Rhizosphere Microbiome Research Articles

Key Chemical Soil Parameters for the Assembly of Rhizosphere Bacteria Associated with Avocado Cv Hass Grafted on Landrace Rootstocks

Avocado cultivation holds significant economic importance in many countries, ranking Colombia as the fifth largest global producer. Particularly, the Hass cultivar plays a pivotal role in Colombia’s avocado industry, especially in the Department of Antioquia, the primary export region. This cultivar is grown under diverse soil and climate conditions and exhibits considerable genetic polymorphism due to the hybridization of varieties of agronomic significance, leading to a diverse array of landrace rootstocks. However, the role of soil conditions and rootstock genotype in structuring rhizosphere bacterial communities is still lacking. In addressing this knowledge gap, we investigated the influence of two soil conditions on the structure of rhizosphere bacterial communities associated with two landrace genotypes of Persea americana cv. Hass, utilizing 16S rRNA sequencing. Notably, no significant differences related to genotypes were observed. This study reports that the rhizosphere bacterial microbiome remains consistent across avocado landrace rootstocks, while variations in key parameters such as phosphorus, pH, Mg, and Ca drive distinct rhizosphere effects. Our results reveal that despite the soils having similar management, increases in these crucial parameters can lead to bacterial communities with lower alpha diversity and a more complex co-occurrence network. In addition, we found substantial variations in beta diversity, bacterial composition, and metagenome predictions between the two farms, underscoring the role of soil variables in shaping the bacterial microbiome. These findings provide valuable insights into the factors influencing the bacterial communities that may play a role in the health and productivity of crops with agro-industrial potential, such as Hass avocado.

Combating wheat yellow mosaic virus through microbial interactions and hormone pathway modulations

BackgroundThe rhizosphere microbiome is critical for promoting plant growth and mitigating soil-borne pathogens. However, its role in fighting soil-borne virus-induced diseases, such as wheat yellow mosaic virus (WYMV) transmitted by Polymyxa graminis zoospores, remains largely underexplored. In this study, we hypothesized that during viral infections, plant microbiomes engage in critical interactions with plants, with key microbes playing vital roles in maintaining plant health. Our research aimed to identify microbial taxa that not only suppress the disease but also boost wheat yield by using a blend of techniques, including field surveys, yield assessments, high-throughput sequencing of plant and soil microbiomes, microbial isolation, hydroponic experiments, and transcriptome sequencing.ResultsWe found that, compared with roots and leaves, the rhizosphere microbiome showed a better performance in predicting wheat yield and the prevalence of P. graminis and WYMV across the three WYMV-impacted regions in China. Using machine learning, we found that healthy rhizospheres were marked with potentially beneficial microorganisms, such as Sphingomonas and Allorhizobium-Neorhizobium-Parararhizobium-Rhizobium, whereas diseased rhizospheres were associated with a higher prevalence of potential pathogens, such as Bipolaris and Fusicolla. Structural equation modeling showed that these biomarkers both directly and indirectly impacted wheat yield by modulating the rhizosphere microbiome and P. graminis abundance. Upon re-introduction of two key healthy rhizosphere biomarkers, Sphingomonas azotifigens and Rhizobium deserti, into the rhizosphere, wheat growth and health were enhanced. This was attributed to the up-regulation of auxin and cytokinin signaling pathways and the regulation of jasmonic acid and salicylic acid pathways during infections.ConclusionsOverall, our study revealed the critical role of the rhizosphere microbiome in combating soil-borne viral diseases, with specific rhizosphere microbes playing key roles in this process.9s7rr2_Gfui1KYKQgMf1m6Video

The microbiome and metatranscriptome of a panel from the Sarracenia mapping population reveal complex assembly and function involving host influence.

Sarracenia provide an optimal system for deciphering the host-microbiome interactions at various levels. We analyzed the pitcher microbiomes and metatranscriptomes of the parental species, and F1 and F2 generations from the mapping population (Sarracenia purpurea X Sarracenia psittacina) utilizing high-throughput sequencing methods. This study aimed to examine the host influences on the microbiome structure and function and to identify the key microbiome traits. Our quality datasets included 8,892,553 full-length bacterial 16s rRNA gene sequences and 65,578 assembled metatranscripts with microbial protein annotations. The correlation network of the bacterial microbiome revealed the presence of 3-7 distinct community clusters, with 8 hub and 19 connector genera. The entire microbiome consisted of viruses, bacterial, archaea, and fungi. The richness and diversity of the microbiome varied among the parental species and offspring genotypes despite being under the same greenhouse environmental conditions. We have discovered certain microbial taxa that are genotype-enriched, including the community hub and connector genera. Nevertheless, there were no significant differences observed in the functional enrichment analysis of the metatranscriptomes across the different genotypes, suggesting a functional convergence of the microbiome. We found that the pitcher microcosm harbors both rhizosphere and phyllosphere microbiomes within its boundaries, resulting in a structurally diverse and functionally complex microbiome community. A total of 50,424 microbial metatranscripts were linked to plant growth-promoting microbial proteins. We show that this complex pitcher microbiome possesses various functions that contribute to plant growth promotion, such as biofertilization, bioremediation, phytohormone signaling, stress regulation, and immune response stimulation. Additionally, the pitcher microbiome exhibits traits related to microbe-microbe interactions, such as colonization of plant systems, biofilm formation, and microbial competitive exclusion. In summary, the demonstrated taxonomical divergence and functionally convergence of the pitcher microbiome are impacted by the host genetics, making it an excellent system for discovering novel beneficial microbiome traits.

Diversity and interactions of rhizobacteria determine multinutrient traits in tomato host plants under nitrogen and water disturbances

Abstract Coevolution within the plant holobiont extends the capacity of host plants for nutrient acquisition and stress resistance. However, the role of the rhizospheric microbiota in maintaining multinutrient utilization (i.e., multinutrient traits) in the host remains to be elucidated. Multinutrient cycling index (MNC), analogous to the widely used multifunctionality index, provides a straightforward and interpretable measure of the multinutrient traits in host plants. Using tomato as a model plant, we characterized MNC (based on multiple aboveground nutrient contents) in host plants under different nitrogen and water supply regimes and explored the associations between rhizospheric bacterial community assemblages and host-plant multinutrient profiles. Rhizosphere bacterial community diversity, quantitative abundance, predicted function, and key topological features of the co-occurrence network were more sensitive to water supply than to nitrogen supply. A core bacteriome comprising 61 genera, such as Candidatus Koribacter and Streptomyces, persisted across different habitats and served as a key predictor of host-plant nutrient uptake. The MNC index increased with greater diversity and higher core taxon abundance in the rhizobacterial community, while decreasing with higher average degree and graph density of rhizobacterial co-occurrence network. Multinutrient absorption by host plants was primarily regulated by community diversity and rhizobacterial network complexity under the interaction of nitrogen and water. The high biodiversity and complex species interactions of the rhizospheric bacteriome play crucial roles in host-plant performance. This study supports the development of rhizosphere microbiome engineering, facilitating effective manipulation of the microbiome for enhanced plant benefits, which supports sustainable agricultural practices and plant health.

Intercropping of tobacco and maize at seedling stage promotes crop growth through manipulating rhizosphere microenvironment.

Changes in the rhizosphere microbiome and metabolites resulting from crop intercropping can significantly enhance crop growth. While there has been an increasing number of studies on various crop combinations, research on the intercropping of tobacco and maize at seedling stage remains limited. This study is the first to explore rhizosphere effects of intercropping between tobacco and maize seedling stages, we analyzed the nitrogen, phosphorus and potassium nutrients in the soil, and revealed the important effects on soil microbial community composition and metabolite profiles, thereby regulating crop growth and improving soil balance. Compared with mono-cropping, intercropping increased the biomass of the two crops and promoted the nutrient absorption of nitrogen, phosphorus and potassium. Under intercropping conditions, the activities of sucrase, catalase and nitrate reductase in tobacco rhizosphere soil and the content of available potassium, the activities of nitrate reductase and acid phosphatase in maize rhizosphere soil were significantly increasing. Rhizosphere soil bacterial and fungal communities such as Sphingomonas, Massilia, Humicola and Penicillium respond differently to crop planting patterns, and soil dominant microbial communities are regulated by environmental factors such as pH, Organic Matter, Available Potassium, Nitrate Reductase, and Urease Enzyme. Network analysis showed that soil microbial communities were more complex after intercropping, and the reciprocal relationship between bacteria and fungi was enhanced. The difference of metabolites in soil between intercropping and monocropping system was mainly concentrated in galactose metabolism, starch and sucrose metabolism pathway, and the content of carbohydrate metabolites was significantly higher than that of monocropping soil. Key metabolites such as D-Sucrose, D-Fructose-6-Phosphate, D-Glucose-1-Phosphatel significantly influence the composition of dominant microbial communities such as Sphingomonas and Penicillium. This study explained the effects of intercropping between flue-cured tobacco and maize on the content of soil metabolites and soil microbial composition in rhizosphere soil, and deepened the understanding that intercropping system can improve the growth of flue-cured crops seedlings through rhizosphere effects.

Impact of arbuscular mycorrhizal fungi on maize rhizosphere microbiome stability under moderate drought conditions.

With an alarming increase in global greenhouse gas emissions, unstable weather conditions are significantly impacting agricultural production. Drought stress is one of the frequent consequences of climate change that affects crop growth and yield. Addressing this issue is critical to ensure stable crop productivity under drought conditions. Arbuscular mycorrhizal fungi (AMF) establish symbiotic relationships with plants and enhance their resistance to adverse conditions. Effects of arbuscular mycorrhizal associations on the rhizosphere microbiome and root transcriptome under drought conditions have not been explored. Here, we investigated the effects of AMF and drought stress on rhizosphere microorganisms and root transcriptome of maize plants grown in chernozem soil. We used high-throughput sequencing data of bacterial 16S rRNA and fungal internal transcribed spacer regions (ITS) to identify rhizosphere microorganisms. Transcriptomic data were used to assess gene expression in maize plants under different treatments. Our results show that AMF maintains the composition of maize rhizosphere microorganisms under drought stress. In particular, the bacterial and fungal phyla maintained were Actinomycetes and Ascomycota, respectively. Transcriptomic data indicated that AMF influenced gene expression in maize plants under drought stress. Under drought stress, the expression of SWEET13, CHIT3, and RPL23A was significantly higher in the presence of AMF than it was without AMF inoculation, indicating better sugar transport, reduced malondialdehyde accumulation, and improved water use efficiency in AMF-inoculated maize plants. These findings suggest that AMF can enhance the resistance of maize to moderate drought stress by stabilising plant physical traits, which may help maintain the structure of the rhizosphere microbial community. This study provides valuable theoretical insights that should aid the utilization of AMF in sustainable agricultural practices.

Assessment of the soil rhizospheric microbiome of maize as influenced under various fertigation levels and weed management practices

Assessment of the soil rhizospheric microbiome of maize as influenced under various fertigation levels and weed management practices

Genetic resistance to Fusarium wilt shapes rhizospheric beneficial microbiota in four banana cultivars

This study explores the dynamics of bacterial communities in the bulk soil, rhizosphere, and endosphere of banana plants, focusing on variations among cultivars with differing levels of genetic resistance to Fusarium wilt. We examined four banana cultivars: one resistant (P), one moderately susceptible (PT), and two susceptible (W and M). Using 16S rDNA sequencing, we analyzed the bacterial community structures in these habitats. The results showed significant differences in bacterial communities across the three habitats and among the cultivars, with the endosphere communities being the most distinct. The rhizosphere and bulk soil communities were more similar, likely due to the soil microbiome's influence on the rhizosphere. Resistant cultivars (PT and P) displayed unique bacterial communities, with notable taxa such as Burkholderia, Leifsonia, and Marmoricola in the rhizosphere, known for their antagonistic properties against Fusarium oxysporum. In contrast, susceptible cultivars (W and M) harbored different dominant genera, such as Reyranella and Mucilaginibacter, which did not play significant defensive roles against Fusarium wilt. Additionally, the endosphere of resistant cultivars featured beneficial genera like Amycolatopsis and Achromobacter, known for promoting plant growth and enhancing disease resistance. The findings underscore the importance of plant genotype in shaping the rhizosphere microbiome, with specific microbial taxa linked to resistance against Fusarium. These insights point to the potential for developing targeted microbial-based strategies to enhance disease resistance and overall plant health. The study identifies key microbial players that could be harnessed for biological control and improved management of Fusarium wilt in banana cultivation. This research advances our understanding of plant-microbe interactions and their implications for sustainable agriculture, particularly in combating soilborne pathogens.

Integrative approaches to improve litchi (Litchi chinensis Sonn.) plant health using bio-transformations and entomopathogenic fungi

Bio-transformations refer to the chemical modifications made by an organism on a chemical compound that often involves the interaction of plants with microbes to alter the chemical composition of soil or plant. Integrating bio-transformations and entomopathogenic fungi into litchi cultivation can enhance symbiotic relationships, microbial enzymatic activity in rhizosphere, disease suppression and promote overall plant health. The integration of biological formulations and entomopathogenic fungi can significantly influence growth, nutrient dynamics, physiology, and rhizosphere microbiome of air-layered litchi (Litchi chinensis Sonn.) saplings. Biological modifications included, K-mobilizers, AM fungi, Pseudomonas florescence and Azotobacter chroococcum along with Metarhizium, entomopathogenic fungi have been used. The treatments included, T1-Litchi orchard soil + sand (1:1); T2-Sand + AM fungi + Azotobacter chroococcum (1:2:1); T3-Sand + Pseudomonas florecence + K-mobilizer (1:1:1); T4- AM fungi + K-mobilizers (1:1); T5, P. Florecence + A. chroococcum + K-mobilizer (1:1:1); T6-Sand + P. florecence (1:2) and T7-Uninoculated control for field performance. Treatments T4-T6 were further uniformly amended with drenching of Metarrhizium in rhizosphere. T2 application significantly increased resident microbe survival, total chlorophyll content and root soil ratio in seedlings. A. chroococcum, Pseudomonas, K-mobilizers and AM fungi increased in microbial biomass of 2.59, 3.39, 2.42 and 2.77 times, respectively. Acidic phosphatases, dehydrogenases and alkaline phosphatases were increased in rhizosphere. Leaf nutrients reflected through DOP were considerably altered by T2 treatment. Based on Eigen value, PCA-induced changes at biological modifications showed maximum total variance. The study inferred that the bio-transformations through microbial inoculants and entomopathogenic fungi could be an encouraging strategy to enhance the growth of plants, health and productivity. Such practices align well with the goals of sustainable agriculture through biological means by reducing dependency on chemical inputs. By delving into these aspects, the research gaps including microbial processes, competitive and symbiotic relationships, resistance in microbes and how complex interactions among bio-transformations, entomopathogenic fungi and microbes can significantly impact the health and productivity of litchi. Understanding and harnessing these interactions can lead to more effective and sustainable farming practices.

Cover crop root exudates impact soil microbiome functional trajectories in agricultural soils

BackgroundCover cropping is an agricultural practice that uses secondary crops to support the growth of primary crops through various mechanisms including erosion control, weed suppression, nutrient management, and enhanced biodiversity. Cover crops may elicit some of these ecosystem services through chemical interactions with the soil microbiome via root exudation, or the release of plant metabolites from roots. Phytohormones are one metabolite type exuded by plants that activate the rhizosphere microbiome, yet managing this chemical interaction remains an untapped mechanism for optimizing plant-soil-microbiome interactions. Currently, there is limited understanding on the diversity of cover crop phytohormone root exudation patterns and our aim was to understand how phytochemical signals selectively enrich specific microbial taxa and functionalities in agricultural soils.ResultsHere, we link variability in cover crop root exudate composition to changes in soil microbiome functionality. Exudate chemical profiles from 4 cover crop species (Sorghum bicolor, Vicia villosa, Brassica napus, and Secale cereal) were used as the chemical inputs to decipher microbial responses. These distinct exudate profiles, along with a no exudate control, were amended to agricultural soil microcosms with microbial responses tracked over time using metabolomes and genome-resolved metatranscriptomes. Our findings illustrated microbial metabolic patterns were unique in response to cover crop exudate inputs over time, particularly by sorghum and cereal rye amended microcosms. In these microcosms, we identify novel microbial members (at the genera and family level) who produced IAA and GA4 over time. Additionally, we identified cover crop exudates exclusively enriched for bacterial nitrite oxidizers, while control microcosms were discriminated for nitrogen transport, mineralization, and assimilation, highlighting distinct changes in microbial nitrogen cycling in response to chemical inputs.ConclusionsWe highlight that root exudate amendments alter microbial community function (i.e., N cycling) and microbial phytohormone metabolisms, particularly in response to root exudates isolated from cereal rye and sorghum plants. Additionally, we constructed a soil microbial genomic catalog of microorganisms responding to commonly used cover crops, a public resource for agriculturally relevant microbes. Many of our exudate-stimulated microorganisms are representatives from poorly characterized or novel taxa, revealing the yet to be discovered metabolic reservoir harbored in agricultural soils. Our findings emphasize the tractability of high-resolution multi-omics approaches to investigate processes relevant for agricultural soils, opening the possibility of targeting specific soil biogeochemical outcomes through biological precision agricultural practices that use cover crops and the microbiome as levers for enhanced crop production.BPG5Z_iDvqR4KrAs2TcSTiVideo

Phosphorus availability influences disease-suppressive soil microbiome through plant-microbe interactions.

Soil nutrient status and soil-borne diseases are pivotal factors impacting modern intensive agricultural production. The interplay among plants, soil microbiome, and nutrient regimes in agroecosystems is essential for developing effective disease management. However, the influence of nutrient availability on soil-borne disease suppression and associated plant-microbe interactions remains to be fully explored. This study aims to elucidate the mechanistic understanding of nutrient impacts on disease suppression, using phosphorous as a target nutrient. A 6-year field trial involving monocropping of tomatoes with varied fertilizer manipulations demonstrated that phosphorus availability is a key factor driving the control of bacterial wilt disease caused by Ralstonia solanacearum. Subsequent greenhouse experiments were then conducted to delve into the underlying mechanisms of this phenomenon by varying phosphorus availability for tomatoes challenged with the pathogen. Results showed that the alleviation of phosphorus stress promoted the disease-suppressive capacity of the rhizosphere microbiome, but not that of the bulk soil microbiome. This appears to be an extension of the plant trade-off between investment in disease defense mechanisms versus phosphorus acquisition. Adequate phosphorus levels were associated with elevated secretion of root metabolites such as L-tryptophan, methoxyindoleacetic acid, O-phosphorylethanolamine, or mangiferin, increasing the relative density of microbial biocontrol populations such as Chryseobacterium in the rhizosphere. On the other hand, phosphorus deficiency triggered an alternate defense strategy, via root metabolites like blumenol A or quercetin to form symbiosis with arbuscular mycorrhizal fungi, which facilitated phosphorus acquisition as well. Overall, our study shows how phosphorus availability can influence the disease suppression capability of the soil microbiome through plant-microbial interactions. These findings highlight the importance of optimizing nutrient regimes to enhance disease suppression, facilitating targeted crop management and boosting agricultural productivity. Video Abstract.

Microbiota responses to mutations affecting NO homeostasis in Arabidopsis thaliana.

Interactions between plants and microorganisms are pivotal for plant growth and productivity. Several plant molecular mechanisms that shape these microbial communities have been identified. However, the importance of nitric oxide (NO) produced by plants for the associated microbiota remains elusive. Using Arabidopsis thaliana isogenic mutants overproducing NO (nox1, NO overexpression) or down-producing NO (i.e. nia1nia2 impaired in the expression of both nitrate reductases NR1/NIA1 and NR2/NIA2; the 35s::GSNOR1 line overexpressing nitrosoglutathione reductase (GSNOR) and 35s::AHB1 line overexpressing haemoglobin 1 (AHB1)), we investigated how altered NO homeostasis affects microbial communities in the rhizosphere and in the roots, soil microbial activity and soil metabolites. We show that the rhizosphere microbiome was affected by the mutant genotypes, with the nox1 and nia1nia2 mutants causing opposite shifts in bacterial and fungal communities compared with the wild-type (WT) Col-0 in the rhizosphere and roots, respectively. These mutants also exhibited distinctive soil metabolite profiles than those from the other genotypes while soil microbial activity did not differ between the mutants and the WT Col-0. Our findings support our hypothesis that changes in NO production by plants can influence the plant microbiome composition with differential effects between fungal and bacterial communities.

Bacillus siamensis orchestrates plant gene reprogramming and rhizosphere microbiome reshaping to bolster maize crop performance

AbstractPlant growth‐promoting rhizobacteria (e.g., Bacillus) confer health benefits to the host. Bacillus siamensis has been used to control plant disease in fruits and vegetables, but its potential effects on crop performance remain unclear. This study investigated changes in the growth, root transcriptomic profile, and rhizosp here microbiome of maize plants (Zea may L.) following inoculation with B. siamensis 33. All inoculated plants grew better than non‐inoculated controls in pots, as exemplified by 24.0% and 6.8% increase in plant height and stem diameter, respectively (p < 0.01). Shoot dry weight also increased by 20.6% upon inoculation, accompanied by 46.9% increase in root dry weight (p < 0.01). Transcriptomic analysis revealed that inoculation induced (2.16‐ to 5.53‐fold) upregulated expression of genes related to auxin signal transduction in maize. The expression of genes involved in phenylpropanoid biosynthesis, glutathione metabolism, and plant defense‐related signal (e.g., jasmonic acid and salicylic acid) transduction was (2.06‐ to 11.30‐fold) upregulated in inoculated plants. Upon inoculation, bacterial α‐diversity trended higher and potentially beneficial taxa (e.g., Sphingobium, Flavihumibacter, and Parasegetibacter) were enriched in the rhizosphere, likely a result of enhanced root exudation of specific metabolites (e.g., flavonoids) and subsequent recruitment of beneficial microbial taxa. Potential microbial functions associated with nitrogen cycling and pollutant degradation were stimulated by inoculation. These findings indicate that B. siamensis 33 mediates the reprogramming of plant gene expression and reshaping of rhizosphere microbiome structure to bolster maize crop performance.

Nitrogen input differentially shapes the rhizosphere microbiome diversity and composition across diverse maize lines

Nitrogen input differentially shapes the rhizosphere microbiome diversity and composition across diverse maize lines

The Role of Phosphate-Solubilizing Microbial Interactions in Phosphorus Activation and Utilization in Plant-Soil Systems: A Review.

To address the issue of phosphorus limitation in agricultural and forestry production and to identify green and economical alternatives to chemical phosphorus fertilizers, this paper reviews the utilization of phosphorus in plant-soil systems and explores the considerable potential for exploiting endogenous phosphorus resources. The application of phosphate-solubilizing microorganisms (PSMs) is emphasized for their role in phosphorus activation and plant growth promotion. A focus is placed on microbial interactions as an entry point to regulate the functional rhizosphere microbiome, introducing the concept of synthetic communities. This approach aims to deepen the understanding of PSM interactions across plant root, soil, and microbial interfaces, providing a theoretical foundation for the development and application of biological regulation technologies to enhance phosphorus utilization efficiency.

Paenibacillus polymyxa J2-4 induces cucumber to enrich rhizospheric Pseudomonas and contributes to Meloidogyne incognita management under field conditions.

Root knot nematodes (RKNs) pose a great threat to agricultural production worldwide. The bacterial nematocides have received increasing attention due to their safe and efficient control against RKNs. Here, we investigated the biocontrol efficacy of Paenibacillus polymyxa J2-4 against Meloidogyne incognita in the field and analyzed the rhizosphere microbiome of cucumber under nematode infection after application of the J2-4 strain. Furthermore, a biomarker strain of Pseudomonas spp. was isolated from the J2-4-inoculated rhizosphere soil, and its nematocidal activity and growth-promoting effect on host plants were determined. In addition, chemotaxis assay of P. fluroescens ZJ5 toward root exudates was carried out. The field experiment demonstrated that P. polymyxa J2-4 could effectively suppressed gall formation in cucumber plants, with the galling index reduced by 67.63% in 2022 and 65.50% in 2023, respectively, compared with controls. Meanwhile, plant height and yield were significantly increased in J2-4 treated plants compared with controls. Metagenomic analysis indicated that J2-4 altered the rhizosphere microbial communities. The relative abundance of Pseudomonas spp. was notably enhanced in the J2-4 group, which was consistent with Linear discriminant analysis Effect Size results that Pseudomonas was determined as one of the biomarkers in the J2-4 group. Furthermore, the ZJ5 strain, one of the biomarker Pseudomonas strains, was isolated from the J2-4-inoculated rhizosphere soil and was identified as Pseudomonas fluorescens. In addition, P. fluorescens ZJ5 exhibited high nematicidal activity in vitro and in vivo, with 99.20% of the mortality rate of M. incognita at 24 h and 69.75% of gall index reduction. The biocontrol efficiency of the synthetic community of ZJ5 plus J2-4 was superior to that of any other single bacteria against M. incognita. Additionally, ZJ5 exhibited great chemotaxis ability toward root exudates inoculated with J2-4. Paenibacillus polymyxa J2-4 has good potential in the biological control against M. incognita under field conditions. Enrichment of the beneficial bacteria Pseudomonas fluorescens ZJ5 in the J2-4-inoculated rhizosphere soil contributes to M. incognita management. © 2024 Society of Chemical Industry.

Features of the isolation of yeast from the root microbiome of winter wheat (Triticum aestivum L.)

Aim. Development of approaches for isolating yeast symbionts from the rhizosphere of various varieties of winter wheat for their further taxonomic identification, as well as studying the influence of yeast species on the growth and development of wheat plants. Methods. Isolation and identification of yeast from the root microbiome of selected wheat varieties was carried out using microbiological and microscopic research methods. Results. As a result of the investigation, conditions were selected, isolation and primary identification of yeast from the root microbiome of winter wheat varieties in different growing periods was carried out. The following yeast species were identified: Saccharomyces serevisiae, Hanseniaspora uvarum, Papiliotrema terrestris, Pichia fementans, Candida subhashii, Torulaspora delbruecki and Candida sp. Conclusions. The difference in the species composition of yeast-symbionts in different periods of development of winter wheat varieties Lisova Pisnya, Pereyaslivka, Bohdana, Smuglyanka, Podolyanka, Kolonia, Reform and Rebel was noted. The obtained data emphasize the importance of studying the rhizosphere microbiome, in particular the functional role of yeast, for understanding the mechanisms of interaction between the plant and the soil, as well as for the development of effective agronomic strategies in the cultivation of wheat and other crops.

Harnessing Belowground Interaction: Re-analyzing the Role of Rhizosphere Microbiome in Plant–Pathogen Interaction Under Water Stress

Harnessing Belowground Interaction: Re-analyzing the Role of Rhizosphere Microbiome in Plant–Pathogen Interaction Under Water Stress

Changes in enzyme activity, structure and growth strategies of the rhizosphere microbiome influenced by elevated temperature and CO2

The impacts of global warming and increased CO2 levels on soil processes and crop growth are concerning. Soil enzymes in the rhizosphere, produced mainly by microbes, play a vital role in nutrients mobilization for plants. Nevertheless, a comprehensive understanding of how microbial communities in the rhizosphere respond to increased temperatures and CO2 levels, particularly in relation to nutrient acquisition, is still lacking. Addressing this problem, we grew soybeans under elevated temperature (ET, +2 °C) and CO2 levels (eCO2, +300 ppm), both individually and in combination (eCO2 + eT), in rhizobox mesocosms. Enzyme activity and microbial communities in soybean rhizospheres were investigated using soil zymography. eCO2 increased enzyme activity by 2.5 % to 8.7 %, while eT expanded the hotspot area from 1.8 % to 3.3 %. The combined factors amplified both the hotspot area by 5.3 % to 10.1 % and enzyme activity by 35.4 % to 67.3 %. Compared to ambient conditions, rhizosphere communities under eCO2 were predominantly comprised of r-strategist keystone taxa, including Acidobacteria, Proteobacteria, and Ascomycota. On the contrary, eT induced a shift in the microbial community towards K-selected taxa, characterized by an increased relative abundance of Basidiomycota and Actinobacteria. Furthermore, the combination of eCO2 and eT led to an increase in the relative abundance of key bacterial species (Acidobacteria, Proteobacteria, and Actinobacteria) as well as fungi (Ascomycota and Basidiomycota). These findings indicate the potential significance of enzyme hotspots in modulating responses to climate change. Changes in enzyme activity and hotspot area could indicate the alteration in microbial growth strategies. The treatments exhibited distinct changes in the composition of microbial communities, in network organization, and in the proportion of species designated as r or K-strategists. Overall, these findings highlight the combined effects of global change factors on bacterial and fungal communities, providing insights into their growth strategies and nutrient mobilization under climate change scenarios.

Optimal Irrigation and Fertilization Enhanced Tomato Yield and Water and Nitrogen Productivities by Increasing Rhizosphere Microbial Nitrogen Fixation

Irrigation and nitrogen application rates have significant effects on greenhouse tomato yields, as well as water and nitrogen use efficiencies, but little is known regarding how these rates affect plant–microbiome interactions and how the associated changes might impact tomato yields. In this greenhouse study conducted over two years, the effects of three irrigation levels (moderate deficit with 65–75% water holding capacity threshold, slight deficit with 75–85%, and sufficient irrigation with 85–95%) and four nitrogen application levels (60, 120, 240, and 360 kg ha−1) on tomato growth, yield, water and nitrogen productivities, and rhizosphere microbial diversities and functions were investigated. The results demonstrated that the highest tomato leaf area, dry biomass, yield, and water and nitrogen productivities were obtained under the treatment with sufficient irrigation. With increasing nitrogen application, the tomato leaf area, dry biomass, yield, and water and nitrogen productivities showed a trend of first increasing and then decreasing. Overall, the treatment (N2W3) with sufficient irrigation and 240 kg ha−1 N was associated with the highest tomato growth, yield, and water and nitrogen productivities. Moreover, optimal irrigation and nitrogen application obviously altered the structures of rhizosphere bacterial and fungal communities, particularly recruiting microbiota conferring benefits to tomato growth and nitrogen fixation—namely, Lysobacter and Bradyrhizobium. Ultimately, optimal irrigation and nitrogen application significantly increased the relative abundances of functions related to carbon, sulfur, and nitrogen metabolism, especially nitrogen fixation. In summary, optimal irrigation and fertilization enhanced tomato yield, as well as water and nitrogen productivities by increasing the nitrogen fixation functions of the rhizosphere microbiome. Our results provide significant implications for tomato cultivation in greenhouses, in terms of optimized irrigation and fertilization.