisia pallens. Here, we report, endophytic treatments with SF2 (21%) and RF1 (9%) in A. paniculata resulted in significant enhancement of andrographolide along with plant primary productivity. Correspondingly, application of fungal endophytes RF1, SF1, and SF2 significantly improved the plant growth (11 to 40%), shoot weight (28 to 34%), oil content (44 to 58%), and oil yield (72 to 122%) in P. graveolens. Interestingly, treatment of A. pallens with three fungal endophytes resulted in significant enhancement of plant productivity and oil content (12 to 80%) and oil yield (32 to 139%). Subsequently, the endophyte treatments RF1 and SF1 enhanced davanone (13 to 22%) and ethyl cinnamate (11 to 22%) content. However, SF2 endophyte-treated plants did not show any improvement in ethyl cinnamate content but enhanced the content of davanone (10%), a signature component of davana essential oil. Overall, results depict cross-functional role of native endophytes of C. forskohlii and repurposing of functional endophytes for sustainable cultivation of economically important medicinal and aromatic crops.

Gut Microbiome Toxicity: Connecting the Environment and Gut Microbiome-Associated Diseases

The human gut microbiome can be easily disturbed upon exposure to a range of toxic environmental agents. Environmentally induced perturbation in the gut microbiome is strongly associated with human disease risk. Functional gut microbiome alterations that may adversely influence human health is an increasingly appreciated mechanism by which environmental chemicals exert their toxic effects. In this review, we define the functional damage driven by environmental exposure in the gut microbiome as gut microbiome toxicity. The establishment of gut microbiome toxicity links the toxic effects of various environmental agents and microbiota-associated diseases, calling for more comprehensive toxicity evaluation with extended consideration of gut microbiome toxicity.

Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using 13CO2 and 13C-Methanol

Stable isotope probing (SIP) enables tracking the nutrient flows from isotopically labeled substrates to specific microorganisms in microbial communities. In proteomic SIP, labeled proteins synthesized by the microbial consumers of labeled substrates are identified with a shotgun proteomics approach. Here, proteomic SIP was combined with targeted metagenomic binning to reconstruct metagenome-assembled genomes (MAGs) of the microorganisms producing labeled proteins. This approach was used to track carbon flows from ¹³CO₂ to the rhizosphere communities of Zea mays, Triticum aestivum, and Arabidopsis thaliana. Rhizosphere microorganisms that assimilated plant-derived ¹³C were capable of metabolic and signaling interactions with their plant hosts, as shown by their MAGs containing genes for phytohormone modulation, quorum sensing, and transport and metabolism of nutrients typical of those found in root exudates. XoxF-type methanol dehydrogenases were among the most abundant proteins identified in the rhizosphere metaproteomes. ¹³C-methanol proteomic SIP was used to test the hypothesis that XoxF was used to metabolize and assimilate methanol in the rhizosphere. We detected 7 ¹³C-labeled XoxF proteins and identified methylotrophic pathways in the MAGs of 8 ¹³C-labeled microorganisms, which supported the hypothesis. These two studies demonstrated the capability of proteomic SIP for functional characterization of active microorganisms in complex microbial communities.

Medicago truncatula root developmental changes by growth-promoting microbes isolated from Fabaceae, growing on organic farms, involve cell cycle changes and WOX5 gene expression

Both root nodules and the rhizosphere of Fabaceae plants grown on organic farms are a rich source of bacteria, mainly from the families Enterobacteriaceae and Pseudomonadaceae. The enhanced root system growth in M. truncatula after inoculation with selected bacteria includes an increase of nuclei in the cell cycle S phase and a reduction in phase G2 as well as an enhanced expression of the WOX5 gene. Synthetic fertilizers and pesticides are commonly used to improve plant quality and health. However, it is necessary to look for other efficient and also environmentally safe methods. One such method involves the use of bacteria known as plant growth-promoting bacteria (PGPB). Seventy-two bacterial isolates from the rhizospheric soil and root nodule samples of legumes, including bean, alfalfa, lupine and barrel medic, grown on an organic farm in Western Pomerania (Poland) were screened for their growth-promoting capacities and 38 selected isolates were identified based on 16S rRNA gene sequencing. The analysis showed the isolates to represent 17 strains assigned to 6 families: Enterobacteriaceae, Pseudomonadaceae, Xanthomonadaceae, Rhizobiaceae, Bacillaceae and Alcaligenaceae. Pot experiments showed that 13 strains, capable of producing indole compounds from tryptophan in vitro, could significantly enhance the root and shoot weight of 10-week-old Medicago truncatula seedlings. Compared to non-inoculated seedlings, the root system of inoculated ones was more branched; in addition, the root length, surface area and, especially, the root volume were higher. The 24-h root inoculation with the three selected strains increased the nuclei population in the G1 and S phases, decreased it in the G2 phase and enhanced the WUSCHEL-related Homeobox5 (WOX5) gene expression in root tips and lateral zones. The "arrest" of nuclei in the S phase and the enhancement of the WOX5 gene expression were observed to gradually disappear once the bacterial suspension was rinsed off the seedling roots and the roots were transferred to water for further growth. This study shows that the nodules and rhizosphere of legumes grown on organic farms are a rich source of different PGPB species and provides new data on the ability of these bacteria to interfere with cell cycle and gene expression during the root development.

Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil

Maize domestication and breeding have resulted in drastic and well documented changes in aboveground traits, but belowground effects on root system functioning and rhizosphere microbial communities remain poorly understood, despite their critical importance for nutrient and water acquisition. We investigated the rhizosphere microbial community composition and structure of ten Zea mays accessions along an evolutionary transect (two teosinte, three inbred maize lines, and five modern maize hybrids) grown in nutrient depleted soil from a low input agricultural system. Microbial community analysis revealed significant differences in community composition between soil compartments (proximal vs. distal rhizosphere) and between plant genetic groups (teosinte, inbred, and modern hybrid). Only a small portion of the microbial community was differentially selected across plant genetic groups: 3.7% of prokaryotic community members and 4.9% of fungal community members were significantly associated with a specific plant genetic group. Indicator species analysis showed the greatest differentiation between modern hybrids and the other two plant genetic groups. Co-occurrence network analysis revealed that microbial co-occurrence patterns of the inbred maize lines’ rhizosphere were significantly more similar to those of the teosintes than to the modern hybrids. Our results suggest that advances in hybrid development significantly impacted rhizosphere microbial communities and network assembly.

Non-targeted metabolomics unravels a media-dependent prodiginines production pathway in Streptomyces coelicolor A3(2)

The genus Streptomyces is the best-known source of therapeutic secondary metabolites, especially antibiotics with pharmaceutical applications. Here, we performed a comparative study based on the time-resolved metabolic disparity in S. coelicolor A3(2) subjected to fermentative cultivation in two different types of media (R2YE and RSM3) in order to investigate secondary metabolite production pathways. The relative abundance of secondary metabolites, such as prodiginines, indoles, germicidins, and selected diketopiperazines, was increased in S. coelicolor A3(2) cultivated in R2YE medium compared to that in RSM3 medium, variably at the late-log and stationary phases of fermentative growth. Correlation analysis indicated that “antibiotic prodiginines” contributed maximally to the absorption maxima (A₅₃₀) of culture supernatants, indicating their optimal production at 96 hours in R2YE medium. A higher abundance of L-proline (48–72 hours) followed by prodiginines (96 hours) was evident, substantiating the intertwined links between precursor and activated prodiginines pathway. Similarly, the higher abundance of indoles was concurrent with tryptophan levels in the shikimate pathway, whereas diketopiperazines were synchronously abundant along with the levels of phenylalanine, leucine, and proline. Additionally, acetyl-CoA induced the acetate pathway, resulting in the production of germicidins. Thus, our results demonstrate that S. coelicolor A3(2) produces specific secondary metabolites by enhancing the dedicated metabolic pathway responsible for their production. In conclusion, our results from this study provide insight into the metabolic pathways of S. coelicolor A3(2), and can be applied to further optimize the production of prodiginines.