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.

Crop residue return sustains global soil ecological stoichiometry balance.

Although soil ecological stoichiometry is constrained in natural ecosystems, its responses to anthropogenic perturbations are largely unknown. Inputs of inorganic fertilizer and crop residue are key cropland anthropogenic managements, with potential to alter their soil ecological stoichiometry. We conducted a global synthesis of 682 data pairs to quantify the responses of soil carbon (C), nitrogen (N), and phosphorus (P) and grain yields to combined inputs of crop residue plus inorganic fertilizer compared with only inorganic fertilizer application. Crop residue inputs enhance soil C (10.5%-12%), N (7.63%-9.2%), and P (2.62%-5.13%) contents, with an increase in C:N (2.51%-3.42%) and C:P (7.27%-8.00%) ratios, and grain yields (6.12%-8.64%), indicating that crop residue alleviated soil C limitation caused by inorganic fertilizer inputs alone and was able to sustain balanced stoichiometry. Moreover, the increase in soil C and C:N(P) ratio reached saturation in ~13-16 years after crop residue return, while grain yield increase trend discontinued. Furthermore, we identified that the increased C, N, and P contents and C:N(P) ratios were regulated by the initial pH and C content, and the increase in grain yield was not only related to soil properties, but also negatively related to the amount of inorganic N fertilizer input to a greater extent. Given that crop residual improvement varies with soil properties and N input levels, we propose a predictive model to preliminary evaluate the potential for crop residual improvement. Particularly, we suggest that part of the global budget should be used to subsidize crop residue input management strategies, achieving to a win-win situation for agricultural production, ecological protection, and climate change mitigation.

Changes in soil fungal communities after onset of wheat yellow mosaic virus disease.

Rhizosphere-associated microbes have important implications for plant health, but knowledge of the association between the pathological conditions of soil-borne virus-infected wheat and soil microbial communities, especially changes in fungal communities, remains limited. We investigated the succession of fungal communities from bulk soil to wheat rhizosphere soil in both infected and healthy plants using amplicon sequencing methods, and assessed their potential role in plant health. The results showed that the diversity of fungi in wheat rhizosphere and bulk soils significantly differed post wheat yellow mosaic virus disease onset. The structure differences in fungal community at the two wheat health states or two compartment niches were evident, soil physicochemical properties (i.e., NH4 +) contribute to differences in fungal community structure and alpha diversity. Comparison analysis showed Mortierellomycetes and Dothideomycetes as dominant communities in healthy wheat soils at class level. The genus Pyronemataceae and Solicoccozyma were significantly are significantly enriched in rhizosphere soil of diseased plant, the genus Cystofilobasidium, Cladosporium, Mortierella, and Stephanonectria are significantly enriched in bulk soil of healthy plant. Co-occurrence network analysis showed that the fungi in healthy wheat soil has higher mutual benefit and connectivity compared with diseased wheat. The results of this study demonstrated that the occurrence of wheat yellow mosaic virus diseases altered both fungal community diversity and composition, and that NH4 + is the most important soil physicochemical factor influencing fungal diversity and community composition.

[Response of Soil Multifunctionality to Reduced Microbial Diversity].

Soil microbial communities play an important role in driving a variety of ecosystem functions and ecological processes and are the primary driving force in maintaining the biogeochemical cycle. It has been observed that soil microbial diversity decreases with land use intensification and climate change in the global background. It is essential to investigate whether the reduction in soil microbial diversity can affect soil multifunctionality. Thus, in this study, the dilution-to-extinction method was used to construct the gradient of soil microbial diversity, combined with high-throughput sequencing to explore the impact of the reduction in bacterial, fungal, and protist diversity on soil multifunctionality. The results showed that the soil microbial alpha diversity (richness and Shannon index) was significantly lower than that of the original soil. Principal coordinate analysis (PCoA) showed that the microbial community structure of original soil was significantly different from that of diluted soil, and the response of bacterial and fungal communities to diluted soil was higher than that of protists. The regression model showed that there was a significant negative linear relationship between the average response value of soil multi-function and the index of microbial diversity, indicating that the change in soil microbial community was the key factor in regulating soil multifunctionality. The regression model showed that there was a significant negative linear relationship between soil multifunctionality and microbial diversity, indicating that the change in soil microbial community was the key factor to regulate soil multi-kinetic energy. Through the aggregated boosted tree analysis (ABT) and regression model, we found that some specific microbial groups, such as the Solacocozyma and Holtermaniella of fungi and Rudaea of bacteria, could significantly promote the change in soil multifunctionality, which showed that key microbial taxa play an indicative role in biological processes. Furthermore, the structural equation model revealed that bacteria could affect soil multifunctionality through the interaction between microbiomes, which was the key biological factor driving the change in soil multifunctionality. This study provided experimental evidence for the impact of soil microbial diversity on soil multifunctionality, and promoted the notion that maintaining a certain diversity of soil microbial community in a single agricultural ecosystem, especially the diversity of key microbial taxa, is of great significance to the sustainable development of ecosystem function in the future.

Characterization of the belowground microbial community and co-occurrence networks of tobacco plants infected with bacterial wilt disease.

Characterizing the microbial communities associated with soil-borne disease incidence is a key approach in understanding the potential role of microbes in protecting crops from pathogens. In this study, we compared the soil properties and microbial composition of the rhizosphere soil and roots of healthy and bacterial wilt-infected tobacco plants to assess their potential influence on plant health. Our results revealed that the relative abundance of pathogens was higher in diseased plants than in healthy plants. Moreover, compared with healthy plants, there was a significantly higher microbial alpha diversity in the roots and rhizosphere soil of diseased plants. In addition, we detected a lower abundance of certain plant microbiota, including species in the genera Penicillium, Trichoderma, and Burkholderia in the rhizosphere of diseased plants, which were found to be significantly negatively associated with the relative abundance of Ralstonia. Indeed, compared with healthy plants, the co-occurrence networks of diseased plants included a larger number of associations linked to plant health. Furthermore, structural equation modeling revealed that these specific microbes were correlated with disease suppression, thereby implying that they may play important roles in maintaining plant health. In conclusion, our findings provide important insights into the relationships between soil-borne disease incidence and changes in the belowground microbial community. These findings will serve as a basis for further research investigating the use of specific plant-associated genera to inhibit soil-borne diseases.

Microbial community changes in different underground compartments of potato affected yield and quality.

Soil microbial communities are critical to plant health and productivity. Crop-associated microbial diversity may exhibit spatial specificity across regions and soil compartments. However, we lack sound evidence for the impact of variation in soil microbial diversity on plant productivity caused by regional differences. The main aims of this study are to explore the structure and functionality of the belowground (potato tuber surface and rhizosphere) microbial communities in three compartments and assess whether these communities contribute to potato productivity. Significant differences in alpha and beta diversities of belowground microbiota were detected in different compartments and regions, mainly due to differences in available soil nutrients and pH. Changes to microbial diversity between bulk soil and rhizosphere or tuber surface soil were significantly negatively correlated with potato yield and nutrient content and positively correlated with starch content. We further found some bacterial (Mucilaginibacter, Dokdonella, and Salinispora) and fungal (Solicoccozyma, Scytalidium, and Humicola) genera closely associated with potato yield and quality. Aggregated boosted tree prediction revealed that soil physicochemical properties and microbial diversity of tuber surface soil contributed more to potato yield; tuber surface soil bacterial contributed more to potato starch and nutrient content. Our findings provide experimental evidence that the significant differences in soil microbial diversity and specific microbial taxa enrichment may potentially influence crop productivity under soil physicochemical property change scenarios in the agricultural ecosystem. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03167-6.

Wheat yellow mosaic enhances bacterial deterministic processes in a plant-soil system.

Understanding the mechanisms that govern microbial community assembly across soil-plant continuum is crucial for predicting the response of ecosystems to environmental changes. However, the impact of the health status of plant on microbial assembly across this continuum still remain poorly understood. Here, we investigated how wheat yellow mosaic (WYM), caused by the wheat mosaic virus transmitted by Polymyxa graminis, affected microbial assembly across soil (bulk soil, rhizosphere soil), and plant (roots and leaves) continuum in a winter wheat (Triticum aestivum L.) system in northern China, using null model analysis. The results showed that deterministic processes dominated the bacterial community assembly, whereas stochastic processes were primarily responsible for the assembly of the fungal communities. With increasing levels of WYM, deterministic processes were greatly enhanced for bacterial community assembly, accompanied by a decrease in community niche breadth. Intensified competition between bacteria and fungi and increased soil total nitrogen (TN) and soil organic carbon (SOC) contents were mainly responsible for the enhanced deterministic processes for bacterial community assembly. Random forest modeling indicated a strong potential of rhizosphere bacterial community assembly for predicting the pathological conditions of wheat. Structural equation modeling showed that disease level was positively correlated with SOC and TN contents, competitions between bacteria and fungi, and the contribution of variable selection processes to the bacterial community assembly in the wheat rhizosphere. Our study revealed the ecological mechanisms underlying the associations between microbial communities and soil-borne disease, and highlighted the significance of microbial community assembly for maintaining soil and plant health.

Enrichment of beneficial rhizosphere microbes in Chinese wheat yellow mosaic virus-resistant cultivars.

The microbial community within the root system, the rhizosphere closely connected to the root, and their symbiotic relationship with the host are increasingly seen as possible drivers of natural pathogen resistance. Resistant cultivars have the most effective strategy in controlling the Chinese wheat yellow mosaic disease, but the roles of the root and rhizosphere microbial interactions among different taxonomic levels of resistant cultivars are still unknown. Thus, we aimed to investigate whether these microbial community composition and network characteristics are related to disease resistance and to analyze the belowground plant-associated microflora. Relatively high microbial diversity and stable community structure for the resistant cultivars were detected. Comparison analysis showed that some bacterial phyla were significantly enriched in the wheat root or rhizosphere of the resistant wheat cultivar. Furthermore, the root and rhizosphere of the resistant cultivars greatly recruited many known beneficial bacterial and fungal taxa. In contrast, the relative abundance of potential pathogens was higher for the susceptible cultivar than for the resistant cultivar. Network co-occurrence analysis revealed that a much more complex, more mutually beneficial, and a higher number of bacterial keystone taxa in belowground microbial networks were displayed in the resistant cultivar, which may have been responsible for maintaining the stability and ecological balance of the microbial community. Overall, compared with the susceptible cultivar, the resistant cultivar tends to recruit more potential beneficial microbial groups for plant and rhizosphere microbial community interactions. These findings indicate that beneficial rhizosphere microbiomes for cultivars should be targeted and evaluated using community compositional profiles. KEY POINTS: • Different resistance levels in cultivars affect the rhizosphere microbiome.. • Resistant cultivars tend to recruit more potential beneficial microbial groups. • Bacteria occupy a high proportion and core position in the microflora network.

Plant developmental stage drives the differentiation in ecological role of the maize microbiome.

BACKGROUND: Plants live with diverse microbial communities which profoundly affect multiple facets of host performance, but if and how host development impacts the assembly, functions and microbial interactions of crop microbiomes are poorly understood. Here we examined both bacterial and fungal communities across soils, epiphytic and endophytic niches of leaf and root, and plastic leaf of fake plant (representing environment-originating microbes) at three developmental stages of maize at two contrasting sites, and further explored the potential function of phylloplane microbiomes based on metagenomics. RESULTS: Our results suggested that plant developmental stage had a much stronger influence on the microbial diversity, composition and interkingdom networks in plant compartments than in soils, with the strongest effect in the phylloplane. Phylloplane microbiomes were co-shaped by both plant growth and seasonal environmental factors, with the air (represented by fake plants) as its important source. Further, we found that bacterial communities in plant compartments were more strongly driven by deterministic processes at the early stage but a similar pattern was for fungal communities at the late stage. Moreover, bacterial taxa played a more important role in microbial interkingdom network and crop yield prediction at the early stage, while fungal taxa did so at the late stage. Metagenomic analyses further indicated that phylloplane microbiomes possessed higher functional diversity at the early stage than the late stage, with functional genes related to nutrient provision enriched at the early stage and N assimilation and C degradation enriched at the late stage. Coincidently, more abundant beneficial bacterial taxa like Actinobacteria, Burkholderiaceae and Rhizobiaceae in plant microbiomes were observed at the early stage, but more saprophytic fungi at the late stage. CONCLUSIONS: Our results suggest that host developmental stage profoundly influences plant microbiome assembly and functions, and the bacterial and fungal microbiomes take a differentiated ecological role at different stages of plant development. This study provides empirical evidence for host exerting strong effect on plant microbiomes by deterministic selection during plant growth and development. These findings have implications for the development of future tools to manipulate microbiome for sustainable increase in primary productivity. Video Abstract.

T4-like Phages Reveal the Potential Role of Viruses in Soil Organic Matter Mineralization.

Viruses are the most abundant biological entities in the world, but their ecological functions in soil are virtually unknown. We hypothesized that greater abundance of T4-like phages will increase bacterial death and thereby suppress soil organic carbon (SOC) mineralization. A range of phage and bacterial abundances were established in sterilized soil by reinoculation with 10-3 and 10-6 dilutions of suspensions of unsterilized soil. The total and viable 16S rRNA gene abundance (a universal marker for bacteria) was measured by qPCR to determine bacterial abundance, with propidium monoazide (PMA) preapplication to eliminate DNA from non-viable cells. Abundance of the g23 marker gene was used to quantify T4-like phages. A close negative correlation between g23 abundance and viable 16S rRNA gene abundance was observed. High abundance of g23 led to lower viable ratios for bacteria, which suggested that phages drove microbial necromass production. The CO2 efflux from soil increased with bacterial abundance but decreased with higher abundance of T4-like phages. Elimination of extracellular DNA by PMA strengthened the relationship between CO2 efflux and bacterial abundance, suggesting that SOC mineralization by bacteria is strongly reduced by the T4-like phages. A random forest model revealed that abundance of T4-like phages and the abundance ratio of T4-like phages to bacteria are better predictors of SOC mineralization (measured as CO2 efflux) than bacterial abundance. Our study provides experimental evidence of phages' role in organic matter turnover in soil: they can retard SOC decomposition but accelerate bacterial turnover.

Diversity and potential biogeochemical impacts of viruses in bulk and rhizosphere soils.

Viruses can affect microbial dynamics, metabolism and biogeochemical cycles in aquatic ecosystems. However, viral diversity and functions in agricultural soils are poorly known, especially in the rhizosphere. We used virome analysis of eight rhizosphere and bulk soils to study viral diversity and potential biogeochemical impacts in an agro-ecosystem. The order Caudovirales was the predominant viral type in agricultural soils, with Siphoviridae being the most abundant family. Phylogenetic analysis of the terminase large subunit of Caudovirales identified high viral diversity and three novel groups. Viral community composition differed significantly between bulk and rhizosphere soils. Soil pH was the main environmental driver of the viral community structure. Remarkably, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes were detected in viromes, including glycoside hydrolases, carbohydrate esterases and carbohydrate-binding modules. These results demonstrate that virus-encoded putative auxiliary metabolic genes or metabolic genes that may change bacterial metabolism and indirectly contribute to biogeochemical cycling, especially carbon cycling, in agricultural soil.

Diazotrophic Community Variation Underlies Differences in Nitrogen Fixation Potential in Paddy Soils Across a Climatic Gradient in China.

Biological nitrogen (N2) fixation as a source of new N input into the soil by free-living diazotrophs is important for achieving sustainable rice agriculture. However, the dominant environmental drivers or factors influencing N2 fixation and the functional significance of the diazotroph community structure in paddy soil across a climatic gradient are not yet well understood. Thus, we characterized the diazotroph community and identified the ecological predictors of N2 fixation potential in four different climate zones (mid-temperate, warm-temperate, subtropical, and tropical paddy soils) in eastern China. Comprehensive nifH gene sequencing, functional activity detection, and correlation analysis with environmental factors were estimated. The potential nitrogenase activity (PNA) was highest in warm-temperate regions, where it was 6.2-, 2.9-, and 2.2-fold greater than in the tropical, subtropical, and mid-temperate regions, respectively; nifH gene abundance was significantly higher in warm-temperate and subtropical zones than in the tropical or mid-temperate zones. Diazotroph diversity was significantly higher in the tropical climate zone and significantly lower in the mid-temperate zone. Non-metric multidimensional scaling and canonical correlation analysis indicated that paddy soil diazotroph populations differed significantly among the four climate zones, mainly owing to differences in climate and soil pH. Structural equation models and automatic linear models revealed that climate and nutrients indirectly affected PNA by affecting soil pH and diazotroph community, respectively, while diazotroph community, C/P, and nifH gene abundance directly affected PNA. And C/P ratio, pH, and the diazotroph community structure were the main predictors of PNA in paddy soils. Collectively, the differences in diazotroph community structure have ecological significance, with important implications for the prediction of soil N2-fixing functions under climate change scenarios.

Host selection shapes crop microbiome assembly and network complexity.

Plant microbiomes are essential to host health and productivity but the ecological processes that govern crop microbiome assembly are not fully known. Here we examined bacterial communities across 684 samples from soils (rhizosphere and bulk soil) and multiple compartment niches (rhizoplane, root endosphere, phylloplane, and leaf endosphere) in maize (Zea mays)-wheat (Triticum aestivum)/barley (Hordeum vulgare) rotation system under different fertilization practices at two contrasting sites. Our results demonstrate that microbiome assembly along the soil-plant continuum is shaped predominantly by compartment niche and host species rather than by site or fertilization practice. From soils to epiphytes to endophytes, host selection pressure sequentially increased and bacterial diversity and network complexity consequently reduced, with the strongest host effect in leaf endosphere. Source tracking indicates that crop microbiome is mainly derived from soils and gradually enriched and filtered at different plant compartment niches. Moreover, crop microbiomes were dominated by a few dominant taxa (c. 0.5% of bacterial phylotypes), with bacilli identified as the important biomarker taxa for wheat and barley and Methylobacteriaceae for maize. Our work provides comprehensive empirical evidence on host selection, potential sources and enrichment processes for crop microbiome assembly, and has important implications for future crop management and manipulation of crop microbiome for sustainable agriculture.

Rare taxa maintain the stability of crop mycobiomes and ecosystem functions.

Plants harbour highly diverse mycobiomes which sustain essential functions for host health and productivity. However, ecological processes that govern the plant-mycobiome assembly, interactions and their impact on ecosystem functions remain poorly known. Here we characterized the ecological role and community assembly of both abundant and rare fungal taxa along the soil-plant continuums (rhizosphere, phyllosphere and endosphere) in the maize-wheat/barley rotation system under different fertilization practices at two contrasting sites. Our results indicate that mycobiome assembly is shaped predominantly by compartment niche and host species rather than by environmental factors. Moreover, crop-associated fungal communities are dominated by few abundant taxa mainly belonging to Sordariomycetes and Dothideomycetes, while the majority of diversity within mycobiomes are represented by rare taxa. For plant compartments, the abundant sub-community is mainly determined by stochastic processes. In contrast, the rare sub-community is more sensitive to host selection and mainly governed by deterministic processes. Furthermore, our results demonstrate that rare taxa play an important role in fungal co-occurrence network and ecosystem functioning like crop yield and soil enzyme activities. These results significantly advance our understanding of crop mycobiome assembly and highlight the key role of rare taxa in sustaining the stability of crop mycobiomes and ecosystem functions.