Soil-plant Continuum Research Articles

Geogenic perspectives on potassium dynamics and plant uptake: insights from natural and submerged conditions across different soil types with machine learning predictions

Four different soil types including red, alluvial, calcareous, and black soils along with rice cultivated on them were collected from various parts of India and analyzed for potassium dynamics in the soil plant continuum. Soil potassium (K) dynamics were studied under submerged and non-submerged conditions, and potassium content was analyzed in rice roots, shoots, and grains, along with other soil properties. Red (S1: 5.9) and alluvial (S5: 5.16) soils were moderately acidic, while black (S8: 8.01) and calcareous (S7: 8.1) soils were alkaline. Black soil (S8) had the highest cation exchange capacity (CEC: 31.25 cmol (p+)/kg) and clay content (41.2%), while alluvial soil had the most organic carbon (S5: 1.74%). Submerged conditions enhanced potassium availability, with red soil showing the highest levels of water-soluble K (WsK), exchangeable K (ExK), and non-exchangeable K (NEK), particularly Step-K and constant rate K (CR-K) forms. Rice potassium content was highest in grains, followed by shoots and roots, with red soil containing the most available potassium. A strong correlation was found between soil potassium forms and rice plant potassium uptake. Sensitivity analysis indicated that WsK and ExK from non-submerged soil to be the most favorable forms for potassium uptake, especially in the rice roots and grains. Machine learning models, particularly Random Forest, accurately predicted potassium availability and uptake, highlighting their potential in optimizing soil fertility and advancing precision agriculture for better crop yields and soil health.

A Comparative Study on Chemical Speciation of Trace Metals as a Function of Solution pH: A Multivariate Analysis and Simulation Approach

ABSTRACT Biogeochemical activity of trace elements in the environment significantly relies on their chemical speciation. Solution pH influences the chemical speciation and biogeochemical activity of trace elements in the soil-plant continuum. The current study was conducted to simulate the influence of solution pH on chemical fractions of 11 trace elements (arsenic, lead, zinc, copper, chromium, cadmium, mercury, nickel, strontium, antimony, and selenium) using Visual Minteq, a chemical equilibrium model used for the calculation of metal speciation, sorption etc. Results delineated that pH-mediated variations in the chemical speciation of trace elements differed with their type. The results of the current study revealed a dominance of chemical trace element species at acidic (1–6), neutral (7.0), and alkaline (8–14) pH. Divalent trace elements (zinc, cadmium, copper, chromium, nickel, and lead) were the dominant species at acidic pH. However, mercury dominance has a narrow pH range (1–3), while strontium dominance has a wider pH range (1–13). Nitrate, sulfate, and phosphate fractions of trace elements also occurred at pH <8. However, at pH >8, trace elements existed in hydroxide (OH) fractions. In the case of arsenic (arsenite As3+ and arsenate As5+), selenium (selenite Se4+ and selenate Se6+), and antimony (antimonite Sb3+ and antimonate Sb5+), their dominant species get oxidized with increasing pH. Multivariate analysis was conducted for various metals for their dominance as a function of pH. Moreover, Principal Component Analysis verified a linear relation of trace element fractions with pH. Results revealed that solution pH affects the chemical fractions and the phytoavailable fraction of trace elements in growth culture and associated health hazards through soil-plant transfer.

Unlocking Biochar's Potential: Innovative Strategies for Sustainable Remediation of Heavy Metal Stress in Tobacco Plants.

Tobacco, being a globally cultivated crop, holds significant social and economic importance. Tobacco plants are susceptible to the adverse effects of heavy metals (HMs), particularly cadmium (Cd), which hinders root development, disrupts water balance, and impedes nutrient absorption. Higher concentrations of HMs, especially Cd, naturally accumulate in tobacco leaves due to complex interactions within the plant-soil continuum. The uptake of Cd by plants from the soil is influenced by several factors, including soil type, pH, irrigation water quality, and the chemical composition of the metal involved. Different techniques, such as bioremediation, phytoremediation, and mycoremediation, have been employed to tackle the issue of HMs. The use of biochar offers a practical solution to mitigate this problem. With its large surface area and porous nature, biochar can effectively alleviate HMs contamination. Under biochar application, metal adsorption primarily occurs through physical adsorption, where metal ions are trapped within the pores of the biochar. Additionally, electrostatic attraction, in which negatively charged biochar surfaces attract positively charged metal ions, is another major mechanism of metal remediation facilitated by biochar. In this review, we documented, compiled, and interpreted novel and recent information on HMs stress on tobacco plants and explored biochar's role in alleviating HMs toxicity. By providing a comprehensive review of the persistent threat posed by Cd to tobacco crops and exploring biochar's potential as a remediation measure, this work aims to enhance our understanding of HMs stress in tobacco and contribute to the development of sustainable agricultural practices.

Distinct spatiotemporal patterns between fungal alpha and beta diversity of soil-plant continuum in rubber tree.

Plants harbor diverse microorganisms in both belowground and aboveground compartments, which play a vital role in plant nitrogen supply and growth promotion. Understanding the spatiotemporal patterns of microbial communities is a prerequisite for harnessing them to promote plant growth. In this study, we show that the alpha and beta diversity of soil-plant continuum in rubber tree exhibited distinct spatiotemporal pattern. Alpha diversity is highly dependent on seasonal changes, while beta diversity only showed a geographical variation pattern. Climatic factors were the most important factors in shaping fungal alpha diversity. Leaf phosphorus (P) and soil available potassium (AK) were major drivers to induce geographical variation.

Spatial variability of hydraulic parameters of a cropped soil using horizontal crosshole ground penetrating radar

AbstractSoil hydraulic parameters (SHP) play a crucial role controlling the spatiotemporal distribution of water in the soil–plant continuum and thus affect water availability for crops. To provide reliable information on the SHP at different scales, measurement techniques with a good spatial resolution and low labor costs are required. In this study, we used crosshole ground penetrating radar (GPR)‐derived soil water contents (SWCs) measured along horizontal rhizotubes under a controlled experimental test site cropped with winter wheat to estimate the unimodal and dual‐porosity soil hydraulic characteristics with different soil layer setups. Therefore, sequential inversion of the GPR‐derived SWCs was performed using the hydrological model HYDRUS‐1D, whereby the SWC data were either averaged prior inversion or used in a spatially distributed way. To analyze if the time‐lapse gathered GPR data contain enough information to estimate the SHP, additional synthetic studies were performed increasing the data resolution to daily GPR measurements. The results showed that the time‐lapse data contained enough information to estimate the SHP accurately. Additionally, spatially distributed soil hydraulic characteristics differed from the one estimated based on averaged SWCs derived from spatially distributed GPR data. Finally, we derived spatially resolved SHP, which can be used for 3D process rhizosphere processes and root–soil interaction modeling.

Processes of assembly of endophytic prokaryotic and rhizosphere fungal communities in table grape are preponderantly deterministic

Understanding the assemblage of microbial communities is important for the health maintenance and post-harvest quality of fruit crops. However, systematic studies on the core microbiomes of table grapes and microbial community assembly of soil-plant continuum are still rare. To address this, samples were collected and analyzed from key microbiome compartments (bulk soil, rhizosphere of new roots and old roots, endosphere of new and old roots, and endosphere of leaves and fruits) of five table grape cultivars (Balado Black, Jingya, Fujimino, Victoria and Kyoho) at the swelling stage and harvest stage in the field plots. Prokaryotic and fungal communities were analyzed using 16S rRNA and ITS rRNA high-throughput sequencing, respectively. The compartment was the major factor attributable to the variations in both prokaryotic (52.5 %) and fungal communities (23.2 %), respectively. The richness and phylogenetic diversity of both prokaryotic and fungal communities decreased significantly along the compartment continuum from soil to fruit endosphere, but did not differ between the five cultivars across all samples. Occupancy-abundance distribution was used to define 97 core bacteria, 29 core fungi for rhizosphere soil and five core bacteria, 172 core fungi for endosphere. Functional annotations of the rhizosphere core bacteria were mostly associated with ureolysis and chemoheterotrophy, while endophytic core bacteria were mostly fermentative and symbiotic. Rhizosphere core fungi were saprophytic and the endophytic fungi were putatively pathogens. From rhizosphere soil to aboveground organs, the relative importance of deterministic processes for prokaryotic community assembly gradually increased but the contribution of stochastic processes increased for fungal community assembly. These findings highlight niche-specific microbial communities and shared core microbiomes in different grapevine cultivars. The deterministic processes contribute more to the assembly of prokaryotic communities in the aboveground than in the belowground while the assembly of fungal communities exhibits opposite trends. Management practices aiming at niche-specific microbiome should be developed for sustainable grape production.

The short-term effect of microplastics in lettuce involves size- and dose-dependent coordinate shaping of root metabolome, exudation profile and rhizomicrobiome

Micro- and nano-plastics (MNPs) in the soil can impact the microbial diversity within rhizospheres and induce modifications in plants' morphological, physiological, and biochemical parameters. However, a significant knowledge gap still needs to be addressed regarding the specific effects of varying particle sizes and concentrations on the comprehensive interplay among soil dynamics, root exudation, and the overall plant system. In this sense, different omics techniques were employed to clarify the mechanisms of the action exerted by four different particle sizes of polyethylene plastics considering four different concentrations on the soil-roots exudates-plant system was studied using lettuce (Lactuca sativa L. var. capitata) as a model plant. The impact of MNPs was investigated using a multi-omics integrated approach, focusing on the tripartite interaction between the root metabolic process, exudation pattern, and rhizosphere microbial modulation.Our results showed that particle size and their concentrations significantly modulated the soil-roots exudates-plant system. Untargeted metabolomics highlighted that fatty acids, amino acids, and hormone biosynthesis pathways were significantly affected by MNPs. Additionally, they were associated with the reduction of rhizosphere bacterial α-diversity, following a size-dependent trend for specific taxa. The omics data integration highlighted a correlation between Pseudomonadata and Actinomycetota phyla and Bacillaceae family (Peribacillus simplex) and the exudation of flavonoids, phenolic acids, and lignans in lettuce exposed to increasing sizes of MNPs. This study provides a novel insight into the potential effects of different particle sizes and concentrations of MNPs on the soil-plant continuum, providing evidence about size- and concentration-dependent effects, suggesting the need for further investigation focused on medium- to long-term exposure.

Microbial species pool-mediated diazotrophic community assembly in crop microbiomes during plant development.

Plant-associated diazotrophs strongly relate to plant nitrogen (N) supply and growth. However, our knowledge of diazotrophic community assembly and microbial N metabolism in plant microbiomes is largely limited. Here we examined the assembly and temporal dynamics of diazotrophic communities across multiple compartments (soils, epiphytic and endophytic niches of root and leaf, and grain) of three cereal crops (maize, wheat, and barley) and identified the potential N-cycling pathways in phylloplane microbiomes. Our results demonstrated that the microbial species pool, influenced by site-specific environmental factors (e.g., edaphic factors), had a stronger effect than host selection (i.e., plant species and developmental stage) in shaping diazotrophic communities across the soil-plant continuum. Crop diazotrophic communities were dominated by a few taxa (~0.7% of diazotrophic phylotypes) which were mainly affiliated with Methylobacterium, Azospirillum, Bradyrhizobium, and Rhizobium. Furthermore, eight dominant taxa belonging to Azospirillum and Methylobacterium were identified as keystone diazotrophic taxa for three crops and were potentially associated with microbial network stability and crop yields. Metagenomic binning recovered 58 metagenome-assembled genomes (MAGs) from the phylloplane, and the majority of them were identified as novel species (37 MAGs) and harbored genes potentially related to multiple N metabolism processes (e.g., nitrate reduction). Notably, for the first time, a high-quality MAG harboring genes involved in the complete denitrification process was recovered in the phylloplane and showed high identity to Pseudomonas mendocina. Overall, these findings significantly expand our understanding of ecological drivers of crop diazotrophs and provide new insights into the potential microbial N metabolism in the phyllosphere.IMPORTANCEPlants harbor diverse nitrogen-fixing microorganisms (i.e., diazotrophic communities) in both belowground and aboveground tissues, which play a vital role in plant nitrogen supply and growth promotion. Understanding the assembly and temporal dynamics of crop diazotrophic communities is a prerequisite for harnessing them to promote plant growth. In this study, we show that the site-specific microbial species pool largely shapes the structure of diazotrophic communities in the leaves and roots of three cereal crops. We further identify keystone diazotrophic taxa in crop microbiomes and characterize potential microbial N metabolism pathways in the phyllosphere, which provides essential information for developing microbiome-based tools in future sustainable agricultural production.

Emerging organic contaminants in the soil-plant-receptor continuum: transport, fate, health risks, and removal mechanisms.

There is a lack of comprehensive reviews tracking emerging organic contaminants (EOCs) within the soil-plant continuum using the source-pathway-receptor-impact-mitigation (SPRIM) framework. Therefore, this review examines existing literature to gain insights into the occurrence, behaviour, fate, health hazards, and strategies for mitigating EOCs within the soil-plant system. EOCs identified in the soil-plant system encompass endocrine-disrupting chemicals, surfactants, pharmaceuticals, personal care products, plasticizers, gasoline additives, flame retardants, and per- and poly-fluoroalkyl substances (PFAS). Sources of EOCs in the soil-plant system include the land application of biosolids, wastewater, and solid wastes rich in EOCs. However, less-studied sources encompass plastics and atmospheric deposition. EOCs are transported from their sources to the soil-plant system and other receptors through human activities, wind-driven processes, and hydrological pathways. The behaviour, persistence, and fate of EOCs within the soil-plant system are discussed, including sorption, degradation, phase partitioning, (bio)transformation, biouptake, translocation, and bioaccumulation in plants. Factors governing the behaviour, persistence, and fate of EOCs in the soil-plant system include pH, redox potential, texture, temperature, and soil organic matter content. The review also discusses the environmental receptors of EOCs, including their exchange with other environmental compartments (aquatic and atmospheric), and interactions with soil organisms. The ecological health risks, human exposure via inhalation of particulate matter and consumption of contaminated food, and hazards associated with various EOCs in the soil-plant system are discussed. Various mitigation measures including removal technologies of EOCs in the soil are discussed. Finally, future research directions are presented.

Rapid positive response of young trees growth to warming reverses nitrogen loss from subtropical soil

Abstract Global warming is widely expected to alter nitrogen (N) cycling in terrestrial ecosystems by accelerating N transformations in soils. However, it is unclear how warming will affect plant–soil N cycling in subtropical ecosystems. Here, we measured the N transformations including net ammoniation, nitrification, nitrous oxide emissions and nitrate in soil solution throughout the plant–soil continuum with 2 years of experimental soil warming (+5°C) in a young subtropical Chinese fir mesocosm. Seasonal variations of soil and plant (foliage and root) N concentrations and isotopes (δ15N), foliar water use efficiency and arbuscular mycorrhizal colonization rate were measured. Soil warming significantly increased net ammonization and nitrification of the soil, together with the transient positive response observed in inorganic N of the soil. Warming increased nitrate N fluxes in soil solution and nitrous oxide emissions in the first year but not in the second year, suggesting N losses through leaching and gaseous in the initial period of warming. Warming primarily induced enrichment of 15N in foliage relative to the soil, which was attributed to the trade‐offs of persistent increases in plant N uptake caused by enhanced tree growth and a decrease in N losses with continuous warming. Furthermore, young trees' growth and N uptake capacity can rapidly acclimate to climate warming as a result of warming‐induced increases in arbuscular mycorrhizal colonization and foliar water use efficiency. Our findings highlight that warming accelerates the plant–soil N cycle and promotes young trees' growth and N uptake, which in turn reduces soil N lost from this subtropical ecosystem. Therefore, our study suggests that the competition for N between plants and microbes governs whether subtropical forests are opened or closed N cycle systems under climate warming. We predict that subtropical young forests can still maintain their high productivity because young trees can maintain their N uptake capacity and adequate soil N supply in facing future climate warming. Read the free Plain Language Summary for this article on the Journal blog.

Evaluating pulse-reserve characteristics of Soil-Plant continuum in India using remote sensing

The pulse-reserve paradigm associated with the plant's increased water uptake following surface soil moisture pulses is not well understood in India. India has a very high spatio-temporal climate and ecological variability. Such ecological and climatological diversity makes the country-scale analysis of the pulse-reserve paradigm challenging. Here, we present the first analysis of this phenomenon using 9 years of space based passive microwave estimates of surface soil moisture and vegetation water content from both X-band and L-band. We observed from both datasets that the pulse-reserve paradigm is widespread in India across seasons and biomes. The seasonal climate in India drives the precipitation characteristics, thus uphold the pulse-reserve paradigm. The estimated Soil Moisture Threshold (SMT), at which the vegetation water content drops, has substantial spatio-temporal variations, unlike other regions worldwide. The comparisons between X-band and L-band products show significant differences in the magnitudes of soil moisture and vegetation optical depths due to inherent properties. However, most of the findings related to the pulse-reserve paradigm, specifically the sensitivity of processes on different factors, remain similar. We found a strong dependence of SMT on seasonal climate, vegetation greenness, and pulse soil moisture. The association of SMT with soil characteristics, such as clay fraction, is weak in India, contrary to global traits. Our analysis provides new insights into the plant water uptake mechanisms in India to improve the parameterization schemes for better representation of the soil–plant continuum structural and functional behavior.

Assembly of cereal crop fungal communities under water stress determined by host niche

Crop-associated fungi play an important role in agroecosystems. However, a comprehensive understanding of the ecological mechanisms governing fungal community assembly is lacking. Here, we established a wheat (Triticum aestivum) and oat (Avena sativa) cropping system and sampled crop associated fungal communities under different water stresses. The results show that fungal community assembly in the soil-plant continuum is mainly determined by host niches rather than water stress and genotype. However, within the same host niche, water stress and genotype significantly influenced the assembly of fungal communities. This finding was further supported by the network complexity and dissimilarity-overlap analysis. Epiphytes and leaf endosphere exhibited a complex network structure, characterized by strong positive interactions among the members of the mycobiome. The network complexity of the phylloplane increased under drought stress. The analysis of microbial source tracking revealed that the fungi in the roots primarily originated from the bulk soil, while most fungi in the leaves originated from unknown sources under different water stress. In addition, crop mycobiome was governed by a few dominant taxa, with Sordariomycetes identified as an important biomarker taxon for roots and Trichosporonales for leaves. This study provides comprehensive empirical evidence on the assembly mechanisms of crop fungal communities.

Culturomics- and metagenomics-based insights into the soil microbiome preservation and application for sustainable agriculture.

Soil health is crucial for global food production in the context of an ever-growing global population. Microbiomes, a combination of microorganisms and their activities, play a pivotal role by biodegrading contaminants, maintaining soil structure, controlling nutrients' cycles, and regulating the plant responses to biotic and abiotic stresses. Microbiome-based solutions along the soil-plant continuum, and their scaling up from laboratory experiments to field applications, hold promise for enhancing agricultural sustainability by harnessing the power of microbial consortia. Synthetic microbial communities, i.e., selected microbial consortia, are designed to perform specific functions. In contrast, natural communities leverage indigenous microbial populations that are adapted to local soil conditions, promoting ecosystem resilience, and reducing reliance on external inputs. The identification of microbial indicators requires a holistic approach. It is fundamental for current understanding the soil health status and for providing a comprehensive assessment of sustainable land management practices and conservation efforts. Recent advancements in molecular technologies, such as high-throughput sequencing, revealed the incredible diversity of soil microbiomes. On one hand, metagenomic sequencing allows the characterization of the entire genetic composition of soil microbiomes, and the examination of their functional potential and ecological roles; on the other hand, culturomics-based approaches and metabolic fingerprinting offer complementary information by providing snapshots of microbial diversity and metabolic activities both in and ex-situ. Long-term storage and cryopreservation of mixed culture and whole microbiome are crucial to maintain the originality of the sample in microbiome biobanking and for the development and application of microbiome-based innovation. This review aims to elucidate the available approaches to characterize diversity, function, and resilience of soil microbial communities and to develop microbiome-based solutions that can pave the way for harnessing nature's untapped resources to cultivate crops in healthy soils, to enhance plant resilience to abiotic and biotic stresses, and to shape thriving ecosystems unlocking the potential of soil microbiomes is key to sustainable agriculture. Improving management practices by incorporating beneficial microbial consortia, and promoting resilience to climate change by facilitating adaptive strategies with respect to environmental conditions are the global challenges of the future to address the issues of climate change, land degradation and food security.

Seeds Act as Vectors for Antibiotic Resistance Gene Dissemination in a Soil-Plant Continuum.

Though the evidence for antibiotic resistance spread via plant microbiome is mounting, studies regarding antibiotic resistome in the plant seed, a reproductive organ and important food resource, are still in their infancy. This study investigated the effects of long-term organic fertilization on seed bacterial endophytes, resistome, and their intergenerational transfer in the microcosm. A total of 99 antibiotic resistance genes (ARGs) and 26 mobile genetic elements (MGEs) were detected by high-throughput quantitative PCR. The amount of organic fertilizer applied was positively correlated to the number and relative abundance of seed-associated ARGs and MGEs. Moreover, the transmission of ARGs from the rhizosphere to the seed was mainly mediated by the shared bacteria and MGEs. Notably, the rhizosphere of progeny seedlings derived from seeds harboring abundant ARGs was found to have a higher relative abundance of ARGs. Using structural equation models, we further revealed that seed resistome and MGEs were key factors affecting the ARGs in the progeny rhizosphere, implying the seed was a potential resistome reservoir for rhizosphere soil. This study highlights the overlooked role of seed endophytes in the dissemination of resistome in the soil-plant continuum, and more attention should be paid to plant seeds as vectors of ARGs within the "One-Health" framework.

Pathogen invasion increases the abundance of predatory protists and their prey associations in the plant microbiome.

Soil and plant-associated protistan communities play a key role in shaping bacterial and fungal communities, primarily through their function as top-down predators. However, our understanding of how pathogen invasion influences these protistan communities and their relationships with bacterial and fungal communities remains limited. Here, we studied the protistan communities along the soil-plant continuum of healthy chilli peppers and those affected by Fusarium wilt disease (FWD), and integrated bacterial and fungal community data from our previous research. Our research showed that FWD was associated with a significant enrichment of phagotrophic protists in roots, and also increased the proportion and connectivity of these protists (especially Cercozoa and Ciliophora) in both intra- and inter-kingdom networks. Furthermore, the microbiome of diseased plants not only showed a higher relative abundance of functional genes related to bacterial anti-predator responses than healthy plants, but also contained a greater abundance of metagenome-assembled genomes with functional traits involved in this response. The increased microbial inter-kingdom associations between bacteria and protists, coupled with the notable bacterial anti-predator feedback in the microbiome of diseased plants, suggest that FWD may catalyse the associations between protists and their microbial prey. These findings highlight the potential role of predatory protists in influencing microbial assembly and functionality through top-down forces under pathogenic stress.

Linking horizontal crosshole GPR variability with root image information for maize crops

AbstractNon‐invasive imaging of processes within the soil–plant continuum, particularly root and soil water distributions, can help optimize agricultural practices such as irrigation and fertilization. In this study, in‐situ time‐lapse horizontal crosshole ground penetrating radar (GPR) measurements and root images were collected over three maize crop growing seasons at two minirhizotron facilities (Selhausen, Germany). Root development and GPR permittivity were monitored at six depths (0.1–1.2 m) for different treatments within two soil types. We processed these data in a new way that gave us the information of the “trend‐corrected spatial permittivity deviation of vegetated field,” allowing us to investigate whether the presence of roots increases the variability of GPR permittivity in the soil. This removed the main non‐root‐related influencing factors: static influences, such as soil heterogeneities and rhizotube deviations, and dynamic effects, such as seasonal moisture changes. This trend‐corrected spatial permittivity deviation showed a clear increase during the growing season, which could be linked with a similar increase in root volume fraction. Additionally, the corresponding probability density functions of the permittivity variability were derived and cross‐correlated with the root volume fraction, resulting in a coefficient of determination (R2) above 0.5 for 23 out of 46 correlation pairs. Although both facilities had different soil types and compaction levels, they had similar numbers of good correlations. A possible explanation for the observed correlation is that the presence of roots causes a redistribution of soil water, and therefore an increase in soil water variability.

Community assembly of endophytic bacteria and fungi differs in soil-root continuum of Carex cepillacea

Endophytic microbes in nutrient-impoverished soils have unique adaptive mechanisms through the dual selection of plants and soil, which is of great research value for exploring the nutritional strategies of nonmycorrhizal plants. However, the assemblage of endophytic microbes associated with Cyperaceae plants in phosphorus-deficient soil remains unclear. We examined fungal and bacterial communities associated with Carex cepillacea in bulk soil, rhizosphere soil and root endosphere, in the alpine grassland of Qinghai-Tibet Plateau. Diverse endophytes were identified, among which some unique endophytes were enriched in the roots. Specifically, 100 % of rhizosphere bacterial dominant taxa and 85 % of rare taxa reached the root endosphere through the root barrier, while only 65.5 % of rhizosphere fungal dominant taxa and 30.1 % of the rare taxa reached the root endosphere. Thus, in the soil-plant continuum, host appears to have a stronger influence on plant-fungal community assembly than on plant-bacterial community assembly. Moreover, pH and soil available phosphorus (AP) were the primary drivers of the microbial structure in the rhizosphere soil and root endosphere, while MAP mostly influenced microbial structure in the rhizosphere soil. Network analyses further found that endophytic fungi tend to have a higher number of network connections than bacteria, suggesting that fungi are more central than bacteria to the community structure of root microbiomes. Solirubrobacterales and Hypocreales contained most of core groups in the root microbiome, including many plants growth-promoting microbes such as phosphate-dissolving and nitrogen-fixing bacteria. These results indicate that Carex cepillacea roots are colonized by diverse and unique endophytes, including some core microbiota that are potentially important in driving the plant adaptability and nutrient uptake. The findings also highlight the different community assembly patterns of fungi and bacteria in the root-soil continuum. Further exploration of the roles of endophytes is of great significance for understanding the nutrient strategies of nonmycorrhizal plants in alpine environments.

Functional genomic analysis of nutrient cycling of plant-soil continuum in the mossy biocrust in the Tengger Desert

The microbiome and metabolic processes occurring in the soil of the moss crust-soil continuum contribute to drive biogeochemical cycles. In this study, soil chemical properties of soil which was attached to bryophyte (BRS) and soil which was dropped from bryophyte (BBS) were analyzed. Differences in microbial species composition, metabolic pathways and related genes of these two different soil types were also analyzed. The results showed that the total organic carbon (TOC), total nitrogen (TN) and ammonium nitrogen (NH4+-N) content of BRS were significantly higher than those of BBS. The dominant phylum in the soil microbiome of the moss crust-soil continuum was Actinobacteria. Genes and metabolic pathways related to the carbon, nitrogen, phosphorus, and sulfur cycle differed between BRS and BBS. The carbon sequestration capacity of BRS was higher than that of BBS. The relative abundance of napA, narH and narI genes involved in denitrification and dissimilatory nitrate reduction in the BRS microbiome was significantly higher than that in the BBS microbiome, while the relative abundance of nasA, NR and nirA genes involved in assimilatory nitrate reduction in the BRS soil microbiome was significantly lower than that in the BBS soil microbiome. The relative abundance of glpQ genes encoding glycerophosphodiester phosphodiesterase in the BRS microbiome was significantly higher than that in the BBS microbime, while the relative abundance of pstS, pstA, pstC, pstB genes responsible for phosphate-specific transport systems in the BRS microbiome was significantly lower than that in the BBS microbiome. The abundance of the assimilatory sulfate-reducing metabolic pathway in the BRS microbiome was significantly higher than that in the BBS microbiome, while the dissimilatory sulfate-reducing metabolic pathway in the BRS microbiome was significantly lower than that in the BBS microbiome. The study found that the microbiome in the soil which was attached to bryophyte plays a more important role in the accumulation of soil nutrients in the Tengger Desert through biodiversity and metabolic activity.

Attribution of dispersal limitation can better explain the assembly patterns of plant microbiota.

Disentangling community assembly processes is crucial for fully understanding the function of microbiota in agricultural ecosystems. However, numerous plant microbiome surveys have gradually revealed that stochastic processes dominate the assembly of the endophytic root microbiota in conflict with strong host filtering effects, which is an important issue. Resolving such conflicts or inconsistencies will not only help accurately predict the composition and structure of the root endophytic microbiota and its driving mechanisms, but also provide important guidance on the correlation between the relative importance of deterministic and stochastic processes in the assembly of the root endophytic microbiota, and crop productivity and nutritional quality. Here, we propose that the inappropriate division of dispersal limitation may be the main reason for such inconsistency, which can be resolved after the proportion of dispersal limitation is incorporated into the deterministic processes. The rationality of this adjustment under the framework of the formation of a holobiont between the microbiome and the plant host is herein explained, and a potential theoretical framework for dynamic assembly patterns of endophytic microbiota along the soil-plant continuum is proposed. Considering that the assembly of root endophytic microbiota is complicated, we suggest caution and level-by-level verification from deterministic processes to neutral components to stochastic processes when deciding on the attribution of dispersal limitation in the future to promote the expansion and application of microbiome engineering in sustainable agricultural development based on community assembly patterns.

Multi-year belowground data of minirhizotron facilities in Selhausen

The production of crops secure the human food supply, but climate change is bringing new challenges. Dynamic plant growth and corresponding environmental data are required to uncover phenotypic crop responses to the changing environment. There are many datasets on above-ground organs of crops, but roots and the surrounding soil are rarely the subject of longer term studies. Here, we present what we believe to be the first comprehensive collection of root and soil data, obtained at two minirhizotron facilities located close together that have the same local climate but differ in soil type. Both facilities have 7m-long horizontal tubes at several depths that were used for crosshole ground-penetrating radar and minirhizotron camera systems. Soil sensors provide observations at a high temporal and spatial resolution. The ongoing measurements cover five years of maize and wheat trials, including drought stress treatments and crop mixtures. We make the processed data available for use in investigating the processes within the soil–plant continuum and the root images to develop and compare image analysis methods.