Soil-plant Continuum Research Articles

Engineering the Crop Microbiota Through Host Genetics.

The microbiota populating the plant-soil continuum defines an untapped resource for sustainable crop production. The host plant is a driver for the taxonomic composition and function of these microbial communities. In this review, we illustrate how the host genetic determinants of the microbiota have been shaped by plant domestication and crop diversification. We discuss how the heritable component of microbiota recruitment may represent, at least partially, a selection for microbial functions underpinning the growth, development, and health of their host plants and how the magnitude of this heritability is influenced by the environment. We illustrate how host-microbiota interactions can be treated as an external quantitative trait and review recent studies associating crop genetics with microbiota-based quantitative traits. We also explore the results of reductionist approaches, including synthetic microbial communities, to establish causal relationships between microbiota and plant phenotypes. Lastly, we propose strategies to integrate microbiota manipulation into crop selection programs. Although a detailed understanding of when and how heritability for microbiota composition can be deployed for breeding purposes is still lacking, we argue that advances in crop genomics are likely to accelerate wider applications of plant-microbiota interactions in agriculture.

Heavy Metals in Vegetables: Screening Health Risks of Irrigation with Wastewater in Peri-Urban Areas of Bhakkar, Pakistan.

One of the key concerns in public health is food security in the food sector. Due to the large amounts of potentially hazardous metals in wastewater, this practice may pose serious environmental and health risks to neighboring residents. In this study, the health effects of heavy metals in vegetables irrigated with wastewater were studied. The findings indicated a massive accumulation of heavy metals in wastewater-irrigated soil and vegetables collected from Bhakkar, Pakistan. The current study looked at the effects of wastewater irrigation on metal buildup in the soil-plant continuum and the health hazards that come with it (Cd, Co, Ni, Mn, Pb, and Fe). Heavy metal concentrations in vegetables cultivated on soil irrigated with untreated wastewater were not significantly lower (p ≥ 0.05) than in vegetables grown on wastewater-irrigated soil and were below the World Health Organization's recommended limits. A considerable amount of the selected hazardous metals was also swallowed by adults and children who consumed these vegetables, according to the research. On soil that had received wastewater irrigation, Ni and Mn were substantially different at p ≥ 0.001 levels. Pb, Ni, and Cd had health risk scores higher than the ones in all ingested vegetables, while Mn had a health risk score greater than the ones in turnips, carrots, and lettuce. The results also showed that both adults and children who consumed these vegetables absorbed a significant amount of the chosen toxic metals. Pb and Cd were shown to be the most dangerous chemical compounds to human health, and everyday consumption of agricultural plants irrigated with wastewater may pose a health risk, according to the health risk criteria.

Mycorrhizae Enhance Soybean Plant Growth and Aluminum Stress Tolerance by Shaping the Microbiome Assembly in an Acidic Soil.

Strongly acidic soils are characterized by high aluminum (Al) toxicity and low phosphorus (P) availability, which suppress legume plant growth and nodule development. Arbuscular mycorrhizal fungi (AMF) stimulate rhizobia and enhance plant P uptake. However, it is unclear how this symbiotic soybean-AMF-rhizobial trio promotes soybean growth in acidic soils. We examined the effects of AMF and rhizobium addition on the growth of two soybean genotypes, namely, Al-tolerant and Al-sensitive soybeans as well as their associated bacterial and fungal communities in an acidic soil. With and without rhizobial addition, AMF significantly increased the fresh shoot and root biomass of Al-tolerant soybean by 47%/87% and 37%/24%, respectively. This increase in plant biomass corresponded to the enrichment of four plant growth-promoting rhizobacteria (PGPR) in the rhizospheric soil, namely, Chitinophagaceae bacterium 4GSH07, Paraburkholderia soli, Sinomonas atrocyanea, and Aquincola tertiaricarbonis. For Al-sensitive soybean, AMF addition increased the fresh shoot and root biomass by 112%/64% and 30%/217%, respectively, with/without rhizobial addition. Interestingly, this significant increase coincided with a decrease in the pathogenic fungus Nigrospora oryzae as well as an increase in S. atrocyanea, A. tertiaricarbonis, and Talaromyces verruculosus (a P-solubilizing fungus) in the rhizospheric soil. Lastly, the compartment niche along the soil-plant continuum shaped microbiome assembly, with pathogenic/saprotrophic microbes accumulating in the rhizospheric soil and PGPR related to nitrogen fixation or stress resistance (e.g., Rhizobium leguminosarum and Sphingomonas azotifigens) accumulating in the endospheric layer. IMPORTANCE Taken together, this study examined the effects of arbuscular mycorrhizal fungi (AMF) and rhizobial combinations on the growth of Al-tolerant and Al-sensitive soybeans as well as their associated microbial communities in acidic soils and concluded that AMF enhances soybean growth and Al stress tolerance by recruiting PGPR and altering the root-associated microbiome assembly in a host-dependent manner. In the future, these findings will help us better understand the impacts of AMF on rhizosphere microbiome assembly and will contribute to the development of soybean breeding techniques for the comprehensive use of PGPR in sustainable agriculture.

Arbuscular Mycorrhizal Fungi Improve the Growth, Water Status, and Nutrient Uptake of Cinnamomum migao and the Soil Nutrient Stoichiometry under Drought Stress and Recovery.

Drought greatly influences the growth and ecological stoichiometry of plants in arid and semi-arid regions such as karst areas, where Cinnamomum migao (C. migao) is an endemic tree species that is used as a bioenergy resource. Arbuscular mycorrhizal fungi (AMF) play a key role in nutrient uptake in the soil-plant continuum, increasing plant tolerance to drought. However, few studies have examined the contribution of AMF in improving the growth of C. migao seedlings and the soil nutrient stoichiometry under drought-stress conditions. A pot experiment was conducted under natural light in a plastic greenhouse to investigate the effects of individual inoculation and Co-inoculation of AMF [Funneliformis mosseae (F. mosseae) and Claroideoglomus etunicatum (C. etunicatum)] on the growth, water status, and nutrient uptake of C. migao as well as the soil nutrient stoichiometry under well-watered (WW) and drought-stress (DS) conditions. The results showed that compared with non-AMF control (CK), AM symbiosis significantly stimulated plant growth and had higher dry mass. Mycorrhizal plants had better water status than corresponding CK plants. AMF colonization notably increased the total nitrogen and phosphorus content of C. migao seedlings compared with CK. Mycorrhizal plants had higher leaf and stem total carbon concentrations than CK. The results indicated that AM symbiosis protects C. migao seedlings against drought stress by improving growth, water status, and nutrient uptake. In general, the C. migao seedlings that formed with C. etunicatum showed the most beneficial effect on plant growth, water status, and nutrient uptake among all treatments. In the future, we should study more about the biological characteristics of each AMF in the field study to understand more ecological responses of AMF under drought stress, which can better provide meaningful guidance for afforestation projects in karst regions.

Microbial technology improved the biomass and root-shoot ratio of a multipurpose tree species: A potential biological solution for degraded agroforest ecosystems

Poor soil health adversely affects farming and forestry sectors worldwide. Microbial fertilizers can improve the plant-soil continuum in degraded ecosystem. In this research, the soil microbiome, plant biomass and root-shoot ratio of 2 mo-old Bauhinia purpurea, transplanted on aseptic soil + sand mixture (1:1) upon inoculation with 5 g of AMF (MYKOCAP®, coded as MCAP and MYKORICH®, coded as MRICH), with or without NFB (Bio-NTM, coded as Bio-N) amendment, were investigated. B. purpurea (Fabaceae), is an important reforestation and fodder species for livestock. The total plant biomass ranged from 18.90 g - 23.33 g, and highest in MRICH. Root-shoot ratio in Bio-N (0.58) was 23.4% higher than the Control. MCAP and Bio-N had increased sporulation and root colonization and NFB communities, respectively. Spore count can explain 32.9% change in primary roots biomass (p=0.013, r2=0.573), while root colonization can explain the 28.3% (p=0.023, r2=0.532), 47.9% (p=0.001, r2=0.692), 48.7% (p=0.001, r2=0.698), 26.5% (p=0.029, r2=0.514), and 39.4% (p=0.005, r2=0.628) change in total biomass, stem biomass, shoot biomass, primary roots biomass, and root biomass, respectively. Microbial fertilizers had increased the biomass and root-shoot ratio of B. purpurea, 90 days after inoculation. Microbial technology and multipurpose tree-based agroforestry are promising biological solutions for degraded agroforest ecosystems.

Stability of C:N:P Stoichiometry in the Plant–Soil Continuum along Age Classes in Natural Pinus tabuliformis Carr. Forests of the Eastern Loess Plateau, China

Ecological stoichiometry is useful for revealing the biogeochemical characteristics of flows of nutrients and energy between plant and soil, as well as the important implications behind these ecological phenomena. However, the ecological stoichiometric linkages among leaf, litter, soil, and enzymes in the natural forests of the Loess Plateau remain largely unknown. Here, leaf, litter, and soil samples were collected from four age classes of natural Pinus tabuliformis Carr. (P. tabuliformis) to explore the deep linkages among these components. We measured the total carbon (C), total nitrogen (N), and total phosphorus (P) concentrations of leaf and litter, as well as the concentrations of soil organic C, total N, total P, nitrate N, ammonium N, available P, and the activities of β-1,4-glucosidase (a C-acquiring enzyme), β-1,4-N-acetylglucosidase (an N-acquiring enzyme), and alkaline phosphatase (a P-acquiring enzyme) in the topsoil (0–20 cm). The average leaf N:P was 6.9 indicated the growth of P. tabuliformis was constrained by N according to the relative resorption theory of nutrient limitation. The C:N, C:P, and N:P ratios in leaf, litter, and soil and the enzyme activity were not significantly different among age classes (p > 0.05). Litter C:N (43.3) was closer to the ratio of leaf C:N (48.8), whereas the litter C:P (257.7) was obviously lower than the ratio of leaf C:P (338.15). We calculated the stoichiometric homeostasis index (1/H) of leaf responses to soil elements and enzyme activities and found that the relationship between leaf C:P and soil C:P was homeostatic (p < 0.05), whereas the remaining indices showed the leaf stoichiometries were strictly homeostatic (p > 0.05). Correlation analysis showed both litter C:P and N:P were positively correlated with leaf and soil C:P, while the stoichiometric ratios of soil elements and enzymes were obviously irrelevant with leaf stoichiometries (p > 0.05). Partial least squares path modeling indicated that litter significantly changed soil element and enzyme characteristics through direct and indirect effects, respectively. However, soil elements and enzymes impacted leaf stoichiometries barely, which was further confirmed by an overall redundancy analysis. In summary, C:N:P stoichiometry within the plant–soil continuum revealed that natural P. tabuliformis is a relatively stable ecosystem in the Loess Plateau, where the element exchanges between plant and soil maintain dynamic balance with forest development. Further studies are needed to capture the critical factors that regulate leaf stoichiometry in the soil system.

Selenium species transforming along soil-plant continuum and their beneficial roles for horticultural crops.

Selenium (Se) acquirement from daily diet can help reduce the risk of many diseases. The edible parts of crop plants are the main source of dietary Se, while the Se content in crops is determined by Se bioavailability in soil. We summarize recent research on the biogeochemical cycle of Se driven by specific microorganisms and emphasize the oxidizing process in the Se cycle. Moreover, we discuss how plant root exudates and rhizosphere microorganisms affect soil Se availability. Finally, we cover beneficial microorganisms, including endophytes, that promote crop quality and improve crop tolerance to environmental stresses. Se availability to plants depends on the balance between adsorption and desorption, reduction, methylation and oxidation, which are determined by interactions among soil properties, microbial communities and plants. Reduction and methylation processes governed by bacteria or fungi lead to declined Se availability, while Se oxidation regulated by Se-oxidizing microorganisms increases Se availability to plants. Despite a much lower rate of Se oxidization compared to reduction and methylation, the potential roles of microbial communities in increasing Se bioavailability are probably largely underestimated. Enhancing Se oxidation and Se desorption are crucial for the promotion of Se bioavailability and uptake, particularly in Se-deficient soils. Beneficial roles of Se are reported in terms of improved crop growth and quality, and enhanced protection against fungal diseases and abiotic stress through improved photosynthetic traits, increased sugar and amino acid contents, and promoted defense systems. Understanding Se transformation along the plant-soil continuum is crucial for agricultural production and even for human health.

Alhagi sparsifolia Harbors a Different Root-Associated Mycobiome during Different Development Stages.

The mycobiome in the rhizosphere and within the roots benefits the nutrition and function of host plants. However, compared with the bacterial community, root-associated mycobiomes of desert plants and the forces that drive their assemblage are limited. Here, we investigated the mycobiomes in bulk soil, rhizosphere, and root compartments of Alhagi sparsifolia Shap., a phreatophyte species dominating in Central Asia. The internal transcribed spacer (ITS) gene phylogenetic profiles displayed significantly diverse mycobiomes across three compartments and host growth times, together explaining 31.45% of the variation in the community composition. The community structure of the perennial stage was markedly different from that of other stages (30 days to 2 years old). Along the soil-plant continuum, the α-diversity (estimated by Chao1) decreased gradually, while concomitantly increasing the community dissimilarity and the influence of edaphic factors. Specific leaf area, soil water content, and soil organic matter levels were common factors driving the composition of the three mycobiome communities. A more complex and connected network was observed in the root community compared with the other compartments. Overall, our work suggests that an age-sensitive host effect restructured the desert-plant-root-associated mycobiome, and that edaphic factors and host growth strategy may play potential roles in this process.

Polyphosphate fertilizer use efficiency strongly relies on soil physicochemical properties and root-microbial activities

Limited phosphorus (P) bioavailability restricts global agriculture and food production. This element is considered the least plant-available nutrient, and it is highly susceptible to immobilization in the soil matrix. Among the mineral fertilizers used to increase soil P fertility, polyphosphates (PolyP) consist of polymers of OrthoP residues and have been shown to improve crop P uptake and resulting yields more than other forms of P amendments. PolyP fertilizers are also known for their progressive hydrolysis, improving P availability in the rhizosphere and plant P uptake throughout crop growth stages. However, PolyP behavior in soils is still understudied, including rhizosphere traits likely to be involved in PolyP use efficiency within the soil-root-microbe interface. To improve our knowledge of PolyP behavioral properties in the soil–plant continuum, this review is among the first studies to compile, discuss, and propose ideas regarding this research while focusing on the key soil biochemical factors responsible for PolyP hydrolysis and use by crop roots. A combination of exuded P-hydrolyzing enzymes and acidification of the rhizosphere can presumably mobilize available P from PolyP and thereby improve crop P acquisition. The importance of root-associated microbes (exhibiting high P-mobilization capacities) is also discussed as a promising rhizosphere trait that could contribute greatly to boost PolyP hydrolysis and thus increase PolyP agronomic efficiency.

The host niches of soybean rather than genetic modification or glyphosate application drive the assembly of root-associated microbial communities.

Plant roots significantly influence soil microbial diversity, and soil microorganisms play significant roles in both natural and agricultural ecosystems. Although the genetically modified (GM) crops with enhanced insect and herbicide resistance are thought to have unmatched yield and stress resistance advantages, thorough and in-depth case studies still need to be carried out in a real-world setting due to the potential effects of GM plants on soil microbial communities. In this study, three treatments were used: a recipient soybean variety Jack, a triple transgenic soybean line JD321, and the glyphosate-treated JD321 (JD321G). Three sampling stages (flowering, seed filling and maturing), as well as three host niches of soybean rhizosphere [intact roots (RT), rhizospheric soil (RS) and surrounding soil (SS)] were established. In comparison to Jack, the rhizospheric soil of JD321G had higher urease activity and lower nitrite reductase at the flowering stage. Different treatments and different sampling stages existed no significant effects on the compositions of microbial communities at different taxonomic levels. However, at the genus level, the relative abundance of three plant growth-promoting fungal genera (i.e. Mortierella, Chaetomium and Pseudombrophila) increased while endophytic bacteria Chryseobacterium and pathogenic bacteria Streptomyces decreased from the inside to the outside of the roots (i.e. RT → RS → SS). Moreover, two bacterial genera, Bradyrhizobium and Ensifer were more abundant in RT than in RS and SS, as well as three species, Agrobacterium radiobacter, Ensifer fredii and Ensifer meliloti, which are closely related to nitrogen-fixation. Furthermore, five clusters of orthologous groups (COGs) associated to nitrogen-fixation genes were higher in RT than in RS, whereas only one COG annotated as dinitrogenase iron-molybdenum cofactor biosynthesis protein was lower. Overall, the results imply that the rhizosphere host niches throughout the soil-plant continuum largely control the composition and function of the root-associated microbiome of triple transgenic soybean.

Impact of Cadmium Stress on Growth and Physio-Biochemical Attributes of Eruca sativa Mill.

Plants may experience adverse effects from Cadmium (Cd). As a result of its toxicity and mobility within the soil-plant continuum, it is attracting the attention of soil scientists and plant nutritionists. In this study, we subjected young Eruca sativa Mill. seedlings to different levels of Cd applications (0, 1.5, 6 and 30 µmol/L) via pot experiment to explore its morpho-physio-biochemical adaptations. Our results revealed a significant Cd accumulation in leaves at high Cd stress. It was also demonstrated that Cd stress inhibited photosynthetic rate and pigment levels, ascorbate peroxidase (APX), guaiacol peroxidase (GPX), catalase (CAT), and superoxide dismutase (SOD) enzyme activities, and increased malondialdehyde (MDA) levels. Conversely, the concentration of total ascorbate (TAS) increased at all levels of Cd application, whereas that of ascorbic acid (ASA), and dehydroascorbate (DHA) increased at 1.5 (non-significant), 6, 30 and 6 µmol/L (significant), though their concentrations decreased non-significantly at 30 µmol/L application. In conclusion, Cd-subjected E. sativa seedlings diverted much energy from growth towards the synthesis of anti-oxidant metabolites and osmolytes. However, they did not seem to have protected the E. sativa seedlings from Cd-induced oxidative stress, causing a decrease in osmotic adjustment, and an increase in oxidative damage, which resulted in a reduction in photosynthesis and growth. Accordingly, we recommend that the cultivation of E. sativa should be avoided on soil with Cd contamination.

Toxicity of ZnO and Fe2O3 nano-agro-chemicals to soil microbial activities, nitrogen utilization, and associated human health risks

BackgroundVarious nano-enabled agrochemicals are being extensively used for soil remediation and to boost crop production by increasing the nutrient efficiency of fertilizers. However, understanding of their potential risks on the manure–soil–plant continuum is limited. These nano-agrochemicals can be potentially toxic to soil microbes and their associated functions, such as nitrogen (N) mineralization and decomposition of organic materials. Moreover, the accumulation of nanoparticles (NPs) in edible crops may reduce food quality, and can cause serious threats to human health. Accordingly, here we investigated how zinc (ZONPs) and iron oxide (IONPs) nanoparticles affect the soil microbial communities, their efficiency of decomposition and N mineralization, radish yield, and plant N recovery after soil application of poultry manure (PM). Furthermore, we studied the associated health risks (DIM, HRI) via dietary intake of radish.ResultsSoil application of ZONPs and IONPs significantly (P < 0.05) increased microbial biomass Zn/Fe indicating their microbial utilization. This decreased the colony-forming units (CFU) of bacteria and fungi. For example, the application of PM with ZONPs and IONPs decreased the CFU of bacteria by 32% and 19%, respectively. In case of fungi, the CFU reductions were slightly different (ZONPs: 28% and IONPs: 23%). Consequently, the N mineralization significantly decreased by 62% and 29% due to ZONPs and IONPs, respectively. Which ultimately resulted in the reduction of radish dry matter yield by 22% and 12%. The respective reductions of the apparent N recovery (ANR) were 65% and 39%. Health risk assessment indicated that DIM and HRI values from both the NPs lie under safe limits.ConclusionsWe conclude that both metal oxide nanoparticles (i.e., ZONPs and IONPs) can significantly affect the soil microbial community, their associated functions, and crop yield with the former being relatively more toxic. However, no evidence was found regarding the health risks to humans via dietary radish intake. These toxicological effects imply restricting the widespread production and use of NPs, and developing strategies for their safe disposal to avoid their contact with soil beneficial microorganisms.

Three-Dimensional Vulnerability Assessment of Peanut (Arachis hypogaea) Based on Comprehensive Drought Index and Vulnerability Surface: A Case Study of Shandong Province, China

Agricultural drought is a major problem facing China’s agricultural production. In this study, the cash crop ‘peanut’ was used as an example to explore vulnerability. Through the atmosphere–plant–soil continuum system, a single index that could represent different types of droughts affecting peanuts was selected and weighted using the CRITIC weighting method to construct a multi-source data fusion drought index (MFDI). Then, Pearson correlation analysis between the comprehensive drought index and relative meteorological yield and the Mann–Kendall trend test for different growth periods of peanuts were used to verify MFDI and analyze the variation over time. A three-dimensional vulnerability assessment method of drought intensity–drought duration–yield reduction rate was established based on the run theory and trend surface analysis. The results show that the constructed multi-source data fusion drought index (MFDI) can more accurately characterize the actual drought conditions of peanuts in Shandong Province. The MFDI results showed that the drought severity in the coastal areas of the study area decreased with the growth and development of peanuts, while the drought became more severe in the western and northern parts during the late growth period of peanuts. The vulnerability surface of the drought intensity–drought duration–yield reduction rate showed that when the drought intensity was &lt; 0.8 and the duration was &lt; 3.5 months, the vulnerability of peanut crops was low, and then with the increase in drought intensity or duration, the vulnerability increased. The impact of drought duration cannot be ignored. In contrast to traditional vulnerability assessment methods, this study established a three-dimensional vulnerability surface, which provides a new approach for agricultural drought vulnerability assessment. The research results are helpful for a deeper understanding of the relationship between drought and crop vulnerability and provide scientific support for local governments in formulating disaster prevention and mitigation policies.

Ecological niche selection shapes the assembly and diversity of microbial communities in Casuarina equisetifolia L.

The plant microbiome profoundly affects many aspects of host performance; however, the ecological processes by which plant hosts govern microbiome assembly, function, and dispersal remain largely unknown. Here, we investigated the bacterial and fungal communities in multiple compartment niches (bulk soil, rhizosphere soil, root endosphere, phylloplane, and leaf endosphere) of Casuarina equisetifolia L. at three developmental stages in Hainan Province, China. We found that microbiome assemblages along the soil-plant continuum were shaped by the compartment niches. Bacterial diversity and richness decreased from the soils to roots to leaves, with the highest network complexity found in the roots and the lowest found in the phylloplane. However, fungal diversity gradually increased from the soils to roots to phyllosphere, whereas fungal richness decreased from the soils to roots but increased from the roots to phyllosphere; the greatest network complexity was found in bulk soils and the lowest was found in the roots. Different biomarker taxa occurred in the different ecological niches. Bacterial and fungal communities exhibited distinct ecological functions; the former played important roles in maintaining plant growth and providing nutrients, whereas the latter predominantly decomposed organic matter. The bacterial community of C. equisetifolia mostly originated from bulk soil, whereas the fungal community was mainly derived from rhizosphere soil and air. Leaf endophytes were positively correlated with organic carbon, and root and soil microorganisms were positively correlated with total nitrogen, total phosphorus, and total potassium. Our findings provide empirical evidence for plant-microbiome interactions and contribute to future research on non-crop management and the manipulation of non-crop microbiomes.

Long‐term Camellia oleifera cultivation influences the assembly process of soil bacteria in different soil aggregate particles

AbstractUnderstanding the mechanisms that govern microbial community assembly across a soil–plant continuum is crucial for predicting the responses of ecosystems to environmental changes. However, the impact of the health status of plants on microbial assemblies across these continuums remains poorly understood. In this study, we investigated the stochastic and deterministic processes associated with different aggregate particles and Camellia oleifera growth stages (sapling, maturity, and degeneration periods). The composition of bacterial communities in C. oleifera soil was significantly affected by cultivation length and aggregate size, and cultivation length plays a more important role in the regulation of bacterial composition. The assembly processes of the bacterial community were dominated by deterministic processes in soil aggregates at different growth stages. Soil structurality determined soil α‐diversity and β‐diversity to a greater extent than soil nutrient content. This study provides a comprehensive understanding of the evolutionary mechanisms of soil bacterial community in different soil aggregates and C. oleifera plantation lengths and highlights the significance of soil physical properties to mediate soil microbial community composition and abundance.

Microbiomes in agroecosystem: Diversity, function and assembly mechanisms.

Soils are a main repository of biodiversity harbouring immense diversity of microbial species that plays a central role in fundamental ecological processes and acts as the seed bank for emergence of the plant microbiome in cropland ecosystems. Crop-associated microbiomes play an important role in shaping plant performance, which includes but not limited to nutrient uptake, disease resistance, and abiotic stress tolerance. Although our understanding of structure and function of soil and plant microbiomes has been rapidly advancing, most of our knowledge comes from ecosystems in natural environment. In this review, we present an overview of the current knowledge of diversity and function of microbial communities along the soil-plant continuum in agroecosystems. To characterize the ecological mechanisms for community assembly of soil and crop microbiomes, we explore how crop host and environmental factors such as plant species and developmental stage, pathogen invasion, and land management shape microbiome structure, microbial co-occurrence patterns, and crop-microbiome interactions. Particularly, the relative importance of deterministic and stochastic processes in microbial community assembly is illustrated under different environmental conditions, and potential sources and keystone taxa of the crop microbiome are described. Finally, we highlight a few important questions and perspectives in future crop microbiome research.

Phosphorus supply chain for sustainable food production will have mitigated environmental pressure with region-specific phosphorus management

Achieving synergy between food security and phosphorus (P) resource sustainability has been a major challenge for sustainable agriculture. However, addressing this challenge by linking region-specific and whole-process P management strategies has not been investigated. In this study, data collected from field experiments throughout China's major agroecological zones were used to explore potential paths to achieving P resource sustainability without compromising crop production. High P fertilizer use for crop production in China was accompanied by high P-related environmental pressure that was highly spatially heterogeneous, with hotspots in North China. In addition, crop production in the P supply chain was responsible for 94.2% and 57.2% of water eutrophication and global warming potentials. P consumption using integrated strategies that consider the plant–soil continuum and P supply chain characteristics can reduce P consumption by 42.5% without compromising crop production. Providing a valuable reference for farmers and policymakers seeking solutions to achieve sustainable agriculture.

Differential assembly of root-associated bacterial and fungal communities of a dual transgenic insect-resistant maize line at different host niches and different growth stages.

Transgenic technology has been widely applied to crop development, with genetically modified (GM) maize being the world’s second-largest GM crop. Despite the fact that rhizosphere bacterial and fungal populations are critical regulators of plant performance, few studies have evaluated the influence of GM maize on these communities. Plant materials used in this study included the control maize line B73 and the mcry1Ab and mcry2Ab dual transgenic insect-resistant maize line 2A-7. The plants and soils samples were sampled at three growth stages (jointing, flowering, and maturing stages), and the sampling compartments from the outside to the inside of the root are surrounding soil (SS), rhizospheric soil (RS), and intact root (RT), respectively. In this study, the results of alpha diversity revealed that from the outside to the inside of the root, the community richness and diversity declined while community coverage increased. Morever, the different host niches of maize rhizosphere and maize development stages influenced beta diversity according to statistical analysis. The GM maize line 2A-7 had no significant influence on the composition of microbial communities when compared to B73. Compared to RS and SS, the host niche RT tended to deplete Chloroflexi, Gemmatimonadetes and Mortierellomycota at phylum level. Nitrogen-fixation bacteria Pseudomonas, Herbaspirillum huttiense, Rhizobium leguminosarum, and Sphingomonas azotifigens were found to be enriched in the niche RT in comparison to RS and SS, whilst Bacillus was found to be increased and Stenotrophomonas was found to be decreased at the maturing stage as compared to jointing and flowering stages. The nitrogen fixation protein FixH (clusters of orthologous groups, COG5456), was found to be abundant in RT. Furthermore, the pathogen fungus that causes maize stalk rot, Gaeumannomyces radicicola, was found to be abundant in RT, while the beneficial fungus Mortierella hyalina was found to be depleted in RT. Lastly, the abundance of G. radicicola gradually increased during the development of maize. In conclusion, the host niches throughout the soil-plant continuum rather than the Bt insect-resistant gene or Bt protein secretion were primarily responsible for the differential assembly of root-associated microbial communities in GM maize, which provides the theoretical basis for ecological agriculture.

Community Assembly of Fungi and Bacteria along Soil-Plant Continuum Differs in a Zoige Wetland.

ABSTRACTDistinct plant associated microbiomes live in rhizosphere soil, roots, and leaves. However, the differences in community assembly of fungi and bacteria along soil-plant continuum are less documented in ecosystems. We examined fungal and bacterial communities associated with leaves, roots, and rhizosphere soil of the dominant arbuscular mycorrhizal (AM) plants Taraxacum mongolicum and Elymus nutans and non-AM plant Carex enervis in the Zoige Wetland by using high throughput sequencing techniques. The operational taxonomic unit (OTU) richness of fungi and bacteria was significantly higher in rhizosphere soil than in roots and leaves, and their community compositions were significantly different in the rhizosphere soil, roots, and leaves in each plant species. The co-occurrence network analysis revealed that the sensitive fungal and bacterial OTUs with various taxonomic positions were mainly clustered into different modules according to rhizosphere soil, roots, and leaves in each plant species. Along the soil-plant continuum, the rhizosphere soil pool contributed more source on bacterial than on fungal communities in roots and leaves of the three plant species, and more source on bacterial and fungal communities in leaves of T. mongolicum and E. nutans compared with C. enervis. Furthermore, the root pool contributed more source on bacterial than on fungal communities in leaves of T. mongolicum and E. nutans but not that of C. enervis. This study highlights that the host plant selection intensity is higher in fungal than in bacterial communities in roots and leaves from rhizosphere soil in each plant species, and differs in fungal and bacterial communities along the soil-plant continuum in AM plants T. mongolicum and E. nutans and non-AM plant C. enervis in the Zoige Wetland.IMPORTANCE Elucidating the community microbiome assemblage alone the soil-plant continuum will help to better understand the biodiversity maintenance and ecosystem functioning. Here, we examined the fungal and bacterial communities in rhizosphere soil, roots, and leaves of two dominant AM plants and a non-AM plant in Zoige Wetland. We found that along the soil – plant continuum, host plant selection intensity is higher in fungal than in bacterial communities in roots and leaves from rhizosphere soil in each plant species, and differs in fungal and bacterial communities in the AM- and non-AM plants. This is the first report provides evidence of different assembly patterns of fungal and bacterial communities along the soil-plant continuum in the AM- and non-AM plants in the Zoige Wetland.

Multicriteria evaluation of the AquaCrop crop model in a hilly rainfed Mediterranean agrosystem

Exploring crop spatial organizations within landscapes is a promising solution for agroecological transitions and climate change adaptation in Mediterranean rainfed hilly agrosystems. A prerequisite is to ensure that crop models can simulate a range of agrohydrological processes in such agrosystems. The current study deepened the evaluation of the AquaCrop model by conducting a multicriteria evaluation (canopy cover CC, dry aboveground biomass AGB, actual evapotranspiration ETa, runoff R, soil water content SWC) for a range of crop and soil combinations, and for contrasted hydroclimatic years in northeastern Tunisia. The data were collected in the Kamech catchment (OMERE Observatory) during nine measurement campaigns on predominant soils and crops. AquaCrop simulations were based on field observations and parameters from the literature. AquaCrop could simulate plant dynamics and water fluxes for contrasted hydroclimatic years, with a slight dependence on soil class and a significant dependence on crop type. Model simulations were of moderate quality for CC (R2 of 0.45, RMSE of 0.24 on average) and of acceptable quality for AGB (R2 of 0.81, RMSE of 0.85 ton ha−1 on average). AquaCrop acceptably simulated water transfer across the soil–plant continuum (R2 of 0.62, RMSE of 0.77 mm day−1 on average for ETa; R2 of 0.68, RMSE of 0.75 mm day−1 on average for R; R2 of 0.86, RMSE of 27.4 mm on average for SWC). The model performances were satisfactory for most cases, with p values larger than 5 % for the Student’s t test on linear regressions of validation. Our results were similar to those reported in previous studies over flat terrain, including delayed senescence by model simulations with subsequent overestimation of CC and AGB observations. Additionally, soil cracks likely altered the AquaCrop ability to simulate runoff. Despite these limitations, our results support the application of AquaCrop to evaluate water productivity in hilly agrosystems.