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• Potential plant growth-promoting rhizobacteria screened from tomato rhizosphere soil. • Biochemical and molecular characterization of selected four isolates were done and taxonomy identified. • Plant growth promoting traits of the candidate strains were evaluated both at laboratory and greenhouse level. • Greenhouse trail and symbiotic effectiveness of the strains conducted using tomato as host plant. • To improve tomato-strain interaction different possible phosphorus sources were added. Numerous phosphate solubilizing bacteria (PSB) are found in the rhizosphere, benefiting the host plant in different mechanisms and promoting sustainable agriculture. They improve soil fertility with minimum cost requirements using an eco-friendly approach, which is an essential attribute for small-scale farm production. Thus, isolation, characterization, and evaluation of symbiotic effectiveness are hierarchical procedures to develop bioinoculants. Using a dual (plate and liquid medium) screening technique and a greenhouse trial, four potential PSB strains (Mk-1–25, Mk-13–16, Mk-20–7, and Mk-20–20) were selected from tomato rhizosphere soil. All isolates exhibited the following traits: produced colony clear-zone, lowered liquid medium pH, gram-positive, produced urease and IAA, dissolved substantial P from various substrates, symbiotically effective, and improved tomato growth and yield. Taxonomically, they belong to Bacillus and Priestia species (i.e., Mk-1–25 Bacillus halotolerance, Mk-13–16 Bacillus amyloliquefaciens, Mk-20–7 Bacillus megaterium, and Mk-20–20 Priestia megaterium). Among the current strains, Bacillus halotolerance recorded higher SI (3.11), was able to grow in extreme conditions (10% salt, up to 45 °C), produced HCN and siderophore, and improved tomatoes' shoot length and weight, in contrast, Mk-20–20 produced HCN, siderophore, was able to fix nitrogen, improved tomato germination, shoot dry weight, and fruit weight. Various P-supplements (Ca 3 (PO 4) 2 , bonemeal, FePO 4 , AlPO 4 , compost, and DAP fertilizer) were added to induce tomato-strain symbiotic interaction; hence, compost substantially promoted the interaction and resulted in higher symbiotic effectiveness. Ca 3 (PO 4) 2 was a good media composite preferred by most PSB strains; consequently, a higher concentration (219 µg/ml) of dissolved P was recorded from the liquid medium after 10 days of incubation than other substrates. Based on the data obtained from laboratory and greenhouse trials, the current strains were found to be potential candidate. Future work should confirm their efficacy at the field level using model host crops at different sites to recommend them as farm inputs and biofertilizer. [ABSTRACT FROM AUTHOR]

In future cropping systems, a focus on belowground plant–soil interactions should exploit the synergy of plant responses to multiple soil factors to maximize the biological potential of roots. Key soil factors include root-zone heterogeneity arising from the physical, biological, and chemical properties varying in time and space. Optimizing the match between root functioning and soil properties is needed to achieve increased crop productivity and improved soil health. The integration of plant and soil sciences, and the application of holistic plant–soil solutions in the crop systems, will provide effective new approaches towards a more sustainable crop production. The Green Revolution transformed agriculture with high-yielding, stress-resistant varieties. However, the urgent need for more sustainable agricultural development presents new challenges: increasing crop yield, improving nutritional quality, and enhancing resource-use efficiency. Soil plays a vital role in crop-production systems and ecosystem services, providing water, nutrients, and physical anchorage for crop growth. Despite advancements in plant and soil sciences, our understanding of belowground plant–soil interactions, which impact both crop performance and soil health, remains limited. Here, we argue that a lack of understanding of these plant–soil interactions hinders sustainable crop production. We propose that targeted engineering of crops and soils can provide a fresh approach to achieve higher yields, more efficient sustainable crop production, and improved soil health. [ABSTRACT FROM AUTHOR]

It remains unclear whether microbial carbon limitation exists in the rhizosphere, a microbial hotspot characterized by intensive labile carbon input. Here, we collected rhizosphere soils attached to absorptive and transport roots and bulk soils in three alpine coniferous forests and evaluated the limiting resources of microbes based on the responses of microbial growth (18O incorporation into DNA) and respiration to full-factorial amendments of carbon, nitrogen, and phosphorus. The results showed that adding carbon enhanced microbial growth and respiration rates in the rhizosphere soils by 1.2- and 10.3-fold, respectively, indicating the existence of carbon limitation for both anabolic and catabolic processes. In contrast, the promoting effects of nutrient addition were weak or manifested only after the alleviation of carbon limitation, suggesting that nutrients were co-limiting or secondarily limiting resources. Moreover, the category and extent of microbial resource limitations were comparable between the rhizosphere of absorptive and transport roots, and between the rhizosphere and bulk soils. Overall, our findings offer direct evidence for the presence of microbial carbon limitation in the rhizosphere. [ABSTRACT FROM AUTHOR]

Predicting soil water status remotely is appealing due to its low cost and large‐scale application. During drought, plants can disconnect from the soil, causing disequilibrium between soil and plant water potentials at pre‐dawn. The impact of this disequilibrium on plant drought response and recovery is not well understood, potentially complicating soil water status predictions from plant spectral reflectance. This study aimed to quantify drought‐induced disequilibrium, evaluate plant responses and recovery, and determine the potential for predicting soil water status from plant spectral reflectance. Two species were tested: sweet corn (Zea mays), which disconnected from the soil during intense drought, and peanut (Arachis hypogaea), which did not. Sweet corn's hydraulic disconnection led to an extended 'hydrated' phase, but its recovery was slower than peanut's, which remained connected to the soil even at lower water potentials (−5 MPa). Leaf hyperspectral reflectance successfully predicted the soil water status of peanut consistently, but only until disequilibrium occurred in sweet corn. Our results reveal different hydraulic strategies for plants coping with extreme drought and provide the first example of using spectral reflectance to quantify rhizosphere water status, emphasizing the need for species‐specific considerations in soil water status predictions from canopy reflectance. Summary Statement: We developed models to accurately predict rhizosphere water status from hyperspectral imaging of roots and soil. We found canopies cannot always accurately predict rhizosphere water status—as our experiment revealed soil–plant disequilibrium in one species (sweet corn) but not another (peanut). [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Background Aims Methods Results Conclusions Liquid organic fertilizer (LOF) and root exudates contain easily decomposable carbon that can stimulate microbial growth. It is unknown what role the amount of organic matter (OM) in the growing media, and potential interactions between root presence and LOF, might play in enhancing the breakdown of OM.The aim was to better understand how the decomposition rate of plant litter is affected by added fertilizer, plant presence, and growing media OM content.A container experiment was conducted with and without tomato plants (Solanum lycopersicum L.; Heinz 5608 variety) present to evaluate the effect of three one‐time fertilizer additions (no fertilizer, LOF, and synthetic fertilizer) on litter decomposition rate. The equivalent amount of nitrogen (N), phosphorus (P), and potassium(K) was added in both fertilizer treatments. The experiment was conducted using two growing media, one containing high OM and one with negligible OM.The presence of tomato roots stimulated litter decomposition in high OM media, but not in low OM media. Adding LOF did not affect decomposition in either growing medium. Adding synthetic fertilizer led to a negative priming effect in low OM media when roots were present. The rate of decomposition was not affected by root traits.When ample OM was available, the presence of plant roots had a strong positive impact on litter decomposition. In both low and high OM media, a one‐time addition of fertilizer had minimal or negative effects on litter decomposition. We speculate that the continuous nature of root exudation leads to sustained changes in the microbial population (both community composition and size). Boosting root length growth via the one‐time addition of inorganic fertilizer when OM was negligible allowed the plant to outcompete decomposing microbes for N, possibly leading to selection for microbes that primarily feed on exudates, which resulted in retarded litter decomposition rates. In conclusion, as adding inorganic fertilizer stimulated plant and root growth more than adding the equivalent nutrients in LOF, particularly in growth media with a high OM content, it is better to add inorganic nutrients than LOF to stimulate OM breakdown when plants are present. [ABSTRACT FROM AUTHOR]

The plant mycobiome plays a crucial role in the host life cycle, influencing both healthy and diseased states, and is essential for plant tolerance to drought. In this study, we used ITS metabarcoding to investigate the fungal community of the drought-resistant plant Malva sylvestris L. in Morocco along a gradient of precipitation, encompassing subhumid and semi-arid environments. We sampled three biotopes: rhizosphere, bulk soil, and root endosphere. Our findings revealed an absence of beta-diversity differences between bulk soil and rhizosphere, indicating that the plant does not selectively influence its rhizosphere mycobiome. Additionally, ASVs belonging to the genus Alternaria represented up to 30% of reads in the plant's roots and correlated with drought (p = 0.006), indicating a potential role for this fungal genus in mitigating drought, possibly as part of the dark septate endophyte group. Root staining and microscopic observation revealed extensive colonization by fungal hyphae and microsclerotia-like structures. Furthermore, ASVs identified as Fusarium equiseti were also correlated with low precipitation and recognized as a hub taxon in the roots. However, it remains uncertain whether this species is pathogenic or beneficial to the plant. These insights contribute to our understanding of the plant mycobiome's role in drought tolerance and highlight the importance of specific fungal taxa in supporting plant health under varying environmental conditions. Future research should focus on characterizing these taxa's functional roles and their interactions with the host plant to further elucidate their contributions to drought resistance. [ABSTRACT FROM AUTHOR]

Background Results Conclusion Reductive soil disinfestation (RSD), which involves creating anaerobic conditions and incorporating large amounts of organic materials into the soil, has been identified as a reliable strategy for reducing soilborne diseases in successive cropping systems. However, limited research exists on the connections between soil microorganism composition and plant diseases under various types of organic material applications. This study aimed to evaluate the effects of distinct RSD strategies (control without soil amendment; RSD with 1500 kg ha−1 molasses powder; RSD with 3000 kg ha−1 molasses powder; RSD with 3000 kg ha−1 molasses powder and 37.5–41.3 kg ha−1 microbial agent) on the plant disease index, bacterial community composition and network structure in rhizosphere soil.RSD treatments significantly reduced the occurrence of black shank disease in tobacco and increased soil bacterial diversity. High amounts of molasses powder in RSD treatments further enhanced disease inhibition and reduced fungal abundance and Shannon index. RSD also increased the relative abundance of bacterial phylum Firmicutes and fungal phylum Ascomycota, while decreasing the relative abundance of bacterial phyla Chloroflexi and Acidobacteriota and fungal phylum Basidiomycota in rhizosphere soil. A multiple regression model identified bacterial positive cohesion as the primary factor influencing the plant disease index, with a greater impact than bacterial negative cohesion and community stability. The competition among beneficial bacteria for creating a healthy rhizosphere environment is likely a key factor in the success of RSD in reducing plant disease risk.RSD, especially with higher rates of molasses powder, is a viable strategy for controlling black shank disease in tobacco and promoting soil health by fostering beneficial microbial communities. This study provides guidelines for soil management and plant disease prevention. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

AbstractThe Korean fir (Abies koreana), a native coniferous species of Korea, predominantly inhabits the subalpine zone. Recently, this species has experienced a significant population decline, primarily attributed to environmental changes in the subalpine zone driven by global warming. Efforts to prevent the extinction of the Korean fir are underway, with a predominant focus on abiotic factors contributing to its decline. However, there is a notable lack of research on the complex interactions between microbial communities and Korean fir, particularly concerning how these interactions vary with the health status of the trees and their impact on population sustainability. Therefore, this study aimed to elucidate the rhizosphere fungal community structure associated with Korean fir trees in Jirisan National Park. We examined different habitat types, including the rhizospheres of native, cultivated, and dead Korean fir and bulk soil. Our findings revealed that the rhizosphere fungal community in the natural habitat of Korean fir predominantly comprises Agaricomycetes. Furthermore, the fungal community structure was more responsive to habitat type variations than seasonal changes. These findings provide basic information for conserving this endangered species and developing alternative habitats for the Korean fir. [ABSTRACT FROM AUTHOR]

Rapid urbanization has exerted immense pressure on urban environments, severely constraining the growth of ancient trees. The growth of ancient trees is closely linked to the microbial communities in their rhizospheres, and studying their community characteristics may provide new insights into promoting the growth and rejuvenation of ancient trees. In this study, the rhizosphere soil and root systems of ancient Ginkgo biloba trees (approximately 200 years old) and adult G. biloba trees (approximately 50 years old) in Shanghai were selected as research subjects. Phospholipid fatty acid (PLFA) analysis and high-throughput sequencing were employed to investigate the diversity of microbial communities in the G. biloba rhizosphere. The results indicated that the 19 PLFA species selected to characterize the soil microbial community structure and biomass were present in the rhizosphere soil of both ancient and adult G. biloba trees. However, the total microbial biomass and the microbial biomass in the rhizosphere soil of ancient G. biloba were lower than the microbial biomass in the rhizosphere soil of adult G. biloba. The biomasses of Gram-negative bacteria (G−), arbuscular mycorrhizal fungi (AMF), and protozoans (P) were significantly different. Total phosphorus, organic matter, and pH may be the key factors influencing the soil microbial community in the rhizosphere zone of ancient G. biloba. An in-depth study of AMF showed that the roots and rhizosphere soil of G. biloba contained abundant AMF resources, which were assigned to 224 virtual taxa using the MaarjAM reference database, belonging to four orders, ten families, and nineteen genera. The first and second most dominant genera were Glomus and Paraglomus, respectively. Archaeospora and Ambispora were more dominant in the rhizosphere than the roots. Furthermore, the abundance of live AMF was significantly higher in ancient G. biloba than in adult G. biloba. Therefore, future research should focus on the improvement of soil environmental characteristics and the identification and cultivation of indigenous dominant AMF in the rhizosphere of ancient G. biloba, aiming for their effective application in the rejuvenation of ancient trees. [ABSTRACT FROM AUTHOR]

Anthracnose caused by Colletotrichum is an increasingly severe disease of common vetch that reduces plant yield and quality. In this study, the effects of anthracnose on the rhizosphere soil microbial community of common vetch were studied via high-throughput sequencing. The relationship among the rhizosphere soil microbes and soil properties were analyzed. Lower fungal diversity was observed in rhizosphere soils of diseased plants. Variations in relative abundance were observed in the fungal phyla Mortierellomycota and Glomeromycota and in the bacterial phyla Acidobacteria, Oxyphotobacteria, and Verrucomicrobia. Gammaproteobacteria and Deltaproteobacteria were significantly more abundant in the rhizosphere soil of healthy plant. The bacterial community in the rhizosphere soil of diseased plant was involved in the synthesis of amino acids (glycine, serine, threonine, alanine, aspartate, and glutamate). Results of a redundancy analysis showed that Colletotrichum was negatively correlated with soil available potassium (AK) and the content of soil organic matter (SOC); however, it was positively correlated with soil pH. The relative abundances of Bacillus showed a negative correlation with soil pH and a positive correlation with AK and SOC content. The present study demonstrated that anthracnose could affect the rhizosphere soil microbial communities in common vetch, and soil properties have a close relationship with the rhizosphere soil microbes of common vetch. [ABSTRACT FROM AUTHOR]

Effective colonization by microbe in the rhizosphere is critical for establishing a beneficial symbiotic relationship with the host plant. Bacillus subtilis, a soil-dwelling bacterium that is commonly found in association with plants and their rhizosphere, has garnered interest for its potential to enhance plant growth, suppress pathogens, and contribute to sustainable agricultural practices. However, research on the dynamic distribution of B. subtilis within the rhizosphere and its interaction mechanisms with plant roots remains insufficient due to limitations in existing in situ detection methodologies. To achieve dynamic in situ detection of the rhizosphere environment, we established iRhizo-Chip, a microfluidics-based platform. Using this device to investigate microbial behavior within the rhizosphere, we found obvious diurnal fluctuations in the growth of B. subtilis in the rhizosphere. Temporal dynamic analysis of rhizosphere dissolved oxygen (DO), pH, dissolved organic carbon, and reactive oxygen species showed that diurnal fluctuations in the growth of B. subtilis are potentially related to a variety of environmental factors. Spatial dynamic analysis also showed that the spatial distribution changes of B. subtilis and DO and pH were similar. Subsequently, through in vitro control experiments, we proved that rhizosphere DO and pH are the main driving forces for diurnal fluctuations in the growth of B. subtilis. Our results show that the growth of B. subtilis is driven by rhizosphere DO and pH, resulting in diurnal fluctuations, and iRhizo-Chip is a valuable tool for studying plant rhizosphere dynamics. [ABSTRACT FROM AUTHOR]

Switchgrass (Panicum virgatum L.) is a native, low-input North American perennial crop primarily grown for bioenergy, livestock forage, and industrial fiber. To achieve no-input switchgrass production that meets biomass needs, several switchgrass genotypes have been identified that have a low or negative response to nitrogen fertilizer, i.e., the biomass accumulation with added nitrogen is less than or equal to that when grown without nitrogen. In order to improve the viability of low-input switchgrass production, a more detailed understanding of the biogeochemical mechanisms active in these select genotypes is needed. 16S and ITS amplicon sequencing and qPCR of key functional genes were applied to switchgrass rhizospheres to elucidate microbial community structure in high-producing, no-input switchgrass families. Rhizosphere microbial community structure differed strongly between sites, and nitrogen responsiveness. [ABSTRACT FROM AUTHOR]

Military sites, both active and decommissioned, are rarely studied and may represent a source of fungal bioresources with potential applications for the remediation of co-contaminated soils. The aims of this study were both deepening the knowledge on fungal communities of a decommissioned military site and identifying indigenous bioresources showing potentialities for downstream mycoremediation applications. The culturable fractions of soil fungal communities of an Italian decommissioned military site were isolated from six representative sampling plots. In addition, the fungal community of the rhizosphere of Plantago lanceolata was also isolated. α and β diversity indices were used to analyze biodiversity data of the isolated fungal communities. A polycyclic aromatic hydrocarbons (PAHs) enrichment microplate experiment in the presence of Zn, Pb, and Zn-Pb co-contamination was conducted, followed by in vitro functional traits screenings, to select the isolates with the best potential for future mycoremediation applications. Globally 101 taxa, accounting for a total of 546 strains, were isolated from the samples. The enrichment results highlighted several fungal species showing the ability to use PAHs as nutritional source, even in the co-presence of potentially toxic elements. Finally, the analysis of their functional traits revealed their potential for biotechnological applications in soil detoxification. [ABSTRACT FROM AUTHOR]

Summary: The onset of stomatal closure reduces transpiration during drought. In seed plants, drought causes declines in plant water status which increases leaf endogenous abscisic acid (ABA) levels required for stomatal closure. There are multiple possible points of increased belowground resistance in the soil–plant atmospheric continuum that could decrease leaf water potential enough to trigger ABA production and the subsequent decreases in transpiration.We investigate the dynamic patterns of leaf ABA levels, plant hydraulic conductance and the point of failure in the soil–plant conductance in the highly embolism‐resistant species Callitris tuberculata using continuous dendrometer measurements of leaf water potential during drought.We show that decreases in transpiration and ABA biosynthesis begin before any permanent decreases in predawn water potential, collapse in soil–plant hydraulic pathway and xylem embolism spread.We find that a dynamic but recoverable increases in hydraulic resistance in the soil in close proximity to the roots is the most likely driver of declines in midday leaf water potential needed for ABA biosynthesis and the onset of decreases in transpiration. [ABSTRACT FROM AUTHOR]

Arsenic (As) contamination of soils threatens the health of millions globally through accumulation in crops. While plants detoxify As via phytochelatin (PC) complexation and efflux of arsenite from roots, arsenite efflux mechanisms are not fully understood. Here, white lupin (Lupinus albus) was grown in semi-hydroponics, and exudation of glutathione (GSH) derivatives and PCs in response to As was measured using LC-MS/MS. Inhibiting synthesis of the PC precursor GSH with l -buthionine sulfoximine (BSO) or ABC transporters with vanadate drastically reduced (>22%) GSH derivative and PC2 exudation, but not PC3 exudation. This was accompanied by As hypersensitivity in plants treated with BSO and moderate sensitivity with vanadate treatment. Investigating As–PC complexation revealed two distinct As–PC complexes, As bound to GSH and PC2 (GS–As–PC2) and As bound to PC3 (As–PC3), in exudates of As-treated lupin plants. Vanadate inhibited As–PC exudation, while BSO inhibited both the synthesis and exudation of As–PC complexes. These results demonstrate a role for GSH derivatives and PC exudation in lupin As tolerance and reveal As–PC exudation as a new potential mechanism contributing to active As efflux in plants. Overall, this study uncovers insights into rhizosphere As detoxification with potential to help mitigate pollution and reduce As accumulation in crops. [ABSTRACT FROM AUTHOR]

Background: Soil bacteria often form close associations with their host plants, particularly within the root compartment, playing a significant role in plant growth and stress resilience. Vachellia tortilis subsp. raddiana, (V. tortilis subsp. raddiana)a leguminous tree, naturally thrives in the harsh, arid climate of the Guelmim region in southern Morocco. This study aims to explore the diversity and potential plant growth-promoting (PGP) activities of bacteria associated with this tree. Results: A total of 152 bacterial isolates were obtained from the rhizosphere of V. tortilis subsp. raddiana. Rep-PCR fingerprinting revealed 25 distinct genomic groups, leading to the selection of 84 representative strains for further molecular identification via 16 S rRNA gene sequencing. Seventeen genera were identified, with Bacillus and Pseudomonas being predominant. Bacillus strains demonstrated significant tolerance to water stress (up to 30% PEG), while Pseudomonas strains showed high salinity tolerance (up to 14% NaCl). In vitro studies indicated variability in PGP activities among the strains, including mineral solubilization, biological nitrogen fixation, ACC deaminase activity, and production of auxin, siderophores, ammonia, lytic enzymes, and HCN. Three elite strains were selected for greenhouse inoculation trials with V. tortilis subsp. raddiana. Strain LMR725 notably enhanced various plant growth parameters compared to uninoculated control plants. Conclusions: The findings underscore the potential of Bacillus and Pseudomonas strains as biofertilizers, with strain LMR725 showing particular promise in enhancing the growth of V. tortilis subsp. raddiana. This strain emerges as a strong candidate for biofertilizer formulation aimed at improving plant growth and resilience in arid environments. [ABSTRACT FROM AUTHOR]

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

The gut microbiome of worms from composting facilities potentially harbors organisms that are beneficial to plant growth and development. In this experiment, we sought to examine the potential impacts of rhizosphere microbiomes derived from Eisenia fetida worm castings (i.e. vermicompost) on tomato (Solanum lycopersicum, L.) plant growth and physiology. Our experiment consisted of a greenhouse trial lasting 17 weeks total in which tomato plants were grown with one of three inoculant treatments: a microbial inoculant created from vermicompost (V), a microbial inoculant created from sterilized vermicompost (SV), and a no-compost control inoculant (C). We hypothesized that living microbiomes from the vermicompost inoculant treatment would enhance host plant growth and gene expression profiles compared to plants grown in sterile and control treatments. Our data showed that bacterial community composition was significantly altered in tomato rhizospheres, but fungal community composition was highly variable in each treatment. Plant phenotypes that were significantly enhanced in the vermicompost and sterile vermicompost treatments, compared to the control, included aboveground biomass and foliar δ15N nitrogen. RNA sequencing revealed distinct gene expression changes in the vermicompost treatment, including upregulation of nutrient transporter genes such as Solyc06g074995 (high affinity nitrate transporter), which exhibited a 250.2-fold increase in expression in the vermicompost treatment compared to both the sterile vermicompost and control treatments. The plant transcriptome data suggest that rhizosphere microbiomes derived from vermicompost can influence tomato gene expression and growth-related regulatory pathways, which highlights the value of RNA sequencing in uncovering molecular responses in plant microbiome studies. [ABSTRACT FROM AUTHOR]

The rhizosphere, the soil region influenced by plant roots, represents a dynamic microenvironment where intricate interactions between plants and microorganisms shape soil health, nutrient cycling, and plant growth. Soil microorganisms are integral players in the transformation of materials, the dynamics of energy flows, and the intricate cycles of biogeochemistry. Considerable research has been dedicated to investigating the abundance, diversity, and intricacies of interactions among different microbes, as well as the relationships between plants and microbes present in the rhizosphere. Metagenomics, a powerful suite of techniques, has emerged as a transformative tool for dissecting the genetic repertoire of complex microbial communities inhabiting the rhizosphere. The review systematically navigates through various metagenomic approaches, ranging from shotgun metagenomics, enabling unbiased analysis of entire microbial genomes, to targeted sequencing of the 16S rRNA gene for taxonomic profiling. Each approach's strengths and limitations are critically evaluated, providing researchers with a nuanced understanding of their applicability in different research contexts. A central focus of the review lies in the practical applications of rhizosphere metagenomics in various fields including agriculture. By decoding the genomic content of rhizospheric microbes, researchers gain insights into their functional roles in nutrient acquisition, disease suppression, and overall plant health. The review also addresses the broader implications of metagenomic studies in advancing our understanding of microbial diversity and community dynamics in the rhizosphere. It serves as a comprehensive guide for researchers, agronomists, and policymakers, offering a roadmap for harnessing metagenomic approaches to unlock the full potential of the rhizosphere microbiome in promoting sustainable agriculture. [ABSTRACT FROM AUTHOR]

Despite gaining significant attention in recent years, it remains unclear whether mycorrhizal fungi distribute meaningful amounts of resources among trees in ways that increase the fitness of the receiving trees. To investigate this, we used pairs of shaded and unshaded Pinus halepensis or Quercus calliprinos saplings, growing in both inter‐ and intra‐specific combinations outdoors in forest soil. We examined the combined effects of indirect and direct below‐ground connections on tree performance and Non‐Structural Carbohydrate (NSC) pools. Although we did not observe any growth benefits, shaded recipient oaks exhibited higher levels of root and branch NSC compared to their control counterparts, which were not connected below‐ground. This finding suggests a potential benefit of establishing below‐ground connections. However, no such benefits were observed among the unshaded pairs or in the other inter‐ and intra‐specific pairs of pines and oaks. We monitored the carbon (C) flow from a 13CO2‐labelled donor pine tree to a below‐ground connected oak tree and demonstrated C transfer from pines to shaded oaks. We also identified the main fungal symbionts interacting with pines and oaks. Our findings indicate that the effects of below‐ground C transfer are context‐dependent, manifesting in nuanced alterations in plant NSC that are not readily apparent through conventional growth metrics. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Gas exchange in the soil is determined by the size and connectivity of air‐filled pores. Root mucilage reduces air‐filled pore connectivity and thus gas diffusivity. It is unclear to what extent mucilage affects soil pore connectivity and tortuosity. The aim of this study was to gain a better understanding of gas diffusion processes in the rhizosphere by explaining the geometric alterations of the soil pore space induced by mucilage. We quantified the effect of a root mucilage analogue collected from chia seeds without intrinsic respiratory activity on oxygen diffusion at different water contents during drying–rewetting cycles in a diffusion chamber experiment. Quantification of oxygen diffusion showed that mucilage decreased the gas diffusion coefficient in dry soil without affecting air‐filled porosity. Without mucilage, a hysteresis in gas diffusion coefficient during a drying–rewetting cycle was observed. The effect depended on particle size and diminished with increasing mucilage content. X‐ray computed tomography imaging indicated a hysteresis in the connectivity of the gas phase during a drying–rewetting cycle for samples without mucilage. This effect was attenuated with increasing mucilage content. Furthermore, electron microscopy showed that mucilage structures formed in drying soil increase with mucilage content, thereby progressively reducing the connectivity of the gas phase. In conclusion, the effect of mucilage on soil gas diffusion highly depends on soil texture and mucilage content. The diminishing hysteresis with the addition of mucilage suggests that plant roots secrete mucilage to balance oxygen availability and water content, even under fluctuating moisture conditions. [ABSTRACT FROM AUTHOR]

Tree lines in high latitudes and high altitudes are considered sentinels of global change. This manifests in accelerated encroachment of trees and shrubs and enhanced plant productivity, with currently unknown implications for the carbon balance of these biomes. Given the large soil organic carbon stocks in many tree line soils, we here wondered whether introducing highly productive plants would accelerate carbon cycling through rhizosphere priming effects and if certain soils would be more vulnerable to carbon loss from positive priming than others.To test this, organic and mineral soils were sampled above and below tree lines in the Swedish sub‐arctic and the Peruvian Andes. A greenhouse experiment was then performed to quantify plant‐induced changes in soil mineralisation rates (rhizosphere priming effect) and new C formation using natural abundance labelling and the C4‐species Cynodon dactylon. Several environmental, plant, soil and microbial parameter were monitored during the experiment to complement the observations on soil C cycling.Priming was predominantly positive at the beginning of the experiment, then systematically decreased in all soils during the plant growth season to be mostly negative at the end of the experiment at plant senescence. Independent of direction of priming, the magnitude of priming was always greater in organic than in corresponding mineral soils, which was best explained by the higher C contents of these soils. Integrated over the entire study period, the overall impact of priming (positive and negative) on the soil C balance was mostly negligible. Though net soil C loss was observed in organic soils from the sub‐arctic tundra in Sweden.Most notably, positive and negative priming effects were not mutually exclusive, rather omnipresent across ecosystems, depending on sampling time. The direction of priming seems to be fluctuating with plant productivity, rhizosphere carbon inputs and nutrient uptake. This highlights the need for integrative long‐term studies if we aim to understand priming effects at ecosystem scale and greenhouse and laboratory studies must be validated in situ to enable reliable ecological upscaling. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Aims This study investigated the bacterial communities in the rhizosphere of two traditional Portuguese olive cultivars, Cobrançosa and Negrinha de Freixo, in relation to soil properties. Additionally, we aimed to isolate and identify bacteria with potential for biocontrol and other plant growth-promoting traits from these rhizosphere communities. Methods and results Bacterial communities in the olive rhizosphere were investigated using a metabarcoding approach and the soil physicochemical properties of the olive groves were also analyzed. Higher bacterial richness was associated with Negrinha de Freixo growing in soil with high organic matter content and water-holding capacity. In contrast, the soils of the Cobrançosa grove presented higher pH and electric conductivity. Negrinha de Freixo rhizosphere was enriched with ASVs (Amplicon Sequence Variants) belonging to Bacillus, Gaiella, Acidothermus, Bradyrhizobium , and uncultured Xanthobacteraceae. On the other hand, the Cobrançosa rhizosphere was characterized by higher relative abundance of Streptomyces and Sphingomonas. Bacterial isolation from the rhizosphere and screening for plant growth-promoting activities were also performed. Six bacteria strains, predominantly Bacillus isolated from Negrinha de Freixo, demonstrated antagonistic activities against the olive fungal pathogen Colletotrichum gloeosporoides and other plant growth promotion (PGP) traits. Conclusions Our findings demonstrate that the structure of rhizosphere bacterial communities associated with olive trees is shaped by both plant cultivar and soil-related factors. The higher number of bacterial species in the rhizosphere of Negrinha de Freixo was related to a higher organic matter content and a greater abundance of isolates with plant growth promotion traits, particularly Bacillus strains. [ABSTRACT FROM AUTHOR]

Vascular plants develop diverse root system architectures and exudates to facilitate acquisition of soil nutrients (nitrogen and phosphorus). Plant species have inherently specific properties of root system architectures and exudates, but some plants exhibit high plasticity to respond to spatiotemporal variations in soil nutrient forms and availability. This paper synthesizes evidence on how plant species diversity and root plasticity contribute to soil nutrient mobilization and uptake in plants from the tropics to the Arctic with varying plant species diversity. The development of finer roots in the surface soil is a well‐known strategy for the acquisition of limited nutrients (especially phosphorus), but the allocation of roots foraging "nutrient hotspots" in deeper soil (podzolic soil or permafrost‐affected soils) is an alternative strategy for coniferous trees tested in the Arctic and boreal forests. This contrasts with findings in tropical forests, where diverse plant species with different capacities of organic acid exudation coexist and species composition shifts in response to phosphorus deficiency. In particular, high malate exudation from roots and rhizosphere microbes stimulates phosphorus solubilization, aluminum detoxification, and lignin degradation in acidic soils. The diversity and plasticity of the root system architecture, root exudation, and the flexibility of nutrient sources mitigate nutrient limitation in soil. Root plasticity facilitating soil nutrient acquisition has a large impact on biogeochemistry and soil formation, such as podzolization, in the long term. [ABSTRACT FROM AUTHOR]

Indiscriminate use of mineral fertilizers has a broad negative impact on soil health. Because of the above, there is an urgent need to search for natural organic alternatives, including using soil microbial resources to replenish soil nutrients for enhanced Agri productivity vis a vis sustainably maintaining soil health. The nitrogen-fixing rhizobacteria (NFR) are such type of bacteria which fix gaseous atmospheric nitrogen in the soil and in nodules of certain plant species in considerable amounts that are readily available for plants' uptake and may be considered as a viable alternative source of mineral nitrogen application. The present study was conducted to isolate the most potent nitrogen-fixing bacteria from the litchi rhizosphere. Hence, Five NFR (NFR1 to NFR5) were isolated from the rhizosphere of litchi orchard of Bihar Agricultural University, Sabour, Bhgalpur, India, based on their ability to fix atmospheric nitrogen in a nitrogen-free mineral salt medium. NFR2 was found to be the most potent in fixing atmospheric nitrogen (11.31 mg N per gram carbon source)among all the isolated rhizobacterial strains. Hence, on the basis of biological nitrogen fixation ability, the isolate NFR2 was subjected to 16S ribosomal RNA (16S rRNA) gene sequencing for molecular characterization. Based on 16S rDNA sequence analysis, NFR2 showed the closest sequence homology with Beijerinckia fluminensis and was identified and reported as Beijerinckia fluminensis strain BAUMS11, Accession number MN533953. The study noticeably indicated that the B. fluminensis strain BAUMS11 was found most efficient in fixing gaseous atmospheric nitrogen and may be used for the manufacturing of nitrogenous biofertilizer, which can fix atmospheric nitrogen to the tune-up to 30 kg N ha-1yr-1. [ABSTRACT FROM AUTHOR]

In recent years, the increase due to the rise in the high yielding verities led to the high-rate application of chemicals and pesticides in the soil. These chemical fertilizers give great responses to the farmers on a short-term basis, but in the long term, they harm the soil and human health by interfering in the food chain. The use of biofertilizers is a very good alternative for crop production in a sustainable and environment-friendly manner. Numerous bacteria and fungi can be used as biofertilizers for making the essential nutrients available to the plants which are associated with the rhizosphere of different crops, either symbiotically or non-symbiotically. Zinc plays a vital role in crop growth and achieving a great yield among the various macro and micronutrients. Zinc is responsible for Auxin synthesis, chlorophyll formation, protein metabolism, carbohydrate fixation, disease and stress tolerance. Zn deficiency is a global issue that gradually lowers crop output and productivity. Using zinc solubilizing microorganisms is one of the most effective sustainable approaches to achieving higher yield and restoring soil productivity. These microorganisms solubilize the available zinc pool in the soil so plants can easily uptake zinc. Bacillus subtilis, Thiobacillus thioxidans, Rhizobium, Pantoea sp., Gluconacetobacter, Saccharomyces sp. and PGPR (Plant Growth Promoting Rhizobacteria) are involved in zinc solubilizing process and boost the soluble zinc in the soil. Using zinc solubilizers can reduce the fertilizer requirement of the crop to about 25-50% in combination with inorganic zinc fertilizers, so it reduces overall fertilizer cost. [ABSTRACT FROM AUTHOR]

The rhizosphere is the hotspot for microbial enzyme activities and contributes to carbon cycling. Precipitation is an important component of global climate change that can profoundly alter belowground microbial communities. However, the impact of precipitation on conifer rhizospheric microbial populations has not been investigated in detail. In the present study, using high-throughput amplicon sequencing, we investigated the impact of precipitation on the rhizospheric soil microbial communities in two Norway Spruce clonal seed orchards, Lipová Lhota (L-site) and Prenet (P-site). P-site has received nearly double the precipitation than L-site for the last three decades. P-site documented higher soil water content with a significantly higher abundance of Aluminium (Al), Iron (Fe), Phosphorous (P), and Sulphur (S) than L-site. Rhizospheric soil metabolite profiling revealed an increased abundance of acids, carbohydrates, fatty acids, and alcohols in P-site. There was variance in the relative abundance of distinct microbiomes between the sites. A higher abundance of Proteobacteria, Acidobacteriota, Ascomycota, and Mortiellomycota was observed in P-site receiving high precipitation, while Bacteroidota, Actinobacteria, Chloroflexi, Firmicutes, Gemmatimonadota, and Basidiomycota were prevalent in L-site. The higher clustering coefficient of the microbial network in P-site suggested that the microbial community structure is highly interconnected and tends to cluster closely. The current study unveils the impact of precipitation variations on the spruce rhizospheric microbial association and opens new avenues for understanding the impact of global change on conifer rizospheric microbial associations. [ABSTRACT FROM AUTHOR]

The "limón sutil" (Citrus aurantifolia) has been widely cultivated and well established for many years in Piura, northwestern Peru, because of its exceptional climate and soil conditions. However, decline and death of C. aurantifolia trees caused by different phytopathogens remain a common problem which has been observed in the last decades. It is known that the microbiota of soil plays an important role with their host and could be the starting point to understand the causes of citrus decline. In this study, we identified through culture-independent methods the bacterial and fungal microbiota associated to C. aurantifolia, C. jambhiri and C. volkameriana rhizospheres in the main areas of Piura. By using a 16S rRNA and ITS-metabarcoding analysis, we evaluated the taxonomic diversity between healthy trees and with decline symptoms and how this diversity could influence the health status of citrus trees. More than 600 and 200 bacterial and fungal ASVs were identified, respectively. Our metabarcoding analysis was able to identify Proteobacteria, Cyanobacteria, Firmicutes, Bacteroidota and Acidobacteriota prokaryotic phyla, while fungal phyla included Ascomycota, Basidiomycota and Glomeromycota. In addition, there were differences between microbial diversity indices in rhizospheres evaluated. Finally, bacterial and fungal genera were shared among the different citrus rhizospheres. These results have allowed us to obtain a preliminary identification of microbiota in the citrus rhizospheres of healthy trees and with decline symptoms. [ABSTRACT FROM AUTHOR]

Moso bamboo is excellent candidate for cadmium (Cd)/lead (Pb) phytoremediation, while rhizosphere microbiome has significant impact on phytoremediation efficiency of host plant. However, little is known about the rhizosphere bacterial communities of moso bamboo in Cd/Pb contaminated soils. Therefore, this study investigated the assembly patterns and key taxa of rhizosphere bacterial communities of moso bamboo in Cd/Pb polluted and unpolluted soils, by field sampling, chemical analysis, and 16S rRNA gene sequencing. The results indicated α-diversity between Cd/Pb polluted and unpolluted soils showed a similar pattern (p > 0.05), while β-diversity was significantly different (p < 0.05). The relative abundance analysis indicated α-proteobacteria (37%) and actinobacteria (31%) were dominant in Cd/Pb polluted soils, while γ-proteobacteria (40%) and α-proteobacteria (22%) were dominant in unpolluted soils. Co-occurrence network analysis indicated microbial networks were less complex and more negative in polluted soils than in unpolluted soils. Mantel analysis indicated soil available phosphorus, organic matter, and available Pb were the most important environmental factors affecting microbial community structure. Correlation analysis showed 11 bacterial genera were significantly positively related to Cd/Pb. Overall, this study identified the bacterial community composition of bamboo rhizosphere in responding to Cd/Pb contamination and provides a theoretical basis for microbe-assistant phytoremediation in the future. Novelty statement: To date, little is known about the bacterial communities in the rhizosphere of moso bamboo under Cd and Pb multiple stresses. This study investigated the assembly patterns and key taxa of rhizospheric bacterial communities of moso bamboo in Cd/Pb polluted and unpolluted soils. It was found that the bacterial community structure in bamboo rhizosphere is easily influenced by soil chemical environment, such as fertilities and heavy metals. The key bacterial taxa identified here could be target microbe in future microbe-assistant phytoremediation. [ABSTRACT FROM AUTHOR]

Soil microorganisms play important roles in vegetation establishment and soil biogeochemical cycling. Ammodendron bifolium is a dominant sand-fixing (i.e., stabilizing sand dunes) and endangered plant in the Takeermohuer Desert, and the bacterial community associated with this plant rhizosphere is still unclear. In this study, we investigated the composition and diversity of the bacterial community from the A. bifolium rhizosphere and bulk soil at different soil depths (i.e., 0–40 cm, 40–80 cm, 80–120 cm) using culture and high-throughput sequencing methods. We preliminarily analyzed the edaphic factors influencing the structure of bacterial communities. The results showed that the high-salinity Takeermohuer Desert has an oligotrophic environment, while the A. bifolium rhizosphere exhibited a relatively nutrient-rich environment due to higher contents of soil organic matter (SOM) and soil alkaline nitrogen (SAN) than bulk soil. The dominant bacterial groups in the desert were Actinobacteria (39.8%), Proteobacteria (17.4%), Acidobacteria (10.2%), Bacteroidetes (6.3%), Firmicutes (6.3%), Chloroflexi (5.6%), and Planctomycetes (5.0%) at the phylum level. However, the relative abundances of Proteobacteria (20.2%) and Planctomycetes (6.1%) were higher in the rhizosphere, and those of Firmicutes (9.8%) and Chloroflexi (6.9%) were relatively higher in barren bulk soil. A large number of Actinobacteria were detected in all soil samples, of which the most abundant genera were Streptomyces (5.4%) and Actinomadura (8.2%) in the bulk soil and rhizosphere, respectively. The Chao1 and PD_whole_tree indices in the rhizosphere soil were significantly higher than those in the bulk soil at the same soil depth and tended to decrease with increasing soil depth. Co-occurrence network analyses showed that the keystone species in the Takeermohuer Desert were the phyla Actinobacteria, Acidobacteria, Proteobacteria, and Chloroflexi. Furthermore, the major edaphic factors affecting the rhizosphere bacterial community were electrical conductivity (EC), SOM, soil total nitrogen (STN), SAN, and soil available potassium (SAK), while the major edaphic factors affecting the bacterial community in bulk soil were distance and ratio of carbon to nitrogen (C/N). We concluded that the A. bifolium rhizosphere bacterial community is different from that of the nonrhizosphere in composition, structure, diversity, and driving factors, which may improve our understanding of the relationship between plant and bacterial communities and lay a theoretical foundation for A. bifolium species conservation in desert ecosystems. [ABSTRACT FROM AUTHOR]

Despite that climate change is currently one of the most pervasive challenges, its effects on the plant-associated microbiome is still poorly studied. The aim of this study was to evaluate the impact of the independent and combinatory effect of climate warming and drought on the microbiome assembly of oak from seed to seedling. In a multifactorial experimental set up, acorns were subjected to different temperatures (15 °C, 20 °C, and 25 °C) and soil moisture levels (drought (15%) and control (60%)) from germination until the seedling stage, after which the bacterial and fungal communities associated to the rhizosphere and phyllosphere were characterized by amplicon sequencing and qPCR. The results showed a stronger effect of temperature on fungal than on bacterial diversity and the effect was more pronounced in the phyllosphere. Under drought condition, temperature had a significantly negative effect on phyllosphere fungal diversity. In the rhizosphere, temperature had a significant effect on the fungal community composition which was primarily caused by species turnover. Regardless of temperature, Actinobacteriota was significantly enriched in drought, a group of bacteria known to increase plant drought tolerance. This study provides new insights into the effect of climate change on the plant microbiome in natural ecosystems. [ABSTRACT FROM AUTHOR]

Polygonatum kingianum Collett & Hemsl., is one of the most important traditional Chinese medicines in China. The purpose of this study is to investigate the relationship between herb quality and microbial-soil variables, while also examining the composition and structure of the rhizosphere microbial community in Polygonatum kingianum, the ultimate goal is to provide a scientific approach to enhancing the quality of P. kingianum. Illumina NovaSeq technology unlocks comprehensive genetic variation and biological functionality through high-throughput sequencing. And in this study it was used to analyze the rhizosphere microbial communities in the soils of five P. kingianum planting areas. Conventional techniques were used to measure the organic elements, pH, and organic matter content. The active ingredient content of P. kingianum was identified by High Performance Liquid Chromatography (HPLC) and Colorimetry. A total of 12,715 bacterial and 5487 fungal Operational Taxonomic Units (OTU) were obtained and taxonomically categorized into 81 and 7 different phyla. Proteobacteria, Bacteroidetes, and Acidobacteriae were the dominant bacterial phyla Ascomycota and Basidiomycota were the dominat fungal phyla. The key predictors for bacterial community structure included hydrolysable nitrogen and available potassium, while for altering fungal community structure, soil organic carbon content (OCC), total nitrogen content (TNC), and total potassium content (TPOC) were the main influencing factors. Bryobacter and Candidatus Solibacter may indirectly increase the polysaccharide content of P. kingianum, and can be developed as potential Plant Growth Promoting Rhizobacteria (PGPR). This study has confirmed the differences in the soil and microorganisms of different origins of P. kingianum, and their close association with its active ingredients. And it also broadens the idea of studying the link between plants and microorganisms. [ABSTRACT FROM AUTHOR]

Abstract\nNOVELTY STATEMENTPersistent crude oil contamination poses a significant environmental challenge. In this study, the efficacy of Vigna unguiculata (L.) and associated rhizospheric microorganisms in remediating crude oil-contaminated soil within a microcosm setting was investigated. A randomized block design was employed, and soil samples were subjected to varying degrees of contamination: 0% (UR), 2.5% (CR2), 5.0% (CR5), 7.5% (CR7), and 10.0% (CR10) w/w crude oil. The investigation aimed to assess the potential of Vigna unguiculata (L.) in mitigating crude oil contamination across these defined contamination gradients. The plant growth and crude oil removal were monitored concurrently post-emergence. Plant emergence and growth were significantly affected due to contamination, especially among plants in CR5 and CR10. The bacterial population was higher in the rhizosphere, and the treatments with lower hydrocarbon contamination. It was shown that plant density encouraged the growth of bacterial communities. Significant reduction in soil TPH was observed in CR2 (76.61%) and CR7 (65.88%). There was a strong correlation between plant growth and oil-utilizing bacterial population (r2 = 0.966) and plant growth and hydrocarbon reduction (r2 = 0.956), signifying the role of plant-bacterial synergy. Saturate fractions (C30 – C32) were significantly degraded to lower molecular weight compounds (C11 – C14). Except in CR5 and CR10, the remediation within the cowpea rhizosphere was effective even at regulatory standards. Understanding the rhizosphere ecological dynamics would further highlight the role the bacteria played; hence, it is recommended.The present study established a direct link between bacterial-plant interaction and biodegradation of crude oil. It extensively explored the nature of the degradation and also the fate of the residual oil. The present study achieved high rate of TPH removal within 12 weeks using cowpea alone as against the several previous reports that used other stimulants. [ABSTRACT FROM AUTHOR]

Zinc (Zn) is an essential micronutrient that is found in almost all classes of enzymes. Its deficiency is a well-documented problem among cereal crops that causes decreased crop yields and nutritional quality. Therefore, an experiment was implemented in a randomized block design which included the treatments of bacterial inoculation consisting of T1 (Control), T2 (100% RDF;100:40:20), T3(100% RDF + 25 kg ZnSO4.7 H2O), T4(100%RDF+ ZnSB1– Bacillus sp. strain BAU_A2 @750 ml ha−1), T5 (100%RDF+ ZnSB2– Priestia megaterium strain BAU_A3 @750 ml ha−1), T6 (100%RDF+ ZnSB3-Bacillus subtilis strain BAU_A5@750 ml ha−1). The mineral NPK was applied as per treatments. The results indicated the maximum values of water soluble exchangeable Zn and organically bounded Zn in treatments consisting ZnSB1, ZnSB2 and ZnSB3, respectively. The WS+EXCH-Zn was significantly increased by 68.57%, 28.26%, 18%, 98.14%, 41.30%, 30.00% and 128.12%, 55.55%, 37.25%, 43%, 62.22% and 43.13% in first year (2018–19) and second year (2019–2020) under the soil treated with ZnSB1-Peribacillus simplex strain BAU_A1, ZnSB2-Bacillus sp. strain BAU__A2 and ZnSB3-Bacillus subtilis strain BAU_A5 along with 100%RDF over control, application of recommended dose of fertilizer with and without application of 25 kg ZnSO4 ha−1, respectively. However, the maximum decrement in Mn-oxide-bounded zinc (1.12 mg kg−1 soil) was observed with T6 which was significantly higher by 158%, 194.4%, 185.71% over control, 100% RDF with and without application of 25 kg ZnSO4 ha−1, which showed the solubilization of zinc with the activity of ZnSB in soil. The study may be beneficial to mitigate the zinc deficiency in soil and malnutrition in children. [ABSTRACT FROM AUTHOR]

Manipulating the rhizosphere microbiome to enhance plant stress tolerance is an environmentally friendly technology and a renewable resource to restore degraded environments. Here we suggest a sustainable bioremediation strategy on the example of Stebnyk mine tailings storage. We consider Salicornia europaea rhizosphere community, and the ability of the phytoremediation plant Salix viminalis to recruit its beneficial microbiome to mediate the pollution stress at the Stebnyk mine tailings storage. The tailings contain large amounts of brine salts and heavy metals that contaminate the ground water and surrounding areas, changing soil biogeochemistry and causing increased erosion. The species richness of the endophytic bacterial community of S. viminalis roots was assessed based on observed OTUs, Shannon-InvSimpson, and evenness index. Our results obtained using the plant-based enrichment strategy show that biodiversity was decreased across the contamination zones and that S. europaea supplementation significantly increased the species richness. Our results also indicate that the number of dominating bacteria was not changed across zones in both S. europaea-treated and untreated bacterial populations, and that the decrease in richness was mainly caused by the low abundant bacterial OTUs. The importance of selecting the bioremediation strains that are likely to harbor a reservoir of genetic traits that aid in bioremediation function from the target environment is discussed [ABSTRACT FROM AUTHOR]

Microbial interactions in the rhizosphere contribute to soil health, making understanding these interactions crucial for sustainable agriculture and ecosystem management. Yet it is difficult to understand what we cannot see; among the limitations in rhizosphere imaging are challenges associated with rapidly and noninvasively imaging microbial cells over field depths relevant to plant roots. Here, we present a bimodal imaging technique called complex-field and fluorescence microscopy using the aperture scanning technique (CFAST) that addresses these limitations. CFAST integrates quantitative phase imaging using synthetic aperture imaging based on Kramers-Kronig relations, along with three-dimensional (3D) fluorescence imaging using an engineered point spread function. We showcase CFAST's practicality and versatility in two ways. First, by harnessing its depth of field of more than 100 µm, we significantly reduce the number of captures required for 3D imaging of plant roots and bacteria in the rhizoplane. This minimizes potential photobleaching and phototoxicity issues. Second, by leveraging CFAST's phase sensitivity and fluorescence specificity, we track microbial growth, competition, and gene expression at early stages of colony biofilm development. Specifically, we resolve bacterial growth dynamics of mixed populations without the need for genetically labeling environmental isolates. Moreover, we find that gene expression related to phosphorus sensing and antibiotic production varies spatiotemporally within microbial populations that are surface attached and appears distinct from their expression in planktonic cultures. Together, CFAST's attributes overcome commercial imaging platform limitations and enable insights to be gained into microbial behavioral dynamics in experimental systems of relevance to the rhizosphere. [ABSTRACT FROM AUTHOR]

Plants release a wealth of metabolites into the rhizosphere that can shape the composition and activity of microbial communities in response to environmental stress. The connection between rhizodeposition and rhizosphere microbiome succession has been suggested, particularly under environmental stress conditions, yet definitive evidence is scarce. In this study, we investigated the relationship between rhizosphere chemistry, microbiome dynamics, and abiotic stress in the bioenergy crop switchgrass grown in a marginal soil under nutrient-limited, moisture-limited, and nitrogen (N)-replete, phosphorus (P)-replete, and NP-replete conditions. We combined 16S rRNA amplicon sequencing and LC-MS/MS-based metabolomics to link rhizosphere microbial communities and metabolites. We identified significant changes in rhizosphere metabolite profiles in response to abiotic stress and linked them to changes in microbial communities using network analysis. N-limitation amplified the abundance of aromatic acids, pentoses, and their derivatives in the rhizosphere, and their enhanced availability was linked to the abundance of bacterial lineages from Acidobacteria, Verrucomicrobia, Planctomycetes, and Alphaproteobacteria. Conversely, N-amended conditions increased the availability of N-rich rhizosphere compounds, which coincided with proliferation of Actinobacteria. Treatments with contrasting N availability differed greatly in the abundance of potential keystone metabolites; serotonin and ectoine were particularly abundant in N-replete soils, while chlorogenic, cinnamic, and glucuronic acids were enriched in N-limited soils. Serotonin, the keystone metabolite we identified with the largest number of links to microbial taxa, significantly affected root architecture and growth of rhizosphere microorganisms, highlighting its potential to shape microbial community and mediate rhizosphere plant-microbe interactions. [ABSTRACT FROM AUTHOR]

The colonization of alien plants in new habitats is typically facilitated by microorganisms present in the soil environment. However, the diversity and structure of the archaeal, bacterial, and fungal communities in the latitudinal spread of alien plants remain unclear. In this study, the rhizosphere and bulk soil of Chromolaena odorata were collected from five latitudes in Pu' er city, Yunnan Province, followed by amplicon sequencing of the soil archaeal, bacterial, and fungal communities. Alpha and beta diversity results revealed that the richness indices and the structures of the archaeal, bacterial, and fungal communities significantly differed along the latitudinal gradient. Additionally, significant differences were observed in the bacterial Shannon index, as well as in the structures of the bacterial and fungal communities between the rhizosphere and bulk soils. Due to the small spatial scale, trends of latitudinal variation in the archaeal, bacterial, and fungal communities were not pronounced. Total potassium, total phosphorus, available nitrogen, available potassium and total nitrogen were the important driving factors affecting the soil microbial community structure. Compared with those in bulk soil, co-occurrence networks in rhizosphere microbial networks presented lower complexity but greater modularity and positive connections. Among the main functional fungi, arbuscular mycorrhizae and soil saprotrophs were more abundant in the bulk soil. The significant differences in the soil microbes between rhizosphere and bulk soils further underscore the impact of C. odorata invasion on soil environments. The significant differences in the soil microbiota along latitudinal gradients, along with specific driving factors, demonstrate distinct nutrient preferences among archaea, bacteria, and fungi and indicate complex microbial responses to soil nutrient elements following the invasion of C. odorata. [ABSTRACT FROM AUTHOR]

Canada thistle is a pervasive perennial weed, causing challenges to agricultural and natural ecosystems globally. Although research has focused on the phenology, genetics, and control of Canada thistle, little is known about the rhizosphere microbiome and the role plant–microbe interactions play in invasion success. This study investigated the rhizosphere microbiome of Canada thistle across diverse climates, soils, and crops in the U.S. northern Great Plains. Soil and rhizosphere samples were collected and bacterial 16S and fungal ITS2 sequencing were performed to characterize the core microbiome and identify potential factors contributing to invasion success. Amplicon sequencing revealed a stable core microbiome that was detected in the Canada thistle rhizosphere across all locations. The core microbiome was dominated by the bacterial phyla Actinobacteriota and Proteobacteria and fungal phyla Ascomycota and Basidiomycota. Differential abundance analysis showed rhizosphere fungal communities were enriched in pathogen-containing genera with a 1.7-fold greater abundance of Fusaria and a 2.6-fold greater abundance of Gibberella compared to bulk soil. Predictive functional profiling showed rhizosphere communities were enriched (p < 0.05, FDR corrected) in plant pathogen fungal guilds which represented 19% of the fungal community. The rhizosphere microbiome was similar in composition across environments, highlighting the stable association between Canada thistle and specific microbial taxa. This study characterized the core microbiome of Canada thistle, and the findings highlight plant–microbe interactions shaping invasive behavior. These findings are important for understanding the ecological impacts of plant invasion and soil-microbe ecological processes. [ABSTRACT FROM AUTHOR]

The taxonomic composition of soil (Technosol and Retisol) bacterial communities near the salt dump of a potassium enterprise (Solikamsk, Perm krai) was analyzed by the method of high-throughput sequencing of the 16S rRNA gene. Soil samples without plants and of the rhizosphere of plants of the species Calamagrostis epigeios (L.) Roth from plots located 1–1.5, 8, and 780 m and 11 km from the salt dump were studied. It was found that bacteria of the phyla Pseudomonadota, Bacteroidota, Actinomycetota, Acidobacteriota, Verrucomicrobiota, and Gemmatimonadota predominated in all soil samples. The impact of halite waste on the taxonomic composition of bacterial communities in soils was the greatest on plots in the salinization zone in the immediate vicinity of the salt dump (1–1.5 m). In soil samples without plants taken in these areas, bacteria of the order "Candidatus Actinomarinales" predominated, the proportion of representatives of the phyla Acidobacteriota and Verrucomicrobiota, the class Actinobacteria, and the family Chitinophagaceae decreased, and the proportion of bacteria of the family Xanthomonadaceae in bacterial communities increased in comparison with nonsaline soils (at a distance of 8 and 780 m and 11 km from the salt dump). In the rhizosphere bacterial communities of plants, growing in the salinization zone, the proportion of representatives of the phylum Acidobacteriota and of the families Chitinophagaceae and Enterobacteriaceae decreased, while the proportion of the families Xanthomonadaceae and Flavobacteriaceae became greater. The influence of the salt dump on soil bacterial communities from plots located 8 m and 730 m from the salt dump was revealed: it was manifested in the presence of representatives of the order "Candidatus Actinomarinales" (1.4–1.6%), of the families Nitrosomonadaceae (3.0–6.1%) and Saprospiraceae (1.0–1.9%), of the genus Ilumatobacter (1.6–2.8%), and of nonculturable bacteria of the family Rhodanobacteraceae (1.3–1.5%). [ABSTRACT FROM AUTHOR]

Previously it was shown that endophytic bacteria had the ability to move out of the roots of pea plant seedlings (Pisum sativum L.) into the rhizosphere. In this study, six distinct bacterial strains were isolated from the root growth medium during the cultivation of seedlings in an aqueous medium. By analyzing the nucleotide sequence of 16S rRNA genes, the taxonomic position of these strains was established. Their morphological and cultural parameters were assessed, and the activity of hydrolytic enzymes (pectinase, cellulase, protease) and the IAA-producing capability were examined. It has been observed that the quantity of endophytic bacteria that appears on the root surface during the growth of pea seedlings significantly surpasses the quantity present in the root tissues. It is assumed that hydrolytic enzymes such as pectinase and cellulase are involved in the release of bacteria into the external environment, causing the destruction of carbohydrate structures in plant cell walls. The metabolic parameters established in the studied strains, and the significance of these endophytic bacteria for the host plant after their exit from the roots into the rhizosphere are under discussion. [ABSTRACT FROM AUTHOR]

Background and aims: The differences in multi-elemental concentrations among plant species provide insightful information for understanding species coexistence in forest ecosystems, known as the biogeochemical niche separation. As most of the studies focused on leaf elemental concentrations, it is unclear whether belowground fine roots exhibit biogeochemical niche separation and whether there are close linkages of elemental concentrations among leaves, fine roots and rhizosphere soils. Methods: Nine element (N, P, K, Ca, Mg, Mn, Zn, Cu, and Fe) concentrations in leaves, fine roots and rhizosphere soils were measured for three tree species, three woody shrub species, and three herbaceous species in three subtropical plantations. Results: Elemental concentrations in leaves and fine roots were significantly different between woody and herbaceous species. Notably, the elemental concentrations differed more significantly for leaves than for fine roots, which indicated that leaves, as the most metabolically active tissues, tended to maintain their unique elemental concentrations within a particular functional type. Despite the different elemental needs between leaves and fine roots, most elemental concentrations of leaves were closely associated with those of the fine roots, highlighting the relationship between leaf and root ecological processes. Elemental concentrations in leaves or fine roots were not significantly correlated with those of the rhizospheres. Conclusions: There is evidence for biogeochemical niche separation between coexisting woody and herbaceous species to avoid competition. Our results generalized the biogeochemical niche hypothesis to belowground tissues, which offered new insights into a better understanding of species evolution and coexistence in ecosystems. [ABSTRACT FROM AUTHOR]

Drought is one of the major yield‐limiting factors under climatic adversaries. The positive role of silicon (Si) in drought tolerance of plants has unfolded a new avenue for enhancing crop productivity through better Si use efficiency. It is hence interesting to understand the mechanistic insights pertaining to its beneficial roles under drought stress conditions. Higher plants sense drought stress via roots which, regulate aboveground plant growth under stress. Cellular and molecular modulations occurring at the root and soil interphases influence the survival and growth of plants under drought stress; therefore, it is intriguing to know how Si influences the soil–root interphase and how this interaction augments overall plant growth under drought. In this review, we summarised the roles of Si in the root systems, rhizosphere and their interactions that could improve plant's growth and development under drought conditions. We have discussed the direct and indirect effects of Si‐induced belowground changes on plant roots, soil physical, chemical and biological properties, and their mutual interactions in eliciting defence signalling, including hormone signalling pathways. A mechanistic model of Si‐induced beneficial effects in water‐limited environments is suggested, which could help improve the management of rainfed croplands through Si fertilisation. [ABSTRACT FROM AUTHOR]

Rhizosphere microbial communities play a substantial role in plant productivity. We studied the rhizosphere bacteria and fungi of 51 distinct potato cultivars grown under similar greenhouse conditions using a metabarcoding approach. As expected, individual cultivars were the most important determining factor of the rhizosphere microbial composition; however, differences were also obtained when grouping cultivars according to their growth characteristics. We showed that plant growth characteristics were related to deterministic and stochastic assembly processes of bacterial and fungal communities, respectively. The bacterial genera Arthrobacter and Massilia (known to produce indole acetic acid and siderophores) exhibited greater relative abundance in high- and medium-performing cultivars. Bacterial co-occurrence networks were larger in the rhizosphere of these cultivars and were characterized by a distinctive combination of plant beneficial Proteobacteria and Actinobacteria along with a module of diazotrophs namely Azospira, Azoarcus , and Azohydromonas. Conversely, the network within low-performing cultivars revealed the lowest nodes, hub taxa, edges density, robustness, and the highest average path length resulting in reduced microbial associations, which may potentially limit their effectiveness in promoting plant growth. Our findings established a clear pattern between plant productivity and the rhizosphere microbiome composition and structure for the investigated potato cultivars, offering insights for future management practices. [ABSTRACT FROM AUTHOR]

Here we review the 400-year history of hydroponic culture and describe a unique management approach that does not require leaching or discarding solution between harvests. Nutrients are maintained at a low and steady concentration by daily additions of a dilute solution that replaces the transpired water along with the nutrients that were removed in growth each day. A stable pH and a low steady-state concentration of ammonium are maintained through automated additions of a solution of nitric acid and ammonium nitrate. Ample solution volume (at least 20 cm deep) stabilizes nutrient concentrations, reduces root density, and improves uniformity. Gentle aeration at ≈100 mL·min-1·L-1 maintains dissolved oxygen near saturation and increases uniformity throughout the rhizosphere. These practices facilitate a uniform, closed, root zone with rigorous pH control that provides the micromolar nutrient concentrations of N and P that are representative of field soils. [ABSTRACT FROM AUTHOR]

The intensive applications of nanomaterials in the agroecosystem led to the creation of several environmental problems. More efforts are needed to discover new insights in the nanomaterial–microbe–plant nexus. This relationship has several dimensions, which may include the transport of nanomaterials to different plant organs, the nanotoxicity to soil microbes and plants, and different possible regulations. This review focuses on the challenges and prospects of the nanomaterial–microbe–plant nexus under agroecosystem conditions. The previous nano-forms were selected in this study because of the rare, published articles on such nanomaterials. Under the study's nexus, more insights on the carbon nanodot–microbe–plant nexus were discussed along with the role of the new frontier in nano-tellurium–microbe nexus. Transport of nanomaterials to different plant organs under possible applications, and translocation of these nanoparticles besides their expected nanotoxicity to soil microbes will be also reported in the current study. Nanotoxicity to soil microbes and plants was investigated by taking account of morpho-physiological, molecular, and biochemical concerns. This study highlights the regulations of nanotoxicity with a focus on risk and challenges at the ecological level and their risks to human health, along with the scientific and organizational levels. This study opens many windows in such studies nexus which are needed in the near future. [ABSTRACT FROM AUTHOR]

It is unclear how elevated CO2 (eCO2) and warming interactively influence soil N mineralization in the rhizosphere of rice (Oryza sativa L.), given that the N mineralization process in anaerobic paddy soils differs from that of aerobic upland soils. In this study, we conducted a rhizobox experiment in open top chambers and used 15N-13C dual-labeling to examine the impacts of eCO2 (700 ppm) and warming (2 °C above the ambient) on N mineralization and associated microbial processes in the rhizosphere of rice plants under anaerobic conditions. Compared to the control, the combination of eCO2 and warming increased rice N uptake by 50% in a no-added-N treatment and 32% under an N-added treatment, with the additional uptake mainly consisting of soil-derived N. Co-elevation of CO2 and temperature increased microbial biomass C and N and increased N mineralization by 41% and 23% in the no-added-N and N-added treatments, respectively. The absolute abundances of the N-mineralization genes chiA, pepA, pepN, and urea hydrolysis gene ureC in the rhizosphere increased by 22–30% under eCO2 and warming, corresponding to the additional N mineralization and photosynthetic C allocation into the soil. However, eCO2 plus warming did not increase the metabolic efficiency of N mineralization (mineralized N per unit microbial N). Our results suggest that the co-elevation of CO2 and temperature stimulated microbially mediated soil N mineralization in the rhizosphere of rice, posing a risk on the acceleration of soil organic matter decomposition. [ABSTRACT FROM AUTHOR]

Background: Peanut (Arachis hypogaea L.) is regarded as a crop with high nutrient use efficiency, but there may be differences between cultivars. Furthermore, there is little information on the strategy of peanut cultivars to adapt to soil P availability and to what extent they explore non‐labile P pools. Aims: Our objective was to evaluate growth, root morphology, enzymatic activity in the rhizosphere, and P uptake of peanut cultivars grown under different soil P status. Methods: The study was conducted in a greenhouse in 6‐L pots. Soils with low P (without fertilization) and high P content (with fertilization) and seven peanut cultivars of different origins, different maturation groups, and release years were investigated. Peanut shoot yield, phosphorus uptake, root growth, soil P fractions as well as phosphatase activity in the rhizosphere soil were determined. Results: In P‐deficient soil, a higher dry matter yield was associated with longer root hairs and root length, which resulted in decreased soil non‐labile P was observed mainly with cultivars developed in Argentina (ARG‐medium‐old and ARG‐medium‐new) and the late maturity Brazilian cultivar (BR I‐late new). These cultivars adapted well to P deficiency and were less dependent on labile P. New Brazilian early and medium maturity cultivars developed less, shorter root hairs, and showed low acid phosphatase activity in the rhizosphere under P deficiency, resulting in lower P uptake and dry matter yield. Under high P availability, new Brazilian cultivars of medium and late maturity showed the highest dry matter yield (9.0 and 9.8 g plant−1, respectively) and longest roots, around 120 m plant−1. High P availability decreased root hairs in all cultivars. Conclusion: Overall, the adaptation of peanut cultivars to P‐deficient soils was lower for the new mid‐ and early‐maturing Brazilian cultivars compared with the Argentinian and old or late‐maturing Brazilian cultivars. The main strategies of P‐efficient cultivars under low P availability are to increase root length, root hair length, and root hair density. [ABSTRACT FROM AUTHOR]