Sustainable Cropping Requires Adaptation to a Heterogeneous Rhizosphere

Colorful windows to the dark rhizosphere

The dynamic and complex interactions between plant and microbiomes in the rhizosphere play a major role in the plant's health and productivities. Using interdisciplinary approaches, Behr et al. studied how farming practices can influence the rhizosphere process, offering an exciting direction for microbial manipulation to enhance agricultural productivity.

Maize functional requirements drive the selection of rhizobacteria under long-term fertilization practices

Rhizosphere microbiomes are pivotal for crop fitness, but the principles underlying microbial assembly during root-soil interactions across soils with different nutrient statuses remain elusive. We examined the microbiomes in the rhizosphere and bulk soils of maize plants grown under six long-term (≥ 29 yr) fertilization experiments in three soil types across middle temperate to subtropical zones. The assembly of rhizosphere microbial communities was primarily driven by deterministic processes. Plant selection interacted with soil types and fertilization regimes to shape the structure and function of rhizosphere microbiomes. Predictive functional profiling showed that, to adapt to nutrient-deficient conditions, maize recruited more rhizobacteria involved in nutrient availability from bulk soil, although these functions were performed by different species. Metagenomic analyses confirmed that the number of significantly enriched Kyoto Encyclopedia of Genes and Genomes Orthology functional categories in the rhizosphere microbial community was significantly higher without fertilization than with fertilization. Notably, some key genes involved in carbon, nitrogen, and phosphorus cycling and purine metabolism were dominantly enriched in the rhizosphere soil without fertilizer input. In conclusion, our results show that maize selects microbes at the root-soil interface based on microbial functional traits beneficial to its own performance, rather than selecting particular species.

Trichoderma-secreted anthranilic acid promotes lateral root development via auxin signaling and RBOHF-induced endodermal cell wall remodeling

Trichoderma spp. have evolved the capacity to communicate with plants by producing various secondary metabolites (SMs). Nonhormonal SMs play important roles in plant root development, while specific SMs from rhizosphere microbes and their underlying mechanisms to control plant root branching are still largely unknown. In this study, a compound, anthranilic acid (2-AA), is identified from T. guizhouense NJAU4742 to promote lateral root development. Further studies demonstrate that 2-AA positively regulates auxin signaling and transport in the canonical auxin pathway. 2-AA also partly rescues the lateral root numbers of CASP1pro:shy2-2, which regulates endodermal cell wall remodeling via an RBOHF-induced reactive oxygen species burst. In addition, our work reports another role for microbial 2-AA in the regulation of lateral root development, which is different from its better-known role in plant indole-3-acetic acid biosynthesis. In summary, this study identifies 2-AA from T. guizhouense NJAU4742, which plays versatile roles in regulating plant root development.

Root plasticity versus elasticity - when are responses acclimative?

Spatiotemporal soil heterogeneity and the resulting edaphic stress cycles can be decisive for crop growth. However, our understanding of the acclimative value of root responses to heterogeneous soil conditions remains limited. We outline a framework to evaluate the acclimative value of root responses that distinguishes between stress responses that are persistent and reversible upon stress release, termed 'plasticity' and 'elasticity', respectively. Using energy balances, we provide theoretical evidence that the advantage of plasticity over elasticity increases with the number of edaphic stress cycles and if responses lead to comparatively high energy gains. Our framework provides a conceptual basis for assessing the acclimative value of root responses to soil heterogeneity and can catalyse research on crop adaptations to heterogeneous belowground environments.

Genotypic differences in systemic root responses to mechanical obstacles

As roots grow through the soil to forage for water and nutrients, they encounter mechanical obstacles such as patches of dense soil and stones that locally impede root growth. Here, we investigated hitherto poorly understood systemic responses of roots to localised root impedance. Seedlings of two wheat genotypes were grown in hydroponics and exposed to impenetrable obstacles constraining the vertical growth of the primary or a single seminal root. We deployed high-resolution in vivo imaging to quantify temporal dynamics of root elongation rate, helical root movement, and root growth direction. The two genotypes exhibited distinctly different patterns of systemic responses to localised root impedance, suggesting different strategies to cope with obstacles, namely stress avoidance and stress tolerance. Shallower growth of unconstrained seminal roots and more pronounced helical movement of unconstrained primary and seminal roots upon localised root impedance characterised the avoidance strategy shown by one genotype. Stress tolerance to localised root impedance, as exhibited by the other genotype, was indicated by relatively fast elongation of primary roots and steeper seminal root growth. These different strategies highlight that the effects of mechanical obstacles on spatiotemporal root growth patterns can differ within species, which may have major implications for resource acquisition and whole-plant growth.

15 N labeling technology reveals enhancement of nitrogen uptake and transfer by root interaction in cotton/soybean intercropping

BACKGROUND

Biological nitrogen fixation in legumes and their transfer of nitrogen to non-legumes in legume/non-legume intercropping systems are considered to be important for the improvement of productivity. However, research on interspecific interaction and root nitrogen transfer in cotton/soybean intercropping systems has rarely been undertaken. In this study, the roots of cotton and soybean were separated with either complete root barriers (CB), using plastic film, or semi-root barriers (SB), using nylon net. No root barrier (NB) was used as the control.

RESULTS

The results showed that cotton produced more above-ground dry matter (DM) than soybean. The above-ground DM and nitrogen uptake of cotton was greatest with the NB treatment. The above-ground DM and nitrogen uptake of soybean was greatest with the CB treatment. At the harvest stage, the nitrogen transfer rate from soybean to cotton was 22.47% with the SB treatment and 40.41% with the NB treatment. Interspecific root interaction increased the nitrogen transfer amount, especially for the cotton roots in the 0-15 cm soil layer and for the soybean roots in the 0-30 cm soil layer. The root distribution of soybean was the key factor affecting nitrogen transfer amount, and nitrogen transfer amount was the key factor affecting nitrogen uptake of cotton in the cotton/soybean intercropping system.

CONCLUSION

These results indicated that nitrogen transfer from soybean to cotton through root interaction improved cotton above-ground DM and nitrogen uptake. © 2023 Society of Chemical Industry.

Divergence in the distribution of di(2-ethylhexyl) phthalate (DEHP) in two soils

Understanding the distribution of di(2-ethylhexyl) phthalate (DEHP) is necessary for future risk evaluation of DEHP in agricultural soils. This study used 14C-labeled DEHP to examine its volatilization, mineralization, extractable residues, and non-extractable residues (NERs) incubated in Chinese typical red and black soil with/without Brassica chinensis L. Results showed that after incubated for 60 days, 46.3% and 95.4% of DEHP were mineralized or transformed into NERs in red and black soil, respectively. The distribution of DEHP in humic substances as NER descended in order: humin > fulvic acids > humic acids. DEHP in black soil was more bioavailable, with 6.8% of initial applied radioactivity left as extractable residues at the end of incubation when compared with red soil (54.5%). Planting restrained the mineralization of DEHP by 18.5% and promoted the extractable residues of DEHP by 1.5% for black soil, but no such restrain was observed in red soil. These findings provide valuable information for understanding the distribution of DEHP in different soils and develop the understanding for the risk assessments of PAEs in typical soils.

The Microbial Connection to Sustainable Agriculture

Microorganisms are an important element in modeling sustainable agriculture. Their role in soil fertility and health is crucial in maintaining plants' growth, development, and yield. Further, microorganisms impact agriculture negatively through disease and emerging diseases. Deciphering the extensive functionality and structural diversity within the plant-soil microbiome is necessary to effectively deploy these organisms in sustainable agriculture. Although both the plant and soil microbiome have been studied over the decades, the efficiency of translating the laboratory and greenhouse findings to the field is largely dependent on the ability of the inoculants or beneficial microorganisms to colonize the soil and maintain stability in the ecosystem. Further, the plant and its environment are two variables that influence the plant and soil microbiome's diversity and structure. Thus, in recent years, researchers have looked into microbiome engineering that would enable them to modify the microbial communities in order to increase the efficiency and effectiveness of the inoculants. The engineering of environments is believed to support resistance to biotic and abiotic stressors, plant fitness, and productivity. Population characterization is crucial in microbiome manipulation, as well as in the identification of potential biofertilizers and biocontrol agents. Next-generation sequencing approaches that identify both culturable and non-culturable microbes associated with the soil and plant microbiome have expanded our knowledge in this area. Additionally, genome editing and multidisciplinary omics methods have provided scientists with a framework to engineer dependable and sustainable microbial communities that support high yield, disease resistance, nutrient cycling, and management of stressors. In this review, we present an overview of the role of beneficial microbes in sustainable agriculture, microbiome engineering, translation of this technology to the field, and the main approaches used by laboratories worldwide to study the plant-soil microbiome. These initiatives are important to the advancement of green technologies in agriculture.

Root-Soil Interactions for Pepper Accessions Grown under Organic and Conventional Farming

Modern agriculture has boosted the production of food based on the use of pesticides and fertilizers and improved plant varieties. However, the impact of some such technologies is high and not sustainable in the long term. Although the importance of rhizospheres in final plant performance, nutrient cycling, and ecosystems is well recognized, there is still a lack of information on the interactions of their main players. In this paper, four accessions of pepper are studied at the rhizosphere and root level under two farming systems: organic and conventional. Variations in soil traits, such as induced respiration, enzymatic activities, microbial counts, and metabolism of nitrogen at the rhizosphere and bulk soil, as well as measures of root morphology and plant production, are presented. The results showed differences for the evaluated traits between organic and conventional management, both at the rhizosphere and bulk soil levels. Organic farming showed higher microbial counts, enzymatic activities, and nitrogen mobilization. Our results also showed how some genotypes, such as Serrano or Piquillo, modified the properties of the rhizospheres in a very genotype-dependent way. This specificity of the soil-plant interaction should be considered for future breeding programs for soil-tailored agriculture.

Resource-dependent biodiversity and potential multi-trophic interactions determine belowground functional trait stability

BACKGROUND

For achieving long-term sustainability of intensive agricultural practices, it is pivotal to understand belowground functional stability as belowground organisms play essential roles in soil biogeochemical cycling. It is commonly believed that resource availability is critical for controlling the soil biodiversity and belowground organism interactions that ultimately lead to the stabilization or collapse of terrestrial ecosystem functions, but evidence to support this belief is still limited. Here, we leveraged field experiments from the Chinese National Ecosystem Research Network (CERN) and two microcosm experiments mimicking high and low resource conditions to explore how resource availability mediates soil biodiversity and potential multi-trophic interactions to control functional trait stability.

RESULTS

We found that agricultural practice-induced higher resource availability increased potential cross-trophic interactions over 316% in fields, which in turn had a greater effect on functional trait stability, while low resource availability made the stability more dependent on the potential within trophic interactions and soil biodiversity. This large-scale pattern was confirmed by fine-scale microcosm systems, showing that microcosms with sufficient nutrient supply increase the proportion of potential cross-trophic interactions, which were positively associated with functional stability. Resource-driven belowground biodiversity and multi-trophic interactions ultimately feedback to the stability of plant biomass.

CONCLUSIONS

Our results indicated the importance of potential multi-trophic interactions in supporting belowground functional trait stability, especially when nutrients are sufficient, and also suggested the ecological benefits of fertilization programs in modern agricultural intensification. Video Abstract.

Rhizosphere engineering for sustainable crop production: entropy-based insights

There is a growing interest in exploring interactions at root-soil interface in natural and agricultural ecosystems, but an entropy-based understanding of these dynamic rhizosphere processes is lacking. We have developed a new conceptual model of rhizosphere regulation by localized nutrient supply using thermodynamic entropy. Increased nutrient-use efficiency is achieved by rhizosphere management based on self-organization and minimized entropy via equilibrium attractors comprising (i) optimized root strategies for nutrient acquisition and (ii) improved information exchange related to root-soil-microbe interactions. The cascading effects through different hierarchical levels amplify the underlying processes in plant-soil system. We propose a strategy for manipulating rhizosphere dynamics and improving nutrient-use efficiency by localized nutrient supply with minimization of entropy to underpin sustainable food/feed/fiber production.

Crop domestication disrupts intercropping benefits: A case study from barley-faba bean mixture under contrasting P inputs

How crop domestication mediates root functional traits and trait plasticity in response to neighboring plants is unclear, but it is important for selecting potential species to be grown together to facilitate P uptake. We grew two barley accessions representing a two-stage domestication process as a sole crop or mixed with faba bean under low and high P inputs. We analyzed six root functional traits associated with P acquisition and plant P uptake in five cropping treatments in two pot experiments. The spatial and temporal patterns of root acid phosphatase activity were characterized in situ with zymography at 7, 14, 21, and 28 days after sowing in a rhizobox. Under low P supply, wild barley had higher total root length (TRL), specific root length (SRL), and root branching intensity (RootBr) as well as higher activity of acid phosphatase (APase) in the rhizosphere, but lower root exudation of carboxylates and mycorrhizal colonization (MC), relative to domesticated barley. In response to neighboring faba bean, wild barley exhibited larger plasticity in all root morphological traits (TRL, SRL, and RootBr), while domesticated barley showed greater plasticity in root exudates of carboxylates and colonization by mycorrhiza. Wild barley with greater root morphology-related trait plasticity was a better match with faba bean than domesticated barley, indicated by higher P uptake benefits in wild barley/faba bean than domesticated barley/faba bean mixtures under low P supply. Our findings indicated that the domestication of barley disrupts the intercropping benefits with faba bean through the shifts of root morphological traits and their plasticity in barley. Such findings provide valuable information for barley genotype breeding and the selection of species combinations to enhance P uptake.

Characterizing bacterial communities in Phragmites australis rhizosphere and non-rhizosphere sediments under pressure of antibiotics in a shallow lake

Introduction

Antibiotics are ubiquitous pollutants and widely found in aquatic ecosystems, which of rhizosphere sediment and rhizosphere bacterial communities had certain correlation. However, the response of bacterial communities in Phragmites australis rhizosphere and non-rhizosphere sediments to antibiotics stress is still poorly understood.

Methods

To address this knowledge gap, the samples of rhizosphere (R) and non-rhizosphere (NR) sediments of P. australis were collected to investigate the differences of bacterial communities under the influence of antibiotics and key bacterial species and dominate environmental factors in Baiyangdian (BYD) Lake.

Results

The results showed that the contents of norfloxacin (NOR), ciprofloxacin (CIP) and total antibiotics in rhizosphere sediments were significantly higher than that in non-rhizosphere sediments, meanwhile, bacterial communities in non-rhizosphere sediments had significantly higher diversity (Sobs, Shannon, Simpsoneven and PD) than those in rhizosphere sediments. Furthermore, total antibiotics and CIP were found to be the most important factors in bacterial diversity. The majority of the phyla in rhizosphere sediments were Firmicutes, Proteobacteria and Campilobacterota, while Proteobacteria, Chloroflexi was the most abundant phyla followed by Bacteroidota, Actinobacteriota in non-rhizosphere sediments. The dominate factors of shaping the bacterial communities in rhizosphere were total antibiotics, pH, sediment organic matter (SOM), and NH₄-N, while dissolved organic carbon (DOC), NO₃-N, pH, and water contents (WC) in non-rhizosphere sediments.

Discussion

It is suggested that antibiotics may have a substantial effect on bacterial communities in P. australis rhizosphere sediment, which showed potential risk for ARGs selection pressure and dissemination in shallow lake ecosystems.

Evaluation of the Ecological Environment Affected by Cry1Ah1 in Poplar

Populus is a genus of globally significant plantation trees used widely in industrial and agricultural production. Poplars are easily damaged by Micromelalopha troglodyta and Hyphantria cunea, resulting in decreasing quality. Bt toxin-encoded by the Cry gene has been widely adopted in poplar breeding because of its strong insect resistance. There is still no comprehensive and sufficient information about the effects of Cry1Ah1-modified (CM) poplars on the ecological environment. Here, we sampled the rhizosphere soils of field-grown CM and non-transgenic (NT) poplars and applied 16S rRNA and internal transcribed spacer amplicon Illumina MiSeq sequencing to determine the bacterial community associated with the CM and NT poplars. Based on the high-throughput sequencing of samples, we found that the predominant taxa included Proteobacteria (about 40% of the total bacteria), Acidobacteria (about 20% of the total bacteria), and Actinobacteria (about 20% of the total bacteria) collected from the natural rhizosphere of NT and CM poplars. In addition, studies on the microbial diversity of poplar showed that Cry1Ah1 expression has no significant influence on rhizosphere soil alkaline nitrogen, but significantly affects soil phosphorus, soil microbial biomass nitrogen, and carbon. The results exhibited a similar bacterial community structure between CM varieties affected by the expression of Cry1Ah1 and non-transgenic poplars. In addition, Cry1Ah1 expression revealed no significant influence on the composition of rhizosphere microbiomes. These results broadly reflect the effect of the Bt toxin-encoded by Cry1Ah1 on the ecology and environment and provide a clear path for researchers to continue research in this field in the future.

Global transcriptome and coexpression network analyses reveal cultivar-specific molecular signatures associated with different rooting depth responses to drought stress in potato

Potato is one of the most important vegetable crops worldwide. Its growth, development and ultimately yield is hindered by drought stress condition. Breeding and selection of deep-rooted and drought-tolerant potato varieties has become a prime approach for improving the yield and quality of potato (Solanum tuberosum L.) in arid and semiarid areas. A comprehensive understanding of root development-related genes has enabled scientists to formulate strategies to incorporate them into breeding to improve complex agronomic traits and provide opportunities for the development of stress tolerant germplasm. Root response to drought stress is an intricate process regulated through complex transcriptional regulatory network. To understand the rooting depth and molecular mechanism, regulating root response to drought stress in potato, transcriptome dynamics of roots at different stages of drought stress were analyzed in deep (C119) and shallow-rooted (C16) cultivars. Stage-specific expression was observed for a significant proportion of genes in each cultivar and it was inferred that as compared to C16 (shallow-rooted), approximately half of the genes were differentially expressed in deep-rooted cultivar (C119). In C16 and C119, 11 and 14 coexpressed gene modules, respectively, were significantly associated with physiological traits under drought stress. In a comparative analysis, some modules were different between the two cultivars and were associated with differential response to specific drought stress stage. Transcriptional regulatory networks were constructed, and key components determining rooting depth were identified. Through the results, we found that rooting depth (shallow vs deep) was largely determined by plant-type, cell wall organization or biogenesis, hemicellulose metabolic process, and polysaccharide metabolic process. In addition, candidate genes responding to drought stress were identified in deep (C119) and shallow (C16) rooted potato varieties. The results of this study will be a valuable source for further investigations on the role of candidate gene(s) that affect rooting depth and drought tolerance mechanisms in potato.

Biodiversity-based cropping systems: A long-term perspective is necessary

Biodiversity-based cropping systems are an interesting option to address the many challenges that agriculture faces. However, benefits of these systems should not obscure the fact that creating biodiversity-based cropping systems represents a major change for farmers. To address this challenge, we argue that designing biodiversity-based cropping systems requires transforming ecological concepts into technical opportunities. Indeed, integrating ecological concepts such as plant-soil feedback and plant functional traits more strongly into cropping system design offers promising opportunities for the provision of ecosystem services, such as pest and disease control, crop production (including crop yield stability), climate regulation and regulation of soil quality. Accordingly, we demonstrate that designing biodiversity-based cropping systems requires considering not only the short term but also the long term. This would ensure that the expected ecosystem services have enough time to build up and provide their full effects, that the cropping systems are resilient and that they avoid the limitations of short-term assessments, which do not sufficiently consider multi-year effects. Considering long-term consequences of system change - induced by biodiversity - is essential to identify potential trade-offs between ecosystem services, as well as agricultural obstacles to and mechanisms of change. Including farmers and other food-chain actors in cropping system design would help find acceptable compromises that consider not only the provision of ecosystem services, but also other dimensions related to economic viability, workload or the technical feasibility of crops, which are identified as major obstacles to crop diversification. This strategy represents an exciting research front for the development of agroecological cropping systems.

Maize and peanut intercropping improves the nitrogen accumulation and yield per plant of maize by promoting the secretion of flavonoids and abundance of Bradyrhizobium in rhizosphere

Belowground interactions mediated by root exudates are critical for the productivity and efficiency of intercropping systems. Herein, we investigated the process of microbial community assembly in maize, peanuts, and shared rhizosphere soil as well as their regulatory mechanisms on root exudates under different planting patterns by combining metabolomic and metagenomic analyses. The results showed that the yield of intercropped maize increased significantly by 21.05% (2020) and 52.81% (2021), while the yield of intercropped peanut significantly decreased by 39.51% (2020) and 32.58% (2021). The nitrogen accumulation was significantly higher in the roots of the intercropped maize than in those of sole maize at 120 days after sowing, it increased by 129.16% (2020) and 151.93% (2021), respectively. The stems and leaves of intercropped peanut significantly decreased by 5.13 and 22.23% (2020) and 14.45 and 24.54% (2021), respectively. The root interaction had a significant effect on the content of ammonium nitrogen (NH₄ ⁺-N) as well as the activities of urease (UE), nitrate reductase (NR), protease (Pro), and dehydrogenase (DHO) in the rhizosphere soil. A combined network analysis showed that the content of NH₄ ⁺-N as well as the enzyme activities of UE, NR and Pro increased in the rhizosphere soil, resulting in cyanidin 3-sambubioside 5-glucoside and cyanidin 3-O-(6-Op-coumaroyl) glucoside-5-O-glucoside; shisonin were significantly up-regulated in the shared soil of intercropped maize and peanut, reshaped the bacterial community composition, and increased the relative abundance of Bradyrhizobium. These results indicate that interspecific root interactions improved the soil microenvironment, regulated the absorption and utilization of nitrogen nutrients, and provided a theoretical basis for high yield and sustainable development in the intercropping of maize and peanut.

Root Foraging Strategy Improves the Adaptability of Tea Plants (Camellia sinensis L.) to Soil Potassium Heterogeneity

Root foraging enables plants to obtain more soil nutrients in a constantly changing nutrient environment. Little is known about the adaptation mechanism of adventitious roots of plants dominated by asexual reproduction (such as tea plants) to soil potassium heterogeneity. We investigated root foraging strategies for K by two tea plants (low-K tolerant genotype “1511” and low-K intolerant genotype “1601”) using a multi-layer split-root system. Root exudates, root architecture and transcriptional responses to K heterogeneity were analyzed by HPLC, WinRHIZO and RNA-seq. With the higher leaf K concentrations and K biological utilization indexes, “1511” acclimated to K heterogeneity better than “1601”. For “1511”, maximum total root length and fine root length proportion appeared on the K-enriched side; the solubilization of soil K reached the maximum on the low-K side, which was consistent with the amount of organic acids released through root exudation. The cellulose decomposition genes that were abundant on the K-enriched side may have promoted root proliferation for “1511”. This did not happen in “1601”. The low-K tolerant tea genotype “1511” was better at acclimating to K heterogeneity, which was due to a smart root foraging strategy: more roots (especially fine roots) were developed in the K-enriched side; more organic acids were secreted in the low-K side to activate soil K and the root proliferation in the K-enriched side might be due to cellulose decomposition. The present research provides a practical basis for a better understanding of the adaptation strategies of clonal woody plants to soil nutrient availability.

Ensuring future food security and resource sustainability: insights into the rhizosphere

Feeding the world’s growing population requires continuously increasing crop yields with less fertilizers and agrochemicals on limited land. Focusing on plant belowground traits, especially root-soil-microbe interactions, holds a great promise for overcoming this challenge. The belowground root-soil-microbe interactions are complex and involve a range of physical, chemical, and biological processes that influence nutrient-use efficiency, plant growth and health. Understanding, predicting, and manipulating these rhizosphere processes will enable us to harness the relevant interactions to improve plant productivity and nutrient-use efficiency. Here, we review the recent progress and challenges in root-soil-microbe interactions. We also highlight how root-soil-microbe interactions could be manipulated to ensure food security and resource sustainability in a changing global climate, with an emphasis on reducing our dependence on fertilizers and agrochemicals.

Short-term effects of polyethene and polypropylene microplastics on soil phosphorus and nitrogen availability

Microplastics are an emerging threat to soils, but little is known about their effects on soil nitrogen (N) and phosphorus (P) cycling. In this study, a three-month soil incubation experiment has been conducted to analyze the effects of polyethene (PE) and polypropylene (PP) microplastics in sizes of 0-1 mm and 1-5 mm on soil available phosphate, nitrate, and ammonium contents under different fertilization regimes. Soil phosphorus and nitrogen availability were continuously determined in-situ by ion-exchange membrane method during the incubation. Microplastic surface chemical composition and the specific surface area were analyzed by FTIR and BET, respectively. The 16s rRNA sequencing of soil bacterial communities as well as soil pH have been determined after the incubation. The results showed that the presence of microplastics could significantly (P < 0.05) decrease soil available phosphate content from 122.61 mg P L^-1 to 63.43 mg P L^-1. The addition of PP microplastics could significantly increase soil available ammonium content from 0.94 mg N L^-1 to 1.53 mg N L^-1. Since microplastics had undetectable specific surface area and limited effects on soil microorganisms, adsorption and microorganism alteration functions might not be the main drivers of microplastic effects on soil phosphorus and nitrogen.

Robust identification of low-Cd rice varieties by boosting the genotypic effect of grain Cd accumulation in combination with marker-assisted selection

Rice (Oryza sativa L.), a staple for half of the world's population, usually accumulates high levels of cadmium (Cd) in the grain when planted in the Cd-contaminated paddy fields. Genetic improvements using natural variation of grain-Cd accumulation is the most cost-effective way to mitigate the risk of excess Cd accumulation. However, as a complex trait, grain-Cd accumulation is susceptible to environmental variation, which challenges to characterize the genetic nature and subsequently the stable performance of grain-Cd accumulation. To boost the genetic effect on grain-Cd performance, we established an approach of normalization using the comparative grain-Cd value (CCd) following a contrasting field design. Identification of the genetic locus responsible for CCd variation help us develop a low-grain-Cd variety de novo, named 'Lushansimiao', which had lower grain-Cd levels in a large-scale field test and can produce Cd-safe rice following prolonged irrigations in the field with intermediate levels of Cd pollution. Combined CCd evaluating and low-Cd allelic genotyping, another six varieties were also identified as low-grain-Cd rice. Our study paves the way to efficiently quantify the genetic nature of grain-Cd accumulation in rice, and the stable low-Cd rice varieties will help to mitigate the risk of excess Cd accumulation in rice.

The Immediate Hotspot of Microbial Nitrogen Cycling in an Oil-Seed Rape (Brassica campestris L.) Soil System Is the Bulk Soil Rather Than the Rhizosphere after Biofertilization

Biofertilizers are substances that promote plant growth through the efficacy of living microorganisms. The functional microbes comprising biofertilizers are effective mediators in plant-soil systems in the regulation of nitrogen cycling, especially in nitrification repression. However, the deterministic or stochastic distribution of the functional hotspot where microbes are active immediately after biofertilization is rarely investigated. Here, pot experiments with oil-seed rape (Brassica campestris L.) were conducted with various chemical and biological fertilizers in order to reveal the distribution of the hotspot after each fertilization. A stimulated dynamic of the nitrogen cycling-related genes in the bulk soil inferred that the bulk soil was likely to be the hotspot where the inoculated bacterial fertilizers dominated the nitrogen cycle. Furthermore, a network analysis showed that bulk soil microbial communities were more cooperative than those in the rhizosphere after biofertilization, suggesting that the microbiome of the bulk soils were more efficient for nutrient cycling. In addition, the relatively abundant ammonia-oxidizing bacteria and archaea present in the networks of bulk soil microbial communities further indicated that the bulk soil was the plausible hotspot after the application of the biofertilizers. Therefore, our research provides a new insight into the explicit practice of plant fertilization and agricultural management, which may improve the implementational efficiency of biofertilization.

Peanut Rotation and Flooding Induce Rhizobacteriome Variation With Opposing Influences on the Growth and Medicinal Yield of Corydalis yanhusuo

Corydalis yanhusuo, a precious herb of the Papaveraceae family, is widely used in multiple traditional Chinese medicines for the treatment of many painful conditions, and its medicinal part is the dried tuber. Yet how to improve this plant's medicinal yield as well as its economic efficiency remains a key problem in its cultivation. The planting of C. yanhusuo in rotation with peanut (Arachis hypogaea L.) aims to improve land utilization efficiency, but the total production of tubers is severely reduced relative to fields without rotation. However, an increased yield was observed in C. yanhusuo plants grown in previously flooded fields (HR field) compared to the ones grown in the fields that had been used to cultivate peanut (PL field) or in fields without rotation or flooding (N field). Based on these phenomena, in this study, we explored the potential factors responsible for the altered growth/yield of C. yanhusuo under different field conditions. Soil physicochemical properties and the diversity and community of rhizobacteriome of C. yanhusuo were both analyzed. By testing several soil physicochemical properties, we found that the cation exchange capacity (CEC), soil organic matter (SOM), total nitrogen (TN), and pH value differed significantly among these three types of fields. 16S rRNA amplicon sequencing revealed stark differences in the composition, diversity, and potential functions of the bacterial community in the rhizosphere of C. yanhusuo plants grown in field with the peanut rotation or flooding. Notably, the Acidobacteria were enriched in the HR field, while Actinobacteria were enriched in the PL field. More importantly, further analysis showed that changed soil physicochemical properties could be one reason for why the rhizospheric bacterial community has changed; hence, soil physicochemical properties might also be affecting plant performance indirectly by regulating the rhizospheric bacterial community. The RDA analysis distinguished CEC as the most important soil physicochemical property influencing the structure and composition of the C. yanhusuo rhizobacteriome. In summary, our results suggest peanut rotation- and flooding-induced soil physicochemical properties changes would further impact the rhizobacteriome of C. yanhusuo albeit differentially, culminating in opposite effects upon the plant growth and medicinal yield of C. yanhusuo.

Engineering Host Microbiome for Crop Improvement and Sustainable Agriculture

Dynamic consortium of microbial communities (bacteria, fungi, protists, viruses, and nematodes) colonizing multiple tissue types and coevolving conclusively with the host plant is designated as a plant microbiome. The interplay between plant and its microbial mutualists supports several agronomic functions, establishing its crucial role in plant beneficial activities. Deeper functional and mechanistic understanding of plant-microbial ecosystems will render many "ecosystem services" by emulating symbiotic interactions between plants, soil, and microbes for enhanced productivity and sustainability. Therefore, microbiome engineering represents an emerging biotechnological tool to directly add, remove, or modify properties of microbial communities for higher specificity and efficacy. The main goal of microbiome engineering is enhancement of plant functions such as biotic/abiotic stresses, plant fitness and productivities, etc. Various ecological-, biochemical-, and molecular-based approaches have come up as a new paradigm for disentangling many microbiome-based agromanagement hurdles. Furthermore, multidisciplinary approaches provide a predictive framework in achieving a reliable and sustainably engineered plant-microbiome for stress physiology, nutrient recycling, and high-yielding disease-resistant genotypes.

Molecular Evolution and Local Root Heterogeneous Expression of the Chenopodium quinoa ARF Genes Provide Insights into the Adaptive Domestication of Crops in Complex Environments

Auxin response factors (ARFs) influence plant growth and development via the coupling of basic biological processes. However, the evolution, expansion, and regulatory mechanisms of ARFs in the domesticated crop quinoa after artificial selection remain elusive. In this study, we systematically identified 30 Chenopodium quinoa ARFs (CqARFs). In this typical domesticated crop, ARFs divided into three subfamilies are subjected to strong purification selection and have a highly conserved evolutionary pattern. Polyploidy is the primary reason for the expansion of the ARF family after quinoa domestication. The expression patterns of CqARFs in different tissues have been differentiated, and CqARF2, 5, 9 and 10 from class A have the characteristics of local heterogeneous expression in different regions of roots, which may be the key factors for crops to respond in complex environments. Overall, we examined the evolution and expansion of ARFs in representative domesticated crops using the genome, transcriptome, and molecular biology and discovered a class A ARF-centered heterogeneous expression network that played an important role in auxin signaling and environmental responses. We provide new insights into how ARFs promote domesticated crop adaptation to artificial selection by polyploid expansion.