Root exudates contribute to belowground ecosystem hotspots: A review

Synergistic interplay of management practices and environmental factors in shaping grassland soil carbon stocks: Insights into the effects of fertilization, mowing, burning, and grazing

Grasslands, which account for over 40 % of the Earth's terrestrial area, play a vital role in mitigating global change and biodiversity loss. These ecosystems serve as critical carbon sinks, regulating the global carbon cycle and supporting diverse flora and fauna. However, their ability to sustain these functions is threatened by land use change and climate disruption. Current challenges revolve around understanding how key management practices such as grazing, mowing, burning, and fertilization, interact with environmental factors to influence grassland soil carbon stocks. This study presents a meta-analysis of the effects of these management practices and environmental factors, such as soil type, depth, texture, temperature, precipitation, and their synergistic interplay. It evaluates how management intensity, duration, and frequency interact with these environmental variables to influence soil carbon storage, providing valuable insights into optimizing grassland management for enhanced soil carbon stock and broader ecosystem stability. The findings reveal that grazing, particularly at high intensity, tends to reduce soil carbon stocks (-0.412, p < 0.001), with the most pronounced effects observed in shallow soils and temperate climates. Mowing also negatively affected carbon stock (-0.416, p = 0.013), especially when carried out frequently and over long durations. On the other hand, burning had mixed results with an overall positive effect (0.340, p = 0.078). Short-term burns promoted carbon accumulation, while frequent burning led to carbon loss. Fertilization, especially with nitrogen and phosphorus, proved beneficial for increasing soil carbon stocks (0.712, p < 0.001), particularly in nutrient-poor soils and semi-arid climates. This study introduces a systems-based approach to grassland management, providing a framework for optimizing carbon-focused strategies. By integrating the role of management practices, particularly their frequency, intensity, and duration, along with soil characteristics and climate, these findings provide actionable insights for policymakers, land managers, and researchers. They guide the development of sustainable management strategies that not only enhance soil carbon stocks but also support ecosystem health and resilience.

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.

Co-inoculation of Trichoderma and tea root-associated bacteria enhance flavonoid production and abundance of mycorrhizal colonization in tea (Camellia sinensis)

Tea is one of the most popular nonalcoholic beverages, that contains several medicinally important flavonoids. Due to seasonal variation and various environmental stresses, the overall consistency of tea flavonoids affects the tea quality. To combat stress, plants stimulate symbiotic relationships with root-associated beneficial microbiomes that sustain nutrient allocation. Therefore, a study has been designed to understand the role of the tea root microbiome in sustaining tea leaf flavonoid production. To enumerate the microbiome, tea root and rhizoplane soil were collected from 3 years of healthy plants from Jalpaiguri district, West Bengal, India. A culture-independent approach was adopted to identify root and rhizosphere microbial diversity (BioSample: SAMN31404869; SRA: SRS15503027 [rhizosphere soil metagenome] BioSample: SAMN31404868;SRA:SRS15503030 [root metagenome]. In addition to diverse microbes, four mycorrhiza fungi, i.e., Glomus intraradices, Glomus irregulare, Paraglomus occultum and Scutellospora heterogama were predominant in collected root samples. A culture-dependent approach was also adopted to isolate several plant growth-promoting bacteria [Bacillus sp. D56, Bacillus sp. D42, Bacillus sp. DR15, Rhizobium sp. DR23 (NCBI Accession: OR821747-OR821750)] and one fungal [Trichoderma sp. AM6 (NCBI Accession:OM915414)] strain. A pot experiment was designed to assess the impact of that isolated microbiome on tea seedlings. After six months of microbiome inoculation, tea plants' physicochemical and transcriptional parameters were evaluated. The results confer that the microbiome-treated treatments [(T1-without any microbial inoculation; NCBI Accession: SAMN33591153), Trichoderma sp. AM6 (T2; NCBI Accession: SAMN33591155) and Trichoderma sp. AM6 +VAM containing tea root+synthetic microbial consortia (T5; NCBI Accession: SAMN33591154)] could enhance the total flavonoid content in tea seedlings by upregulating certain transcripts associated with the flavonoid biosynthesis pathway of tea.

Intraspecific plant-soil feedbacks alter root traits in a perennial grass

Drought is a common stressor faced by plants and their associated microbiomes. Projected climate data point toward an increase in the severity and frequency of extreme precipitation events, such as drought. Previous research has shown that long-term exposure to drought can shape plants' genomes, resulting in genetic variation for drought tolerance. We hypothesized that these genetic changes also affect patterns of microbial colonization in the rhizosphere, potentially feeding back to influence plant drought responses. Here, we tested 33 rhizosphere soils conditioned by 33 genotypes of Tripsacum dactyloides (eastern gamagrass) that originated from native populations across a precipitation gradient in the southern plains of the United States. We used these 33 rhizosphere soils as inocula for a fully factorial experiment to test the responses of conspecific plants to the differentially conditioned soils under drought or well-watered conditions. Variation in aboveground traits such as shoot length, weight, and root-to-shoot ratios was primarily explained by watering treatment. However, many belowground traits, such as root anatomical and architectural traits, were more likely to be affected by the genotype of the conditioning plant. Of the traits we measured, only aerenchyma area was affected by the interaction between current watering treatment and genotype of the conditioning plant. Ultimately, both the current watering treatment and conditioning plant genotype altered plant physiological traits and the associated microbiome. The differential intraspecies plant-soil feedback dynamics driven by plant local adaptation will be key to understanding future plants' responses to rapidly shifting climates, in both restoration projects and agricultural systems.

Beneficial microorganisms: Regulating growth and defense for plant welfare

Beneficial microorganisms (BMs) promote plant growth and enhance stress resistance. This review summarizes how BMs induce growth promotion by improving nutrient uptake, producing growth-promoting hormones and stimulating root development. How BMs enhance disease resistance and help protect plants from abiotic stresses has also been explored. Growth-defense trade-offs are known to affect the ability of plants to survive under unfavourable conditions. This review discusses studies demonstrating that BMs regulate growth-defense trade-offs through microbe-associated molecular patterns and multiple pathways, including the leucine-rich repeat receptor-like kinase pathway, abscisic acid signalling pathway and specific transcriptional factor regulation. This multifaceted relationship underscores the significance of BMs in sustainable agriculture. Finally, the need for integration of artificial intelligence to revolutionize biofertilizer research has been highlighted. This review also elucidates the cutting-edge advancements and potential of plant-microbe synergistic microbial agents.

Assembly Mechanisms and Functional Adaptations of Soil Fungal Communities of Different Plant Rhizospheres in Ilmenite Mining Area

This study investigated the mechanisms of structural assembly and functional adaptations of fungal communities in the rhizosphere soils of seven different plants grown in the ilmenite zone. We analyzed changes in the rhizosphere soil fungal communities using ITS sequencing. The results revealed that different plants affected the properties of the rhizosphere soil. The contents of organic matter, total nitrogen, and total potassium in the rhizosphere soil exhibited significant variations compared to the soil that was not occupied by plants. Soil fungal composition analysis revealed that Ascomycota and Basidiomycota were the dominant phyla in the soil of this mining area. At the genus level, compared to the mineral soil without plants, the proportion of Epicoccum increased in the rhizosphere soils of different plants, while the proportion of Fusarium decreased. Alpha diversity studies revealed that fungal diversity in the rhizospheres of different plants changed significantly. Beta diversity studies showed a significant differentiation in the fungal community structure of different plant rhizosphere soils compared to the KB group. The FunGuild predictions indicated that different plant rhizosphere soils are enriched with different guilds and trophic patterns of fungi. In addition, we found that soil physical and chemical properties were significantly correlated with the abundance and diversity of fungal communities. The above results indicate that plant species and soil physicochemical properties are important factors influencing the assembly of soil fungal communities in the rhizosphere. This research provides insights into the assembly mechanisms and functional adaptations of fungal community structures in the rhizosphere soils of seven plant species in ilmenite iron mining areas. This helps us to screen plant and fungal community assemblages that can promote soil restoration in ilmenite mining areas and provide a theoretical basis for future ecological restoration in ilmenite areas.

The occurrence of wheat crown rot correlates with the microbial community and function in rhizosphere soil

Wheat crown rot (WCR) is a significant soil-borne disease affecting wheat production worldwide. Understanding the impact of wheat crown rot on the structure and function of microbial communities in the wheat rhizosphere soil can provide a theoretical basis for the mining biological control resources against WCR. In this study, rhizosphere soils with varying WCR severities (light, moderate, severe) were analyzed for chemical properties, microbial community composition and functions using high-throughput sequencing. The results revealed that WCR decreased rhizosphere soil pH, the content of available nitrogen and phosphorus, and the abundance of beneficial taxa such as Bacillus and Streptomyces. Additionally, functional predictions showed that microbial communities adapted to WCR by enhancing signaling pathways and reducing their anabolic activity. From soil with light WCR occurrence, we isolated Bacillus velezensis BF-237, whose abundance was reduced by WCR. Greenhouse experiments demonstrated that BF-237 achieved a control efficiency of 56.61% against WCR in artificially inoculated sterilized soil and 53.32% in natural soil. This study clarifies the impact of wheat crown rot on the community structure, and function of rhizosphere soil microorganisms, alongside identifying a promising biocontrol agent. These findings contribute to understanding WCR pathogenesis and offer practical resources for its management.

Absorption and transport of different ZnO nanoparticles sizes in Agrostis stolonifera: Impacts on physiological, biochemical responses, root exudation, and microbial community structure

Nanomaterials play a crucial role in various applications, but their environmental impact necessitates effective recycling strategies. This study investigates the effects of different ZnO nanoparticles (ZnO-NPs) sizes (0, 30, 50, and 90 nm) on Agrostis stolonifera, focusing on physiological and biochemical responses, root exudate, and microbial community structure. The results showed that the most optimal physiological and biochemical responses, including enhanced plant growth and increased activities of superoxide dismutase, peroxidase, and catalase, were observed at 50 nm ZnO-NPs. Agrostis stolonifera accumulated more ZnO-NPs at 30 nm, with Zn content in root and leaf tissues reaching 186 mg/kg and 294 mg/kg, respectively. Meanwhile, SEM-Mapping and TEM analyses confirmed the absorption and transport of ZnO-NPs within Agrostis stolonifera. Furthermore, root exudates analysis revealed an increase in the types of organic matter secreted by roots at 30 nm and 50 nm ZnO-NPs, while 90 nm ZnO-NPs had the opposite effect. 16S rRNA gene sequencing showed that the species diversity and uniformity of root microorganisms exhibited contrasting trends with increasing ZnO-NPs size, with roots exposed to 50 nm ZnO-NPs showed higher species richness than those exposed to 30 nm or 90 nm. However, beneficial microorganisms such as Bryobacter and Methylophilus were inhibited by 90 nm ZnO-NPs. This study provides novel insights into a potential ZnO-NPs recycling strategy in soil using Agrostis stolonifera, offering a means to mitigate nanoparticle-induced damage to soil and crops.

Natural variation in root exudate composition in the genetically structured Arabidopsis thaliana in the Iberian Peninsula

Plant root exudates are involved in nutrient acquisition, microbial partnerships, and inter-organism signaling. Yet, little is known about the genetic and environmental drivers of root exudate variation at large geographical scales, which may help understand the evolutionary trajectories of plants in heterogeneous environments. We quantified natural variation in the chemical composition of Arabidopsis thaliana root exudates in 105 Iberian accessions. We identified up to 373 putative compounds using ultra-high-performance liquid chromatography coupled with mass spectrometry. We estimated the broad-sense heritability of compounds and conducted a genome-wide association (GWA) study. We associated variation in root exudates to variation in geographic, environmental, life history, and genetic attributes of Iberian accessions. Only 25 of 373 compounds exhibited broad-sense heritability values significantly different from zero. GWA analysis identified polymorphisms associated with 12 root exudate compounds and 26 known genes involved in metabolism, defense, signaling, and nutrient transport. The genetic structure influenced root exudate composition involving terpenoids. We detected five terpenoids related to plant defense significantly varying in mean abundances in two genetic clusters. Our study provides first insights into the extent of root exudate natural variation at a regional scale depicting a diversified evolutionary trajectory among A. thaliana genetic clusters chiefly mediated by terpenoid composition.

A tale for two roles: Root-secreted methyl ferulate inhibits P. nicotianae and enriches the rhizosphere Bacillus against black shank disease in tobacco

BACKGROUND

Root exudates serve as chemical signaling molecules that regulate rhizosphere interactions and control soil-borne diseases. The interactions between plants and the soil microbiome play dynamic and crucial roles in regulating the resistance of plants to biotic stress. However, the specific roles of many root exudates in plant pathogens remain unclear. The root exudate methyl ferulate, a naturally occurring and relatively non-toxic antifungal agent, has been applied to control postharvest pathogens and preserve foodstuffs and has not been used in plant disease control.

RESULTS

This study investigated the role of the root exudate methyl ferulate in controlling tobacco black shank disease. We observed that methyl ferulate was secreted in greater quantities in the tobacco resistant cultivar Gexin 3 following inoculation with P. nicotianae than in the susceptible cultivar Xiaohuangjin 1025. Our findings also revealed that methyl ferulate strongly inhibited P. nicotianae (EC50 = 67.51 µg/mL), effectively controlling tobacco black shank disease by impairing NADH dehydrogenase function (the activity decreased by 50%). Furthermore, methyl ferulate recruited disease-suppressive rhizosphere microbes, such as Bacillus (the relative abundance of these microbes increases from 4.69% to 13.79%), thereby increasing disease resistance. The overexpression of caffeic acid O-methyltransferase NtCOMT10 resulted in increased methyl ferulate secretion (increased to 221.09% compared with that of the wild-type), concomitant improvement in the disease suppression of tobacco black shank disease (disease index decreased from 20% to less than 10%) and enrichment of beneficial microbes. In addition, methyl ferulate exerted antagonistic effects on other phytopathogens, such as B. cinerea, P. aphanidermatum, P. sojae, C. lagenarium and F. oxysporum.

CONCLUSIONS

Our findings indicated that methyl ferulate, a component of root exudates regulated by NtCOMT10, can inhibit phytopathogens and enrich rhizosphere Bacillus against plant disease. The great dual effect of methyl ferulate on the control of phytopathogens and its low cost enable a novel potential avenue for controlling soil-borne fungal diseases. This study provides ingenious insights into controlling soil-borne diseases through beneficial root exudates. Video Abstract.

Modulation of Zn Ion Toxicity in Pisum sativum L. by Phycoremediation

Microalgae offer a promising alternative for heavy metal removal, and the search for highly efficient strains is ongoing. This study investigated the potential of two microalgae, Coelastrella sp. BGV (Chlorophyta) and Arthronema africanum Schwabe & Simonsen (Cyanoprokaryota), to bind zinc ions (Zn2⁺) and protect higher plants. Hydroponically grown pea (Pisum sativum L.) seedlings were subjected to ZnSO4 treatment for 7 days in either a nutrient medium (Knop) or a microalgal suspension. The effects of increasing Zn2⁺ concentrations were evaluated through solution parameters, microalgal dry weight, pea growth (height, biomass), and physiological parameters, including leaf gas exchange, chlorophyll content, and normalized difference vegetation index (NDVI). Zinc accumulation in microalgal and plant biomass was also analyzed. The results revealed that microalgae increased pH and oxygen levels in the hydroponic medium while enhancing Zn accumulation in pea roots. At low ZnSO4 concentrations (2-5 mM), microalgal suspensions stimulated pea growth and photosynthetic performance. However, higher ZnSO4 levels (10-15 mM) caused Zn accumulation, leading to nutrient deficiencies and growth suppression in microalgae, which ultimately led to physiological disturbances in peas. Coelastrella sp. BGV exhibited greater tolerance to Zn stress and provided a stronger protective effect when co-cultivated with peas, highlighting its potential for phycoremediation applications.

Rhizosphere microbial community structure and PICRUSt2 predicted metagenomes function in heavy metal contaminated sites: A case study of the Blesbokspruit wetland

This study investigated the microbial diversity inhabiting the roots (rhizosphere) of macrophytes thriving along the Blesbokspruit wetland, South Africa's least conserved Ramsar site. The wetland suffers from decades of pollution from mining wastewater, agriculture, and sewage. The current study focused on three macrophytes: Phragmites australis (common reed), Typha capensis (bulrush), and Eichhornia crassipes (water hyacinth). The results revealed a greater abundance and diversity of microbes (Bacteria and Fungi) associated with the free-floating E. crassipes compared to P. australis and T. capensis. Furthermore, the correlation between microbial abundance and metals, showed a strong correlation between fungal communities and metals such as nickel (Ni) and arsenic (As), while bacterial communities correlated more with lead (Pb) and chromium (Cr). The functional analysis predicted by PICRUSt2 identified genes related to xenobiotic degradation, suggesting the potential of these microbes to break down pollutants. Moreover, specific bacterial groups - Proteobacteria, Verrucomicrobia, Cyanobacteria, and Bacteroidetes - were linked to this degradation pathway. These findings suggest a promising avenue for microbe-assisted phytoremediation, a technique that utilizes plants and their associated microbes to decontaminate polluted environments.

Atmospheric methane consumption in arid ecosystems acts as a reverse chimney and is accelerated by plant-methanotroph biomes

Drylands cover one-third of the Earth's surface and are one of the largest terrestrial sinks for methane. Understanding the structure-function interplay between members of arid biomes can provide critical insights into mechanisms of resilience toward anthropogenic and climate-change-driven environmental stressors-water scarcity, heatwaves, and increased atmospheric greenhouse gases. This study integrates in situ measurements with culture-independent and enrichment-based investigations of methane-consuming microbiomes inhabiting soil in the Anza-Borrego Desert, a model arid ecosystem in Southern California, United States. The atmospheric methane consumption ranged between 2.26 and 12.73 μmol m2 h-1, peaking during the daytime at vegetated sites. Metagenomic studies revealed similar soil-microbiome compositions at vegetated and unvegetated sites, with Methylocaldum being the major methanotrophic clade. Eighty-four metagenome-assembled genomes were recovered, six represented by methanotrophic bacteria (three Methylocaldum, two Methylobacter, and uncultivated Methylococcaceae). The prevalence of copper-containing methane monooxygenases in metagenomic datasets suggests a diverse potential for methane oxidation in canonical methanotrophs and uncultivated Gammaproteobacteria. Five pure cultures of methanotrophic bacteria were obtained, including four Methylocaldum. Genomic analysis of Methylocaldum isolates and metagenome-assembled genomes revealed the presence of multiple stand-alone methane monooxygenase subunit C paralogs, which may have functions beyond methane oxidation. Furthermore, these methanotrophs have genetic signatures typically linked to symbiotic interactions with plants, including tryptophan synthesis and indole-3-acetic acid production. Based on in situ fluxes and soil microbiome compositions, we propose the existence of arid-soil reverse chimneys, an empowered methane sink represented by yet-to-be-defined cooperation between desert vegetation and methane-consuming microbiomes.

Novel weapon-aided plant protection in the underground battlefield

Ralstonia solanacearum and R. pseudosolanacearum, the causative agents of bacterial wilt, ranks as the second most devastating phytopathogens, affecting over 310 plant species and causing substantial economic losses worldwide. R. solanacearum and R. pseudosolanacearum infect plants through the underground root system, where it interacts with both the host and the surrounding microbiota and multiply in the xylem where bacteria cell and its polysaccharide product block the water transportation from root to aboveground. Currently, effective control methods are limited, as resistance genes are unavailable and antibiotics prove ineffective. In current Commentary, we review recent advancements in combating bacterial wilt, categorizing the approaches (weapons) into three distinct strategies. The physical and chemical weapons focus on leveraging sound waves to trigger crop immunity and reducing bacterial virulence signaling, respectively. The biological weapon employs predatory protists to directly consume Ralstonia cells in the root zone, while also reshaping the protective rhizosphere microbiome to fortify the plant. We believe that these novel methods hold the potential to revolutionize crop protection from bacterial wilt and inspire new era in sustainable agriculture.

Early allelopathic input and later nutrient addition mediated by litter decomposition of invasive Solidago canadensis affect native plant and facilitate its invasion

Litter decomposition is essential for nutrient and chemical cycling in terrestrial ecosystems. Previous research on in situ litter decomposition has often underestimated its impact on soil nutrient dynamics and allelopathy. To address this gap, we conducted a comprehensive study involving both field and greenhouse experiments to examine the decomposition and allelopathic effects of the invasive Solidago canadensis L. in comparison with the native Phalaris arundinacea L. In the field, a 6-month litter bag experiment using leaf litter from S. canadensis and P. arundinacea was conducted across three community types: invasive, native, and mixed. Seed germination tests were also performed to investigate the allelopathic effects of decomposing litter. In the greenhouse, a pot experiment with lettuce as a bioindicator was performed to examine the allelochemical inputs from litter decomposition over various time intervals (0, 30, 60, 120, and 180 days). Subsequently, a soil-plant feedback experiment was carried out to further evaluate the effects of decomposing litter on soil biochemistry and plant dynamics. The findings of this study revealed that S. canadensis litter decomposed more rapidly and exhibited greater nitrogen (N) remaining mass compared with P. arundinacea in both single and mixed communities. After 180 days, the values for litter mass remaining for S. canadensis and P. arundinacea were 36% and 43%, respectively, when grown separately and were 32% and 44%, respectively, in mixed communities. At the invasive site, the soil ammonia and nitrate for S. canadensis increased gradually, reaching 0.89 and 14.93 mg/kg by day 120, compared with the native site with P. arundinacea. The soil organic carbon for S. canadensis at the invasive site also increased from 10.6 mg/kg on day 0 to 15.82 mg/kg on day 120, showing a higher increase than that at the native site with P. arundinacea. During the initial decomposition stages, all litters released almost all of their allelochemicals. However, at the later stages, litters continued to input nutrients into the soil, but had no significant impact on the soil carbon (C) and N cycling. Notably, litter-mediated plant-soil feedback facilitated the invasion of S. canadensis. In conclusion, this study highlights the significance of litter decomposition as a driver of transforming soil biochemistry, influencing the success of invasive S. canadensis.

Plant-microbe interactions: PGPM as microbial inoculants/biofertilizers for sustaining crop productivity and soil fertility

Plant-microbe interactions play pivotal roles in sustaining crop productivity and soil fertility, offering promising avenues for sustainable agricultural practices. This review paper explores the multifaceted interactions between plants and various microorganisms, highlighting their significance in enhancing crop productivity, combating pathogens, and promoting soil health. Understanding these interactions is crucial for harnessing their potential in agricultural systems to address challenges such as food security and environmental sustainability. Therefore, the introduction of beneficial microbes into agricultural ecosystems by bio-augmentation reduces the negative effects of intensive, non-sustainable agriculture on the environment, society, and economy, into the mechanisms underlying the application of plant growth promoting microbes as microbial inoculants/biofertilizers; their interactions, the factors influencing their dynamics, and the implications for agricultural practices, emerging technologies and strategies that leverage plant-microbe interactions for improving crop yields, soil fertility, and overall agricultural sustainability.

A 2-year pure biochar addition enhances soil carbon sequestration and reduces aggregate stability in understory conditions

The enhancement of soil aggregate size and stability is crucial for mitigating climate change and improving carbon sequestration in forest ecosystems. Biochar, derived from rice husks, has been suggested as an effective mean to increase soil carbon storage. However, isolating biochar's specific effects on soil aggregate formation and carbon sink capacity can be complex due to the overlapping influences of fertilization and understory vegetation cultivation. Our study circumvented these variables by incorporating different amounts of biochar into plantation soil without any additional cultivation or fertilization, conducting a detailed two-year field experiment. The findings revealed that biochar significantly increased the organic carbon content and density in the uncultivated under-forest Ferralsols, thus enhancing its carbon sink function. Intriguingly, while biochar raised the proportion of small soil aggregates (< 0.25 mm) and their organic carbon levels, it decreased the fraction of larger aggregates (> 0.25 mm), adversely affecting soil aggregate stability. These results suggest that biochar may compromise soil aggregate structure and stability in the absence of plant growth. The positive impact of biochar on soil carbon storage was found to depend more on its inherent inert carbon content than on soil type. Moreover, biochar alone was insufficient to increase the quantity of soil macroaggregates without the binding action of plant root exudates. Biochar's key function appears to be in enhancing the soil aggregate-forming processes facilitated by plant roots and microorganisms. Therefore, for optimal carbon sequestration in forest soils, integrating biochar application with appropriate agricultural practices is advisable.

Rice rhizobiome engineering for climate change mitigation

The year 2023 was the warmest year since 1850. Greenhouse gases, including CO2 and methane, played a significant role in increasing global warming. Among these gases, methane has a 25-fold greater impact on global warming than CO2. Methane is emitted during rice cultivation by a group of rice rhizosphere microbes, termed methanogens, in low oxygen (hypoxic) conditions. To reduce methane emissions, it is crucial to decrease the methane production capacity of methanogens through water and fertilizer management, breeding of new rice cultivars, regulating root exudation, and manipulating rhizosphere microbiota. In this opinion article we review the recent developments in hypoxia ecology and methane emission mitigation and propose potential solutions based on the manipulation of microbiota and methanogens for the mitigation of methane emissions.

Molecular Communication of Microbial Plant Biostimulants in the Rhizosphere Under Abiotic Stress Conditions

Microbial plant biostimulants offer a promising, sustainable solution for enhancing plant growth and resilience, particularly under abiotic stress conditions such as drought, salinity, extreme temperatures, and heavy metal toxicity. These biostimulants, including plant growth-promoting rhizobacteria, mycorrhizal fungi, and nitrogen-fixing bacteria, enhance plant tolerance through mechanisms such as phytohormone production, nutrient solubilization, osmotic adjustment, and antioxidant enzyme activation. Advances in genomics, metagenomics, transcriptomics, and proteomics have significantly expanded our understanding of plant-microbe molecular communication in the rhizosphere, revealing mechanisms underlying these interactions that promote stress resilience. However, challenges such as inconsistent field performance, knowledge gaps in stress-related molecular signaling, and regulatory hurdles continue to limit broader biostimulant adoption. Despite these challenges, microbial biostimulants hold significant potential for advancing agricultural sustainability, particularly amid climate change-induced stresses. Future studies and innovation, including Clustered Regularly Interspaced Short Palindromic Repeats and other molecular editing tools, should optimize biostimulant formulations and their application for diverse agro-ecological systems. This review aims to underscore current advances, challenges, and future directions in the field, advocating for a multidisciplinary approach to fully harness the potential of biostimulants in modern agriculture.

Unveiling the impacts of microplastic pollution on soil health: A comprehensive review

Soil contamination by microplastics (MPs) has emerged as a significant global concern. Although traditionally associated with crop production, contemporary understanding of soil health has expanded to include a broader range of factors, including animal safety, microbial diversity, ecological functions, and human health protection. This paradigm shifts underscores the imperative need for a comprehensive assessment of the effects of MPs on soil health. Through an investigation of various soil health indicators, this review endeavors to fill existing knowledge gaps, drawing insights from recent studies conducted between 2021 and 2024, to elucidate how MPs may disrupt soil ecosystems and compromise their crucial functions. This review provides a thorough analysis of the processes leading to MP contamination in soil environments and highlights film residues as major contributors to agricultural soils. MPs entering the soil detrimentally affect crop productivity by hindering growth and other physiological processes. Moreover, MPs hinder the survival, growth, and reproductive rates of the soil fauna, posing potential health risks. Additionally, a systematic evaluation of the impact of MPs on soil microbes and nutrient cycling highlights the diverse repercussions of MP contamination. Moreover, within soil-plant systems, MPs interact with other pollutants, resulting in combined pollution. For example, MPs contain oxygen-containing functional groups on their surfaces that form high-affinity hydrogen bonds with other pollutants, leading to prolonged persistence in the soil environment thereby increasing the risk to soil health. In conclusion, we succinctly summarize the current research challenges related to the mediating effects of MPs on soil health and suggest promising directions for future studies. Addressing these challenges and adopting interdisciplinary approaches will advance our understanding of the intricate interplay between MPs and soil ecosystems, thereby providing evidence-based strategies for mitigating their adverse effects.

Miscanthus sp. root exudate alters rhizosphere microbial community to drive soil aggregation for heavy metal immobilization

The heavy metals (HMs) spatial distribution in soil is intricately shaped by aggregation processes involving chemical reactions and biological activities, which modulate HMs toxicity, migration, and accumulation. Pioneer plants play a central role in preventing HMs at source, yet the precise mechanisms underlying their involvement in soil aggregation remain unclear. This study investigates HMs distribution within rhizosphere and bulk soil aggregates of Miscanthus sp. grown in tailings to elucidate the impact of root exudates (REs) and rhizosphere microbes. The results indicate that Miscanthus sp. enhance soil stability, increasing the proportion of macroaggregates by 4.06 %-9.78 %. HMs tend to concentrate in coarse-aggregates, particularly within rhizosphere environments, while diminishing in fine-aggregates. Under HMs stress, lipids and lipid-like molecules are the most abundant REs produced by Miscanthus sp., accounting for under up to 26.74 %. These REs form complex with HMs, promoting microaggregates formation. Charged components such as sugars and amino acids further contribute to soil aggregation. REs also regulates rhizosphere bacteria and fungi, with Acidobacteriota, Chloroflexi were the dominant bacterial phyla, while Ascomycota and Basidiomycota dominate the fungal community. The synergistic effect of REs and microorganisms impact soil organic matter and nutrient content, facilitating HMs nanoparticle heteroaggregation and macroaggregates formation. Consequently, soil structure and REs shape the distribution of HMs in soil aggregation. Pioneer plants mediate REs interaction with rhizosphere microbes, promoting the distribution of HMs into macroaggregates, leading to immobilization. This study sheds light on the role of pioneer plants in regulating soil HMs, offering valuable insights for soil remediation strategies.

Investigating the bacterial community of gray mangroves (Avicennia marina) in coastal areas of Tabuk region

Mangrove vegetation, a threatened and unique inter-tidal ecosystem, harbours a complex and largely unexplored bacterial community crucial for nutrient cycling and the degradation of toxic pollutants in coastal areas. Despite its importance, the bacterial community composition of the gray mangrove (Avicennia marina) in the Red Sea coastal regions remains under-studied. This study aims to elucidate the structural and functional diversity of the microbiome in the bulk and rhizospheric soils associated with A. marina in the coastal areas of Ras Alshabaan-Umluj (Umluj) and Almunibrah-Al-Wajh (Al-Wajh) within the Tabuk region of Saudi Arabia. Amplicon sequencing targeting the 16S rRNA was performed using the metagenomic DNAs from the bulk and rhizospheric soil samples from Umluj and Al-Wajh. A total of 6,876 OTUs were recovered from all samples, of which 1,857 OTUs were common to all locations while the total number of OTUs unique to Al-wajh was higher (3,011 OTUs) than the total number of OTUs observed (1,324 OTUs) at Umluj site. Based on diversity indices, overall bacterial diversity was comparatively higher in rhizospheric soil samples of both sites. Comparing the diversity indices for the rhizosphere samples from the two sites revealed that the diversity was much higher in the rhizosphere samples from Al-Wajh as compared to those from Umluj. The most dominant genera in rhizosphere sample of Al-Wajh were Geminicoccus and Thermodesulfovibrio while the same habitat of the Umluj site was dominated by Propionibacterium, Corynebacterium and Staphylococcus. Bacterial functional potential prediction analyses showed that bacteria from two locations have almost similar patterns of functional genes including amino acids and carbohydrates metabolisms, sulfate reduction and C-1 compound metabolism and xenobiotics biodegradation. However, the rhizosphere samples of both sites harbour more genes involved in the utilization and assimilation of C-1 compounds. Our results reveal that bacterial communities inhabiting the rhizosphere of A. marina differed significantly from those in the bulk soil, suggesting a possible role of A. marina roots in shaping these bacterial communities. Additionally, not only vegetation but also geographical location appears to influence the overall bacterial composition at the two sites.

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.

A "love match" score to compare root exudate attraction and feeding of the plant growth-promoting rhizobacteria Bacillus subtilis, Pseudomonas fluorescens, and Azospirillum brasilense

Introduction

The rhizosphere is the zone of soil surrounding plant roots that is directly influenced by root exudates released by the plant, which select soil microorganisms. The resulting rhizosphere microbiota plays a key role in plant health and development by enhancing its nutrition or immune response and protecting it from biotic or abiotic stresses. In particular, plant growth-promoting rhizobacteria (PGPR) are beneficial members of this microbiota that represent a great hope for agroecology, since they could be used as bioinoculants for sustainable crop production. Therefore, it is necessary to decipher the molecular dialog between roots and PGPR in order to promote the establishment of bioinoculants in the rhizosphere, which is required for their beneficial functions.

Methods

Here, the ability of root exudates from rapeseed (Brassica napus), pea (Pisum sativum), and ryegrass (Lolium perenne) to attract and feed three PGPR (Bacillus subtilis, Pseudomonas fluorescens, and Azospirillum brasilense) was measured and compared, as these responses are directly involved in the establishment of the rhizosphere microbiota.

Results

Our results showed that root exudates differentially attracted and fed the three PGPR. For all beneficial bacteria, rapeseed exudates were the most attractive and induced the fastest growth, while pea exudates allowed the highest biomass production. The performance of ryegrass exudates was generally lower, and variable responses were observed between bacteria. In addition, P. fluorescens and A. brasilense appeared to respond more efficiently to root exudates than B. subtilis. Finally, we proposed to evaluate the compatibility of each plant-PGPR couple by assigning them a "love match" score, which reflects the ability of root exudates to enhance bacterial rhizocompetence.

Discussion

Taken together, our results provide new insights into the specific selection of PGPR by the plant through their root exudates and may help to select the most effective exudates to promote bioinoculant establishment in the rhizosphere.

The Potential of Helichsryum splendidum (Thunb.) Less. for the Restoration of Sites Polluted with Coal Fly Ash

The disposal of coal fly ash (CFA) generated from coal-fired power stations has serious impact on the ecosystem, by converting large pieces of land to barren ash dams with the potential to contaminate groundwater, surface water, air and soil. The aim of this study was to clarify the potential of phytoremediation using Helichrysum splendidum (Thunb.) Less. in areas polluted by CFA through conduction of pot trial experiments for 14 weeks. Plants of the same age were cultivated in CFA to assess their growth, photosynthetic rate and tolerance towards metal toxicity. This study revealed that the CFA was moderately polluted with heavy metals, and a lower photosynthetic rate was recorded for the CFA plants in comparison to the controls (plants grown in soil). Although the CO2 assimilation rate was lower for the CFA plants, increased growth was recorded for all the plants tested. Inductively coupled plasma mass spectrometry (ICP-MS) was used to quantify the amount of trace elements in samples and parameters including translocation factor (TF) and bioconcentration factor (BCF) were used to evaluate the phytoremediation potential of H. splendidum (Thunb.) Less. The results revealed that higher concentrations of Cd, Co, Cr, Cu, Mn and Pb were accumulated in the roots, while As, Ni and Zn were found in the shoots. Elements including As, Cr and Zn reported TF values above 1, indicating the plants' phytoextraction potential. The BCF values for As, Cu and Zn were 1.22, 1.19 and 1.03, indicating effectiveness in the phytostabilization processes. A removal rate efficiency ranging from 18.0 to 56.7% was recorded confirming that, H. splendidum (Thunb.) Less. can be employed for restoration of CFA dams.

Efficiency of metal(loid) phytostabilization by white lupin (Lupinus albus L.), common vetch (Vicia sativa L.), and buckwheat (Fagopyrum esculentum Moench)

Erosion and leaching of metal(loid)s from contaminated sites can spread pollution to adjacent ecosystems and be a source of toxicity for living organisms. Phytostabilization consists of selecting plant species accumulating little or no metal(loid)s in aerial parts to establish a vegetation cover and thus to stabilize the contaminants in the soil. Seeds of white lupin, common vetch, and buckwheat were sown in greenhouse on soils from former French mines (Pontgibaud and Vaulry) contaminated with metal(loid)s including high concentrations of As and Pb (772 to 1064 and 121 to 12,340 mg kg-1, respectively). After 3 weeks of exposure, the growth of white lupin was less affected than that of the 2 other species probably because metal(loid) concentrations in roots and aerial parts of lupins were lower (5-20 times less Pb in lupin leaves on Pontgibaud soil and 5-10 times less As in lupin leaves on Vaulry soil than in vetch and buckwheat). To limit oxidation and/or scavenge metal(loid)s, white lupin increased the content of proline and total phenolic compounds (TPC) in leaves and roots by a factor 2 whereas buckwheat stimulated the production of TPC by a factor 1.5-2, and non-protein thiols (NPT) by factors around 1.75 in leaves and 6-12 in roots. Vetch accumulated more proline than white lupin but less NPT than buckwheat and less TPC than the 2 other plant species. The level of oxidation was however higher than in control plants for the 3 species indicating that defense mechanisms were not completely effective. Overall, our results showed that white lupin was the best species for phytostabilization but amendments should be tested to improve its tolerance to metal(loid)s.

Variation of root traits and its influences on soil organic carbon stability in response to altered precipitation in an alpine meadow

Soil organic carbon (SOC) dynamics are strongly controlled by plant roots. Yet, how variation of root traits under precipitation change influences SOC stability remains unclear. As part of a 5-year field experiment manipulating precipitation including 90 % (0.1P), 50 % (0.5P), 30 % (0.7P) decrease, and 50 % increase (1.5P), this study was designed to assess the effects of changing precipitation on root traits and production dynamics by minirhizotron and examine how such influences regulate SOC stability in an alpine meadow on the Qinghai-Tibetan Plateau. We found that root length density (RLD), specific root length (SRL), root branching intensity (RBI), and root residue carbon input (RC input) exhibited no significant response, whereas root turnover (RT), root carbon (C), nitrogen (N) concentrations and C/N ratio were altered by precipitation change with nonlinear trends. Absorptive root RT positively correlated to manipulated precipitation within the interannual precipitation range in topsoil, but it showed no significant change under extreme drought treatment. Alpine meadows can maintain the SOC content and density under varied precipitation. However, it showed significant variation in aggregate stability and organic carbon (OC) distribution in aggregates in topsoil, which were mainly due to the strong direct effects of soil moisture and partly related to RLD and RC input of transport roots. Although subsurface soil aggregate stability and OC associated with aggregates were not modified, our results indicated a risk of SOC stability variation in subsurface soil if absorptive root RT and SRL changed. These findings provide vital information to predict responses of SOC dynamics of alpine meadow to future climate change.

RhizoMAP: a comprehensive, nondestructive, and sensitive platform for metabolic imaging of the rhizosphere

BACKGROUND

Elucidating the intricate structural organization and spatial gradients of biomolecular composition within the rhizosphere is critical to understanding important biogeochemical processes, which include the mechanisms of root-microbe interactions for maintaining sustainable plant ecosystem services. While various analytical methods have been developed to assess the spatial heterogeneity within the rhizosphere, a comprehensive view of the fine distribution of metabolites within the root-soil interface has remained a significant challenge. This is primarily due to the difficulty of maintaining the original spatial organization during sample preparation without compromising its molecular content.

RESULTS

In this study, we present a novel approach, RhizoMAP, in which the rhizosphere molecules are imprinted on selected polymer membranes and then spatially profiled using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI). We enhanced the performance of RhizoMAP by combining the use of two thin (< 20 μm) membranes (polyester and polycarbonate) with distinct MALDI sample preparations. This optimization allowed us to gain insight into the distribution of over 500 different molecules within the rhizosphere of poplar (Populus trichocarpa) grown in rhizoboxes filled with mycorrhizae soil. These two membranes, coupled with three different sample preparation conditions, enabled us to capture the distribution of a wide variety of molecules that included phytohormones, amino acids, sugars, sugar glycosides, polycarboxylic acids components of the Krebs cycle, fatty acids, short aldehydes and ketones, terpenes, volatile organic compounds, fertilizers from the soil, and others. Their spatial distribution varies greatly, with some following root traces, others showing diffusion from roots, some associated with soil particles, and many having distinct hot spots along the plant root or surrounding soil. Moreover, we showed how RhizoMAP can be used to localize the origin of the molecules and molecular transformation during root growth. Finally, we demonstrated the power of RhizoMAP to capture molecular distributions of key metabolites throughout a 20 cm deep rhizosphere.

CONCLUSIONS

RhizoMAP is a method that provides nondestructive, untargeted, broad, and sensitive metabolite imaging of root-associated molecules, exudates, and soil organic matter throughout the rhizosphere, as demonstrated in a lab-controlled native soil environment.

The rootstock modifies the arbuscular mycorrhizal community of the root system, while the influence of the scion is limited in grapevines

Understanding the effects of grapevine rootstock and scion genotypes on arbuscular mycorrhizal fungi (AMF), as well as the roles of these fungi in plant development, could provide new avenues for adapting viticulture to climate change and reducing agrochemical inputs. The root colonization of 10 rootstock/scion combinations was studied using microscopy and metabarcoding approaches and linked to plant development phenotypes. The AMF communities were analysed using 18S rRNA gene sequencing. The 28S rRNA gene was also sequenced for some combinations to evaluate whether the method changed the results. Root colonization indexes measured by microscopy were not significantly different between genotypes. Metabarcoding analyses showed an effect of the rootstock genotype on the β-diversity and the enrichment of several taxa with both target genes, as well as an effect on the Chao1 index with the 18S rRNA gene. We confirm that rootstocks recruit different AMF communities when subjected to the same pedoclimatic conditions, while the scion has little or no effect. Significant correlations were observed between AMF community composition and grapevine development, suggesting that AMF have a positive effect on plant growth. Given these results, it will be important to define consensus methods for studying the role of these beneficial micro-organisms in vineyards.

Molecular Mechanisms of Plant Responses to Copper: From Deficiency to Excess

Copper (Cu) is an essential nutrient for plant growth and development. This metal serves as a constituent element or enzyme cofactor that participates in many biochemical pathways and plays a key role in photosynthesis, respiration, ethylene sensing, and antioxidant systems. The physiological significance of Cu uptake and compartmentalization in plants has been underestimated, despite the importance of Cu in cellular metabolic processes. As a micronutrient, Cu has low cellular requirements in plants. However, its bioavailability may be significantly reduced in alkaline or organic matter-rich soils. Cu deficiency is a severe and widespread nutritional disorder that affects plants. In contrast, excessive levels of available Cu in soil can inhibit plant photosynthesis and induce cellular oxidative stress. This can affect plant productivity and potentially pose serious health risks to humans via bioaccumulation in the food chain. Plants have evolved mechanisms to strictly regulate Cu uptake, transport, and cellular homeostasis during long-term environmental adaptation. This review provides a comprehensive overview of the diverse functions of Cu chelators, chaperones, and transporters involved in Cu homeostasis and their regulatory mechanisms in plant responses to varying Cu availability conditions. Finally, we identified that future research needs to enhance our understanding of the mechanisms regulating Cu deficiency or stress in plants. This will pave the way for improving the Cu utilization efficiency and/or Cu tolerance of crops grown in alkaline or Cu-contaminated soils.

Phytobial remediation advances and application of omics and artificial intelligence: a review

Industrialization and urbanization increased the use of chemicals in agriculture, vehicular emissions, etc., and spoiled all environmental sectors. It causes various problems among living beings at multiple levels and concentrations. Phytoremediation and microbial association are emerging as a potential method for removing heavy metals and other contaminants from soil. The treatment uses plant physiology and metabolism to remove or clean up various soil contaminants efficiently. In recent years, omics and artificial intelligence have been seen as powerful techniques for phytobial remediation. Recently, AI and modeling are used to analyze large data generated by omics technologies. Machine learning algorithms can be used to develop predictive models that can help guide the selection of the most appropriate plant and plant growth-promoting rhizobacteria combination that is most effective at remediation. In this review, emphasis is given to the phytoremediation techniques being explored worldwide in soil contamination.

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

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

Underwater light source changes microecosystem constructed by Vallisneria spinulosa Yan for water restoration: Efficiency of water purification, characteristics of growth, and rhizosphere

Submerged macrophytes are effective in ecological restoration of water bodies polluted by nitrogen and phosphorus, and its restoration capacity depends on underwater illumination condition. This study explored the influencing mechanism of illumination on Vallisneria spinulosa Yan (V. spinulosa Yan) for water restoration. Addition of underwater light source increased the total nitrogen, ammonia nitrogen, total phosphorus, and phosphate removal loads of the V. spinulosa Yan growth system by 61.5, 39.2, 8.5, and 5.0 mg m-2 d-1, respectively. Meanwhile, the growth of V. spinulosa Yan was obviously promoted, even with high water turbidity. Although the biological nitrogen removal processes were inhibited by adding underwater light source, the growth of V. spinulosa Yan can be significantly improved, thus enhancing the efficiency of water purification via the absorption of nitrogen and phosphorus by V. spinulosa Yan. This study provides a theoretical foundation and technical support for application of submerged macrophytes in ecological water restoration.

Sustainable strategy for rehabilitating phosphate mining sites and valorisation of phosphate industry by-products and sludge using pistachio tree (Pistacia atlantica), false pepper (Schinus molle), and eucalyptus (Eucalyptus globulus) trees

The development of anthroposols has been proposed as a new environmentally friendly approach to ensuring the successful revegetation of phosphate mining sites. The phosphate industry's by-products, including phosphogypsum (PG), phosphate sludge (PS), and sewage sludge (SS), can be valuable resources in restoring the ecological balance of mined soil areas. The aim of this study was to safely and sustainably restore the ecological integrity of the phosphate mining site through the evaluation of nutrients and heavy metals dynamics in soil and plant tissues of three tree species and treated by-products containing 65 % PG, 30 % PS, and 5 % SS. The tree species used were Pistacia atlantica, Schinus molle, and Eucalyptus globulus. The experimental layout was a randomised complete block design with six replicates and three treatments. Growth diameter, height, nutrient uptakes and heavy metal dynamic were evaluated from the rhizosphere soils and plant tissues over two years. Hierarchical head maps of correlations between the measured growth parameters, soil and nutrient uptakes of the tree species were analysed using a phylogenetic generalised linear mixed model. S. molle and E. globulus had higher average diameter and height than P. atlantica plants. P. atlantica and S. molle showed greater nitrogen, phosphorus, potassium, calcium, and magnesium concentrations than E. globulus trees. Tree growth parameters were closely linked to soil nutrient bioavailability. The heavy metal accumulation ratio was higher in the E. globulus and S. molle leaves than in stems. Using by-products could be valorised for rehabilitating mine sites together with E. globulus and S. molle species.

Rhizosphere metabolic cross-talk from plant-soil-microbe tapping into agricultural sustainability: Current advance and perspectives

Rhizosphere interactions from plant-soil-microbiome occur dynamically all the time in the "black microzone" underground, where we can't see intuitively. Rhizosphere metabolites including root exudates and microbial metabolites act as various chemical signalings involving in rhizosphere interactions, and play vital roles on plant growth, development, disease suppression and resistance to stress conditions as well as proper soil health. Although rhizosphere metabolites are a mixture from plant roots and soil microbes, they often are discussed alone. As a rapid appearance of various omics platforms and analytical methods, it offers possibilities and opportunities for exploring rhizosphere interactions in unprecedented breadth and depth. However, our comprehensive understanding about the fine-tuning mechanisms of rhizosphere interactions mediated by these chemical compounds still remain clear. Thus, this review summarizes recent advances systemically including the features of rhizosphere metabolites and their effects on rhizosphere ecosystem, and looks forward to the future research perspectives, which contributes to facilitating better understanding of biochemical communications belowground and helping identify novel rhizosphere metabolites. We also address challenges for promoting the understanding about the roles of rhizosphere metabolites in different environmental stresses.

Both the scion and rootstock of grafted grapevines influence the rhizosphere and root endophyte microbiomes, but rootstocks have a greater impact

BACKGROUND

Soil microorganisms play an extensive role in the biogeochemical cycles providing the nutrients necessary for plant growth. Root-associated bacteria and fungi, originated from soil, are also known to influence host health. In response to environmental stresses, the plant roots exude specific molecules influencing the composition and functioning of the rhizospheric and root microbiomes. This response is host genotype-dependent and is affected by the soil microbiological and chemical properties. It is essential to unravel the influence of grapevine rootstock and scion genotypes on the composition of this microbiome, and to investigate this relationship with plant growth and adaptation to its environment. Here, the composition and the predicted functions of the microbiome of the root system were studied using metabarcoding on ten grapevine scion-rootstock combinations, in addition to plant growth and nutrition measurements.

RESULTS

The rootstock genotype significantly influenced the diversity and the structure of the bacterial and fungal microbiome, as well as its predicted functioning in rhizosphere and root compartments when grafted with the same scion cultivar. Based on β-diversity analyses, 1103P rootstock showed distinct bacterial and fungal communities compared to the five others (RGM, SO4, 41B, 3309 C and Nemadex). The influence of the scion genotype was more variable depending on the community and the investigated compartment. Its contribution was primarily observed on the β-diversity measured for bacteria and fungi in both root system compartments, as well as for the arbuscular mycorrhizal fungi (AMF) in the rhizosphere. Significant correlations were established between microbial variables and the plant phenotype, as well as with the plant mineral status measured in the petioles and the roots.

CONCLUSION

These results shed light on the capacity of grapevine rootstock and scion genotypes to recruit different functional communities of microorganisms, which affect host growth and adaptation to the environment. Selecting rootstocks capable of associating with positive symbiotic microorganisms is an adaptation tool that can facilitate the move towards sustainable viticulture and help cope with environmental constraints.

Neighbour-induced changes in root exudation patterns of buckwheat results in altered root architecture of redroot pigweed

Roots are crucial in plant adaptation through the exudation of various compounds which are influenced and modified by environmental factors. Buckwheat root exudate and root system response to neighbouring plants (buckwheat or redroot pigweed) and how these exudates affect redroot pigweed was investigated. Characterising root exudates in plant-plant interactions presents challenges, therefore a split-root system which enabled the application of differential treatments to parts of a single root system and non-destructive sampling was developed. Non-targeted metabolome profiling revealed that neighbour presence and identity induces systemic changes. Buckwheat and redroot pigweed neighbour presence upregulated 64 and 46 metabolites, respectively, with an overlap of only 7 metabolites. Root morphology analysis showed that, while the presence of redroot pigweed decreased the number of root tips in buckwheat, buckwheat decreased total root length and volume, surface area, number of root tips, and forks of redroot pigweed. Treatment with exudates (from the roots of buckwheat and redroot pigweed closely interacting) on redroot pigweed decreased the total root length and number of forks of redroot pigweed seedlings when compared to controls. These findings provide understanding of how plants modify their root exudate composition in the presence of neighbours and how this impacts each other's root systems.

Unique dissolved organic matter molecules and microbial communities in rhizosphere of three typical crop soils and their significant associations based on FT-ICR-MS and high-throughput sequencing analysis

Using cucumber, maize, and ryegrass as model plants, the diversity and uniqueness of the molecular compositions of dissolved organic matter (DOM) and the structures of microbial communities in typical crop rhizosphere soils, as well as their associations, were investigated based on high-resolution mass spectrometry combined with high-throughput sequencing. The results showed that the rhizosphere contained 2200 organic molecules that were not identified in the non-rhizosphere soils, as characterized by FT-ICR-MS. The rhizosphere DOM molecules generally contained more N, S, and P heteroatoms, stronger hydrophilicity, and more refractory organic matter, representing high and complex chemical diversity characteristics. 16SrRNA sequencing results demonstrated that Proteobacteria, Actinomycetes and Firmicutes were the dominant flora in the soils. Plant species could significantly change the composition and relative abundance of rhizosphere microbial populations. The microbial community structures of rhizosphere and non-rhizosphere soils showed significant differences at both the phylum and class levels. Multiple interactions between the microorganisms and DOM compositions formed a complex network of relationships. There were strong and remarkable positive or negative couplings between different sizes and categories of DOM molecules and the specific microbial groups (P < 0.05, |R| ≥ 0.9) in the rhizosphere soils as shown by network profiles. The correlations between DOM molecules and microbial groups in rhizosphere soils had plant species specificity. The results above emphasized the relationship between the heterogeneity of DOM and the diversity of microbial communities, and explored the molecular mechanisms of the biochemical associations in typical plant rhizosphere soils, providing a foundation for in-depth understanding of plant-soil-microbe interactions.

Root-exuded specialized metabolites reduce arsenic toxicity in maize

By releasing specialized metabolites, plants modify their environment. Whether and how specialized metabolites protect plants against toxic levels of trace elements is not well understood. We evaluated whether benzoxazinoids, which are released into the soil by major cereals, can confer protection against arsenic toxicity. Benzoxazinoid-producing maize plants performed better in arsenic-contaminated soils than benzoxazinoid-deficient mutants in the greenhouse and the field. Adding benzoxazinoids to the soil restored the protective effect, and the effect persisted to the next crop generation via positive plant-soil feedback. Arsenate levels in the soil and total arsenic levels in the roots were lower in the presence of benzoxazinoids. Thus, the protective effect of benzoxazinoids is likely soil-mediated and includes changes in soil arsenic speciation and root accumulation. We conclude that exuded specialized metabolites can enhance protection against toxic trace elements via soil-mediated processes and may thereby stabilize crop productivity in polluted agroecosystems.

Impacts of cobalt and zinc on improving peanuts nutrient uptake, yield and irrigation water use efficiency under different irrigation levels

The knowledge of proper fertigation across various irrigation levels is necessary for maximizing peanut yield and irrigation use efficiency in arid areas, and it also can effectively alleviate the risk of nutrient deficiency induced by water stress. This study evaluated the effectiveness of cobalt combined with two zinc application methods on peanut nutrient uptake, yield, and irrigation water use efficiency across varying irrigation levels. A split-split plot experiment was carried out in 2021 and 2022. Three peanut gross water requirement (GWR) levels (100%, 80%, and 60%) were designated for main plots. Subplots featured plants treated with either 0 or 7.5 mg L-1 of cobalt. The sub-sub plots assessed chelated zinc effects at rates of 0 and 2 g L-1 via foliar and soil applications. In comparison to the control (100% GWR), nutrient uptake decreased, with sodium being the exception, and there was an increase in soil pH at 60% GWR. The results showed also significant reductions in yield and water use by approximately 60.3% and 38.1%, respectively. At this irrigation level, applying zinc via soil, either alone or combined with cobalt, led to significant yield increases of 89.7% and 191.3% relative to the control. Also, it's crucial to note that cobalt application negatively affected iron and copper at 60% GWR, but this impact was lessened with soil-applied zinc. Hence, under a similar circumstance, treating stressed peanut plants with additional foliar applications of iron + copper and applying zinc via soil, could enhance nutrient uptake and improve yield. On the other hand, at 80% GWR, a combination of foliar-applied zinc and cobalt, had a tremendous impact on the absorption of (nitrogen, phosphorus, magnesium, and zinc), resulting in enhanced agronomic traits and decreased water losses. Additionally, at this irrigation level, foliar zinc application alone yielded a 32.4% increase compared to the 80% GWR control. When combined with cobalt, there was a 70.0% surge in water use. Based on this knowledge, the study suggests using 80% GWR and treating peanut plants with a combination of foliar-applied zinc and cobalt. This strategy aids plants in countering the adverse effects of water stress, ultimately leading to enhanced yield and irrigation water use efficiency.

Dynamics of benthic microeukaryotic communities in a mangrove wetland invaded by Spartina alterniflora: Effects of vegetation, seasonality, and sediment depth

Benthic microeukaryotes are crucial mediators of biogeochemical cycles in coastal wetland ecosystems, yet their spatial and temporal variability remains poorly understood. This study delineates the diversity patterns of benthic microeukaryotes in a Spartina alterniflora-invaded mangrove ecosystem in Fujian, China. Using high-throughput sequencing of 18S rRNA gene transcripts, we identified the influences of vegetation, seasonality, and sediment depth on microeukaryotic communities. We discovered that vegetation cover significantly affects community composition, primarily driven by nutrient concentrations and pH. The community structure of microeukaryotes varied seasonally and vertically, correlating with changes in sediment temperature, pH, salinity, and fucoxanthin concentration. Notably, invasive Spartina alterniflora habitats showed enhanced heterotrophic interactions, suggesting that invasive species can reshape benthic microeukaryotic co-occurrence patterns. Seasonal co-occurrence patterns revealed dominant Bacillariophyta assemblages exhibited distinct network modules enriched in the cold (spring) and warm (summer and fall) seasons, respectively, which indicated potential ecological niche differentiation. Our findings reveal the complex relationships between environmental factors and benthic microeukaryotic diversity, offering insights into microbial responses to natural and invasive vegetation influences.

The Multiple Promoting Effects of Suaeda glauca Root Exudates on the Growth of Alfalfa under NaCl Stress

Under abiotic stress, plant root exudates can improve plant growth performance. However, studies on the effect of root exudates on the stress resistance of another plant are insufficient. In this study, root exudates (REs) were extracted from Suaeda glauca to explore their effect on alfalfa seedlings under salt stress. The results showed that the plant height and fresh weight of alfalfa significantly increased by 47.72% and 53.39% after 7 days of RE treatment at a 0.4% NaCl concentration. Under 1.2% salt stress, REs reduced the Malondialdehyde content in alfalfa by 30.14% and increased the activity of its antioxidant enzymes (peroxidase and catalase) and the content of its osmotic regulators (soluble sugar and proline) by 60.68%, 52%, 45.67%, and 38.67%, respectively. Soil enzyme activity and the abundance of soil-beneficial bacteria were increased by REs. Spearman analysis showed that urease and neutral phosphatase were related to the richness of beneficial bacteria. Redundancy analysis confirmed that urease affected the composition of the soil bacterial community. The partial least squares structural equation model (PLS-SEM) revealed that REs had a direct positive effect on alfalfa growth under salt stress by regulating the plant's injury and antioxidant systems, and the soil bacterial community had an indirect positive effect on alfalfa growth through soil enzyme activity.

Use of wastewater alum-coagulation sludge as a phosphorus fertiliser - a mini review

The use of aluminium (Al) salts, particularly alum, in coagulation is a widespread and conventional treatment method for eliminating pollutants, including phosphorus (P) which can cause eutrophication, from wastewater. However, a significant challenge of this process is the substantial amount of sludge generated, necessitating proper disposal. Historically, land disposal has been a common practice, but it poses potential issues for plant life on these lands. Despite the associated drawbacks, sludge contains elevated concentrations of vital plant nutrients like P and nitrogen, presenting an opportunity for beneficial use in agriculture. Given the imminent scarcity of P fertilizers due to the eventual depletion of high-grade P ores, this review explores the potential advantages and challenges of utilizing Al sludge as a P source for plants and proposes measures for its beneficial application. One primary concern with land application of Al sludge is its high levels of soluble Al, known to be toxic to plants, particularly in acidic soils. Another issue arises from the elevated Al concentration is P fixation and subsequently reducing P uptake by plants. To address these issues, soil treatment options such as lime, gypsum, and organic matter can be employed. Additionally, modifying the coagulation process by substituting part of the Al salts with cationic organic polymers proves effective in reducing the Al content of the sludge. The gradual release of P from sludge into the soil over time proves beneficial for plants with extended growth periods.

Relationships between root exudation and root morphological and architectural traits vary with growing season

Plants allocate a substantial amount of C belowground for root exudates and for the construction and adjustment of root morphological and architectural traits. What relationships exist between root exudates and other root traits and these relationships change with growing season, however, remain unclear. We quantified the root exudation rate and root morphological traits, including total root length (RL), total root surface area (RS), root diameter (RD), specific root length (SRL), specific root area (SRA) and root tissue density (RTD), and architectural traits, such as branching intensity (BI), and investigated their associations during the rapidly growing season (April and August) and the slowly growing season (December) of three common native tree species, Liquidambar formosana, Michelia maudiae and Schima superba, in subtropical China. We found that the linkages of RD, SRL, SRA, RTD and BI did not change with the growing season, reflecting their highly conservative relationships. The root exudation rate varied significantly with growing season (P < 0.05) and produced various associations with other root traits at different growing seasons. During the rapidly growing season (i.e., April), the exudation rate was the highest and was positively correlated with RL. The exudation rate was the lowest during the slowly growing season (i.e., December) and was negatively associated with RL, RS and RTD. Our findings demonstrate the seasonality of the linkages of root exudation rate with other root traits, which highlights the highly plastic and complex associations of belowground root traits. These findings help to deepen our understanding of plant nutrient acquisition strategies.

Emerging sensing, imaging, and computational technologies to scale nano-to macroscale rhizosphere dynamics - Review and research perspectives

The soil region influenced by plant roots, i.e., the rhizosphere, is one of the most complex biological habitats on Earth and significantly impacts global carbon flow and transformation. Understanding the structure and function of the rhizosphere is critically important for maintaining sustainable plant ecosystem services, designing engineered ecosystems for long-term soil carbon storage, and mitigating the effects of climate change. However, studying the biological and ecological processes and interactions in the rhizosphere requires advanced integrated technologies capable of decoding such a complex system at different scales. Here, we review how emerging approaches in sensing, imaging, and computational modeling can advance our understanding of the complex rhizosphere system. Particularly, we provide our perspectives and discuss future directions in developing in situ rhizosphere sensing technologies that could potentially correlate local-scale interactions to ecosystem scale impacts. We first review integrated multimodal imaging techniques for tracking inorganic elements and organic carbon flow at nano- to microscale in the rhizosphere, followed by a discussion on the use of synthetic soil and plant habitats that bridge laboratory-to-field studies on the rhizosphere processes. We then describe applications of genetically encoded biosensors in monitoring nutrient and chemical exchanges in the rhizosphere, and the novel nanotechnology-mediated delivery approaches for introducing biosensors into the root tissues. Next, we review the recent progress and express our vision on field-deployable sensing technologies such as planar optodes for quantifying the distribution of chemical and analyte gradients in the rhizosphere under field conditions. Moreover, we provide perspectives on the challenges of linking complex rhizosphere interactions to ecosystem sensing for detecting biological traits across scales, which arguably requires using the best-available model predictions including the model-experiment and image-based modeling approaches. Experimental platforms relevant to field conditions like SMART (Sensors at Mesoscales with Advanced Remote Telemetry) soils testbed, coupled with ecosystem sensing and predictive models, can be effective tools to explore coupled ecosystem behavior and responses to environmental perturbations. Finally, we envision that with the advent of novel high-resolution imaging capabilities at nano- to macroscale, and remote biosensing technologies, combined with advanced computational models, future studies will lead to detection and upscaling of rhizosphere processes toward ecosystem and global predictions.

Shrub expansion raises both aboveground and underground multifunctionality on a subtropical plateau grassland: coupling multitrophic community assembly to multifunctionality and functional trade-off

Introduction

Shrubs have expanded into grasslands globally. However, the relative importance of aboveground and underground diversity and the relative importance of underground community assembly and diversity in shaping multifunctionality and functional trade-offs over shrub expansion remains unknown.

Methods

In this study, aboveground and underground multitrophic communities (abundant and rare archaea, bacteria, fungi, nematodes, and protists) and 208 aboveground and underground ecosystem properties or indicators were measured at three stages (Grass, Mosaic, Shrub) of shrub expansion on the Guizhou subtropical plateau grassland to study multifunctionality and functional trade-offs.

Results

The results showed that shrub expansion significantly enhanced aboveground, underground, and entire ecosystem multifunctionality. The functional trade-off intensities of the aboveground, underground, and entire ecosystems showed significant V-shaped changes with shrub expansion. Shrub expansion improved plant species richness and changed the assembly process and species richness of soil abundant and rare subcommunities. Plant species diversity had a greater impact on multifunctionality than soil microbial diversity by more than 16%. The effect of plant species diversity on functional trade-offs was only one-fifth of the effect of soil microbial diversity. The soil microbial species richness did not affect multifunctionality, however, the assembly process of soil microbial communities did. Rather than the assembly process of soil microbial communities, the soil microbial species richness affected functional trade-offs.

Discussion

Our study is the first to couple multitrophic community assemblies to multifunctionality and functional trade-offs. Our results would boost the understanding of the role of aboveground and underground diversity in multifunctionality and functional trade-offs.

Stabilisation of soil organic matter with rock dust partially counteracted by plants

Soil application of Ca- and Mg-rich silicates can capture and store atmospheric carbon dioxide as inorganic carbon but could also have the potential to stabilise soil organic matter (SOM). Synergies between these two processes have not been investigated. Here, we apply finely ground silicate rock mining residues (basalt and granite blend) to a loamy sand in a pot trial at a rate of 4% (equivalent to 50 t ha-1 ) and investigate the effects of a wheat plant and two watering regimes on soil carbon sequestration over the course of 6 months. Rock dust addition increased soil pH, electric conductivity, inorganic carbon content and soil-exchangeable Ca and Mg contents, as expected for weathering. However, it decreased exchangeable levels of micronutrients Mn and Zn, likely related to the elevated soil pH. Importantly, it increased mineral-associated organic matter by 22% due to the supply of secondary minerals and associated sites for SOM sorption. Additionally, in the nonplanted treatments, rock supply of Ca and Mg increased soil microaggregation that subsequently stabilised labile particulate organic matter as organic matter occluded in aggregates by 46%. Plants, however, reduced soil-exchangeable Mg and Ca contents and hence counteracted the silicate rock effect on microaggregates and carbon within. We suggest this cation loss might be attributed to plant exudates released to solubilise micronutrients and hence neutralise plant deficiencies. The effect of enhanced silicate rock weathering on SOM stabilisation could substantially boost its carbon sequestration potential.

Effects of varying nano-ZnO concentrations on the physiology, biochemistry, root exudate, and root microbial community of Agrostis stolonifera

This study investigates the adsorption and transport of nano-ZnO in Agrostis stolonifera, focusing on its effects on plant physiology, biochemistry, root exudate, and root microbial community.

Persistence of Root Exudates of Sorghum bicolor and Solidago canadensis: Impacts on Invasive and Native Species

Root exudates of the invasive Solidago canadensis and the cereal crop Sorghum bicolor (L.) Moench cv. 'Hybridsorgo' were tested for allelopathic interactions against native and invasive plant species in a controlled environment. After the surface was sterilized, the seeds of two invasive species (Bromus sterilis and Veronica persica) and two native species (Youngia japonica and Rumex acetosa) were germinated and transplanted into the soil (1:1 mixture of coco peat and sand) that had been conditioned for one month by the cultivation of Solidago canadensis and Sorghum bicolor, both in combination or as unplanted controls. After an additional eight weeks of growth, morphometric measurements of the shoot and root, including foliar characteristics and above- and below-ground biomass accumulation, were performed. The results revealed significant inhibitory effects of root exudates released by Sorghum bicolor and Solidago canadensis on native species' productivity and physiology. The invasive species exhibited variable growth responses, with Veronica persica showing reduced shoot and root expansion, but Bromus sterilis revealed increased shoot and root biomass allocation and nutrition under the exudate treatments. Exudates from Solidago canadensis and Sorghum bicolor together showed synergistic negative effects on native species, while they promoted growth and nutrition in Veronica persica. Taken together, the differential species responses indicate that the tested native species were more sensitive to the allelopathic compounds than the invasive species, which is in line with the theory of novel weapons. The legacy effects of root exudates of both Sorghum bicolor and Solidago canadensis could promote invasive establishment through imposing allelochemical interference competition against native plant species. Understanding the specific allelopathic mechanisms may help with the development of integrated strategies for managing invasive species.

Research progress of nano-scale secondary ion mass spectrometry (NanoSIMS) in soil science: Evolution, applications, and challenges

Nano-scale secondary ion mass spectrometry (NanoSIMS) has emerged as a powerful analytical tool for investigating various aspects of soils. In recent decades, the widespread adoption of advanced instrumentation and methods has contributed significantly to our understanding of organic-mineral assemblages. However, few literature reviews have comprehensively summarized NanoSIMS and its evolution, applications, limitations, and integration with other analytical techniques. In this review, we addressed this gap by comprehensively overviewing the development of NanoSIMS as an analytical tool in soils. This review covers studies on soil organic matter (SOM) cycling, soil-root interactions, and the behavior of metals, discussing the capability and limitations related to the distribution, composition, and interactions of various soil components that occur at mineral-organic interfaces. Furthermore, we examine recent advancements in high-resolution imaging and mass spectrometry technologies and their impact on the utilization of NanoSIMS in soils, along with potential new applications such as utilizing multiple ion beams and integrating them with other analytical techniques. The review emphasizes the importance of employing advanced techniques and methods to explore micro-interfaces and provide in situ descriptions of organic-mineral assemblages in future research. The ongoing development and refinement of NanoSIMS may yield new insights and breakthroughs in soil science, deepening our understanding of the intricate relationships between soil components and the processes that govern soil health and fertility.