The role of root exudates in rhizosphere interactions with plants and other organisms

Catabolic pathway acquisition by rhizosphere bacteria readily enables growth with a root exudate component but does not affect root colonization

Horizontal gene transfer (HGT) is a fundamental evolutionary process that plays a key role in bacterial evolution. The likelihood of a successful transfer event is expected to depend on the precise balance of costs and benefits resulting from pathway acquisition. Most experimental analyses of HGT have focused on phenotypes that have large fitness benefits under appropriate selective conditions, such as antibiotic resistance. However, many examples of HGT involve phenotypes that are predicted to provide smaller benefits, such as the ability to catabolize additional carbon sources. We have experimentally simulated the consequences of one such HGT event in the laboratory, studying the effects of transferring a pathway for catabolism of the plant-derived aromatic compound salicyl alcohol between rhizosphere isolates from the Pseudomonas genus. We find that pathway acquisition enables rapid catabolism of salicyl alcohol with only minor disruptions to the existing metabolic and regulatory networks of the new host. However, this new catabolic potential does not confer a measurable fitness advantage during competitive growth in the rhizosphere. We conclude that the phenotype of salicyl alcohol catabolism is readily transferable but is selectively neutral under environmentally relevant conditions. We propose that this condition is common and that HGT of many pathways will be self-limiting because the selective benefits are small.IMPORTANCEHorizontal gene transfer (HGT) is a key process in microbial evolution, but the factors limiting HGT are poorly understood. Aside from the rather unique scenario of antibiotic resistance, the evolutionary benefits of pathway acquisition are still unclear. To experimentally test the effects of pathway acquisition, we transferred a pathway for catabolism of a plant-derived aromatic compound between soil bacteria isolated from the roots of poplar trees and determined the resulting phenotypic and fitness effects. We found that pathway acquisition allowed bacteria to grow using the plant-derived compound in the laboratory, but that this new phenotype did not provide an advantage when the bacteria were reinoculated onto plant roots. These results suggest that the benefits of pathway acquisition may be small when measured under ecologically-relevant conditions. From an engineering perspective, efforts to alter microbial community composition in situ by manipulating catabolic pathways or nutrient availability will be challenging when gaining access to a new niche does not provide a benefit.

Two rice cultivars recruit different rhizospheric bacteria to promote aboveground regrowth after mechanical defoliation

Plants have evolved the ability to regrow after mechanical defoliation and environmental stresses. However, it is unclear whether and how defoliated plants exploit beneficial microbiota from the soil to promote aboveground regrowth. Here, we compared the defoliation-triggered changes in the root exudation and bacterial microbiome of two rice cultivars (Oryza sativa L ssp.), indica/xian cultivar Minghui63 and japonica/geng cultivar Nipponbare. The results show that reciprocal growth promotion existed between defoliated Minghui63 seedlings and soil bacteria. After the leaves were removed, the Minghui63 seedlings displayed approximately 1.5- and 2.1-fold higher root exudation and leaf regrowth rates, respectively, than did the Nipponbare seedlings. In field trials, Minghui63 and Nipponbare enriched taxonomically and functionally distinct bacteria in the rhizosphere and root. In particular, Minghui63 rhizosphere and root communities depleted bacteria whose functions are related to xenobiotics biodegradation and metabolism. The microbiome data implied that the bacterial family Rhodocyclaceae was specifically enriched during the regrowth of defoliated Minghui63 rice. We further isolated a Rhodocyclaceae strain, Uliginosibacterium gangwonense MDD1, from rice root. Compared with germ-free conditions, MDD1 inoculation promoted the aboveground regrowth of defoliated Minghui63 by 61% but had a weaker effect on Nipponbare plants, suggesting cultivar-specific associations between regrowth-promoting bacteria and rice. This study provides novel insight into microbiota‒root‒shoot communication, which is implicated in the belowground microbiome and aboveground regrowth in defoliated rice. These data will be helpful for microbiome engineering to increase rice resilience to defoliation and environmental stresses.IMPORTANCEAs sessile organisms, plants face a multitude of abiotic and biotic stresses which often result in defoliation. To survive, plants have evolved the ability to regrow leaves after stresses and wounding. Previous studies revealed that the rhizosphere microbiome affected plant growth and stress resilience; however, how belowground microbiota modulates the aboveground shoot regrowth is unclear. To address this question, we used rice, an important crop worldwide, to analyze the role of rhizosphere microbiota in leaf regrowth after defoliation. Our data indicate mutual growth promotion between defoliated rice and rhizosphere bacteria and such beneficial effect is cultivar specific. The microbiome analysis also led us to find a Uliginosibacterium gangwonense strain that promoted rice cv. MH63 leaf regrowth. Our findings therefore present a novel insight into plant-microbiome function and provide beneficial strains that potentially enhance rice stress resilience.

Interaction between root exudates and PFOS mobility: Effects on rhizosphere microbial health in wetland ecosystems

Perfluorooctanesulfonate (PFOS), a persistent organic pollutant, poses significant ecological risks. This study investigates the effects of PFOS on rhizosphere microbial communities of two wetland plants, Lythrum salicaria (LS) and Phragmites communis (PC). We conducted microcosm experiments to analyze the physiological status of soil microbes under varying PFOS concentrations and examined the role of root exudates in modulating PFOS mobility. Flow cytometry and soil respiration measurements revealed that PFOS exposure increased microbial mortality, with differential impacts observed between LS and PC rhizospheres. LS root exudates intensified microbial stress, whereas PC exudates mitigated PFOS toxicity. Thin-layer chromatography indicated that LS exudates decreased PFOS mobility, leading to higher local concentrations and increased microbial toxicity, while PC exudates enhanced PFOS mobility, reducing its local impact. Fourier-transform infrared spectroscopy and excitation-emission matrix fluorescence spectroscopy of root exudates identified compositional shifts under PFOS stress, highlighting distinct defense strategies in LS and PC. These findings underscore the importance of plant-microbe interactions and root exudate composition in determining microbial resilience to PFOS contamination.

Taming of the microbial beasts: Plant immunity tethers potentially pathogenic microbiota members

Plants are in intimate association with taxonomically structured microbial communities called the plant microbiota. There is growing evidence that the plant microbiota contributes to the holistic performance and general health of plants, especially under unfavorable situations. Despite the attached benefits, surprisingly, the plant microbiota in nature also includes potentially pathogenic strains, signifying that the plant hosts have tight control over these microbes. Despite the conceivable role of plant immunity in regulating its microbiota, we lack a complete understanding of its role in governing the assembly, maintenance, and function of the plant microbiota. Here, we highlight the recent progress on the mechanistic relevance of host immunity in orchestrating plant-microbiota dialogues and discuss the pluses and perils of these microbial assemblies.

Enhancing the Resilience of Agroecosystems Through Improved Rhizosphere Processes: A Strategic Review

As farming practices evolve and climate conditions shift, achieving sustainable food production for a growing global population requires innovative strategies to optimize environmentally friendly practices and minimize ecological impacts. Agroecosystems, which integrate agricultural practices with the surrounding environment, play a vital role in maintaining ecological balance and ensuring food security. Rhizosphere management has emerged as a pivotal approach to enhancing crop yields, reducing reliance on synthetic fertilizers, and supporting sustainable agriculture. The rhizosphere, a dynamic zone surrounding plant roots, hosts intense microbial activity fueled by root exudates. These exudates, along with practices such as green manure application and intercropping, significantly influence the soil's microbial community structure. Beneficial plant-associated microbes, including Trichoderma spp., Penicillium spp., Aspergillus spp., and Bacillus spp., play a crucial role in improving nutrient cycling and promoting plant health, yet their interactions within the rhizosphere remain inadequately understood. This review explores how integrating beneficial microbes, green manures, and intercropping enhances rhizosphere processes to rebuild microbial communities, sequester carbon, and reduce greenhouse gas emissions. These practices not only contribute to maintaining soil health but also foster positive plant-microbe-rhizosphere interactions that benefit entire ecosystems. By implementing such strategies alongside sound policy measures, sustainable cropping systems can be developed to address predicted climate challenges. Strengthening agroecosystem resilience through improved rhizosphere processes is essential for ensuring food security and environmental sustainability in the future. In conclusion, using these rhizosphere-driven processes, we could develop more sustainable and resilient agricultural systems that ensure food security and environmental preservation amidst changing climate situations.

Phlomoides rotata adapts to low-nitrogen environments by promoting root growth and increasing root organic acid exudate

Nitrogen (N) is one of the three major elements required for plant growth and development. It is of great significance to study the effects of different nitrogen application levels on the growth and root exudates of Phlomoides rotata, and can provide a theoretical basis for its scientific application of fertilizer to increase production. In this study, Phlomoides rotata were grown under different nitrogen conditions for two months. Soil and plant analyzer development (SPAD) values, bioaccumulation, root morphology, root exudate composition, nitrogen metabolism enzyme and antioxidant enzyme activity were evaluated. The results showed that compared with CK (no N fertilizer), N2 (CO(NH2)2 80 mg/kg) and N3 (CO(NH2)2 160 mg/kg) through significantly improved the activities of nitrogen metabolism enzyme nitrite reductase (NiR), glutamate dehydrogenase (GDH) and glutamine synthetase (GS), enhanced the nitrogen metabolism process, and increased the accumulation of plant soluble sugars (SS) and soluble protein (SP), thus improving Phlomoides rotata biomass yield. After 60 days of treatment, low nitrogen (N1, CO(NH2)2 40 mg/kg) increased root length, root volume, root surface area, average root diameter, significantly increased the diversity of organic acids in root exudates, and enhanced the activity of antioxidant enzymes to adapt the nitrogen deficiency environment. This study can provide new ideas for understanding the mechanism of nitrogen tolerance in Phlomoides rotata and developing scientific fertilization management strategies for plateau plants and medicinal plants.

Root Exudation: An In-Depth Experimental Guide

Plants exude a wide variety of compounds into the rhizosphere, modulating soil functioning and diversity. The number of studies investigating exudation has exponentially increased over the past decades. Yet, the high inter-study variability of the results is slowing down our understanding of root-soil interactions. This variability is partly due to the absence of harmonized methodologies to collect and characterize exudation. Here, we discuss how various experimental aspects influence exudation profiles by performing a literature review, and we suggest best practices for different experimental setups. We discuss state-of-the-art of spatially resolved exudate collection, collection in controlled versus field conditions and plant growth setups ranging from hydroponics to soil. We highlight the importance of preparing experimental blanks, in situ versus ex situ exudate collection, various collection media and timing of collection, exudate storage and processing and analytical considerations. We summarize best practices for experimental setup and reporting of parameters in an easily accessible table format to facilitate discussion of best practices in the field. An increased standardization in the field together with the systematic studies suggested will improve our knowledge of how plant exudation shapes interactions with organisms in soil.

Ralstonia solanacearum infection induces tobacco root to secrete chemoattractants to recruit antagonistic bacteria and defensive compounds to inhibit pathogen

BACKGROUND

Plant root exudates play crucial roles in maintaining the structure and function of the whole belowground ecosystem and regulating the interactions between roots and soil microorganisms. Ralstonia solanacearum causes bacterial wilt disease in many plants, while root exudate-mediated inhibition of pathogen infection is poorly understood. Here, we characterize the chemical divergence between root exudates of healthy and diseased tobacco plants and the effects of that variability on the rhizosphere microbial community and the occurrence of bacterial wilt.

RESULTS

Compared with the healthy plants, root exudates in diseased plants showed distinct exudation patterns and metabolite profiles including increased amounts of flavonoids, phenylpropanoids, terpenoids and defense-related hormones, as well as distinct bacterial community composition, as illustrated by an increased abundance of Ralstonia and decreased abundances of Bacillus and Streptomyces in diseased plants rhizosphere. Pathogen infection stimulated roots to secrete more defensive compounds to inhibit pathogen growth. Change of root exudates modulated rhizosphere microbial community. Specific root exudates could benefit plants by attracting antagonistic Bacillus amyloliquefaciens and inhibiting pathogens. Bacillus amyloliquefaciens could utilize specific root exudates as carbon sources. Benzyl cinnamatel promoted the biofilm formation and colonization of B. amyloliquefaciens on roots.

CONCLUSION

To defend against pathogen invasion, tobacco plants recruited antagonistic and plant growth-promoting rhizobacteria to the rhizosphere by modifying root exudate profiles. Specific signal molecules are recommended to recruit beneficial microorganisms for controlling bacterial wilt. The results provide insights concerning the metabolic divergence of root exudates integral to understanding root-microorganism interaction. © 2024 Society of Chemical Industry.

Selenium nanoboosting of plant-beneficial microbiome

In the dynamic theater of plant-microbe interactions, a new conductor has emerged: selenium nanoparticles. As unveiled by Sun et al. in this issue of Cell Host & Microbe, these microbially synthesized nanoparticles recruit plant growth-promoting microbes, orchestrating a synergy between plants and the rhizosphere microbiome.

Antibiotic resistance genes transfer risk: Contributions from soil erosion and sedimentation activities, agricultural cycles, and soil chemical contamination

The transfer of antibiotic resistance genes (ARGs) pose environmental risks that are influenced by soil activity and pollution. Soil erosion and sedimentation accelerate degradation and migration, thereby affecting soil distribution and contamination. This study quantified the vertical and horizontal transfer capabilities of ARGs and simulated soil environments under various scenarios, such as erosion, agricultural cycles, and chemical pollution. The results showed that slope, runoff, and sediment volume significantly affected soil erosion and ARG transfer risks. The response of environmental factors to the transfer risk of ARGs is as follows: the promotion effect of soil deposition (average: 21.41 %) is significantly greater than the inhibitory effect of soil erosion (average: -11.31 %); the planting period (average: -64.654) is greater than the harvest period (average: -56.225); the response to soil chemical pollution is: the impact of phosphate fertilizer residues, antibiotics, and pesticide pollution is more significant. This study constructed a vertical and horizontal transfer system of ARGs in soil erosion and sedimentation environments and proposed a response analysis method for the impact of factors, such as soil erosion and sedimentation activities, agricultural cycles, and soil chemical pollution, on ARGs transfer capabilities.

Teosinte populations exhibit weak local adaptation to their rhizosphere biota despite strong effects of biota source on teosinte fitness and traits

While biotic interactions often impose selection, species and populations vary in whether they are locally adapted to biotic interactions. Evolutionary theory predicts that environmental conditions drive this variable local adaptation by altering the fitness impacts of species interactions. To investigate the influence of an environmental gradient on adaptation between a plant and its associated rhizosphere biota, we cross-combined teosinte (Zea mays ssp. mexicana) and rhizosphere biota collected across a gradient of decreasing temperature, precipitation, and nutrients in a greenhouse common garden experiment. We measured both fitness and phenotypes expected to be influenced by biota, including concentrations of nutrients in leaves. Independent, main effects of teosinte and biota source explained most variation in teosinte fitness and traits. For example, biota from warmer sites provided population-independent fitness benefits across teosinte hosts. Effects of biota that depended on teosinte genotype were often not specific to their local hosts, and most traits had similar relationships to fitness across biota treatments. However, we found weak patterns of local adaptation between teosinte and biota from colder sites, suggesting environmental gradients may alter the importance of local adaptation in teosinte-biota interactions, as evolutionary theory predicts.

Untargeted Metabolomic Analysis Reveals a Potential Role of Saponins in the Partial Resistance of Pea (Pisum sativum) Against a Root Rot Pathogen, Aphanomyces euteiches

In soilborne diseases, the plant-pathogen interaction begins as soon as the seed germinates and develops into a seedling. Aphanomyces euteiches, an oomycete, stays dormant in soil and is activated by sensing the host through chemical signals present in the root exudates. The composition of plant exudates may, thus, play an important role during the early phase of infection. To better understand the role of root exudates in plant resistance, we investigated the interaction between partially resistant lines (PI660736 and PI557500) and susceptible pea cultivars (CDC Meadow and AAC Chrome) against A. euteiches during the pre-invasion phase. The root exudates of the two sets of cultivars clearly differed from each other in inducing oospore germination. PI557500 root exudate not only had diminished induction but also inhibited the oospore germination. The contrast between the root exudates of resistant and susceptible cultivars was reflected in their metabolic profiles. Data from fractionation and oospore germination inhibitory experiments identified a group of saponins that accumulated differentially in susceptible and resistant cultivars. We detected 56 saponins and quantified 44 of them in pea root and 30 from root exudate; the majority of them, especially soyasaponin I and dehydrosoyasaponin I with potent in vitro inhibitory activities, were present in significantly higher amounts in both roots and root exudates of PI660736 and PI557500 compared with Meadow and Chrome. Our results provide evidence for saponins as deterrents against A. euteiches, which might have contributed to the resistance against root rot in the studied pea cultivars. [Formula: see text] Copyright © 2024 His Majesty the King in Right of Canada, as represented by the Minister of Agriculture and Agri-Food Canada and the National Research Council of Canada. This is an open access article distributed under the CC BY 4.0 International license.

Multifaceted effects of microplastics on soil-plant systems: Exploring the role of particle type and plant species

Microplastics have emerged as a global environmental concern, yet their impact on terrestrial environments, particularly agricultural soils, remains underexplored. Agricultural soils, due to intensive farming, may serve as significant sinks for microplastics. This study investigated the effects of different types of microplastics-polyester microfibers, polyethylene terephthalate microfragments, and polystyrene microspheres-on soil properties and radish growth, while a complementary experiment examined the impact of polyester microfibers on the growth of lettuce and Chinese cabbage. Through both horizontal and vertical comparisons, this research comprehensively evaluated the interactions between microplastic particles and plant species in soil-plant systems. The results showed that polyester microfibers significantly affected soil bulk density, with effects varying based on planting conditions (p < 0.01). Polyethylene terephthalate microfragments and polystyrene microspheres reduced the proportion of small soil macroaggregates under radish cultivation (p < 0.01). Additionally, polystyrene microspheres significantly altered the total organic carbon stock in radish-growing soil, potentially affecting the microclimate (p < 0.01). Interestingly, polyester microfibers promoted lettuce seed germination and significantly enhanced the root biomass of Chinese cabbage (p < 0.05). Overall, the environmental effects of microplastic exposure varied depending on the type of particle and plant species, suggesting that microplastics are not always harmful to soil-plant systems and may even offer benefits in certain scenarios. Given the crucial role of soil-plant systems in terrestrial ecosystems, and their direct connection to food safety, human health, and global change, further research should explore both the positive and negative impacts of microplastics on agricultural practices.

Soil microbiological assessment on diversified annual cropping systems in China

Recent studies have demonstrated that monocropping of flue-cured tobacco can lead to various issues, including nutrient deficiencies, accumulation of allelopathic substances, and disturbance in soil microbial flora. While diversification in cropping systems has proven effective in alleviating monocropping barriers, however, further exploration is needed to understand the potential microbial mechanisms involved in this process. In our study, we set five cropping systems (RR: rice monocropping; TR: tobacco-rice rotation over 20 years; TRA: tobacco-rice-astragalus rotation; TRW: tobacco-rice-wheat rotation; TRO: tobacco-rice-oilseed rape rotation) to explore the impact on crop yield and quality, soil chemical properties, and microbial diversity. The results showed that the yield and gross margin were significantly decreased. Following diversification in cropping systems, particularly after implementing the TRA treatment, the yield and gross margin increased by 27.35% and 38.67%, respectively, compared to the TR treatment. Additionally, the presence of tobacco in the soil resulted in acidification, reduced soil fertility, and suppression of soil microorganism diversity and metabolite abundance. With diversification in cropping systems, there was an increase in soil pH, carbon and nitrogen cycle enzyme activities, and the relative abundance of beneficial microorganisms (acidobacteria, nitrospirillum, and ascomycota) and soil metabolites. Diversification in cropping systems has the potential to increase crop biomass, soil fertility, and soil microbial environment. Our results suggest a scientific foundation for implementing effective nutrient management practices and rational crop rotation systems.

Allelopathic effects of leaf extracts of Eucalyptus camaldulensis Dehnh. on morphological, physiological, and yield traits of Ethiopian wheat (Triticum durum L.) cultivars

Allelochemicals released into the soil from the leaves of eucalyptus species affect the growth and physiology of various crops. This study aimed to evaluate the allelopathic effects of aqueous and methanolic leaf extracts from Eucalyptus camaldulensis on three Ethiopian wheat cultivars (Assasa, Mukiye and Ude) of Triticum durum L. It was conducted as a pot experiment, and it utilized four concentrations of the extracts (Control (0%), 10%, 15%, and 20%) in a completely randomized design with three replicates. Results indicated that both extracts inhibited plant growth, biomass, and yield, with the methanolic extract showing stronger inhibitory effects. For instance, a concentration of 20% methanolic leaf extracts decreased chlorophyll fluorescence in the Assasa, Ude, and Mukiye cultivars by 53.97%, 36.36%, and 36.51%, respectively. The growth of both shoots and roots in Assasa, Ude, and Mukiye was significantly reduced at higher concentrations. Increasing concentrations of the extracts led to greater reductions in seedling traits and overall crop yield, with significant impacts observed (p ≤ 0.05). The findings suggest that eucalyptus should not be planted on agricultural land due to its negative impact on crop productivity.

Microbial biofilms: a comprehensive review of their properties, beneficial roles and applications

Biofilms are microbial communities nested in self-secreted extracellular polymeric substances that can provide microorganisms with strong tolerance and a favorable living environment. Deepening the understanding and research on positive effects of microbial biofilms is consequently necessary, since most researches focuses on how to control biofilms formation to reduce food safety issues. This paper highlights beneficial roles of biofilms including the formation mechanism, influencing factors, health benefits, strategies to improve its film-forming efficiency, as well as applications especially in fields of food industry, agriculture and husbandry, and environmental management. Beneficial biofilms can be affected by multiple factors such as strain characteristics, media composition, signal molecules, and carrier materials. The biofilm barrier composed of beneficial bacteria provides a more favorable microecological environment, keeping bacteria survival longer, and its derived metabolites are better conducive to health. However, in the practical application of biofilms, there are still significant challenges, especially in terms of film-forming efficiency, stability, and safety assessment. Continuous research is needed to discover innovative methods of utilizing biofilms for sustainable food development in the future, in order to fully unleash its potential and promote its application in the food industry.

Compost mediates the recruitment of core bacterial communities in alfalfa roots to enhance their productivity potential in saline-sodic soils

Introduction

Composting is one of the effective environmental protection and sustainable measures for improving soil quality and increasing crop yield. However, due to the special physical and chemical properties of saline-sodic soil and the complex rhizosphere microecological environment, the potential mechanism of regulating plant growth after applying compost in saline-sodic soil remains elusive.

Methods

Here, we investigated the effects of different compost addition rates (0, 5, 15, 25%) on plant growth traits, soil chemical properties, and rhizosphere bacterial community structure.

Results

The results showed that compost promoted the accumulation of plant biomass and root growth, increased soil nutrients, and enhanced the diversity and complexity of the rhizosphere bacterial communities. Moreover, the enriched core bacterial ASVs (Amplicon Sequence Variants) in compost treatment could be reshaped, mainly including dominant genera, such as Pseudomonas, Devosia, Novosphingobium, Flavobacterium, and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium. The functions of these ASVs were energy resources and nitrogen cycle functions, suggesting the roles of these ASVs in improving plant root nutrient resource acquisition for alfalfa growth. The contents of available potassium, available phosphorus, total nitrogen, and organic carbon of the soil surrounding the roots, the root length, root surface area, root volume, and root tips affected the abundance of the core bacterial ASVs, and the soil chemical properties contributed more to the effect of plant biomass.

Discussion

Overall, our study strengthens the understanding of the potentially important taxa structure and function of plant rhizosphere bacteria communities, and provides an important reference for developing agricultural microbiome engineering techniques to improve root nutrient uptake and increase plant productivity in saline-sodic soils.

Rhizosphere microbiome regulation: Unlocking the potential for plant growth

Rhizosphere microbial communities are essential for plant growth and health maintenance, but their recruitment and functions are affected by their interactions with host plants. Finding ways to use the interaction to achieve specific production purposes, so as to reduce the use of chemical fertilizers and pesticides, is an important research approach in the development of green agriculture. To demonstrate the importance of rhizosphere microbial communities and guide practical production applications, this review summarizes the outstanding performance of rhizosphere microbial communities in promoting plant growth and stress tolerance. We also discuss the effect of host plants on their rhizosphere microbes, especially emphasizing the important role of host plant species and genes in the specific recruitment of beneficial microorganisms to improve the plants' own traits. The aim of this review is to provide valuable insights into developing plant varieties that can consistently recruit specific beneficial microorganisms to improve crop adaptability and productivity, and thus can be applied to green and sustainable agriculture in the future.

Gluconacetobacter diazotrophicus AZ0019 requires functional nifD gene for optimal plant growth promotion in tomato plants

Gluconacetobacter diazotrophicus is a nitrogen fixing bacterium able to colonise a wide range of host plants and is marketed as a biofertiliser due to its ability to promote plant growth. This study aims to investigate how biological nitrogen fixation (BNF) competency affects the growth promotion of inoculated tomato plants and to describe the colonisation mechanism of this bacterium in dicot systems. A nitrogen fixation impaired mutant (Gd nifD- ) was produced by disrupting the nifD gene, which encodes the nitrogenase Mo-Fe subunit, in order to assess its plant growth promotion (PGP) capability in comparison to G. diazotrophicus wild type strain (Gd WT). Furthermore, tagged strains were employed to monitor the colonisation process through qPCR analyses and fluorescence microscopy. Following a preliminary glass house trial, Gd WT or Gd nifD- were applied to hydroponically grown tomato plants under nitrogen-replete and nitrogen-limiting conditions. Bacteria reisolation data and plant growth parameters including height, fresh weight, and chlorophyll content were assessed 15 days post inoculation (dpi). Gd WT significantly enhanced plant height, fresh weight, and chlorophyll content in both nitrogen conditions, while Gd nifD- showed a reduced PGP effect, particularly in terms of chlorophyll content. Both strains colonised plants at similar levels, suggesting that the growth advantages were linked to BNF capacity rather than colonisation differences. These findings indicate that a functional nifD gene is a fundamental requirement for optimal plant growth promotion by G. diazotrophicus.

Harnessing Pseudomonas spp. for sustainable plant crop protection

This review examines the role of Pseudomonas spp. bacteria as biocontrol agents against crop diseases, focusing on their mechanisms of action, efficacy, and potential applications in sustainable agriculture. Pseudomonas spp., ubiquitous in soil ecosystems and root microbiomes, have attracted attention for their ability to suppress phytopathogens and enhance plant health through various mechanisms. These include direct competition for nutrients, production of antimicrobial compounds and volatile organic compounds, competition using type VI secretion systems, and indirect induction of systemic resistance. Our review shows that Pseudomonas strains effectively control a wide range of diseases across diverse plant species, with some strains demonstrating efficacy comparable to chemical fungicides. However, the review also highlights challenges in achieving consistent performance when using Pseudomonas inoculants under field conditions due to various biotic and abiotic factors. Strategies to optimize biocontrol potential, such as formulation techniques, application methods, and integration with other management practices, are discussed. The advantages of Pseudomonas-based biocontrol for sustainable agriculture include reduced reliance on chemical pesticides, enhanced crop productivity, and improved environmental sustainability. Future research directions should focus on understanding the complex interactions within the plant microbiome, optimizing delivery systems, and addressing regulatory hurdles for commercial deployment. This review underscores the significant potential of Pseudomonas spp. in sustainable crop protection while acknowledging the need for further research to fully harness their capabilities in agricultural systems.

Arsenic-induced enhancement of diazotrophic recruitment and nitrogen fixation in Pteris vittata rhizosphere

Heavy metal contamination poses an escalating global challenge to soil ecosystems, with hyperaccumulators playing a crucial role in environmental remediation and resource recovery. The enrichment of diazotrophs and resulting nitrogen accumulation promoted hyperaccumulator growth and facilitated phytoremediation. Nonetheless, the regulatory mechanism of hyperaccumulator biological nitrogen fixation has remained elusive. Here, we report the mechanism by which arsenic regulates biological nitrogen fixation in the arsenic-hyperaccumulator Pteris vittata. Field investigations and greenhouse experiments, based on multi-omics approaches, reveal that elevated arsenic stress induces an enrichment of key diazotrophs, enhances plant nitrogen acquisition, and thus improves plant growth. Metabolomic analysis and microfluidic experiments further demonstrate that the upregulation of specific root metabolites plays a crucial role in recruiting key diazotrophic bacteria. These findings highlight the pivotal role of nitrogen-acquisition mechanisms in the arsenic hyperaccumulation of Pteris vittata, and provide valuable insights into the plant stress resistance.

Drought stimulates root exudation of organic nitrogen in cotton (Gossypium hirsutem)

Root exudation of N is a plant input to the soil environment and may be differentially regulated by the plant during drought. Organic N released by root systems has important implications in rhizosphere biogeochemical cycling considering the intimate coupling of C and N dynamics by microbial communities. Besides amino acids, diverse molecules exuded by root systems constitute a significant fraction of root exudate organic N but have yet to receive a metabolomic and quantitative investigation during drought. To observe root exudation of N during drought, mature cotton plants received progressive drought and recovery treatments in an aeroponic system throughout their reproductive stage and were compared to control plants receiving full irrigation. Root exudates were nondestructively sampled from the same plants at 9 timepoints over 18 days. Total organic C and N were quantified by combustion, inorganic N with spectrophotometric methods, free amino acids by high performance liquid chromatography (HPLC), and untargeted metabolomics by Fourier-transform ion cyclotron resonance-mass spectrometry (FT-ICR-MS). Results indicate that organic N molecules in root exudates were by far the greatest component of root exudate total N, which accounted for 20-30% of root exudate mass. Drought increased root exudation of organic N (62%), organic C (6%), and free amino acid-N (562%), yet free amino acids were <5% of the N balance. Drought stress significantly increased root exudation of serine, aspartic acid, asparagine, glutamic acid, tryptophan, glutamine, phenylalanine, and lysine compared to the control. There was a total of 3,985 molecules detected across root exudate samples, of which 41% contained N in their molecular formula. There were additionally 349 N-containing molecules unique to drought treatment and 172 unique to control. Drought increased the relative abundance and redistributed the molecular weights of low molecular weight N-containing molecules. Time-series analysis revealed root exudation of organic N was stimulated by drought and was sensitive to the degree of drought stress.

Evolution of phosphate scouting in the terrestrial biosphere

Chemistry assigns phosphorus and its most oxidized form, inorganic phosphate, unique roles for propelling bioenergetics and metabolism in all domains of life, possibly since its very origin on prebiotic Earth. For plants, access to the vital mineral nutrient profoundly affects growth, development and vigour, thus constraining net primary productivity in natural ecosystems and crop production in modern agriculture. Unlike other major biogenic elements, the low abundance and uneven distribution of phosphate in Earth's crust result from the peculiarities of phosphorus cosmochemistry and geochemistry. Here, we trace the chemical evolution of the element, the geochemical phosphorus cycle and its acceleration during Earth's history until the present (Anthropocene) as well as during the evolution and rise of terrestrial plants. We highlight the chemical and biological processes of phosphate mobilization and acquisition, first evolved in bacteria, refined in fungi and algae and expanded into powerful phosphate-prospecting strategies during land plant colonization. Furthermore, we review the evolution of the genetic and molecular networks from bacteria to terrestrial plants, which monitor intracellular and extracellular phosphate availabilities and coordinate the appropriate responses and adjustments to fluctuating phosphate supply. Lastly, we discuss the modern global phosphorus cycle deranged by human activity and the challenges imposed ahead. This article is part of the theme issue 'Evolution and diversity of plant metabolism'.

Transcriptomic response of wetland microbes to root influence

Wetlands are hotspots for carbon and nutrient cycling. The important role of plant-microbe interactions in driving wetland biogeochemistry is widely acknowledged, prompting research into their molecular biological basis for a deeper understanding of these processes. We analyzed transcriptomic responses of soil microbes to root exudates in coastal wetland soils using 13CO2 pulse labeling. Metatranscriptomics revealed 388 upregulated and 11 downregulated genes in response to root exudates. The Wood-Ljungdahl pathway and dissimilatory sulfate reduction/oxidation were the most active microbial pathways independent of root influence, whereas pathways with the strongest upregulation in response to root influence were related to infection, stress response, and motility. We demonstrate shifts within the active community toward higher relative abundances of Betaproteobacteria, Campylobacterota, Kiritimatiellota, Lentisphaerota, and Verrucomicrobiota in response to exudates. Overall, this study improves our mechanistic understanding of wetland plant-soil microbe interactions by revealing the phylogenetic and transcriptional response of soil microorganisms to root influence and exudate input.

Molecular and morphoanatomical characterization of Urocystis heteropogonis sp. nov.: a novel smut fungus infecting Heteropogon contortus

BACKGROUND

A new species of smut fungus, Urocystis heteropogonis, was discovered infecting Heteropogon contortus in Shawar Valley, Swat district, Khyber Pakhtunkhwa, Pakistan. The study aimed to characterize this fungus based on its morpho-anatomical and molecular features and clarify its phylogenetic position within the genus Urocystis.

RESULTS

Urocystis heteropogonis was identified as a novel species, distinct from other Urocystis species. Morphologically, it is characterized by larger spore balls (14-69 × 11-45 μm) and central spores that are 14-28 × 11-20 μm in size, with each spore containing1-8 central spores. The spore walls measure 0.9-2.5 μm in thickness and the species differs in infection patterns compared to other Urocystis species. Phylogenetic analysis based on the ITS and LSU regions of nuclear ribosomal DNA (nrDNA) further confirmed the novelty of the species, placing it within a distinct clade alongside U. agropyri, U. occulta, U. piptatheri, and U. tritici.

CONCLUSIONS

The discovery of Urocystis heteropogonis adds to the diversity of smut fungi infecting grasses and highlights the need for further research into its ecological and agricultural implications. Future studies should focus on the disease's spread, management, and potential impact on host populations.

Microbial necromass in soil profiles increases less efficiently than root biomass in long-term fenced grassland: Effects of microbial nitrogen limitation and soil depth

Grassland fencing is acknowledged as a crucial initiative to enhance biodiversity and to increase soil organic carbon (SOC) content in ecologically fragile regions or barren systems. Theoretical perspectives propose that fencing induced an increase in root biomass, and its penetration into the soil profile introduced organic matter that facilitated SOC formation through microbial necromass and root residues. It is hypothesized that long-term grassland fencing increases root biomass, thereby enhancing SOC formation within the soil profile through microbial residues in badland ecosystems. To test this hypothesis, we selected grasslands subjected to varying durations of fencing post-grazing (i.e., 10, 15, 20, 30, and 40 y). Our investigation aimed to clarify microbial necromass dynamics in 0-100 cm soil profiles after fencing and to identify the influencing factors. Long-term grassland fencing (i.e., >30 y) increased root biomass by 160 %, SOC by 69 %, and necromass by 41 % compared to grazed grassland within the 0-40 cm horizon; in contrast, increased root biomass by 870 %, SOC by 111 %, and necromass by 46 % in the 40-100 cm horizon. Necromass in deep soil (40-100 cm) accounted for about 50 % of total residues in the 0-100 cm profile. Increased root and living microbial biomass stimulated the necromass accumulation, with a more pronounced increase in fungal residues compared with bacterial residues. Nonetheless, microbial nutrient limitation increases C or N-acquisition enzyme coefficients, which subsequently reduced fungal and bacterial residues and stimulated their recycling. Despite substantial increases in root biomass within the soil profile after fencing, limitation of microbial N and depth reduced the effectiveness of enhancing SOC and necromass. In conclusion, although microbial residues were the important source of SOC in grasslands of the Loess Plateau, microbial N limitation impeded necromass accumulation, and the interplay of root biomass, soil depth, and nutrient limitation regulated the dynamics of necromass following grassland fencing.

Mechanisms of rhizosphere plant-microbe interactions: molecular insights into microbial colonization

The rhizosphere, as the "frontline" of plant life, connects plant roots, rhizosphere microorganisms, and surrounding soil, plays a crucial role in plant growth and health, particularly in sustainable agriculture. Despite the well-established contribution of plant-microbe interactions to plant health, the specific molecular mechanisms remain insufficiently understood. This review aims to summarize the physiological adjustments and signal modulation that both plants and microorganisms undergo within this unique ecological niche to ensure successful colonization. By analyzing key processes such as chemotaxis, root attachment, immune evasion, and biofilm formation, we uncover how plants precisely modulate root exudates to either recruit or repel specific microorganisms, thereby shaping their colonization patterns. These findings provide new insights into the complexity of plant-microbe interactions and suggest potential directions for future research in sustainable agriculture.

Altitudinal variation in rhizosphere microbial communities of the endangered plant Lilium tsingtauense and the environmental factors driving this variation

The rhizosphere soil properties and microbial communities of Lilium tsingtauense, an endangered wild plant, have not been examined in previous studies. Here, we characterized spatial variation in soil properties and microbial communities in the rhizosphere of L. tsingtauense. We measured the abundance of L. tsingtauense at different altitudes and collected rhizosphere and bulk soils at three representative altitudes. The results showed that L. tsingtauense was more abundant, and the rhizosphere soil was richer in nitrogen, phosphorus, potassium, water content, and organic matter and more acidic at high altitudes than at lower altitudes. The diversity and richness of rhizosphere bacteria and fungi increased with altitude and were higher in rhizosphere soil than in bulk soil. In addition, ectomycorrhizal fungi, endophytic fungi, and nitrogen-fixing bacteria were more abundant, and plant-pathogenic fungi were less abundant at high altitudes. Co-occurrence network analysis identified four key phyla (Bacteroidota, Proteobacteria, Ascomycota, and Basidiomycota) in the microbial communities. We identified a series of microbial taxa (Acidobacteriales, Xanthobacteraceae, and Chaetomiaceae) and rhizosphere soil metabolites (phosphatidylcholine and phosphatidylserine) that are crucial for the survival of L. tsingtauense. Correlation analysis and random forest analysis showed that some environmental factors were closely related to the rhizosphere soil microbial community and played an important role in predicting the distribution and growth status of L. tsingtauense. In sum, the results of this study revealed altitudinal variation in the rhizosphere microbial communities of L. tsingtauense and the factors driving this variation. Our findings also have implications for habitat restoration and the conservation of this species.

IMPORTANCE

Our study highlighted the importance of the rhizosphere microbial community of the endangered plant L. tsingtauense. We found that soil pH plays an important role in the survival of L. tsingtauense. Our results demonstrated that a series of microbial taxa (Acidobacteriales, Xanthobacteraceae, Aspergillaceae, and Chaetomiaceae) and soil metabolites (phosphatidylcholine and phosphatidylserine) could be essential indicators for L. tsingtauense habitat. We also found that some environmental factors play an important role in shaping rhizosphere microbial community structure. Collectively, these results provided new insights into the altitudinal distribution of L. tsingtauense and highlight the importance of microbial communities in their growth.

A molecular perspective on the role of FERONIA in root growth, nutrient uptake, stress sensing and microbiome assembly

BACKGROUND

Roots perform multifaceted functions in plants such as movement of nutrients and water, sensing stressors, shaping microbiome, and providing structural support. How roots perceive and respond above traits at the molecular level remains largely unknown. Despite the enormous advancements in crop improvement, the majority of recent efforts have concentrated on above-ground traits leaving significant knowledge gaps in root biology. Also, studying root system architecture (RSA) is more difficult due to its intricacy and the difficulties of observing them during plant life cycle which has made it difficult to identify desired root traits for the crop improvement. However, with the aid of high-throughput phenotyping and genotyping tools many developmental and stress-mediated regulation of RSA has emerged in both model and crop plants leading to new insights in root biology. Our current understanding of upstream signaling events (cell wall, apoplast) in roots and how they are interconnected with downstream signaling cascades has largely been constrained by the fact that most research in plant systems concentrate on cytosolic signal transduction pathways while ignoring the early perception by cells' exterior parts. In this regard, we discussed the role of FERONIA (FER) a cell wall receptor-like kinase (RLK) which acts as a sensor and a bridge between apoplast and cytosolic signaling pathways in root biology.

AIM OF THE REVIEW

The goal of this review is to provide valuable insights into present understanding and future research perspectives on how FER regulates distinct root responses related to growth and stress adaptation.

KEY SCIENTIFIC CONCEPTS OF REVIEW

In plants, FER is a unique RLK because it can act as a multitasking sensor and regulates diverse growth, and adaptive traits. In this review, we mainly highlighted its role in root biology like how it modulates distinct root responses such as root development, sensing abiotic stressors, mechanical stimuli, nutrient transport, and shaping microbiome. Further, we provided an update on how FER controls root traits by involving Rapid Alkalinization Factor (RALF) peptides, calcium, reactive oxygen species (ROS) and hormonal signaling pathways.. We also highlight number of outstanding questions in FER mediated root responses that warrants future investigation. To sum up, this review provides a comprehsive information on the role of FER in root biology which can be utilized for the development of future climate resilient and high yielding crops based on the modified root system.

Long-Life Inoculant: Bradyrhizobium Stored in Biodegradable Beads for Four Years Shows Optimal Cell Vitality, Interacts with Peanut Roots, and Promotes Early Growth

Currently, bacterial inoculant technology focuses on improving long-term storage conditions to ensure adequate rhizobia numbers and their effectiveness as plant growth promoters. This study aimed to investigate whether storage at 4 °C for four years of alginate beads immobilizing Bradyrhizobium sp. SEMIA6144 maintains bacterial vitality, efficacy in growth promotion, and ability to establish early interactions with Arachis hypogaea L. The recovery of viable SEMIA6144 cells decreased over time (10% at six months, 1% at one year, and 0.01% at four years), while cell vitality remained high at 94.1%, 90.2%, and 93.4%, respectively. The unsaturated/saturated fatty acid ratio declined during storage, reducing membrane fluidity and metabolic activity. Mobility and root adhesion of SEMIA6144 decreased after one and four years. However, growth promotion in peanuts inoculated with SEMIA6144 beads was observed through increased biomass, total chlorophyll, leaf number, leaf area, and decreased chlorophyll fluorescence compared to non-inoculated plants. Although nodulation was low in plants inoculated with four-year-old beads, leghemoglobin levels were maintained. These results demonstrate that Bradyrhizobium sp. SEMIA6144 can be stored for four years in alginate beads at 4 °C, maintaining its vitality and ability to establish a symbiosis that stimulates early peanut growth. Understanding these physiological changes could be valuable for the future improvement of long-lasting inoculants.

Understanding the root of the problem for tackling pea root rot disease

Pea (Pisum sativum), a crop historically significant in the field of genetics, is regaining momentum in sustainable agriculture due to its high protein content and environmental benefits. However, its cultivation faces significant challenges from root rot, a complex disease caused by multiple soil-borne pathogens prevalent across most pea growing regions. This disease leads to substantial yield losses, further complicated by the dynamic interactions among pathogens, soil conditions, weather, and agricultural practices. Recent advancements in molecular diagnostics provide promising tools for the early and precise detection of these pathogens, which is critical for implementing effective disease management strategies. In this review, we explore how the availability of latest pea genomic resources and emerging technologies, such as CRISPR and cell-specific transcriptomics, will enable a deeper understanding of the molecular basis underlying host-pathogen interactions. We emphasize the need for a comprehensive approach that integrates genetic resistance, advanced diagnostics, cultural practices and the role of the soil microbiome in root rot. By leveraging these strategies, it is possible to develop pea varieties that can withstand root rot, ensuring the crop's resilience and its continued importance in global agriculture.

The epidemic occurrence of decline disease in bayberry trees altered plant and soil related microbiome and metabolome

BACKGROUND

In China, decline disease with unknown etiology appeared as an epidemic among bayberry trees in the southern area of the Yangtze River. Furthermore, the use of beneficial microbes has been reported to be able to reduce the incidence of this disease, emphasizing the association of this disease with microorganisms. Therefore, it has become critical to uncover the microbiome's function and related metabolites in remodeling the immunity of bayberry trees under biotic or abiotic stresses.

RESULTS

The amplicon sequencing data revealed that decline disease significantly altered bacterial and fungal communities, and their metabolites in the four distinct niches, especially in the rhizosphere soils and roots. Furthermore, the microbial communities in the four niches correlated with the metabolites of the corresponding niches of bayberry plants, and the fungal and bacterial networks of healthy trees were shown to be more complex than those of diseased trees. In addition, the role of microbiome in the resistance of bayberry trees to the occurrence of decline disease was justified by the isolation, identification, and characterization of important microorganisms such as significantly enriched Bacillus ASV804, Pseudomonas ASV815 in healthy plants, and significantly enriched Stenotrophomonas ASV719 in diseased plants.

CONCLUSION

Overall, our study revealed that the occurrence of decline disease altered the microbiome and its metabolites in four ecological niches in particular rhizosphere soils and roots of bayberry, which provides new insight into the control of bayberry decline disease.

Using fungal-bacterial community analysis to explore potential microbiomes to manage Meloidogyne incongnita

Rhizosphere microbial communities strongly affect outbreaks of root-knot nematode (RKN) disease. However, little is known about the interactions among fungi, bacteria and RKN. The bacterial and fungal community compositions in the rhizospheres of four representative tobacco varieties, both resistant and susceptible to RKN, were characterized using 16S rRNA gene sequencing for bacteria and internal transcribed spacer gene sequencing for fungi. Our findings revealed that the fungi played crucial roles in facilitating the cross-kingdom and symbiotic fungal-bacterial interactions to suppress RKN. Moreover, our investigation suggested Microbacterium as a potential microbial antagonist against RKN based on its enhanced presence in RKN-resistant tobacco genotypes, and the relative abundance of Microbacterium was 34.49% greater in the rhizosphere of resistant tobacco than that of susceptible tobacco significantly. Notably, the richness of fungal community enhanced tobacco's microbe-associated resistance to RKN through the positive regulation of the richness and diversity of bacterial community and the relative abundance of Microbacterium. This study underscores the critical role of the fungus-dominated fungal-bacterial community in bolstering tobacco resistance against RKN. The potential antagonistic role of Microbacterium presents promising avenues for innovative RKN management strategies.

Microbial community composition and co-occurrence network analysis of the rhizosphere soil of the main constructive tree species in Helan Mountain of Northwest China

To understand the microbial diversity and community composition within the main constructive tree species, Picea crassifolia, Betula platyphylla, and Pinus tabuliformis, in Helan Mountain and their response to changes in soil physicochemical factors, a high throughput sequencing technology was used to analyze the bacterial and fungal diversity and community structure. RDA (Redundancy Analysis) and Pearson correlation analysis were used to explore the influence of soil physicochemical factors on microbial community construction, and co-occurrence network analysis was conducted on the microbial communities. The results showed that the fungal and bacterial diversity was highest in B. platyphylla, and lowest in P. crassifolia. Additionally, the fungal/bacterial richness was greatest in the rhizosphere soils of P. tabuliformis and B. platyphylla. RDA and Pearson correlation analysis revealed that NN (nitrate nitrogen) and AP (available phosphorus) were the main determining factors of the bacterial community, while NN and SOC (soil water content) were the main determining factors of the fungal community. Pearson correlation analysis between soil physicochemical factors and the alpha diversity of the microbial communities revealed a significant positive correlation between pH and the bacterial and fungal diversity, while SOC, TN (total nitrogen), AP, and AN (available nitrogen) were significantly negatively correlated with the bacterial and fungal diversity. Co-occurrence network analysis revealed that the soil bacterial communities exhibit richer network nodes, edges, greater diversity, and greater network connectivity. Indicating that bacterial communities exhibit more complex and stable interaction patterns in soil. This study reveals the complex interactive relationship between microbial communities and soil physicochemical factors in forest ecosystems. By analyzing the response of rhizosphere microbial communities of major tree species in Helan Mountain to nutrient dynamics and pH changes, we can deepen our understanding of the role of microorganisms in regulating ecosystem functions and provide theoretical basis for soil improvement and ecological restoration strategies.

Organic acids released by submerged macrophytes with damaged leaves alter the denitrification microbial community in rhizosphere

Submerged macrophytes have important impacts on the denitrification and anaerobic ammonia-oxidizing (anammox) processes. Leaf damage in these plants probably changes the rhizosphere environment, affecting organic acid release and denitrifying bacteria. However, there is a lack of comprehensive understanding of the specific changes. This study investigated these changes in the rhizosphere of Potamogeton crispus with four degrees of leaf excision. When 0 %, 30 %, 50 % and 70 % of leaves were excised, the concentrations of total organic acid were 31.45, 32.67, 38.26, and 35.16 mg/L, respectively. The abundances of nirS-type denitrifying bacteria were 2.10 × 1010, 1.59 × 1010, 2.54 × 1010, and 4.67 × 1010 copies/g dry sediment, respectively. The abundances of anammox bacteria were 7.58 × 109, 4.59 × 109, 3.81 × 109, and 3.90 × 109 copies/g dry sediment, respectively. The concentration of total organic acids and the abundance of two denitrification microorganisms in the rhizosphere zone were higher than those in the root zone and non-rhizosphere zone. With increasing leaf damage, the number of OTUs in the Pseudomonas genus of nirS-type denitrifying bacteria first increased and then decreased, while that of the Thauera genus was relatively stable. The overall increase in the OTU number of anammox bacteria indicated that leaf damage promotes root exudates release, thereby leading to an increase in their diversity. The co-occurrence network revealed that the two denitrification microorganisms had about 60.52 % positive connections in rhizosphere while 64.73 % negative connections in non-rhizosphere. The abundance and community composition of both denitrification microorganisms were positively correlated with the concentrations of various substances such as oxalic acid, succinic acid, total organic acids and NO2--N. These findings demonstrate that submerged plant damage has significantly impacts on the structure of denitrification microbial community in the rhizosphere, which may alter the nitrogen cycling process in the deposit sediment. SYNOPSIS: This study reveals leaf damage of macrophyte changed the rhizosphere denitrification microbial community, which is helpful to further understand the process of nitrogen cycle in water.

Dynamic alterations and ecological implications of rice rhizosphere bacterial communities induced by an insect-transmitted reovirus across space and time

BACKGROUND

Cereal diseases caused by insect-transmitted viruses are challenging to forecast and control because of their intermittent outbreak patterns, which are usually attributed to increased population densities of vector insects due to cereal crop rotations and indiscriminate use of pesticides, and lack of resistance in commercial varieties. Root microbiomes are known to significantly affect plant health, but there are significant knowledge gaps concerning epidemics of cereal virus diseases at the microbiome-wide scale under a variety of environmental and biological factors.

RESULTS

Here, we characterize the diversity and composition of rice (Oryza sativa) root-associated bacterial communities after infection by an insect-transmitted reovirus, rice black-streaked dwarf virus (RBSDV, genus Fijivirus, family Spinareoviridae), by sequencing the bacterial 16S rRNA gene amplified fragments from 1240 samples collected at a consecutive 3-year field experiment. The disease incidences gradually decreased from 2017 to 2019 in both Langfang (LF) and Kaifeng (KF). BRSDV infection significantly impacted the bacterial community in the rice rhizosphere, but this effect was highly susceptible to both the rice-intrinsic and external conditions. A greater correlation between the bacterial community in the rice rhizosphere and those in the root endosphere was found after virus infection, implying a potential relationship between the rice-intrinsic conditions and the rhizosphere bacterial community. The discrepant metabolites in rhizosphere soil were strongly and significantly correlated with the variation of rhizosphere bacterial communities. Glycerophosphates, amino acids, steroid esters, and triterpenoids were the metabolites most closely associated with the bacterial communities, and they mainly linked to the taxa of Proteobacteria, especially Rhodocyclaceae, Burkholderiaceae, and Xanthomonadales. In addition, the greenhouse pot experiments demonstrated that bulk soil microbiota significantly influenced the rhizosphere and endosphere communities and also regulated the RBSDV-mediated variation of rhizosphere bacterial communities.

CONCLUSIONS

Overall, this study reveals unprecedented spatiotemporal dynamics in rhizosphere bacterial communities triggered by RBSDV infection with potential implications for disease intermittent outbreaks. The finding has promising implications for future studies exploring virus-mediated plant-microbiome interactions. Video Abstract.

Analysis of rhizosphere fungal diversity in lavender at different planting years based on high-throughput sequencing technology

Continuous cropping is a common cultivation practice in lavender cultivation, and the structure of the soil microbial community is one of the main reasons affecting the continuous cropping disorder in lavender; however, the relationship between the number of years of cultivation and inter-root microbial composition has not yet been investigated; using Illumina high-throughput sequencing we detected fungal community structure of rhizosphere soil under 1 (L1), 3 (L3), 5 (L5) and 0 (L0) years' of lavender cultivation in Yili, Xinjiang China. The results showed that with the extension of planting years, the physical-chemical characteristics of the soil shifted, and the diversity of the fungal communities shrank, the abundance and richness of species decreased and then increased, and the phylogenetic diversity increased, The structure of the soil fungal communities varied greatly. At phylum level, dominant fungal phyla were Ascomycetes, Basidiomycetes, etc. At genus level, dominant genera were Gibberella, Mortierella, etc, whose absolute abundance all increased with increasing planting years (P < 0.05); redundancy analysis showed that thesoil physicochemical characteristics significantly correlated with dominant bacterial genera. The FUN Guild prediction showed that six groups of plant pathogens and plant saprotrophs changed significantly (P < 0.05), the amount of harmful bacteria in the soil increased while the amount of arbuscular mycorrhizal fungui (AMF) decreased, leading to a continuous cropping obstacle of lavender. The findings of this study provida theoretical foundation for the management of continuous cropping and the prevention fungus-related diseases in lavender.

Effects of decomposed and undecomposed straw of three crops on clubroot disease of Chinese cabbage and soil nutrients

AIMS

Straw turnover plays an important role in reducing soil diseases, improving the ecological environment of plowland and realizing the effective ecological utilization of straw.

METHODS

Pot and field experiments were carried out to investigate the effects of maize, rice and wheat straws on the growth, clubroot disease of Chinese cabbage and soil nutrients. Undecomposed and decomposed maize, rice and wheat straws were quantitatively added to the monocultural soil of Chinese cabbage, and the crops without straw were taken as the control.

RESULTS

The results showed that the addition of maize, wheat and rice straws could promote the growth of monocultural Chinese cabbage, inhibit the occurrence of clubroot disease, increase soil pH value, the content of soil organic matter, alkaline hydrolyzable nitrogen and available potassium in pot experiment. Exogenous straw application could reduce the incidence rate by 22.54 ~ 47.85%, increase the plot yield of field 95.15 ~ 365.81%.

CONCLUSIONS

In terms of inhibiting clubroot disease and improving soil properties, undecomposed rice straw is superior to maize and wheat straw, while decomposed maize straw is superior to rice and wheat straw.

Defense Molecules of the Invasive Plant Species Ageratum conyzoides

Ageratum conyzoides L. is native to Tropical America, and it has naturalized in many other tropical, subtropical, and temperate countries in South America, Central and Southern Africa, South and East Asia, Eastern Austria, and Europe. The population of the species has increased dramatically as an invasive alien species, and it causes significant problems in agriculture and natural ecosystems. The life history traits of Ageratum conyzoides, such as its short life cycle, early reproductive maturity, prolific seed production, and high adaptive ability to various environmental conditions, may contribute to its naturalization and increasing population. Possible evidence of the molecules involved in the defense of Ageratum conyzoides against its natural enemies, such as herbivore insects and fungal pathogens, and the allelochemicals involved in its competitive ability against neighboring plant species has been accumulated in the literature. The volatiles, essential oils, extracts, residues, and/or rhizosphere soil of Ageratum conyzoides show insecticidal, fungicidal, nematocidal, and allelopathic activity. The pyrrolizidine alkaloids lycopsamine and echinatine, found in the species, are highly toxic and show insecticidal activity. Benzopyran derivatives precocenes I and II show inhibitory activity against insect juvenile hormone biosynthesis and trichothecene mycotoxin biosynthesis. A mixture of volatiles emitted from Ageratum conyzoides, such as β-caryophyllene, β-bisabolene, and β-farnesene, may work as herbivore-induced plant volatiles, which are involved in the indirect defense function against herbivore insects. Flavonoids, such as nobiletin, eupalestin, 5'-methoxynobiletin, 5,6,7,3',4',5'-hexamethoxyflavone, and 5,6,8,3,4',5'-hexamethoxyflavone, show inhibitory activity against the spore germination of pathogenic fungi. The benzoic acid and cinnamic acid derivatives found in the species, such as protocatechuic acid, gallic acid, p-coumaric acid, p-hydroxybenzoic acid, and ferulic acid, may act as allelopathic agents, causing the germination and growth inhibition of competitive plant species. These molecules produced by Ageratum conyzoides may act as defense molecules against its natural enemies and as allelochemicals against neighboring plant species, and they may contribute to the naturalization of the increasing population of Ageratum conyzoides in new habitats as an invasive plant species. This article presents the first review focusing on the defense function and allelopathy of Ageratum conyzoides.

Inoculation of multi-metal-resistant Bacillus sp. to a hyperaccumulator plant Sedum alfredii for facilitating phytoextraction of heavy metals from contaminated soil

Co-contamination of soil by multiple heavy metals is a significant global challenge. An effective strategy to address this issue involves using hyperaccumulators such as Sedum alfredii (S. alfredii). The efficiency of phytoremediation can be improved by supplementing with plant growth-promoting bacteria (PGPB). However, bacteria resources of PGPB resistant to multi-heavy metal contamination are still lacking. This study focused nine different strains of Bacillus and screened for resistance to heavy metals including cadmium (Cd), zinc (Zn), copper (Cu), and lead (Pb). A superior strain, Bacillus subtilis PY79 (B. subtilis), showed tolerance for all tested metals. Inoculation with B. subtilis in the rhizosphere of S. alfredii increased the accumulation of Cd, Zn, Cu, and Pb by 88.02%, 58.99%, 90.22%, and 54.97% in the plant shoots after 30 days respectively. B. subtilis application lowered the pH of the rhizosphere soil, thereby increasing the bioavailability of nutrients and heavy metals. Furthermore, B. subtilis helped S. alfredii recruit PGPB and heavy metal-resistant bacteria such as Edaphobacter, Niastella, and Chitinophaga, enhancing the growth and phytoremediation efficiency. Moreover, inoculation with B. subtilis not only upregulated genes of the ABC, HMA, ZIP, and MTP families involved in the translocation and detoxification of heavy metals but also increased the secretion of antioxidants within the cells. These findings indicate that B. subtilis enhances the tolerance, uptake, and translocation of heavy metals in S. alfredii, offering valuable insights for the phytoremediation of multi-metal-contaminated soils.

Microbial volatile organic compounds 2-heptanol and acetoin control Fusarium crown and root rot of tomato

Some microbial volatile organic compounds (mVOCs) can act as antagonistic weapons against plant pathogens, but little information is available on the contribution of individual mVOC to biocontrol and how they interact with plant pathogens. In this study, the Bacillus subtilis strain N-18 isolated from the rhizosphere of healthy plants grown in areas where Fusarium crown and root rot (FCRR) of tomato occurs could reduce the 30% of the incidence of FCRR. Moreover, the volatile organic compounds (VOCs) produced by N-18 had inhibitory effects on Fusarium oxysporum f. sp. radicis-lycopersici (FORL). The identification of VOCs of N-18 was analyzed by the solid-phase microextraction coupled to gas chromatography-mass spectrometry. Meanwhile, we conducted sensitivity tests with these potential active ingredients and found that the volatile substances acetoin and 2-heptanol can reduce the 41.33% and 35% of the incidence of FCRR in tomato plants. In addition, the potential target protein of acetoin, found in the cheminformatics and bioinformatics database, was F. oxysporum of hypothetical protein AU210_012600 (FUSOX). Molecular docking results further predicted that acetoin interacts with FUSOX protein. These results reveal the VOCs of N-18 and their active ingredients in response to FORL and provide a basis for further research on regulating and controlling FCRR.

Root exudates facilitate the regulation of soil microbial community function in the genus Haloxylon

Introduction

Root exudates act as the "language" of plant-soil communication, facilitating crucial interactions, information exchange, and energy transfer between plants and soil. The interactions facilitated by root exudates between plants and microorganisms in the rhizosphere are crucial for nutrient uptake and stress resilience in plants. However, the mechanism underlying the interaction between root exudates and rhizosphere microorganisms in desert plants under drought conditions remains unclear, especially among closely related species.

Methods

To reveal the ecological strategies employed by the genus Haloxylon in different habitats. Using DNA extraction and sequencing and UPLC-Q-Tof/MS methods, we studied root exudates and soil microorganisms from two closely related species, Haloxylon ammodendron (HA) and Haloxylon persicum (HP), to assess differences in their root exudates, soil microbial composition, and interactions.

Results

Significant differences were found in soil properties and root traits between the two species, among which soil water content (SWC) and soil organic carbon (SOC) in rhizosphere and bulk soils (P < 0.05). While the metabolite classification of root exudates was similar, their components varied, with terpenoids being the main differential metabolites. Soil microbial structure and diversity also exhibited significant differences, with distinct key species in the network and differential functional processes mainly related to nitrogen and carbon cycles. Strong correlations were observed between root exudate-mediated root traits, soil microorganisms, and soil properties, although the complex interactions differed between the two closely relative species. The primary metabolites found in the network of HA include sugars and fatty acids, while HP relies on secondary metabolites, steroids and terpenoids.

Discussion

These findings suggest that root exudates are key in shaping rhizosphere microbial communities, increasing microbial functionality, fostering symbiotic relationships with hosts, and bolstering the resilience of plants to environmental stress.

Genotype of pioneer plant Miscanthus is not a key factor in the structure of rhizosphere bacterial community in heavy metal polluted sites

Miscanthus is a common pioneer plant with abundant genetic variation in abandoned mines in southern China. However, the extent to which genetic differentiation among species modulates rhizosphere bacterial communities remains unclear. Miscanthus samples were collected from 26 typical abandoned heavy-metal mines with different soil types in southern China, tested using 14 pairs of simple sequence repeats (SSR) primers, and classified into two genotypes based on Nei's genetic distance. The structure and diversity of rhizosphere bacterial communities were examined using 16 S rRNA sequencing. The results showed that among the factors affecting the rhizosphere bacterial community structure of Miscanthus samples, the role of genotype was not significant, and geographical conditions were the most important factors, followed by pH and total organic carbon (TOC). The process of rhizospheric community assembly varied among different genotypes; however, the recruited species and their abundances were similar. Collectively, we provided an approach based on genetic differentiation to quantify the relative contribution of genotypes to the rhizosphere bacterial community, demonstrating that genotypes contribute less than soil conditions. Our findings provide new insights into the role of host genetics in the ecological processes of plant rhizosphere bacterial communities in abandoned mines and provide theoretical support for microbe-assisted phytoremediation.

Cover crop species influences soil fungal species richness and community structure

Despite the well documented link between cover cropping and soil microbiology, the influence of specific cover crop species on soil microbes remains poorly understood. We evaluated how soil fungal communities in a no till system respond to four cover crop treatments: no cover crop (REF), cereal ryegrass (CRYE), wild pennycress (WPEN), and a mix of pea, clover, radish, and oat (PCRO). Soil samples were collected from experimental plots following termination of cover crops from depths of 0-2 cm and 2-4 cm where cover crops had significantly increased soil organic matter. There was no significant interaction between soil depth and cover crop treatment on either alpha diversity or beta diversity. All cover crop treatments (CRYE, PCRO, and WPEN) enhanced soil fungal richness but only CRYE enhanced soil fungal diversity and altered the fungal community structure. Soil depth altered the fungal community structure but had no effect on fungal diversity and richness. Genus Fusarium which includes some of the most economically destructive pathogens was more abundant in REF and PCRO treatments compared to CRYE and WPEN. In contrast, genus Mortierella which is known to promote plant health was more abundant in all cover crop treatments relative to the REF. These findings demonstrate that cover cropping can increase soil fungal species richness and alter fungal community structure, potentially promoting the abundance of beneficial fungi and reducing the abundance of some plant pathogens within the genus Fusarium. These effects are dependent on cover crop species, a factor that should be considered when selecting appropriate cover crops for a particular cropping system.

The Role of Low-Molecular-Weight Organic Acids in Metal Homeostasis in Plants

Low-molecular-weight organic acids (LMWOAs) are essential O-containing metal-binding ligands involved in maintaining metal homeostasis, various metabolic processes, and plant responses to biotic and abiotic stress. Malate, citrate, and oxalate play a crucial role in metal detoxification and transport throughout the plant. This review provides a comparative analysis of the accumulation of LMWOAs in excluders, which store metals mainly in roots, and hyperaccumulators, which accumulate metals mainly in shoots. Modern concepts of the mechanisms of LMWOA secretion by the roots of excluders and hyperaccumulators are summarized, and the formation of various metal complexes with LMWOAs in the vacuole and conducting tissues, playing an important role in the mechanisms of metal detoxification and transport, is discussed. Molecular mechanisms of transport of LMWOAs and their complexes with metals across cell membranes are reviewed. It is discussed whether different endogenous levels of LMWOAs in plants determine their metal tolerance. While playing an important role in maintaining metal homeostasis, LMWOAs apparently make a minor contribution to the mechanisms of metal hyperaccumulation, which is associated mainly with root exudates increasing metal bioavailability and enhanced xylem loading of LMWOAs. The studies of metal-binding compounds may also contribute to the development of approaches used in biofortification, phytoremediation, and phytomining.

Study on the migration behaviour of heavy metals at the improved mine soil-plant rhizosphere interface

With the increasing shortage of land resources and the aggravation of soil pollution in mining areas, the remediation of soil in abandoned mining areas has gradually attracted people's attention. The remediation of heavy metal contaminated soil in mining areas is the key to reduce the harm of heavy metals to the environment and human health. In this study, municipal sludge and phytoremediation technology were combined to investigate the migration and transformation of heavy metals at the soil-plant interface in improved mining areas through indoor pot experiments. The results showed that heavy metals in non-rhizosphere soil entered the rhizosphere environment with the growth of plants, leading to the increase of heavy metal content in rhizosphere soil. The cumulative amounts of Cu, Zn, Pb and Cd were 1299.32, 832.10, 347.89 and 71.34 mg/kg, respectively. The content of oxidized Cu and Zn decreased with increasing planting days, while the oxidized Pb and Cd showed an increasing trend. Under acidic conditions, H+ is easy to compete with heavy metal ions for exchangeable positions in the clay mineral layer, so that the reducible heavy metals are easy to be converted into exchangeable states. In this paper, the effects of various factors on the distribution of heavy metals were discussed by adjusting soil pH, adding humic acid and root exudates, so as to analyse the migration and transformation mechanism of heavy metals at the soil-plant interface, and provide a reliable theoretical basis for soil remediation in mining areas.

A systematic review and meta-analysis on the root effects and toxic mechanisms of rare earth elements

Rare earth elements (REEs) have attracted much attention because of their unique physical and chemical properties. The root system is the plant organ most directly in contact with REEs, and it is critical to understand the mechanisms of interaction between the two. This paper investigates the effects of REEs on plant enrichment and fractionation, as well as on various developmental and toxicity indices of the root system. REEs are more likely to be deposited on the root surface under the influence of root secretion. The complexation between the two affects the uptake and fractionation of REEs and the altered pattern of root secretion. The toxicity mechanisms of REEs on plant root cells were lied in: (1) REEs generate reactive oxygen species after entering the plant, leading to oxidative stress and damage to plant cells; (2) REEs with higher charge-to-volume ratios compete for organic ligands with or displace Ca2+, further disrupting the normal function of plant root cells. It was shown that the sensitivity of inter-root microorganisms to REEs varied depending on the content and physicochemical properties of REEs. The paper also concluded with a meta-analysis of phytotoxicity induced by REEs, which showed that REEs affect plant physiological parameters. REEs, as a source of oxidative stress, triggered lipid peroxidation damage in plants and enhanced the activity of antioxidant enzymes, thus revealing the significant toxicity of REEs to plants. The phytotoxic effects of REEs increased with time and concentration. These results help to elucidate the ecotoxicology of rare earth-induced phytotoxicity.

Saltbush seedlings (Atriplex spp.) shed border-like cells from closed-type root apical meristems

Australian saltbush (Atriplex spp.) survive in exceptionally saline environments and are often used for pasture in semi-arid areas. To investigate the impact of salinity on saltbush root morphology and root exudates, three Australian native saltbush species (Atriplex nummularia , Atriplex amnicola , and Atriplex vesicaria ) were grown in vitro in optimised sterile, semi-hydroponic systems in media supplemented with different concentrations of salt (NaCl). Histological stains and chromatographic techniques were used to characterise the root apical meristem (RAM) type and root exudate composition of the saltbush seedlings. We report that saltbush species have closed-type RAMs, which release border-like cells (BLCs). Monosaccharide content, including glucose and fructose, in the root mucilage of saltbush was found to be uniquely low, suggesting that saltbush may minimise carbon release in polysaccharides of root exudates. Root mucilage also contained notable levels of salt, plus increasing levels of unidentified compounds at peak salinity. Un-esterified homogalacturonan, xyloglucan, and arabinogalactan proteins between and on the surface of BLCs may aid intercellular adhesion. At the highest salinity levels, root cap morphology was altered but root:shoot ratio remained consistent. While questions remain about the identity of some components in saltbush root mucilage other than the key monosaccharides, this new information about root cap morphology and cell surface polysaccharides provides avenues for future research.

Plant microRNAs regulate the defense response against pathogens

MicroRNAs (miRNAs) are a class of small non-coding RNAs, typically 20-25 nucleotides in length, that play a crucial role in regulating gene expression post-transcriptionally. They are involved in various biological processes such as plant growth, development, stress response, and hormone signaling pathways. Plants interact with microbes through multiple mechanisms, including mutually beneficial symbiotic relationships and complex defense strategies against pathogen invasions. These defense strategies encompass physical barriers, biochemical defenses, signal recognition and transduction, as well as systemic acquired resistance. MiRNAs play a central role in regulating the plant's innate immune response, activating or suppressing the transcription of specific genes that are directly involved in the plant's defense mechanisms against pathogens. Notably, miRNAs respond to pathogen attacks by modulating the balance of plant hormones such as salicylic acid, jasmonic acid, and ethylene, which are key in activating plant defense mechanisms. Moreover, miRNAs can cross boundaries into fungal and bacterial cells, performing cross-kingdom RNA silencing that enhances the plant's disease resistance. Despite the complex and diverse roles of miRNAs in plant defense, further research into their function in plant-pathogen interactions is essential. This review summarizes the critical role of miRNAs in plant defense against pathogens, which is crucial for elucidating how miRNAs control plant defense mechanisms.

Short-Term Effects of Cenchrus fungigraminus/Potato or Broad Bean Interplanting on Rhizosphere Soil Fertility, Microbial Diversity, and Greenhouse Gas Sequestration in Southeast China

Cenchrus fungigraminus is a new species and is largely used as forage and mushroom substrate. However, it can usually not be planted on farmland on account of local agricultural land policy. Interplanting Cenchrus fungigraminus with other crops annually (short-term) is an innovative strategy to promote the sustainable development of the grass industry in southern China. To further investigate this, C. fungigraminus mono-planting (MC), C. fungigraminus-potato interplanting (CIP) and C. fungigraminus-broad bean interplanting (CIB) were performed. Compared to MC, soil microbial biomass carbon (SMBC), soil organic matter (SOM), ammoniacal nitrogen (AMN), pH and soil amino sugars had a positive effect on the rhizosphere soil of CIP and CIB, as well as enhancing soil nitrogenase, nitrite reductase, and peroxidase activities (p < 0.05). Moreover, CIP improved the root vitality (2.08 times) and crude protein (1.11 times). In addition, CIB enhanced the crude fiber of C. fungigraminus seedlings. These two interplanting models also improved the microbial composition and diversity (Actinobacteria, Firmicutes, and Bacteroidota, etc.) in the rhizosphere soil of C. fungigraminus seedlings. Among all the samples, 189 and 59 genes were involved in methane cycling and nitrogen cycling, respectively, which improved the presence of the serine cycle, ribulose monophosphate, assimilatory nitrate reduction, methane absorption, and glutamate synthesis and inhibited denitrification. Through correlation analysis and the Mantel test, the putative functional genes, encoding functions in both nitrogen and methane cycling, were shown to have a significant positive effect on pH, moisture, AMN, SOM, SMBC, and soil peroxidase activity, while not displaying a significant effect on soil nitrogenase activity and total amino sugar (p < 0.05). The short-term influence of the interplanting model was shown to improve land use efficiency and economic profitability per unit land area, and the models could provide sustainable agricultural production for rural revitalization.