Plant-associated Microbes Research Articles

Appearance of green tea compounds in plasma following acute green tea consumption is modulated by the gut microbiome in mice.

Studies have suggested that phytochemicals in green tea have systemic anti-inflammatory and neuroprotective effects. However, the mechanisms behind these effects are poorly understood, possibly due to differential metabolism of phytochemicals resulting from variation in gut microbiome composition. To unravel this complex relationship, our team utilized a novel combined microbiome analysis and metabolomics approach applied to low complexity microbiome (LCM) and human colonized (HU) gnotobiotic mice treated with an acute dose of powdered matcha green tea. A total of 20 LCM mice received 10 distinct human fecal slurries for an n=2 mice per human gut microbiome; 9 LCM mice remained un-colonized with human slurries throughout the experiment. We performed untargeted metabolomics on green tea and plasma to identify green tea compounds that were found in plasma of LCM and HU mice that had consumed green tea. 16S ribosomal RNA gene sequencing was performed on feces of all mice at study end to assess microbiome composition. We found multiple green tea compounds in plasma associated with microbiome presence and diversity (including acetylagmatine, lactiflorin, and aspartic acid negatively associated with diversity). Additionally, we detected strong associations between bioactive green tea compounds in plasma and specific gut bacteria, including associations between spiramycin and Gemmiger, and between wildforlide and Anaerorhabdus. Additionally, some of the physiologically relevant green tea compounds are likely derived from plant-associated microbes, highlighting the importance of considering foods and food products as meta-organisms. Overall, we describe a novel workflow for discovering relationships between individual food compounds and composition of the gut microbiome.

Cotton-mycorrhizal symbiosis: a comprehensive review of benefits for sustainable agriculture

Abstract Fertilizers and plant protection chemicals have played crucial role in modern agriculture. However, their excessive and imbalanced use over decades has resulted in the degradation and deterioration of soil health. The sustainability of agricultural systems largely depends on improving soil health. In this context, the arbuscular mycorrhizal fungi (AMF) association is a well-known interaction among plant microbial symbiotic associations that plays a multifunctional role in maintaining plant-soil health. More than 90% of terrestrial crop plants, including cultivated cotton, have a mutualistic symbiotic association with AMF. Symbiosis provides several benefits, such as the acquisition of mineral nutrients (primarily phosphorus), protection against biotic and abiotic stresses, and improved yield and fiber quality, contributing to the growth and development of the host plant. Under controlled conditions, the percent root length colonization of cotton was 50 to 70%, indicating the potential of AMF as a biological agent and plant growth promoter for sustainable cotton production. This review provides an updated and comprehensive overview of cotton-mycorrhizal symbiosis and its benefits.

Genome sequences of Microvirga spp. CF3062 and CF3016 isolated from nodules found on herbarium specimens collected in 2004 and 2015.

We present the genomes of two Microvirga isolates isolated from nodules found on Medicago lupulina herbarium specimens at the Marion Ownbey Herbarium at Washington State University. These genomes and others from herbarium specimens offer an unprecedented opportunity to study the bacterial evolution of plant-associated microbes over long time scales.

From synthetic communities to synthetic ecosystems: exploring causalities in plant-microbe-environment interactions.

The plant microbiota research field has rapidly shifted from efforts aimed at gaining a descriptive understanding of microbiota composition to a focus on acquiring mechanistic insights into microbiota functions and assembly rules. This evolution was driven by our ability to establish comprehensive collections of plant-associated microbes and to reconstruct meaningful microbial synthetic communities (SynComs). We argue that this powerful deconstruction-reconstruction strategy can be used to reconstitute increasingly complex synthetic ecosystems (SynEcos) and mechanistically understand high-level biological organization. The transitioning from simple to more advanced, fully tractable and programmable gnotobiotic SynEcos is ongoing and aims at rationally simplifying natural ecosystems by engineering them. Such reconstitution ecology approaches represent an untapped strategy for bridging the gap between ecology and functional biology and for unraveling plant-microbiota-environment mechanisms that modulate ecosystem health, assembly, and functioning.

Effect of pathogen Globisporangium ultimum on plant growth and colonizing bacterial communities

Plants recruit plant-associated microbes from soil to enhance their growth and mitigate the adverse effects of pathogen invasion on plant health. How pathogens impact the interactions of the plant-associated microbes and plant growth is poorly understood. We established S-microsystems (sterile soil inoculated with 101 bacteria isolated from humus soil with Artemisia annua, Oryza sativa or Houttuynia cordata), and N-microsystems (natural soil with these plants) to evaluate the effects of the fungus Globisporangium ultimum on plant growth and their colonizing bacterial communities (CBCs). S-microsystems and N-microsystems were inoculated with and without G. ultimum, respectively. Their seedling growth and CBCs were investigated. Plant height and root numbers in A. annua, O. sativa and H. cordata S-microsystems with G. ultimum were 34.5 % and 52.8 %, 23.1 % and 31.3 %, 102.1 % and 45.0 % higher than those without G. ultimum, respectively. The CBCs were diverse among S-microsystems of A. annua, O. sativa and H. cordata, and the CBC abundances in the three S-microsystems without G. ultimum were higher than those with G. ultimum. The relative abundances of bacterial genera Rhizobium, Pseudomonas, Brevundimonas and Cupriavidus were significantly positively related to plant growth. We determined that the CBCs in A. annua, O. sativa and H. cordata were selective and related to the plant species, and can mitigate disadvantageous influences of G. ultimum on seedling growth. The plants and their CBCs’ abundance and composition were differentially affected by G. ultimum. Our results provide evidence that CBCs promote plant growth due to dynamic changes in the composition and abundance of CBC members, which were affected by plant species and biotic factors.

Plant-Associated Volatile Organic Compound (VOC) Database (PVD): A Resource Supporting Research on VOCs Produced by Plants and Plant-Associated Microbes

Diverse volatile organic compounds (VOCs) perform functions crucial for plant growth and health. However, studies on the nature and mechanisms of action of bioactive VOCs, except those mediating plant-insect interactions, lag considerably behind those on waterborne compounds. We built the Plant-Associated VOC Database (PVD) to facilitate research on VOCs released by plants and plant-associated microbes. This platform presents the physicochemical characteristics, biosynthetic pathways, and known or hypothesized functions of VOCs. We present the design, utility, and planned expansion of PVD. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Microbial Contributions to Heavy Metal Phytoremediation in Agricultural Soils: A Review.

Phytoremediation is a sustainable technique that employs plants to reinforce polluted environments such as agroecosystems. In recent years, new strategies involving the plant microbiome as an adjuvant in remediation processes have been reported. By leveraging this microbial assistance to remediate soils contaminated with heavy metals such As, Pb, Cd, Hg, and Cr, plants can sequester, degrade, or stabilize contaminants more efficiently. Remarkably, some plant species are known for their hyper-accumulative traits in synergy with their microbial partners and can successfully mitigate heavy metal pollutants. This sustainable biotechnology based on plant-microbe associations not only aids in environmental cleanup but also enhances biodiversity, improves soil structure, and promotes plant growth and health, making it a promising solution for addressing agro-pollution challenges worldwide. The current review article emphasizes the potential of synergistic plant-microbe interactions in developing practical and sustainable solutions for heavy metal remediation in agricultural systems, which are essential for food security.

Unveiling the positive impacts of the genus Rhodococcus on plant and environmental health

Organic farming has emerged as a sustainable solution to the adverse effects (diminished nutritional value, compromised food quality, environmental contamination, and public health hazards) that are usually associated with harmful chemical pesticides. To overcome such loss, one must explore the plant-associated microbes that are the naturally occurring root commensal and could positively improve crop health. In this review, we highlight the importance of the bacterial genus Rhodococcus, a subset of Actinobacteria that carries immense potential in enhancing crop yield and is associated with bioremediation of toxic pesticides and other chemicals to improve soil health. However, it has been noticed that few species of Rhodococcus are pathogenic for the plant (R. fascians) as well as humans/animals (R. equi). But still, the majority of Rhodococcus isolates are found to be non-pathogenic and carry substantial beneficial traits. Here, we have attempted to comprise those beneficial traits of the different members of the genus Rhodococcus. The main emphasis of this review article is to explore the major areas such as enzyme production, phytohormone synthesis, growth regulation, siderophore production, bioremediation, organic compound degradation, and environmental pollution control. Opinions towards the applications of advanced methodologies for utilizing the cumulative prospective potential of the genus Rhodococcus have also been discussed in the different sections of the review. Conclusively, this article gathers the scattered information from the past and recent literature about this bacteria and provides the future direction about how it can improve plant/soil health and eliminate toxic chemicals and environmental pollutants.

Plasmodiophora brassicae effector PbPE23 induces necrotic responses in both host and non-host plants.

Plasmodiophora brassicae is an obligate biotroph that causes clubroot disease in cruciferous plants, including canola and Arabidopsis. In contrast to most known bacterial, oomycete and fungal pathogens that colonize at the host apoplastic space, the protist P. brassicae establishes an intracellular colonization within various types of root cells and secretes a plethora of effector proteins to distinct cellular compartments favourable for survival and growth of the pathogen during pathogenesis. Identification and functional characterization of P. brassicae effectors has been hampered by the limited understanding of this unique pathosystem. Here, we report a P. brassicae effector, PbPE23, containing a Ser/Thr kinase domain, that induces necrosis after heterologous expression by leaf infiltration in both host and non-host plants. While PbPE23 is an active kinase, the kinase activity itself is not required for triggering the necrosis in plants. PbPE23 shows a nucleocytoplasmic localization in Nicotiana benthamiana and its N-terminal 25TPdPAQKQ32 sequence, resembling the contiguous hydrophilic TPAP motif and Q-rich region in many Nep1-like proteins (NLPs) from plant-associated microbes, is required for the induction of necrosis. Further, transcript profiling of PbPE23 reveals its high expression at the transition stages from primary to secondary infection, suggesting its potential involvement in the development of clubroot disease.

Diverse RNA viruses discovered in multiple seagrass species.

Seagrasses are marine angiosperms that form highly productive and diverse ecosystems. These ecosystems, however, are declining worldwide. Plant-associated microbes affect critical functions like nutrient uptake and pathogen resistance, which has led to an interest in the seagrass microbiome. However, despite their significant role in plant ecology, viruses have only recently garnered attention in seagrass species. In this study, we produced original data and mined publicly available transcriptomes to advance our understanding of RNA viral diversity in Zostera marina, Zostera muelleri, Zostera japonica, and Cymodocea nodosa. In Z. marina, we present evidence for additional Zostera marina amalgavirus 1 and 2 genotypes, and a complete genome for an alphaendornavirus previously evidenced by an RNA-dependent RNA polymerase gene fragment. In Z. muelleri, we present evidence for a second complete alphaendornavirus and near complete furovirus. Both are novel, and, to the best of our knowledge, this marks the first report of a furovirus infection naturally occurring outside of cereal grasses. In Z. japonica, we discovered genome fragments that belong to a novel strain of cucumber mosaic virus, a prolific pathogen that depends largely on aphid vectoring for host-to-host transmission. Lastly, in C. nodosa, we discovered two contigs that belong to a novel virus in the family Betaflexiviridae. These findings expand our knowledge of viral diversity in seagrasses and provide insight into seagrass viral ecology.

Exploring bioremediation strategies for heavy metals and POPs pollution: the role of microbes, plants, and nanotechnology

Heavy metal and Persistent Organic Pollutants (POPs) pollution stemming from industrialization, intensive agriculture, and other human activities pose significant environmental and health threats. These contaminants persist in the air, soil, and water, particularly in industrialized nations, adversely affecting human health and ecosystems. While physical and chemical methods exist for detoxifying contaminated soil, they often have drawbacks such as high cost and technical complexity. Bioremediation, utilizing plants and microbes, offers a promising solution. Certain microorganisms like Streptomyces, Aspergillus and plant species such as Hibiscus and Helianthus show high metal adsorption capacities, making them suitable for bioremediation. However, plants’ slow growth and limited remediation efficiency have been challenges. Recent advancements involve leveraging plant-associated microbes to enhance heavy metal removal. Additionally, nanotechnology, particularly nano-bioremediation, shows promise in efficiently removing contaminants from polluted environments by combining nanoparticles with bioremediation techniques. This review underscores bioremediation methods for heavy metals using plants and microbes, focusing on the role of Plant Growth Promoting Rhizobacteria (PGPR) in promoting phytoremediation. It also explores the implementation of nanotechnologies for eliminating metals from polluted soil, emphasizing the significance of soil microbiomes, nanoparticles, and contaminant interactions in developing effective nano-remediation strategies for optimizing agriculture in contaminated fields.

Association of Microbiome Diversity with Disease Symptoms in Brassica oleracea Leaves

Cabbage (Brassica oleracea), a crop of major economic importance worldwide, is affected by numerous diseases, which are caused by a wide range of microorganisms, including fungi, oomycetes, bacteria, and viruses, which lead to important losses in yield and quality. The increasing availability of reference genomes of plant-associated microbes together with recent advances in metagenomic approaches provide new opportunities to identify microbes linked to distinct symptomatology in Brassica leaves. In this study, shotgun metagenomics was used to investigate the microbial community in leaves of B. oleracea plants from agricultural farmlands. Compared with conventional techniques based on culture-based methods, whole-genome shotgun sequencing allows the reliable identification of the microbial population inhabiting a plant tissue at the species level. Asymptomatic and symptomatic leaves showing different disease symptoms were examined. In the asymptomatic leaves, Xanthomonas species were the most abundant taxa. The relative abundance of bacterial and fungal communities varied depending on disease symptoms on the leaf. The microbiome of the leaves showing mild to severe levels of disease was enriched in bacterial populations (Sphingomonas, Methylobacterium, Paracoccus) and to a lesser degree in some fungal taxa, such as Alternaria and Colletotrichum (e.g., in leaves with high levels of necrotic lesions). Sclerotinia species were highly abundant in severely damaged leaves (S. sclerotium, S. trifolium, S. bolearis), followed by Botrytis species. The common and specific bacterial and fungal species associated to disease symptoms were identified. Finally, the analysis of the gene functions in the metagenomic data revealed enrichment in carbohydrate-active enzymes potentially involved in pathogenicity, whose distribution also varied among disease severity groups. Understanding the B. oleracea leaf microbiome in agricultural ecosystems will pave the way for the efficient management of diseases in this crop.

The Root Endophytic Microbiome Shifts Under Drought in High-Performing Sorghum

Plant-associated microbes contribute to crop health and resilience, potentially extending or complementing plant traits under abiotic stress. Here we tested a series of hypotheses centered on the fungal mycobiome and bacterial microbiome of field-grown sorghum ( Sorghum bicolor), an emerging model crop for drought resilience, which we cultivated under arid conditions. Overall, the sorghum mycobiome and microbiome differed in composition between the exterior and interior of plant tissues, between roots and leaves, and among sorghum genotypes. We did not observe variation in fungal and bacterial endophytes among performance classes of sorghum when water was plentiful, but the root endophytic mycobiome and microbiome both shifted markedly under water limitation, with similar shifts in composition observed among multiple plant genotypes. The root endophytic microbiome of high-performing sorghum was especially responsive to water limitation. Network analysis suggested that water limitation did not directly remodel these root endophytic microbiomes, such that interactions of the microbiome with the host plant, rather than interactions among microbes within the microbiome, may be the most dynamic element of change when water is limited. Overall, our study points to shifts in the prevalence of particular taxa under abiotic stress and suggests that high-performing lines may have distinctive features as substrates or strategies for actively recruiting diverse, abundant, and distinctive microbial communities to roots under water limitation. Such findings are important in the arid lands that frame marginal agriculture today and comprise an increasing proportion of agriculture in a changing world.

Influence of humic acid on the p-tert-Butylphenol removal efficiency by Spirodela polyrhiza-Tas13 association

Plant-microbe remediation technique is considered as a promising technology in removal of organic pollutants and its remediation efficiency is largely affected by a variety of surrounding environmental factors. Humic acid (HA) is the complex organic substance ubiquitous in environment, which characterized by its surfactant-like micelle microstructure and various reaction activity. In our study, a plant-microbe association with high p-tert-Butylphenol (PTBP) degradation potential constructed by Spirodela polyrhiza and Sphingobium phenoxybenzoativorans Tas13 has been used, and the influence of HA on the PTBP degradation efficiency of S. polyrhiza-Tas13 association was investigated. The result showed that the presence of HA greatly improved PTBP removal efficiency of S. polyrhiza-Tas13. The reason accounted for this may be due to the presence of HA promoted bacterial cell propagation, altered bacterial cell wall permeability, increased catechol 2,3-dioxygenase (C23O) enzyme activity of strain Tas13, rather than increasing the colonization ability of strain Tas13 on to the root surface. This study will greatly facilitate the application of aquatic plant-microbe association in environmental remediation.

Prevalence and underlying mechanisms of phylosymbiosis in land plants

Abstract Phylosymbiosis, the congruence of microbiome composition with host phylogeny, is a valuable framework for investigating plant–microbe associations and their evolutionary ecology. This review assesses the prevalence of phylosymbiosis across the plant kingdom, elucidates the fundamental ecological and evolutionary processes contributing to its occurrence based on previous research and explores commonly used methods for identifying phylosymbiosis. We find that the presence of phylosymbiosis may be influenced by both phylogenetic distance and the taxonomic level at which host plants are examined, with the strength of associations potentially decreasing as the taxonomic scale becomes finer. Notably, the endophytic microbiome exhibits a stronger phylosymbiosis signal compared with the epiphytic or rhizosphere-associated microbiomes. Microorganisms such as fungi and bacteria can yield highly variable evidence for phylosymbiosis due to differences in colonization, transmission or functional characteristics. We also outline how the four community assembly processes (dispersal, selection, diversification and drift) contribute to the establishment and maintenance of host–microbe phylosymbiosis. Furthermore, we highlight the diversity of methods employed to detect phylosymbiosis, which involves three key processes: constructing host phylogenies, assessing microbial data and statistically evaluating the correlation between host phylogeny and microbial composition. Remarkably different methodologies across studies make comparisons between findings challenging. To advance our understanding, future research is expected to explore phylosymbiosis at lower taxonomic levels and investigate different microbial communities coexisting synergistically within the same host. Understanding the relative importance of community assembly processes in driving phylosymbiosis will be critical for gaining deeper insights into the ecology and evolution of host–microbe interactions.

Exploring the Hidden Treasures: Isolation, Characterization and Screening of Phosphate Solubilizing Bacteria (PSB) for Plant Growth-Promoting Traits from Chilli Field Weeds Rhizosphere

Plant-associated microbes affect growth, nutrient acquisition, tolerance to different stress conditions and etc. by the plant. However, beneficial microbes influencing weeds biosynthesis remain largely unexplored and unexploited. Phosphorus is one of essential macro-minerals for the growth and development of chilli plants. The main objective of this study was to isolate characterize and evaluation of the PGPR characters of PSB from weed rhizosphere of the chilli ecosystem. Totally 40 PSB isolates were isolated from different weeds in the chilli ecosystem and were subjected to biochemical characterization where 13 isolates were found positive for starch hydrolysis, 35 isolates were positive for acid production, 12isolates were positive for gas production, 40 isolates were positive for catalase production, 5 isolates were positive for H2S production, 13 isolates were positive for urease production and remaining all isolated were negative for the respective tests. Based on morphological and biochemical characterization, the isolates were tentatively identified as Bacillus sp and Pseudomonas sp.

Structure and dynamics of microbial communities associated with the resurrection plant Boea hygrometrica in response to drought stress.

The resurrection plant Boea hygrometrica selectively recruits and assembles drought-specific microbial communities across the plant-soil compartments, which may benefit plant growth and fitness under extreme drought conditions. Plant-associated microbes are essential for facilitating plant growth and fitness under drought stress. The resurrection plant Boea hygrometrica in natural habitats with seasonal rainfall can survive rapid desiccation, yet their interaction with microbiomes under drought conditions remains unexplored. This study examined the bacterial and fungal microbiome structure and drought response across plant-soil compartments of B. hygrometrica by high-throughput amplicon sequencing of 16S rRNA gene and internal transcribed spacer. Our results demonstrated that the diversity, composition, and functional profile of the microbial community varied considerably across the plant-soil compartments and were strongly affected by drought stress. Bacterial and fungal diversity was significantly reduced from soil to endosphere and belowground to aboveground compartments. The compartment-specific enrichment of the dominant bacteria phylum Cyanobacteriota and genus Methylorubrum in leaf endosphere, genera Pseudonocardia in rhizosphere soil and Actinoplanes in root endosphere, and fungal phylum Ascomycota in the aboveground compartments and genera Knufia in root endosphere and Cladosporium in leaf endosphere composed part of the core microbiota with corresponding enrichment of beneficial functions for plant growth and fitness. Moreover, the recruitment of dominant microbial genera Sphingosinicella and Plectosphaerella, Ceratobasidiaceae mycorrhizal fungi, and numerous plant growth-promoting bacteria involving nutrient supply and auxin regulation was observed in desiccated B. hygrometrica plants. Our results suggest that the stable assembled drought-specific microbial community of B. hygrometrica may contribute to plant survival under extreme environments and provide valuable microbial resources for the microbe-mediated drought tolerance enhancement in crops.

Insight into saffron associated microbiota from different origins and explore the endophytes for enhancement of bioactive compounds

Crocus sativus L. is a perennial crop for its valuable active compounds. Plant-associated microbes impact on the quality and efficacy of medicinal herbs by promoting bioactive components accumulation. However, how microbes influence the accumulation of bioactive components in saffron have not been well studied. Here, the microbiome in C. sativus derived from 3 core production areas were deciphered by 16S rDNA sequencing and the relationship between endophytes and bioactive ingredients were further investigated. The main results are as follows: (1) Both Comamonadaceae and Burkholderiaceae were positively correlated with the content of bioactive components in the stigmas. (2) The synthesis of crocin was positively correlated with Xanthomonadaceae, negatively correlated with Lachnospiraceae and Prevotellaceae. Therefore, further investigation is required to determine whether Xanthomonadaceae plays an unknown function in the synthesis of crocin. These findings provide guidelines for disentangling the function of endophytes in the production of bioactive ingredients and thus for microbe-mediated breeding.

Bioprospecting of endophytic diazotrophic microbes in sustainable agriculture: Review and prospects

Endophytic diazotrophic bacteria play an important role in developing sustainable modern agriculture. Endophytic bacteria can increase plant growth and yield by exhibiting antibiosis against phytopathogens. Biological mechanisms of atmospheric nitrogen fixation, phosphate solubilization, production of phytohormones and inhibition of plant pathogens and pests promote plant growth avoiding the need for chemical fertilizers and control agents. This review evaluates the groups of different endophytic bacteria, their prospects and challenges for sustainable agriculture. Several new bacterial strains were protected as bioinoculants or biopesticides. Formulations containing endophytic bacteria mainly were intended for seed coating or spraying and acted directly in the control of pests and diseases, as well as in increasing resistance to environmental stress. In many cases, they performed well in promoting the growth of plants by producing hormones that regulate or increase nutrient uptake. Bioprospecting in the case of this review is a systematic overview of the rational approach in harnessing beneficial plant-associated microbes to ensure food security in the future.

Leaf Endophytes Relationship with Host Metabolome Expression in Tropical Gymnosperms.

Plant-microbe interactions play a pivotal role in shaping host fitness, especially concerning chemical defense mechanisms. In cycads, establishing direct correlations between specific endophytic microbes and the synthesis of highly toxic defensive phytochemicals has been challenging. Our research delves into the intricate relationship between plant-microbe associations and the variation of secondary metabolite production in two closely related Zamia species that grow in distinct habitats; terrestrial and epiphytic. Employing an integrated approach, we combined microbial metabarcoding, which characterize the leaf endophytic bacterial and fungal communities, with untargeted metabolomics to test if the relative abundances of specific microbial taxa in these two Zamia species were associated with different metabolome profiles. The two species studied shared approximately 90% of the metabolites spanning diverse biosynthetic pathways: alkaloids, amino acids, carbohydrates, fatty acids, polyketides, shikimates, phenylpropanoids, and terpenoids. Co-occurrence networks revealed positive associations among metabolites from different pathways, underscoring the complexity of their interactions. Our integrated analysis demonstrated to some degree that the intraspecific variation in metabolome profiles of the two host species was associated with the abundance of bacterial orders Acidobacteriales and Frankiales, as well as the fungal endophytes belonging to the orders Chaetothyriales, Glomerellales, Heliotiales, Hypocreales, and Sordariales. We further associate individual metabolic similarity with four specific fungal endophyte members of the core microbiota, but no specific bacterial taxa associations were identified. This study represents a pioneering investigation to characterize leaf endophytes and their association with metabolomes in tropical gymnosperms, laying the groundwork for deeper inquiries into this complex domain.