A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application

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.

Unearthing the power of microbes as plant microbiome for sustainable agriculture

In recent years, research into the complex interactions and crosstalk between plants and their associated microbiota, collectively known as the plant microbiome has revealed the pivotal role of microbial communities for promoting plant growth and health. Plants have evolved intricate relationships with a diverse array of microorganisms inhabiting their roots, leaves, and other plant tissues. This microbiota mainly includes bacteria, archaea, fungi, protozoans, and viruses, forming a dynamic and interconnected network within and around the plant. Through mutualistic or cooperative interactions, these microbes contribute to various aspects of plant health and development. The direct mechanisms of the plant microbiome include the enhancement of plant growth and development through nutrient acquisition. Microbes have the ability to solubilize essential minerals, fix atmospheric nitrogen, and convert organic matter into accessible forms, thereby augmenting the nutrient pool available to the plant. Additionally, the microbiome helps plants to withstand biotic and abiotic stresses, such as pathogen attacks and adverse environmental conditions, by priming the plant's immune responses, antagonizing phytopathogens, and improving stress tolerance. Furthermore, the plant microbiome plays a vital role in phytohormone regulation, facilitating hormonal balance within the plant. This regulation influences various growth processes, including root development, flowering, and fruiting. Microbial communities can also produce secondary metabolites, which directly or indirectly promote plant growth, development, and health. Understanding the functional potential of the plant microbiome has led to innovative agricultural practices, such as microbiome-based biofertilizers and biopesticides, which harness the power of beneficial microorganisms to enhance crop yields while reducing the dependency on chemical inputs. In the present review, we discuss and highlight research gaps regarding the plant microbiome and how the plant microbiome can be used as a source of single and synthetic bioinoculants for plant growth and health.

Disease Resistance Correlates with Core Microbiome Diversity in Cotton

Understanding the resident microbial communities and their above and below ground interactions with plants will provide necessary information for crop disease protection and stress management. In this study, we show how diversity of core microbiome varies with disease susceptibility of a crop. To test this hypothesis, we have focused on identifying the core microbial species of cotton leaf curl disease (CLCuD) susceptible Gossypium hirsutum and CLCuD resistant Gossypium arboreum under viral infestation. Derivation of core membership is challenging as it depends on an occupancy threshold of microbial species in a sampling pool, whilst accounting for different plant compartments. We have used an abundance-occupancy distribution approach where we dynamically assess the threshold for core membership, whilst marginalizing for occupancy in four compartments of the cotton plant, namely, leaf epiphyte, leaf endophyte, rhizosphere, and root endophyte. Additionally, we also fit a neutral model to the returned core species to split them into three groups, those that are neutral, those that are selected by the plant environment, and finally those that are dispersal limited. We have found strong inverse relationship between diversity of core microbiome and disease susceptibility with the resistant variety, G. arboreum, possessing higher diversity of microbiota. A deeper understanding of this association will aid in the development of biocontrol agents for improving plant immunity against biotrophic pathogens.

Response of sweet potato cultivars to Bacillus velezensis T149-19 and Bacillus safensis T052-76 used as biofertilizers

The global market of sweet potato (Ipomoea batatas (L.) Lam.) is continuously growing and, consequently, demands greater productivity from the agricultural sector. The use of biofertilizers facilitates plant growth by making essential nutrients available to crops or providing resistance against different abiotic and biotic factors. The strains Bacillus safensis T052-76 and Bacillus velezensis T149-19 have previously been inoculated in the sweet potato cultivar Ourinho, showing positive effects on plant shoot growth and inhibiting the phytopathogen Plenodomus destruens. To elucidate the effects of these strains on sweet potato growth, four different cultivars of sweet potato were selected: Capivara, IAPAR 69, Rosinha de Verdan and Roxa. The plants were grown in pots in a greenhouse and inoculated with the combined strains according to a randomized block design. A control (without the inoculation of both strains) was also used. A slight positive effect of the inoculation of the two Bacillus strains was observed on the aerial parts of some of the cultivars. An increase in the fresh weight of the sweet potatoes of the inoculated plants was obtained, varying from 2.7 to 11.4 %. The number of sweet potatoes obtained from the inoculated cultivars IAPAR 69 and Roxa increased 15.2 % and 16.7 %, respectively. The rhizosphere soil of each cultivar was further sampled for DNA extraction, and the 16S rRNA gene metabarcoding technique was used to determine how the introduction of these Bacillus strains influenced the rhizosphere bacterial community. The bacterial communities of the four different cultivars were dominated by Actinobacteria, Proteobacteria and Firmicutes. Nonmetric multidimensional scaling (NMDS) revealed that the rhizosphere bacterial communities of plants inoculated with Bacillus strains were more similar to each other than to the bacterial communities of uninoculated plants. This study highlights the contribution of these Bacillus strains to the promotion of sweet potato growth.

Natural fermentation of fresh Jasmine flowers inspired the development of a biotechnological ingredient with global anti-ageing properties

OBJECTIVE

This study focused on the development of a new-to-world ingredient harnessing the natural potential of fresh Jasminum grandiflorum flowers to self-ferment by its phytobiome revealing flower content. Analytical investigations were conducted to highlight specific phytocompounds generated during the natural fermentation of flowers in comparison to a conventional extraction. The synergy with another extraction technology maximized the generation of biocompounds for an interesting efficacy.

METHODS

Jasmine extract was elaborated by combining two patented technologies: the phytofermentology™, inspired by plant-microorganisms interaction and designed to develop ingredients obtained by natural fermentation of the vegetal using its own phytobiota; and the PSR™ technology allowing the extraction of bioactive phytocompounds such as small RNAs from plants.

RESULTS

Analytical investigations of Jasmine extract highlighted uniqueness and richness of the phytocompound profiles, such as organics acids and phenolic compounds, markers of fermentation only obtained after phytofermentology in comparison to conventional extraction. Jasmine extract has the particularity to contain jasmintides, flower small peptides belonging to the family of cysteine-rich peptides (CRPs). Antioxidant and global anti-ageing properties were investigated in cell-free assays demonstrating interesting results: about 20% scavenging of free radicals from 0.5% of Jasmine extract and protection from DNA damage of 26% in comparison to a stressed control.

CONCLUSION

Phytofermentology™ technology combined with PSR™ technology, meant to be respectful of the environment, allowed to development of biofunctionals very close to nature with a unique analytical signature as Jasmine extract, using the potential of fresh flowers phytobiota to self-ferment. The efficacy of the ingredient on global antioxidation and anti-ageing via hyaluronidase/tyrosinase inhibitions was highlighted by cell-free evaluation assays. Further and complementary studies should be conducted to confirm the bioefficacy of this ingredient with in vitro / ex vivo assays.

Medicinal Plant Root Exudate Metabolites Shape the Rhizosphere Microbiota

The interactions between plants and rhizosphere microbes mediated by plant root exudates are increasingly being investigated. The root-derived metabolites of medicinal plants are relatively diverse and have unique characteristics. However, whether medicinal plants influence their rhizosphere microbial community remains unknown. How medicinal plant species drive rhizosphere microbial community changes should be clarified. In this study involving high-throughput sequencing of rhizosphere microbes and an analysis of root exudates using a gas chromatograph coupled with a time-of-flight mass spectrometer, we revealed that the root exudate metabolites and microorganisms differed among the rhizosphere soils of five medicinal plants. Moreover, the results of a correlation analysis indicated that bacterial and fungal profiles in the rhizosphere soils of the five medicinal plants were extremely significantly or significantly affected by 10 root-associated metabolites. Furthermore, among the 10 root exudate metabolites, two (carvone and zymosterol) had opposite effects on rhizosphere bacteria and fungi. Our study findings suggest that plant-derived exudates modulate changes to rhizosphere microbial communities.

Species pool and soil properties in mangrove habitats influence the species-immigration process of diazotrophic communities across southern China

Microbial immigration is an ecological process in natural environments; however, the ecological trade-off mechanisms that govern the balance between species extinction and migration are still lacking. In this study, we investigated the mechanisms underlying the migration of diazotrophic communities from soil to leaves across six natural mangrove habitats in southern China. The results showed that the diazotrophic alpha and beta diversity exhibited significant regional and locational variations. The diazotrophic species pool gradually increased from the leaves to nonrhizosphere soil at each site, exhibiting a vertical distribution pattern. Mantel test analyses suggested that climate factors, particularly mean annual temperature, significantly influenced the structure of the diazotrophic community. The diazotrophic community assembly was mainly governed by dispersal limitation in soil and root samples, whereas dispersal limitation and ecological drift were dominant in leaves. Partial least squares path modeling revealed that the species pool and soil properties, particularly the oxidation-reduction potential and pH, were closely linked to the species-immigration ratio of diazotrophic communities. Our study provides novel insights for understanding the ecological trait diversity patterns and spread pathways of functional microbial communities between below- and aboveground habitats in natural ecosystems.IMPORTANCEEnvironmental selection plays key roles in microbial transmission. In this study, we have provided a comprehensive framework to elucidate the driving patterns of the ecological trade-offs in diazotrophic communities across large-scale mangrove habitats. Our research revealed that Bradyrhizobium japonicum, Marinobacterium lutimaris, and Agrobacterium tumefaciens were more abundant in root-associated soil than in leaves by internal and external pathways. The nonrhizospheric and rhizospheric soil samples harbored the most core amplicon sequence variants, indicating that these dominant diazotrophs could adapt to broader ecological niches. Correlation analysis indicated that the diversities of the diazotrophic community were regulated by biotic and abiotic factors. Furthermore, this study found a lower species immigration ratio in the soil than in the leaves. Both species pool and soil properties regulate the species-immigration mechanisms of the diazotrophic community. These results suggest that substantial species immigration is a widespread ecological process, leading to alterations in local community diversity across diverse host environments.

Rhizosphere-xylem sap connections in the olive tree microbiome: implications for biostimulation approaches

AIMS

Climate change is endangering olive groves. Farmers are adapting by exploring new varieties of olive trees and examining the role of microbiomes in plant health.The main objectives of this work were to determine the primary factors that influence the microbiome of olive trees and to analyze the connection between the rhizosphere and endosphere compartments.

METHODS AND RESULTS

The rhizosphere and xylem sap microbiomes of two olive tree varieties were characterized by next-generation 16S rRNA amplicon sequencing, and soil descriptors were analyzed. Bacterial communities in the rhizosphere of olive trees were more diverse than those found in the xylem sap. Pseudomonadota, Actinobacteriota, Acidobacteriota, and Bacillota were the dominant phyla in both compartments. At the genus level, only very few taxa were shared between soil and sap bacterial communities.

CONCLUSIONS

The composition of the bacteriome was more affected by the plant compartment than by the olive cultivar or soil properties, and a direct route from the rhizosphere to the endosphere could not be confirmed. The large number of plant growth-promoting bacteria found in both compartments provides promising prospects for improving agricultural outcomes through microbiome engineering.

Endophytic diazotrophic communities from rice roots are diverse and weakly associated with soil diazotrophic community composition and soil properties

AIM

Bacteria that promote plant growth, such as diazotrophs, are valuable tools for achieving a more sustainable production of important non-legume crops like rice. Different strategies have been used to discover new bacteria capable of promoting plant growth. This work evaluated the contribution of soil diazotrophs to the endophytic communities established in the roots of rice seedlings cultivated on seven representative soils from Uruguay.

METHODS AND RESULTS

The soils were classified into two groups according to the C and clay content. qPCR, terminal restriction fragment length polymorphism (T-RFLP), and 454-pyrosequencing of the nifH gene were used for analyzing diazotrophs in soil and plantlets' roots grown from seeds of the same genotype for 25 days under controlled conditions. A similar nifH abundance was found among the seven soils, roots, or leaves. The distribution of diazotrophs was more uneven in roots than in soils, with dominance indices significantly higher than in soils (nifH T-RFLP). Dominant soils' diazotrophs were mainly affiliated to Alphaproteobacteria and Planctomycetota. Conversely, Alpha, Beta, Gammaproteobacteria, and Bacillota were predominant in different roots, though undetectable in soils. Almost no nifH sequences were shared between soils and roots.

CONCLUSIONS

Root endophytic diazotrophs comprised a broader taxonomic range of microorganisms than diazotrophs found in soils from which the plantlets were grown and showed strong colonization patterns.

Lipid transfer protein StLTPa enhances potato disease resistance against different pathogens by binding and disturbing the integrity of pathogens plasma membrane

Potato is the third most important food crop worldwide. Potato production suffers from severe diseases caused by multiple detrimental plant pathogens, and broad-spectrum disease resistance genes are rarely identified in potato. Here we identified the potato non-specific lipid transfer protein StLTPa, which enhances species none-specific disease resistance against various pathogens, such as the oomycete pathogen Phytophthora infestans, the fungal pathogens Botrytis cinerea and Verticillium dahliae, and the bacterial pathogens Pectobacterium carotovorum and Ralstonia solanacearum. The StLTPa overexpression potato lines do not show growth penalty. Furthermore, we provide evidence that StLTPa binds to lipids present in the plasma membrane (PM) of the hyphal cells of P. infestans, leading to an increased permeability of the PM. Adding of PI(3,5)P2 and PI(3)P could compete the binding of StLTPa to pathogen PM and reduce the inhibition effect of StLTPa. The lipid-binding activity of StLTPa is essential for its role in pathogen inhibition and promotion of potato disease resistance. We propose that StLTPa enhances potato broad-spectrum disease resistance by binding to, and thereby promoting the permeability of the PM of the cells of various pathogens. Overall, our discovery illustrates that increasing the expression of a single gene in potato enhances potato disease resistance against different pathogens without growth penalty.

Bacillus B2 promotes root growth and enhances phosphorus absorption in apple rootstocks by affecting MhMYB15

Due to the chelation of phosphorus in the soil, it becomes unavailable for plant growth and development. The mechanisms by which phosphorus-solubilizing bacteria activate immobilized phosphorus to promote the growth and development of woody plants, as well as the intrinsic molecular mechanisms, are not clear. Through the analysis of microbial communities in the rhizosphere 16S V3-V4 and a homologous gene encoding microbial alkaline phosphomonoesterase (phoD) in phosphate-efficient (PE) and phosphate-inefficient apple rootstocks, it was found that PE significantly enriched beneficial rhizobacteria. The best phosphorus-solubilizing bacteria, Bacillus sp. strain 7DB1 (B2), was isolated, purified, and identified from the rhizosphere soil of PE rootstocks. Incubating with Bacillus B2 into the rhizosphere of apple rootstocks significantly increased the soluble phosphorus and flavonoid content in the rhizosphere soil. Simultaneously, this process stimulates the root development of the rootstocks and enhances plant phosphorus uptake. After root transcriptome sequencing, candidate transcription factor MhMYB15, responsive to Bacillus B2, was identified through heatmap and co-expression network analysis. Yeast one-hybrid, electrophoretic mobility shift assay, and LUC assay confirmed that MhMYB15 can directly bind to the promoter regions of downstream functional genes, including chalcone synthase MhCHS2 and phosphate transporter MhPHT1;15. Transgenic experiments with MhMYB15 revealed that RNAi-MhMYB15 silenced lines failed to induce an increase in flavonoid content and phosphorus levels in the roots under the treatment of Bacillus B2, and plant growth was slower than the control. In conclusion, MhMYB15 actively responds to Bacillus B2, regulating the accumulation of flavonoids and the uptake of phosphorus, thereby influencing plant growth and development.

Uncovering the effect of waterlogging stress on plant microbiome and disease development: current knowledge and future perspectives

Waterlogging is a constant threat to crop productivity and ecological biodiversity. Plants face multiple challenges during waterlogging stress like metabolic reprogramming, hypoxia, nutritional depletion, reduction in gaseous exchange, pH modifications, microbiome alterations and disease promotion all of which threaten plants survival. Due to global warming and climatic change, the occurrence, frequency and severity of flooding has dramatically increased posing a severe threat to food security. Thus, developing innovative crop management technologies is critical for ensuring food security under changing climatic conditions. At present, the top priority among scientists is to find nature-based solutions to tackle abiotic or biotic stressors in sustainable agriculture in order to reduce climate change hazards to the environment. In this regard, utilizing plant beneficial microbiome is one of the viable nature based remedial tool for mitigating abiotic stressors like waterlogging. Beneficial microbiota provides plants multifaceted benefits which improves their growth and stress resilience. Plants recruit unique microbial communities to shield themselves against the deleterious effects of biotic and abiotic stress. In comparison to other stressors, there has been limited studies on how waterlogging stress affects plant microbiome structure and their functional traits. Therefore, it is important to understand and explore how waterlogging alters plant microbiome structure and its implications on plant survival. Here, we discussed the effect of waterlogging stress in plants and its microbiome. We also highlighted how waterlogging stress promotes pathogen occurrence and disease development in plants. Finally, we highlight the knowledge gaps and areas for future research directions on unwiring how waterlogging affects plant microbiome and its functional traits. This will pave the way for identifying resilient microbiota that can be engineered to promote their positive interactions with plants during waterlogging stress.

Mechanistic and future prospects in rhizospheric engineering for agricultural contaminants removal, soil health restoration, and management of climate change stress

Climate change, food insecurity, and agricultural pollution are all serious challenges in the twenty-first century, impacting plant growth, soil quality, and food security. Innovative techniques are required to mitigate these negative outcomes. Toxic heavy metals (THMs), organic pollutants (OPs), and emerging contaminants (ECs), as well as other biotic and abiotic stressors, can all affect nutrient availability, plant metabolic pathways, agricultural productivity, and soil-fertility. Comprehending the interactions between root exudates, microorganisms, and modified biochar can aid in the fight against environmental problems such as the accumulation of pollutants and the stressful effects of climate change. Microbes can inhibit THMs uptake, degrade organic pollutants, releases biomolecules that regulate crop development under drought, salinity, pathogenic attack and other stresses. However, these microbial abilities are primarily demonstrated in research facilities rather than in contaminated or stressed habitats. Despite not being a perfect solution, biochar can remove THMs, OPs, and ECs from contaminated areas and reduce the impact of climate change on plants. We hypothesized that combining microorganisms with biochar to address the problems of contaminated soil and climate change stress would be effective in the field. Despite the fact that root exudates have the potential to attract selected microorganisms and biochar, there has been little attention paid to these areas, considering that this work addresses a critical knowledge gap of rhizospheric engineering mediated root exudates to foster microbial and biochar adaptation. Reducing the detrimental impacts of THMs, OPs, ECs, as well as abiotic and biotic stress, requires identifying the best root-associated microbes and biochar adaptation mechanisms.

Invisible Inhabitants of Plants and a Sustainable Planet: Diversity of Bacterial Endophytes and their Potential in Sustainable Agriculture

Uncontrolled usage of chemical fertilizers, climate change due to global warming, and the ever-increasing demand for food have necessitated sustainable agricultural practices. Removal of ever-increasing environmental pollutants, treatment of life-threatening diseases, and control of drug-resistant pathogens are also the need of the present time to maintain the health and hygiene of nature, as well as human beings. Research on plant-microbe interactions is paving the way to ameliorate all these sustainably. Diverse bacterial endophytes inhabiting the internal tissues of different parts of the plants promote the growth and development of their hosts by different mechanisms, such as through nutrient acquisition, phytohormone production and modulation, protection from biotic or abiotic challenges, assisting in flowering and root development, etc. Notwithstanding, efficient exploitation of endophytes in human welfare is hindered due to scarce knowledge of the molecular aspects of their interactions, community dynamics, in-planta activities, and their actual functional potential. Modern "-omics-based" technologies and genetic manipulation tools have empowered scientists to explore the diversity, dynamics, roles, and functional potential of endophytes, ultimately empowering humans to better use them in sustainable agricultural practices, especially in future harsh environmental conditions. In this review, we have discussed the diversity of bacterial endophytes, factors (biotic as well as abiotic) affecting their diversity, and their various plant growth-promoting activities. Recent developments and technological advancements for future research, such as "-omics-based" technologies, genetic engineering, genome editing, and genome engineering tools, targeting optimal utilization of the endophytes in sustainable agricultural practices, or other purposes, have also been discussed.

Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling

Engineering natural microbiomes for biotechnological applications remains challenging, as metabolic interactions within microbiomes are largely unknown, and practical principles and tools for microbiome engineering are still lacking. Here, we present a combinatory top-down and bottom-up framework to engineer natural microbiomes for the construction of function-enhanced synthetic microbiomes. We show that application of herbicide and herbicide-degrader inoculation drives a convergent succession of different natural microbiomes toward functional microbiomes (e.g., enhanced bioremediation of herbicide-contaminated soils). We develop a metabolic modeling pipeline, SuperCC, that can be used to document metabolic interactions within microbiomes and to simulate the performances of different microbiomes. Using SuperCC, we construct bioremediation-enhanced synthetic microbiomes based on 18 keystone species identified from natural microbiomes. Our results highlight the importance of metabolic interactions in shaping microbiome functions and provide practical guidance for engineering natural microbiomes.

Evolution and adaptation of terrestrial plant-associated Plantibacter species into remote marine environments

Microbes are thought to be distributed and circulated around the world, but the connection between marine and terrestrial microbiomes remains largely unknown. We use Plantibacter, a representative genus associated with plants, as our research model to investigate the global distribution and adaptation of plant-related bacteria in plant-free environments, particularly in the remote Southern Ocean and the deep Atlantic Ocean. The marine isolates and their plant-associated relatives shared over 98% whole-genome average nucleotide identity (ANI), indicating recent divergence and ongoing speciation from plant-related niches to marine environments. Comparative genomics revealed that the marine strains acquired new genes via horizontal gene transfer from non-Plantibacter species and refined existing genes through positive selection to improve adaptation to new habitats. Meanwhile, marine strains retained the ability to interact with plants, such as modifying root system architecture and promoting germination. Furthermore, Plantibacter species were found to be widely distributed in marine environments, revealing an unrecognized phenomenon that plant-associated microbiomes have colonized the ocean, which could serve as a reservoir for plant growth-promoting microbes. This study demonstrates the presence of an active reservoir of terrestrial plant growth-promoting bacteria in remote marine systems and advances our understanding of the microbial connections between plant-associated and plant-free environments at the genome level.

The interplay between the inoculation of plant growth-promoting rhizobacteria and the rhizosphere microbiome and their impact on plant phenotype

Microbial inoculation stands as a pivotal strategy, fostering symbiotic relationships between beneficial microorganisms and plants, thereby enhancing nutrient uptake, bolstering resilience against environmental stressors, and ultimately promoting healthier and more productive plant growth. However, while the advantageous roles of inoculants are widely acknowledged, the precise and nuanced impacts of inoculation on the intricate interactions of the rhizosphere microbiome remain significantly underexplored. This study explores the impact of bacterial inoculation on soil properties, plant growth, and the rhizosphere microbiome. By employing various bacterial strains and a synthetic community (SynCom) as inoculants in common bean plants, the bacterial and fungal communities in the rhizosphere were assessed through 16 S rRNA and ITS gene sequencing. Concurrently, soil chemical parameters, plant traits, and gene expression were evaluated. The findings revealed that bacterial inoculation generally decreased pH and V%, while increasing H+Al and m% in the rhizosphere. It also decreased gene expression in plants related to detoxification, photosynthesis, and defense mechanisms, while enhancing bacterial diversity in the rhizosphere, potentially benefiting plant health. Specific bacterial strains showed varied impacts on rhizosphere microbiome assembly, predominantly affecting rhizospheric bacteria more than fungi, indirectly influencing soil conditions and plants. Notably, Paenibacillus polymyxa inoculation improved plant nitrogen (by 5.2%) and iron levels (by 28.1%), whereas Bacillus cereus boosted mycorrhization rates (by 70%). Additionally, inoculation led to increased complexity in network interactions within the rhizosphere (∼15%), potentially impacting plant health. Overall, the findings highlight the significant impact of introducing bacteria to the rhizosphere, enhancing nutrient availability, microbial diversity, and fostering beneficial plant-microbe interactions.

Epiphytic and endophytic bacteria on Camellia oleifera phyllosphere: exploring region and cultivar effect

The epiphytic and endophytic bacteria play an important role in the healthy growth of plants. Both plant species and growth environmental influence the bacterial population diversity, yet it is inconclusive whether it is the former or the latter that has a greater impact. To explore the communities of the epiphytic and endophytic microbes in Camellia oleifera, this study assessed three representative C. oleifera cultivars from three areas in Hunan, China by Illumina high-throughput sequencing. The results showed that the diversity and species richness of endophytic microbial community in leaves were significantly higher than those of microbial community in the epiphytic. The diversity and species richness of epiphytic and endophytic microbes are complex when the same cultivar was grown in different areas. The C. oleifera cultivars grown in Youxian had the highest diversity of epiphytic microbial community, but the lowest abundance, while the cultivars grown in Changsha had the highest diversity and species richness of endophytic microbes in leaves. It was concluded that the dominant phylum mainly included Proteobacteria, Actinobacteriota and Firmicutes through the analysis of the epiphytic and endophytic microbial communities of C. oleifera. The species and relative abundances of epiphytic and endophytic microbial community were extremely different at the genus level. The analysis of NMDS map and PERMANOVA shows that the species richness and diversity of microbial communities in epiphytes are greatly influenced by region. However, the community structure of endophytic microorganisms in leaves is influenced by region and cultivated varieties, but the influence of cultivars is more significant. Molecular ecological network analysis showed that the symbiotic interaction of epiphytic microbial community was more complex.

Root-secreted nucleosides: signaling chemoattractants of rhizosphere bacteria

The rhizosphere is a complex ecosystem, consisting of a narrow soil zone influenced by plant roots and inhabited by soil-borne microorganisms. Plants actively shape the rhizosphere microbiome through root exudates. Some metabolites are signaling molecules specifically functioning as chemoattractants rather than nutrients. These elusive signaling molecules have been sought for several decades, and yet little progress has been made. Root-secreted nucleosides and deoxynucleosides were detected in exudates of various plants by targeted ultra-performance liquid chromatography-mass spectrometry/mass spectrometry. Rhizobacteria were isolated from the roots of Helianthemum sessiliflorum carrying the mycorrhizal desert truffle Terfezia boudieri. Chemotaxis was determined by a glass capillary assay or plate assays on semisolid agar and through a soil plate assay. Nucleosides were identified in root exudates of plants that inhabit diverse ecological niches. Nucleosides induced positive chemotaxis in plant beneficial bacteria Bacillus pumilus, Bacillus subtilis, Pseudomonas turukhanskensis spp., Serratia marcescens, and the pathogenic rhizobacterium Xanthomonas campestris and E coli. In a soil plate assay, nucleosides diffused to substantial distances and evoked chemotaxis under conditions as close as possible to natural environments. This study implies that root-secreted nucleosides are involved in the assembly of the rhizosphere bacterial community by inducing chemotaxis toward plant roots. In animals, nucleoside secretion known as "purinergic signaling" is involved in communication between cells, physiological processes, diseases, phagocytic cell migration, and bacterial activity. The coliform bacterium E. coli that inhabits the lower intestine of warm-blooded organisms also attracted to nucleosides, implying that nucleosides may serve as a common signal for bacterial species inhabiting distinct habitats. Taken together, all these may indicate that chemotaxis signaling by nucleosides is a conserved universal mechanism that encompasses living kingdoms and environments and should be given further attention in plant rhizosphere microbiome research.

Microbial diversity and functions in saline soils: A review from a biogeochemical perspective

BACKGROUND

Soil salinization threatens food security and ecosystem health, and is one of the important drivers to the degradation of many ecosystems around the world. Soil microorganisms have extremely high diversity and participate in a variety of key ecological processes. They are important guarantees for soil health and sustainable ecosystem development. However, our understanding of the diversity and function of soil microorganisms under the change of increased soil salinization is fragmented.

AIM OF REVIEW

Here, we summarize the changes in soil microbial diversity and function under the influence of soil salinization in diverse natural ecosystems. We particularly focus on the diversity of soil bacteria and fungi under salt stress and the changes in their emerging functions (such as their mediated biogeochemical processes). This study also discusses how to use the soil microbiome in saline soils to deal with soil salinization for supporting sustainable ecosystems, and puts forward the knowledge gaps and the research directions that need to be strengthened in the future.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Due to the rapid development of molecular-based biotechnology (especially high-throughput sequencing technology), the diversity and community composition and functional genes of soil microorganisms have been extensively characterized in different habitats. Clarifying the responding pattern of microbial-mediated nutrient cycling under salt stress and developing and utilizing microorganisms to weaken the adverse effects of salt stress on plants and soil, which are of guiding significance for agricultural production and ecosystem management in saline lands.

Plant Growth-Promoting Bacteria Influence Microbial Community Composition and Metabolic Function to Enhance the Efficiency of Hybrid pennisetum Remediation in Cadmium-Contaminated Soil

The green and efficient remediation of soil cadmium (Cd) is an urgent task, and plant-microbial joint remediation has become a research hotspot due to its advantages. High-throughput sequencing and metabolomics have technical advantages in analyzing the microbiological mechanism of plant growth-promoting bacteria in improving phytoremediation of soil heavy metal pollution. In this experiment, a pot trial was conducted to investigate the effects of inoculating the plant growth-promoting bacterium Enterobacter sp. VY on the growth and Cd remediation efficiency of the energy plant Hybrid pennisetum. The test strain VY-1 was analyzed using high-throughput sequencing and metabolomics to assess its effects on microbial community composition and metabolic function. The results demonstrated that Enterobacter sp. VY-1 effectively mitigated Cd stress on Hybrid pennisetum, resulting in increased plant biomass, Cd accumulation, and translocation factor, thereby enhancing phytoremediation efficiency. Analysis of soil physical-chemical properties revealed that strain VY-1 could increase soil total nitrogen, total phosphorus, available phosphorus, and available potassium content. Principal coordinate analysis (PCoA) indicated that strain VY-1 significantly influenced bacterial community composition, with Proteobacteria, Firmicutes, Chloroflexi, among others, being the main differential taxa. Redundancy analysis (RDA) revealed that available phosphorus, available potassium, and pH were the primary factors affecting bacterial communities. Partial Least Squares Discriminant Analysis (PLS-DA) demonstrated that strain VY-1 modulated the metabolite profile of Hybrid pennisetum rhizosphere soil, with 27 differential metabolites showing significant differences, including 19 up-regulated and eight down-regulated expressions. These differentially expressed metabolites were primarily involved in metabolism and environmental information processing, encompassing pathways such as glutamine and glutamate metabolism, α-linolenic acid metabolism, pyrimidine metabolism, and purine metabolism. This study utilized 16S rRNA high-throughput sequencing and metabolomics technology to investigate the impact of the plant growth-promoting bacterium Enterobacter sp. VY-1 on the growth and Cd enrichment of Hybrid pennisetum, providing insights into the regulatory role of plant growth-promoting bacteria in microbial community structure and metabolic function, thereby improving the microbiological mechanisms of phytoremediation.

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.

Cereals can trap endophytic bacteria with potential beneficial traits when grown ex-situ in harsh soils

Microbial communities associated with plants growing in harsh conditions, including salinity and water deficiency, have developed adaptive features which permit them to grow and survive under extreme environmental conditions. In the present study, an ex-situ plant trapping method has been applied to collect the culturable microbial diversity associated with the soil from harsh and remote areas. Oryza sativa cv. Baldo and Triticum durum Primadur plants were used as recruiters, while the soil surrounding the roots of Oryza glaberrima plants from remote regions of Mali (West Africa) was used as substrate for their growth. The endophytic communities recruited by the two plant species belonged to Proteobacteria and Firmicutes, and the dominant genera were Bacillus, Kosakonia, and Enterobacter. These endophytes were characterized by analyzing some of the most common plant growth promoting traits. Halotolerant, inorganic phosphate-solubilizing and N-fixing strains were found, and some of them simultaneously showing these three traits. We verified that 'Baldo' recruited mostly halotolerant and P-solubilizers endophytes, while the endophytes selected by 'Primadur' were mainly N-fixers. The applied ex-situ plant trapping method allowed to isolate endophytes with potential beneficial traits that could be applied for the improvement of rice and wheat growth under adverse environmental conditions.

Halophytic Bacterial Endophyte Microbiome from Coastal Desert-Adapted Wild Poaceae Alleviates Salinity Stress in the Common Wheat Triticum aestivum L

Abiotic stresses threaten the strategic crops of Poaceae (Gramineae) worldwide. Habitat-adapted microbiome of wild plants has the potential to alleviate abiotic stresses in alternate hosts. Persian Gulf's coastal deserts are colonized by halophyte plants hosting habitat-adapted halophytic microbiota. Here, endophytic bacteria from wild Poaceae in coastal deserts of the north Persian Gulf at Hormozgan province, Iran, were isolated and screened for mitigating salinity stress in wheat. Accordingly, seven dominant species of wild Poaceae in the region, i.e., Aeloropus lagopoides, Aeloropus litiralis, Chrysopogon aucheri, Cymbopogon olivieri, Desmostachya sp., Halopayrum mucronatum, and Sporbuls arabicus, were explored. In total, 367 endophytic bacteria were isolated, 90 of which tolerated 2.5-M NaCl. Of these, 38 strains were selected based on their bioactivity and applied for in vitro wheat-interaction assays under 250-mM NaCl stress. Five superior strains promoted seed germination and growth indices in rain-fed winter wheat cv. Sardari, i.e., Bacillus subtilis B14, B19, & B27, Bacillus sp. B21, and Bacillus licheniformis Ba38. In planta assays in saline soil (2.7 dS m-1) using the superior strains indicated that Bacillus sp. B21 and Bacillus licheniformis Ba38 increased germination and root and shoot lengths and their dry and fresh weights in wheat seedlings. Moreover, phenolics and flavonoids contents of wheat seedlings were influenced by endophyte application. Thus, the coastal desert-adapted microbiome of wild Poaceae could alleviate abiotic stress and promote growth in cultivated species of Poaceae, such as wheat.

Rhizosphere microbial markers (micro-markers): A new physical examination indicator for traditional Chinese medicines

Rhizosphere microorganisms, as one of the most important components of the soil microbiota and plant holobiont, play a key role in the medicinal plant-soil ecosystem, which are closely related to the growth, adaptability, nutrient absorption, stress tolerance and pathogen resistance of host plants. In recent years, with the wide application of molecular biology and omics technologies, the outcomes of rhizosphere microorganisms on the health, biomass production and secondary metabolite biosynthesis of medicinal plants have received extensive attention. However, whether or to what extent rhizosphere microorganisms can contribute to the construction of the quality evaluation system of Chinese medicinal materials is still elusive. Based on the significant role of rhizosphere microbes in the survival and quality formation of medicinal plants, this paper proposed a new concept of rhizosphere microbial markers (micro-markers), expounded the relevant research methods and ideas of applying the new concept, highlighted the importance of micro-markers in the quality evaluation and control system of traditional Chinese medicines (TCMs), and introduced the potential value in soil environmental assessment, plant pest control and quality assessment of TCMs. It provides reference for developing ecological planting of TCMs and ensuring the production of high quality TCMs by regulating rhizosphere microbial communities.

Microbiome Analysis Revealed Acholeplasma as a Possible Factor Influencing the Susceptibility to Bacterial Leaf Blight Disease of Two Domestic Rice Cultivars in Vietnam

The microbiomes of two important rice cultivars in Vietnam which differ by their susceptibility to the bacterial leaf blight (BLB) disease were analyzed through 16S rRNA amplicon technology. A higher number of operational taxonomic units and alpha-diversity indices were shown in the BLB-resistant LA cultivar than in the BLB-susceptible TB cultivar. The BLB pathogen Xanthomonas was scantly found (0.003%) in the LA cultivar, whereas was in a significantly higher ratio in the TB cultivar (1.82%), reflecting the susceptibility to BLB of these cultivars. Of special interest was the genus Acholeplasma presented in the BLB-resistant LA cultivar at a high relative abundance (22.32%), however, was minor in the BLB-sensitive TB cultivar (0.09%), raising a question about its roles in controlling the Xanthomonas low in the LA cultivar. It is proposed that Acholeplasma once entered the host plant would hamper other phytopathogens, i.e. Xanthomonas, by yet unknown mechanisms, of which the triggering of the host plants to produce secondary metabolites against pathogens could be a testable hypothesis.

The Bacterial and Fungal Compositions in the Rhizosphere of Asarum heterotropoides Fr. Schmidt var. mandshuricum (Maxim.) Kitag. in a Typical Planting Region

Asarum is a traditional Chinese medicinal plant, and its dried roots are commonly used as medicinal materials. Research into the traits of the bacteria and fungus in the Asarum rhizosphere and how they relate to the potency of medicinal plants is important. During four cropping years and collecting months, we used ITS rRNA gene amplicon and sequencing to assess the population, diversity, and predominant kinds of bacteria and fungus in the rhizosphere of Asarum. HPLC was used to determine the three bioactive ingredients, namely asarinin, aristolochic acid I, and volatile oil. The mainly secondary metabolites of Asarum, relationships between microbial communities, soil physicochemical parameters, and possible influences on microbial communities owing to various cropping years and collecting months were all statistically examined. The cropping years and collecting months affected the abundance and diversity of rhizosphere bacteria and fungi, but the cropping year had a significant impact on the structures and compositions of the bacterial communities. The rhizosphere microorganisms were influenced by both the soil physicochemical properties and enzyme activities. Additionally, this study revealed that Trichoderma was positively correlated with the three bioactive ingredients of Asarum, while Tausonia showed entirely opposite results. Gibberella and Leptosphaeria demonstrated a significantly negative correlation with asarinin and violate oil, but they were weakly correlated with the aristolochic acid I content. This study revealed variations in the Asarum rhizosphere microorganism population, diversity, and dominant types across four cropping years and collecting months. The relationship between Asarum secondary metabolites, the soil physicochemical properties, enzyme activities, and rhizosphere microorganisms was discussed. Our results will guide the exploration of the soil characteristics and rhizosphere microorganisms' structures by regulating the microbial community to enhance Asarum quality.

Common mycorrhizal network: the predominant socialist and capitalist responses of possible plant-plant and plant-microbe interactions for sustainable agriculture

Plants engage in a variety of interactions, including sharing nutrients through common mycorrhizal networks (CMNs), which are facilitated by arbuscular mycorrhizal fungi (AMF). These networks can promote the establishment, growth, and distribution of limited nutrients that are important for plant growth, which in turn benefits the entire network of plants. Interactions between plants and microbes in the rhizosphere are complex and can either be socialist or capitalist in nature, and the knowledge of these interactions is equally important for the progress of sustainable agricultural practice. In the socialist network, resources are distributed more evenly, providing benefits for all connected plants, such as symbiosis. For example, direct or indirect transfer of nutrients to plants, direct stimulation of growth through phytohormones, antagonism toward pathogenic microorganisms, and mitigation of stresses. For the capitalist network, AMF would be privately controlled for the profit of certain groups of plants, hence increasing competition between connected plants. Such plant interactions invading by microbes act as saprophytic and cause necrotrophy in the colonizing plants. In the first case, an excess of the nutritional resources may be donated to the receiver plants by direct transfer. In the second case, an unequal distribution of resources occurs, which certainly favor individual groups and increases competition between interactions. This largely depends on which of these responses is predominant ("socialist" or "capitalist") at the moment plants are connected. Therefore, some plant species might benefit from CMNs more than others, depending on the fungal species and plant species involved in the association. Nevertheless, benefits and disadvantages from the interactions between the connected plants are hard to distinguish in nature once most of the plants are colonized simultaneously by multiple fungal species, each with its own cost-benefits. Classifying plant-microbe interactions based on their habitat specificity, such as their presence on leaf surfaces (phyllospheric), within plant tissues (endophytic), on root surfaces (rhizospheric), or as surface-dwelling organisms (epiphytic), helps to highlight the dense and intricate connections between plants and microbes that occur both above and below ground. In these complex relationships, microbes often engage in mutualistic interactions where both parties derive mutual benefits, exemplifying the socialistic or capitalistic nature of these interactions. This review discusses the ubiquity, functioning, and management interventions of different types of plant-plant and plant-microbe interactions in CMNs, and how they promote plant growth and address environmental challenges for sustainable agriculture.

Exploring the potential of endophyte-plant interactions for improving crop sustainable yields in a changing climate

Climate change poses a major threat to global food security, significantly reducing crop yields as cause of abiotic stresses, and for boosting the spread of new and old pathogens and pests. Sustainable crop management as a route to mitigation poses the challenge of recruiting an array of solutions and tools for the new aims. Among these, the deployment of positive interactions between the micro-biotic components of agroecosystems and plants can play a highly significant role, as part of the agro-ecological revolution. Endophytic microorganisms have emerged as a promising solution to tackle this challenge. Among these, Arbuscular Mycorrhizal Fungi (AMF) and endophytic bacteria and fungi have demonstrated their potential to alleviate abiotic stresses such as drought and heat stress, as well as the impacts of biotic stresses. They can enhance crop yields in a sustainable way also by other mechanisms, such as improving the nutrient uptake, or by direct effects on plant physiology. In this review we summarize and update on the main types of endophytes, we highlight several studies that demonstrate their efficacy in improving sustainable yields and explore possible avenues for implementing crop-microbiota interactions. The mechanisms underlying these interactions are highly complex and require a comprehensive understanding. For this reason, omic technologies such as genomics, transcriptomics, proteomics, and metabolomics have been employed to unravel, by a higher level of information, the complex network of interactions between plants and microorganisms. Therefore, we also discuss the various omic approaches and techniques that have been used so far to study plant-endophyte interactions.

Bacteria Associated with Spores of Arbuscular Mycorrhizal Fungi Improve the Effectiveness of Fungal Inocula for Red Raspberry Biotization

Intensive crop production leads to the disruption of the symbiosis between plants and their associated microorganisms, resulting in suboptimal plant productivity and lower yield quality. Therefore, it is necessary to improve existing methods and explore modern, environmentally friendly approaches to crop production. One of these methods is biotization, which involves the inoculation of plants with appropriately selected symbiotic microorganisms which play a beneficial role in plant adaptation to the environment. In this study, we tested the possibility of using a multi-microorganismal inoculum composed of arbuscular mycorrhizal fungi (AMF) and AMF spore-associated bacteria for biotization of the red raspberry. Bacteria were isolated from the spores of AMF, and their plant growth-promoting properties were tested. AMF inocula were supplemented with selected bacterial strains to investigate their effect on the growth and vitality of the raspberry. The investigations were carried out in the laboratory and on a semi-industrial scale in a polytunnel where commercial production of seedlings is carried out. In the semi-industrial experiment, we tested the growth parameters of plants and physiological response of the plant to temporary water shortage. We isolated over fifty strains of bacteria associated with spores of AMF. Only part of them showed plant growth-promoting properties, and six of these (belonging to the Paenibacillus genus) were used for the inoculum. AMF inoculation and co-inoculation of AMF and bacteria isolated from AMF spores improved plant growth and vitality in both experimental setups. Plant dry weight was improved by 70%, and selected chlorophyll fluorescence parameters (the contribution of light to primary photochemistry and fraction of reaction centre chlorophyll per chlorophyll of the antennae) were increased. The inoculum improved carbon assimilation, photosynthetic rate, stomatal conductance and transpiration after temporary water shortage. Raspberry biotization with AMF and bacteria associated with spores has potential applications in horticulture where ecological methods based on plant microorganism interaction are in demand.

Copper-Containing Bionanocomposites Based on Natural Raw Arabinogalactan as Effective Vegetation Stimulators and Agents against Phytopathogens

Novel copper-containing bionanocomposites based on the natural raw arabinogalactan have been obtained as universal effective agents against phytopathogen Clavibacter sepedonicus and development stimulants of agricultural plants. Thus, the use of such nanosystems offers a solution to the tasks set in biotechnology while maintaining high environmental standards using non-toxic, biocompatible, and biodegradable natural biopolymers. The physicochemical characteristics of nanocomposites were determined using a number of analytical methods (elemental analysis, transmission electron microscopy and spectroscopic parameters of electron paramagnetic resonance, UV-visible, etc.). The results of the study under the influence of the nanocomposites on the germination of soybean seeds (Glycine max L.) and the vegetation of potatoes (Solanum tuberosum L.) showed the best results in terms of biometric indicators. It is especially worth noting the pronounced influence of the nanocomposite on the development of the root system, and the increase in the mass of the potato root system reached 19%. It is also worth noting that the nanocomposites showed a stimulating effect on the antioxidant system and did not have a negative effect on the content of pigments in potato tissues. Moreover, the resulting bionanocomposite showed a pronounced antibacterial effect against the phytopathogenic bacterium. During the co-incubation of phytopathogen Clavibacter sepedonicus in the presence of the nanocomposite, the number of cells in the bacterial suspension decreased by up to 40% compared to that in the control, and a 10% decrease in the dehydrogenase activity of cells was also detected.

The Synergistic Impact of Arbuscular Mycorrhizal Fungi and Compost Tea to Enhance Bacterial Community and Improve Crop Productivity under Saline-Sodic Condition

Soil salinity has a negative impact on the biochemical properties of soil and on plant growth, particularly in arid and semi-arid regions. Using arbuscular mycorrhizal fungi (Glomus versiform) and foliar spray from compost tea as alleviating treatments, this study aimed to investigate the effects of alleviating salt stress on the growth and development of maize and wheat grown on a saline-sodic soil during the period of 2022/2023. Six treatments were used in the completely randomized factorial design experiment. The treatments included Arbuscular mycorrhizal fungus (AMF0, AMF1) and varied concentrations of compost tea (CT0, CT50, and CT100). AMF colonization, the bacterial community and endosphere in the rhizosphere, respiration rate, growth parameters, and the productivity were all evaluated. The application of AMF and CT, either separately or in combination, effectively mitigated the detrimental effects caused by soil salinity. The combination of AMF and CT proved to be highly efficient in improving the infection rate of AMF, the bacterial community in the rhizosphere and endosphere, growth parameters, and grain yield of maize and wheat. Therefore, it can be proposed that the inoculation of mycorrhizal fungi with compost tea in saline soils is an important strategy for enhancing salt tolerance in maize and wheat plants through improving microbial activity, the infection rate of AMF, and overall maize and wheat productivity.

The potato rhizosphere microbiota correlated to the yield of three different regions in Korea

We examined potato rhizosphere bacterial and fungal communities across three regions: Cheongju, Pyeongchang, and Gangneung. These regions have varying soil and climate conditions, resulting in different yields. We found that precipitation was the main limiting factor in our study while soil physiochemical factors affect bacterial and fungal microbiota in correlation with yield. Both bacterial and fungal microbiota showed distinct patterns according to the regions. ASVs positively correlated with yield were predominantly found in the Pyeongchang region which also produced the highest yields, while ASVs negatively correlated with yield were associated with Gangneung where the lowest yields were observed. The greatest bacterial and fungal diversity was detected in Pyeongchang consisting of Propionibacteriales, Burkholderiales, and Vicinamibacteriales. Gangneung, on the other hand primarily belong to Sordariales, Mortierellales, Cystofilobasidiales, and Tremellales. The putative yield-negative ASVs detected in Gangneung may have been influenced by drought stress. This work has highlighted key bacterial and fungal taxa as well as core taxa that may potentially be associated with high and low yields of potato in relation to metadata which includes soil chemical and physical parameters as well as weather data. Taken together we suggest that this information can be used to assess site suitability for potato production.

Unveiling the microbiome of hydroponically cultivated lettuce: impact of Phytophthora cryptogea infection on plant-associated microorganisms

Understanding the complex interactions between plants and their associated microorganisms is crucial for optimizing plant health and productivity. While microbiomes of soil-bound cultivated crops are extensively studied, microbiomes of hydroponically cultivated crops have received limited attention. To address this knowledge gap, we investigated the rhizosphere and root endosphere of hydroponically cultivated lettuce. Additionally, we sought to explore the potential impact of the oomycete pathogen Phytophthora cryptogea on these microbiomes. Root samples were collected from symptomatic and nonsymptomatic plants in three different greenhouses. Amplicon sequencing of the bacterial 16S rRNA gene revealed significant alterations in the bacterial community upon P. cryptogea infection, particularly in the rhizosphere. Permutational multivariate analysis of variance (perMANOVA) revealed significant differences in microbial communities between plants from the three greenhouses, and between symptomatic and nonsymptomatic plants. Further analysis uncovered differentially abundant zero-radius operational taxonomic units (zOTUs) between symptomatic and nonsymptomatic plants. Interestingly, members of Pseudomonas and Flavobacterium were positively associated with symptomatic plants. Overall, this study provides valuable insights into the microbiome of hydroponically cultivated plants and highlights the influence of pathogen invasion on plant-associated microbial communities. Further research is required to elucidate the potential role of Pseudomonas and Flavobacterium spp. in controlling P. cryptogea infections within hydroponically cultivated lettuce greenhouses.

Cultural techniques capture diverse phosphate-solubilizing bacteria in rock phosphate-enriched habitats

Phosphorus (P) deficiency is a common problem in croplands where phosphate-based fertilizers are regularly used to maintain bioavailable P for plants. However, due to their limited mobility in the soil, there has been an increased interest in microorganisms that can convert insoluble P into a bioavailable form, and their use to develop phosphate-solubilizing bioinoculants as an alternative to the conventional use of P fertilizers. In this study, we proposed two independent experiments and explored two entirely different habitats to trap phosphate-solubilizing bacteria (PSBs). In the first experiment, PSBs were isolated from the rhizoplane of native plant species grown in a rock-phosphate (RP) mining area. A subset of 24 bacterial isolates from 210 rhizoplane morphotypes was selected for the inorganic phosphate solubilizing activities using tricalcium phosphate (TCP) as the sole P source. In the second experiment, we proposed an innovative experimental setup to select mycohyphospheric bacteria associated to arbuscular mycorrhizal fungal hyphae, indigenous of soils where agronomic plant have been grown and trapped in membrane bag filled with RP. A subset of 25 bacterial isolates from 44 mycohyphospheric morphotypes was tested for P solubilizing activities. These two bacterial subsets were then screened for additional plant growth-promoting (PGP) traits, and 16S rDNA sequencing was performed for their identification. Overall, the two isolation experiments resulted in diverse phylogenetic affiliations of the PSB collection, showing only 4 genera (24%) and 5 species (17%) shared between the two communities, thus underlining the value of the two protocols, including the innovative mycohyphospheric isolate selection method, for selecting a greater biodiversity of cultivable PSB. All the rhizoplane and mycohyphospheric PSB were positive for ammonia production. Indol-3-acetic acid (IAA) production was observed for 13 and 20 isolates, respectively among rhizoplane and mycohyphospheric PSB, ranging, respectively, from 32.52 to 330.27 μg mL-1 and from 41.4 to 963.9 μg mL-1. Only five rhizoplane and 12 mycohyphospheric isolates were positively screened for N2 fixation. Four rhizoplane PSB were identified as siderophore producers, while none of the mycohyphospheric isolates were. The phenotype of one PSB rhizoplane isolate, assigned to Pseudomonas, showed four additive PGP activities. Some bacterial strains belonging to the dominant genera Bacillus and Pseudomonas could be considered potential candidates for further formulation of biofertilizer in order to develop bioinoculant consortia that promote plant P nutrition and growth in RP-enriched soils.

Pseudomonas chlororaphis IRHB3 assemblies beneficial microbes and activates JA-mediated resistance to promote nutrient utilization and inhibit pathogen attack

Introduction

The rhizosphere microbiome is critical to plant health and resistance. PGPR are well known as plant-beneficial bacteria and generally regulate nutrient utilization as well as plant responses to environmental stimuli. In our previous work, one typical PGPR strain, Pseudomonas chlororaphis IRHB3, isolated from the soybean rhizosphere, had positive impacts on soil-borne disease suppression and growth promotion in the greenhouse, but its biocontrol mechanism and application in the field are not unclear.

Methods

In the current study, IRHB3 was introduced into field soil, and its effects on the local rhizosphere microbiome, disease resistance, and soybean growth were comprehensively analyzed through high-throughput sequencing and physiological and molecular methods.

Results and discussion

We found that IRHB3 significantly increased the richness of the bacterial community but not the structure of the soybean rhizosphere. Functional bacteria related to phosphorus solubilization and nitrogen fixation, such as Geobacter, Geomonas, Candidatus Solibacter, Occallatibacter, and Candidatus Koribacter, were recruited in rich abundance by IRHB3 to the soybean rhizosphere as compared to those without IRHB3. In addition, the IRHB3 supplement obviously maintained the homeostasis of the rhizosphere microbiome that was disturbed by F. oxysporum, resulting in a lower disease index of root rot when compared with F. oxysporum. Furthermore, JA-mediated induced resistance was rapidly activated by IRHB3 following PDF1.2 and LOX2 expression, and meanwhile, a set of nodulation genes, GmENOD40b, GmNIN-2b, and GmRIC1, were also considerably induced by IRHB3 to improve nitrogen fixation ability and promote soybean yield, even when plants were infected by F. oxysporum. Thus, IRHB3 tends to synergistically interact with local rhizosphere microbes to promote host growth and induce host resistance in the field.

A comprehensive examination of microbial hazards and risks during indoor soilless leafy green production

Produce grown under controlled environment agriculture (CEA) is often assumed to have a reduced risk of pathogen contamination due to the low chance of exposure to outdoor contaminant factors. However, the 2021 outbreak and numerous recalls of CEA-grown lettuce and microgreens demonstrate the possibility of pathogen introduction during indoor production when there is a failure in the implementation of food safety management systems. Indoor production of commercial leafy greens, such as lettuce and microgreens, is performed across a range of protective structures from primitive household setups to advanced and partially automatized growing systems. Indoor production systems include hydroponic, aquaponic, and aeroponic configurations. Hydroponic systems such as deep water culture and nutrient film technique comprised of various engineering designs represent the main system types used by growers. Depending on the type of leafy green, the soilless substrate, and system selection, risk of microbial contamination will vary during indoor production. In this literature review, science-based pathogen contamination risks and mitigation strategies for indoor production of microgreens and more mature leafy greens are discussed during both pre-harvest and post-harvest stages of production.

Antimicrobial profile of the culturable olive sporobiota and its potential as a source of biocontrol agents for major phytopathogens in olive agriculture

BACKGROUND

The phytopathogens Xylella fastidiosa and Verticillium dahliae present an unparalleled threat to olive agriculture. However, there is no efficient field treatment available today for either pest. Spore-forming bacteria (i.e., the sporobiota) are known for their extraordinary resistance properties and antimicrobial activity. The aim of this study was thus to identify potential novel sustainable spore-forming biocontrol agents derived from the culturable olive microbiome, termed the sporobiota, in general and in particular against X. fastidiosa and V. dahliae.

RESULTS

We demonstrate the wide-ranging antimicrobial profile of 415 isolates from the culturable olive sporobiota towards human and plant pathogens. We further identified five candidates with antagonistic activity against X. fastidiosa and V. dahliae. These belong to the Bacillus subtilis, Bacillus cereus and Peribacillus simplex clade. The activity was related to the species and their relative origin (soil versus leaf endophytic). It is of particular interest that two of these candidates are already naturally present at the site of disease-development that is, plant interior. We further confirmed the presence of lipopeptide genes potentially associated with the reported bioactivity.

CONCLUSIONS

The study provides insights into how members of the olive sporobiota may support the olive plant to ward off detrimental pathogens. It further yields five promising candidates for the development of eco-friendly, multi-active biocontrol agents in olive agriculture. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Exploiting the microbiome associated with normal and abnormal sprouting rice (Oryza sativa L.) seed phenotypes through a metabarcoding approach

Rice germination and seedlings' growth are crucial stages that influence crop establishment and productivity. These performances depend on several factors, including the abundance and diversity of seed microbial endophytes. Two popular rainfed rice varieties cultivated in Cameroon, NERICA 3 and NERICA 8, were used for investigating the seed-associated microbiome using the Illumina-based 16 S rRNA gene. Significant differences were observed in terms of richness index between normal and abnormal seedlings developed from sprouting seeds, although no significant species evenness index was assessed within either phenotype. Two hundred ninety-two bacterial amplicon sequence variants were identified in seed microbiome of the rice varieties, and principal coordinate analysis revealed that microbial communities formed two distinct clusters in normal and abnormal seedling phenotypes. Overall, 38 bacteria genera were identified, belonging to 6 main phyla. Furthermore, the core microbiome was defined, and the differential abundance of 28 bacteria genera was assessed. Based on the collected results, putative bacterial genera were directly correlated with the development of normal seedlings. For most genera that are recognised to include beneficial species, such as Brevundimonas, Sphingomonas, Exiguobacterium, Luteibacter, Microbacterium and Streptomyces, a significant increase of their relative abundance was found in normal seedlings. Additionally, in abnormal seedlings, we also observed an increased abundance of the genera Kosakonia and Paenibacillus, which might have controversial aspects (beneficial or pathogenic), together with the presence of some genera (Clostridium sensu stricto) that are commonly correlated to sick plants. The putative functional gene annotation revealed the higher abundance of genes related to the metabolic biosynthesis of soluble carbohydrates and starch, tryptophan, nucleotides and ABC transporters in normal seedlings. Data presented in this study may help in further understanding the importance of the seed endophyte microbiome for driving a correct development of rice plants at the early stages and to identify possible beneficial bacteria for technological applications aimed to increase seed quality and crop productivity.

From concept to reality: Transforming agriculture through innovative rhizosphere engineering for plant health and productivity

The plant rhizosphere is regarded as a microbial hotspot due to a wide array of root exudates. These root exudates comprise diverse organic compounds such as phenolic, polysaccharides, flavonoids, fatty acids, and amino acids that showed chemotactic responses towards microbial communities and mediate significant roles in root colonization. The rhizospheric microbiome is a crucial driver of plant growth and productivity, contributing directly or indirectly by facilitating nutrient acquisition, phytohormone modulation, and phosphate solubilization under normal and stressful conditions. Moreover, these microbial candidates protect plants from pathogen invasion by secreting antimicrobial and volatile organic compounds. To enhance plant fitness and yield, rhizospheric microbes are frequently employed as microbial inoculants. However, recent developments have shifted towards targeted rhizosphere engineering or microbial recruitments as a practical approach to constructing desired plant rhizospheres for specific outcomes. The rhizosphere, composed of plants, microbes, and soil, can be modified in several ways to improve inoculant efficiency. Rhizosphere engineering is achieved through three essential mechanisms: a) plant-mediated modifications involving genetic engineering, transgenics, and gene editing of plants; b) microbe-mediated modifications involving genetic alterations of microbes through upstream or downstream methodologies; and c) soil amendments. These mechanisms shape the rhizospheric microbiome, making plants more productive and resilient under different stress conditions. This review paper comprehensively summarizes the various aspects of rhizosphere engineering and their potential applications in maintaining plant health and achieving optimum agricultural productivity.

Consistent spatial patterns in microbial taxa of red squirrel gut microbiomes

Gut microbiomes are diverse ecosystems whose drivers of variation remain largely unknown, especially in time and space. We analysed a dataset with over 900 red squirrel (Tamiasciurus hudsonicus) gut microbiome samples to identify the drivers of gut microbiome composition in this territorial rodent. The large-scale spatiotemporal replication in the data analysed was an essential component of understanding the assembly of these microbial communities. We identified that the spatial location of the sampled squirrels in their local environment is a key contributor to gut microbial community composition. The non-core gut microbiome (present in less than 75% of gut microbiome samples) had highly localised spatial patterns throughout different seasons and different study areas in the host squirrel population. The core gut microbiome, on the other hand, showed some spatial patterns, though fewer than in the non-core gut microbiome. Environmental transmission of microbiota is the likely contributor to the spatiotemporal distribution observed in the North American red squirrel gut microbiome.

Bacterially enhanced plant-growing media for controlled environment agriculture

Microbe-plant interactions in the root zone not only shape crop performance in soil but also in hydroponic cultivation systems. The biological and physicochemical properties of the plant-growing medium determine the root-associated microbial community and influence bacterial inoculation effectiveness, which affects plant growth. This study investigated the combined impact of plant-growing media composition and bacterial community inoculation on the root-associated bacterial community of hydroponically grown lettuce (Lactuca sativa L.). Ten plant-growing media were composed of varying raw materials, including black peat, white peat, coir pith, wood fibre, composted bark, green waste compost, perlite and sand. In addition, five different bacterial community inocula (BCI S1-5) were collected from the roots of lettuce obtained at different farms. After inoculation and cultivation inside a vertical farm, lettuce root-associated bacterial community structures, diversity and compositions were determined by evaluating 16S rRNA gene sequences. The study revealed distinct bacterial community structures among experimental replicates, highlighting the influence of raw material variations on root-associated bacterial communities, even at the batch level. However, bacterial community inoculation allowed modulation of the root-associated bacterial communities independently from the plant-growing medium composition. Bacterial diversity was identified as a key determinant of plant growth performance with green waste compost introducing Bacilli and Actinobacteria, and bacterial community inoculum S3 introducing Pseudomonas, which positively correlated with plant growth. These findings challenge the prevailing notion of hydroponic cultivation systems as sterile environments and highlight the significance of proper plant-growing media raw material selection and bacterial community inoculation in shaping root-associated microbiomes that provide stability through microbial diversity. This study supports the concept of creating bacterially enhanced plant-growing media to promote plant growth in controlled environment agriculture.

Identification of synthetic consortia from a set of plant-beneficial bacteria

The use of microbial inoculants in agriculture as biofertilisers and/or biopesticides is an appealing alternative to replace or reduce the practice of agrochemicals. Plant microbiota studies are revealing the different bacterial groups which are populating plant microbiomes re-energising the plant probiotic bacteria (PPB) translational research sector. Some single-microbial strain bioinoculants have proven valid in agriculture (e.g., based on Trichoderma, mycorrhiza or rhizobia); however, it is now recommended to consider multistrain consortia since plant-beneficial effects are often a result of community-level interactions in plant microbiomes. A limiting step is the selection of a fitting combination of microbial strains in order to accomplish the best beneficial effect upon plant inoculation. In this study, we have used a subset of 23 previously identified and characterised rice-beneficial bacterial colonisers to design and test a series of associated experiments aimed to identify potential PPB consortia which are able to co-colonise and induce plant growth promotion. Bacterial strains were co-inoculated in vitro and in planta using several different methods and their co-colonisation and co-persistence monitored. Results include the identification of two 5-strain and one 2-strain consortia which displayed plant growth-promoting features. Future practical applications of microbiome research must include experiments aimed at identifying consortia of bacteria which can be most effective as crop amendments.

Harnessing root exudates for plant microbiome engineering and stress resistance in plants

A wide range of abiotic and biotic stresses adversely affect plant's growth and production. Under stress, one of the main responses of plants is the modulation of exudates excreted in the rhizosphere, which consequently leads to alterations in the resident microbiota. Thus, the exudates discharged into the rhizospheric environment play a preponderant role in the association and formation of plant-microbe interactions. In this review, we aimed to provide a synthesis of the latest and most pertinent literature on the diverse biochemical and structural compositions of plant root exudates. Also, this work investigates into their multifaceted role in microbial nutrition and intricate signaling processes within the rhizosphere, which includes quorum-sensing molecules. Specifically, it explores the contributions of low molecular weight compounds, such as carbohydrates, phenolics, organic acids, amino acids, and secondary metabolites, as well as the significance of high molecular weight compounds, including proteins and polysaccharides. It also discusses the state-of-the-art omics strategies that unveil the vital role of root exudates in plant-microbiome interactions, including defense against pathogens like nematodes and fungi. We propose multiple challenges and perspectives, including exploiting plant root exudates for host-mediated microbiome engineering. In this discourse, root exudates and their derived interactions with the rhizospheric microbiota should receive greater attention due to their positive influence on plant health and stress mitigation.

Microbiome-Mediated Strategies to Manage Major Soil-Borne Diseases of Tomato

The tomato (Solanum lycopersicum L.) is consumed globally as a fresh vegetable due to its high nutritional value and antioxidant properties. However, soil-borne diseases can severely limit tomato production. These diseases, such as bacterial wilt (BW), Fusarium wilt (FW), Verticillium wilt (VW), and root-knot nematodes (RKN), can significantly reduce the yield and quality of tomatoes. Using agrochemicals to combat these diseases can lead to chemical residues, pesticide resistance, and environmental pollution. Unfortunately, resistant varieties are not yet available. Therefore, we must find alternative strategies to protect tomatoes from these soil-borne diseases. One of the most promising solutions is harnessing microbial communities that can suppress disease and promote plant growth and immunity. Recent omics technologies and next-generation sequencing advances can help us develop microbiome-based strategies to mitigate tomato soil-borne diseases. This review emphasizes the importance of interdisciplinary approaches to understanding the utilization of beneficial microbiomes to mitigate soil-borne diseases and improve crop productivity.

Scientific and technological advances in the development of sustainable disease management tools: a case study on kiwifruit bacterial canker

Plant disease outbreaks are increasing in a world facing climate change and globalized markets, representing a serious threat to food security. Kiwifruit Bacterial Canker (KBC), caused by the bacterium Pseudomonas syringae pv. actinidiae (Psa), was selected as a case study for being an example of a pandemic disease that severely impacted crop production, leading to huge economic losses, and for the effort that has been made to control this disease. This review provides an in-depth and critical analysis on the scientific progress made for developing alternative tools for sustainable KBC management. Their status in terms of technological maturity is discussed and a set of opportunities and threats are also presented. The gradual replacement of susceptible kiwifruit cultivars, with more tolerant ones, significantly reduced KBC incidence and was a major milestone for Psa containment - which highlights the importance of plant breeding. Nonetheless, this is a very laborious process. Moreover, the potential threat of Psa evolving to more virulent biovars, or resistant lineages to existing control methods, strengthens the need of keep on exploring effective and more environmentally friendly tools for KBC management. Currently, plant elicitors and beneficial fungi and bacteria are already being used in the field with some degree of success. Precision agriculture technologies, for improving early disease detection and preventing pathogen dispersal, are also being developed and optimized. These include hyperspectral technologies and forecast models for Psa risk assessment, with the latter being slightly more advanced in terms of technological maturity. Additionally, plant protection products based on innovative formulations with molecules with antibacterial activity against Psa (e.g., essential oils, phages and antimicrobial peptides) have been validated primarily in laboratory trials and with few compounds already reaching field application. The lessons learned with this pandemic disease, and the acquired scientific and technological knowledge, can be of importance for sustainably managing other plant diseases and handling future pandemic outbreaks.

Evaluation of ready-to-use freezer stocks of a synthetic microbial community for maize root colonization

IMPORTANCE

Synthetic communities (SynComs) are an invaluable tool to characterize and model plant-microbe interactions. Multimember SynComs approximate intricate real-world interactions between plants and their microbiome, but the complexity and time required for their construction increase enormously for each additional member added to the SynCom. Therefore, researchers who study a diversity of microbiomes using SynComs are looking for ways to simplify the use of SynComs. In this manuscript, we evaluate the feasibility of creating ready-to-use freezer stocks of a well-studied seven-member SynCom for maize roots. The frozen ready-to-use SynCom stocks work according to the principle of "just add buffer and apply to sterilized seeds or seedlings" and thus can save time applied in multiple days of laborious growing and combining of multiple microorganisms. We show that ready-to-use SynCom stocks provide comparable results to those of freshly constructed SynComs and thus allow for significant time savings when working with SynComs.

Depletion of protective microbiota promotes the incidence of fruit disease

Plant-associated microbiomes play important roles in plant health and productivity. However, despite fruits being directly linked to plant productivity, little is known about the microbiomes of fruits and their potential association with fruit health. Here, by integrating 16S rRNA gene, ITS high-throughput sequencing data, and microbiological culturable approaches, we reported that roots and fruits (pods) of peanut, a typical plant that bears fruits underground, recruit different bacterial and fungal communities independently of cropping conditions and that the incidence of pod disease under monocropping conditions is attributed to the depletion of Bacillus genus and enrichment of Aspergillus genus in geocarposphere. On this basis, we constructed a synthetic community (SynCom) consisting of three Bacillus strains from geocarposphere soil under rotation conditions with high culturable abundance. Comparative transcriptome, microbiome profiling, and plant phytohormone signaling analysis reveal that the SynCom exhibited more effective Aspergillus growth inhibition and pod disease control than individual strain, which was underpinned by a combination of molecular mechanisms related to fungal cell proliferation interference, mycotoxins biosynthesis impairment, and jasmonic acid-mediated plant immunity activation. Overall, our results reveal the filter effect of plant organs on the microbiome and that depletion of key protective microbial community promotes the fruit disease incidence.

Deterministic and stochastic processes generating alternative states of microbiomes

The structure of microbiomes is often classified into discrete or semi-discrete types potentially differing in community-scale functional profiles. Elucidating the mechanisms that generate such "alternative states" of microbiome compositions has been one of the major challenges in ecology and microbiology. In a time-series analysis of experimental microbiomes, we here show that both deterministic and stochastic ecological processes drive divergence of alternative microbiome states. We introduced species-rich soil-derived microbiomes into eight types of culture media with 48 replicates, monitoring shifts in community compositions at six time points (8 media × 48 replicates × 6 time points = 2304 community samples). We then confirmed that microbial community structure diverged into a few state types in each of the eight medium conditions as predicted in the presence of both deterministic and stochastic community processes. In other words, microbiome structure was differentiated into a small number of reproducible compositions under the same environment. This fact indicates not only the presence of selective forces leading to specific equilibria of community-scale resource use but also the influence of demographic drift (fluctuations) on the microbiome assembly. A reference-genome-based analysis further suggested that the observed alternative states differed in ecosystem-level functions. These findings will help us examine how microbiome structure and functions can be controlled by changing the "stability landscapes" of ecological community compositions.

Isolation and Identification of Growth-Promoting Bacteria from Plants Growing Under Abiotic Stresses

Identification and isolation of plant growth-promoting bacteria (PGPB) are critical steps toward understanding the role of these bacteria in stress tolerance in plants. This procedure also provides essential knowledge about the microbes needed to formulate effective biofertilizers. This chapter describes culture-dependent and culture-independent strategies to identify and isolate PGPB. The culture-dependent strategy commonly involves growing PGPB on general and selective media. However, the culture-independent strategy involves next-generation sequencing technologies. A combination of both strategies would identify the structure of the bacterial communities and isolate bacteria from their environments. Therefore, this chapter describes a comprehensive strategy where the methods are sequentially applied to identify and isolate epiphytic and endophytic PGPB from a particular environmental sample. However, a single procedure can also be employed to identify and isolate a specific type of PGPB.