Dataset Information

Characterization of Cover Crop Rooting Types from Integration of Rhizobox Imaging and Root Atlas Information.

ABSTRACT: Plant root systems are essential for sustainable agriculture, conveying resource-efficient genotypes and species with benefits to soil ecosystem functions. Targeted selection of species/genotypes depends on available root system information. Currently there is no standardized approach for comprehensive root system characterization, suggesting the need for data integration across methods and sources. Here, we combine field measured root descriptors from the classical Root Atlas series with traits from controlled-environment root imaging for 10 cover crop species to (i) detect descriptors scaling between distant experimental methods, (ii) provide traits for species classification, and (iii) discuss implications for cover crop ecosystem functions. Results revealed relation of single axes measures from root imaging (convex hull, primary-lateral length ratio) to Root Atlas field descriptors (depth, branching order). Using composite root variables (principal components) for branching, morphology, and assimilate investment traits, cover crops were classified into species with (i) topsoil-allocated large diameter rooting type, (ii) low-branched primary/shoot-born axes-dominated rooting type, and (iii) highly branched dense rooting type, with classification trait-dependent distinction according to depth distribution. Data integration facilitated identification of root classification variables to derive root-related cover crop distinction, indicating their agro-ecological functions.

SUBMITTER: Bodner G

PROVIDER: S-EPMC6918168 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Characterization of Cover Crop Rooting Types from Integration of Rhizobox Imaging and Root Atlas Information.

Bodner Gernot G Loiskandl Willibald W Hartl Wilfried W Erhart Eva E Sobotik Monika M

Plants (Basel, Switzerland) 20191117 11

Plant root systems are essential for sustainable agriculture, conveying resource-efficient genotypes and species with benefits to soil ecosystem functions. Targeted selection of species/genotypes depends on available root system information. Currently there is no standardized approach for comprehensive root system characterization, suggesting the need for data integration across methods and sources. Here, we combine field measured root descriptors from the classical Root Atlas series with traits ...[more]

PMID: 31744188

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Project description:BackgroundCover cropping is an agricultural practice that uses secondary crops to support the growth of primary crops through various mechanisms including erosion control, weed suppression, nutrient management, and enhanced biodiversity. Cover crops may elicit some of these ecosystem services through chemical interactions with the soil microbiome via root exudation, or the release of plant metabolites from roots. Phytohormones are one metabolite type exuded by plants that activate the rhizosphere microbiome, yet managing this chemical interaction remains an untapped mechanism for optimizing plant-soil microbiome interactions. Currently, there is limited understanding on the diversity of cover crop phytohormone root exudation patterns and how these chemical messages selectively enrich specific microbial taxa and functionalities in agricultural soils.ResultsHere, we link variability in cover crop root exudate composition to changes in soil microbiome functionality. Exudate chemical profiles from 4 cover crop species (Sorghum bicolor, Vicia villosa, Brassica napus, and Secale cereal) were used as the chemical inputs to decipher microbial responses. These distinct exudate profiles, along with a no exudate control, were amended to agricultural soil microcosms with microbial responses tracked over time using metabolomes and genome-resolved metatranscriptomes. Our findings illustrated microbial metabolic patterns were unique in response to cover crop exudate inputs over time, particularly by sorghum and cereal rye amended microcosms where we identify novel microbial members (at the genera and family level) who produced IAA and GA4 over time. We also identify broad changes in microbial nitrogen cycling in response chemical inputs.ConclusionsWe highlight that root exudate amendments alter microbial community function and phytohormone metabolisms, particularly in response to root exudates isolated from cereal rye and sorghum plants. Additionally, we constructed a soil microbial genomic catalog of microorganisms responding to commonly used cover crops, a public resource for agriculturally-relevant microbes. Many of our exudate-stimulated microorganisms are representatives from poorly characterized or novel taxa, highlighting the yet to be discovered metabolic reservoir harbored in agricultural soils. Our findings emphasize the tractability of high-resolution multiomics approaches to investigate processes relevant for agricultural soils, opening the possibility of targeting specific soil biogeochemical outcomes through biological precision agricultural practices that use cover crops and the microbiome as levers for enhanced crop production.

Project description:Background and Aims:Roots facilitate acquisition of macro- and micronutrients, which are crucial for plant productivity and anchorage in the soil. Phosphorus (P) is rapidly immobilized in the soil and hardly available for plants. Adaptation to P scarcity relies on changes in root morphology towards rooting systems well suited for topsoil foraging. Root-system architecture (RSA) defines the spatial organization of the network comprising primary, lateral and stem-derived roots and is important for adaptation to stress conditions. RSA phenotyping is a challenging task and essential for understanding root development. Methods:In this study, 19 traits describing RSA were analysed in a diversity panel comprising 194 sorghum genotypes, fingerprinted with a 90-k single-nucleotide polymorphism (SNP) array and grown under low and high P availability. Key Results:Multivariate analysis was conducted and revealed three different RSA types: (1) a small root system; (2) a compact and bushy rooting type; and (3) an exploratory root system, which might benefit plant growth and development if water, nitrogen (N) or P availability is limited. While several genotypes displayed similar rooting types in different environments, others responded to P scarcity positively by developing more exploratory root systems, or negatively with root growth suppression. Genome-wide association studies revealed significant quantitative trait loci (P < 2.9 × 10-6) on chromosomes SBI-02, SBI-03, SBI-05 and SBI-09. Co-localization of significant and suggestive (P < 5.7 × 10-5) associations for several traits indicated hotspots controlling root-system development on chromosomes SBI-02 and SBI-03. Conclusions:Sorghum genotypes with a compact, bushy and shallow root system provide potential adaptation to P scarcity in the field by allowing thorough topsoil foraging, while genotypes with an exploratory root system may be advantageous if N or water is the limiting factor, although such genotypes showed highest P uptake levels under the artificial conditions of the present study.

Project description:Pore structure is a key determinant of soil functioning, and both root growth and activity of soil fauna are modified by and interact with pore structure in multiple ways. Cover cropping is a rapidly growing popular strategy for improving agricultural sustainability, including improvements in pore structure. However, since cover crop species encompass a variety of contrasting root architectures, they can have disparate effects on formation of soil pores and their characteristics, thus on the pore structure formation. Moreover, utilization of the existing pore systems and its modification by new root growth, in conjunction with soil fauna activity, can also vary by cover crop species, affecting the dynamics of biopores (creation and demolition). The objectives of this study were (i) to quantify the influence of 5 cover crop species on formation and size distribution of soil macropores (>36 μm Ø); (ii) to explore the changes in the originally developed pore architecture after an additional season of cover crop growth; and (iii) to assess the relative contributions of plant roots and soil fauna to fate and modifications of biopores. Intact soil cores were taken from 5 to 10 cm depth after one season of cover crop growth, followed by X-ray computed micro-tomography (CT) characterization, and then, the cores were reburied for a second root growing period of cover crops to explore subsequent changes in pore characteristics with the second CT scanning. Our data suggest that interactions of soil fauna and roots with pore structure changed over time. While in the first season, large biopores were created at the expense of small pores, in the second year these biopores were reused or destroyed by the creation of new ones through earthworm activities and large root growth. In addition, the creation of large biopores (>0.5 mm) increased total macroporosity. During the second root growing period, these large sized macropores, however, are reduced in size again through the action of soil fauna smaller than earthworms, suggesting a highly dynamic equilibrium. Different effects of cover crops on pore structure mainly arise from their differences in root volume, mean diameter as well as their reuse of existing macropores.

Project description:BackgroundPlant roots release a variety of organic compounds into the soil which alter the physical, chemical and biological properties of the rhizosphere. Root exudates are technically challenging to measure in soil because roots are difficult to access and exudates can be bound by minerals or consumed by microorganisms. Exudates are easier to measure with hydroponically-grown plants but, even here, simple compounds such as sugars and organic acids can be rapidly assimilated by microorganisms. Sterile hydroponic systems avoid this shortcoming but it is very difficult to maintain sterility for long periods especially for larger crop species. As a consequence, studies often use small model species such as Arabidopsis to measure exudates or use seedlings of crop plants which only have immature roots systems.ResultsWe developed a simple hydroponic system for cultivating large crop plants in sterile conditions for more than 30 days. Using this system wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) plants were grown in sterile conditions for 30 days by which time they had reached the six-leaf stage and developed mature root systems with seminal, nodal and lateral roots. To demonstrate the utility of this system we characterized the aluminium-activated exudation of malate from the major types of wheat roots for the first time. We found that all root types measured released malate but the amounts were two-fold greater from the seminal and nodal axile roots compared with the lateral roots. Additionally, we showed that this sterile growth system could be used to collect exudates from intact whole root systems of barley.ConclusionsWe developed a simple hydroponic system that enables cereal plants to be grown in sterile conditions for longer periods than previously recorded. Using this system we measured, for the first time, the aluminium-activated efflux of malate from the major types of wheat roots. We showed the system can also be used for collecting exudates from intact root systems of 30-day-old barley plants. This hydroponic system can be modified for various purposes. Importantly it enables the study of exudates from crop species with mature root systems.

Project description:Increasing the use of cover crops (CCs) is a necessity in sustainable viticulture, although it might clash with possible excessive competition towards vines. Especially in a climate-change scenario, the latter feature should be minimized while maintaining ecosystem services. Aimed at identifying CCs for vineyard floor management, the trial characterized several species according to their evapotranspiration (ET) rates, root growth patterns, and soil aggregate stability potential. The study was performed in 2020 in Piacenza (Northern Italy) on 15 CC species grown in pots kept outdoor and classified as grasses (GR), legumes (LE) and creeping (CR). Together with bare soil (control), they were arranged in a complete randomized block design. CCs ET was assessed through a gravimetric method, starting before mowing and then repeated 2, 8, 17 and 25 days thereafter. Above-ground dry biomass (ADW), root length density (RLD), root dry weight (RDW) and root diameter class length (DCL) were measured, and mean weight diameter (MWD) was calculated within 0-20 cm depth. Before mowing, ET was the highest in LE (18.6 mm day-1) and the lowest in CR (8.1 mm day-1) the latter being even lower than the control (8.5 mm day-1). The high ET rates shown by LE were mainly related to very fast development after sowing, rather than to a higher transpiration per unit of leaf area. After mowing, the 15 species' ET reduction (%) plotted vs leaf area index (LAI, m2 m-2) yielded a very close fit (R2 = 0.94), suggesting that (i) a linear decrease in water use is expected anytime starting with an initial LAI of 5-6, (ii) a saturation effect seems to be reached beyond this limit. Selection of cover crop species to be used in the vineyard was mainly based on diurnal and seasonal water use rates as well as dynamic and extent of root growth patterns. Among GR, Festuca ovina stood out as the one with the lowest ET due to its "dwarfing" characteristics, making it suitable for a permanent inter-row covering. CR species confirmed their potential for under-vine grassing, assuring rapid soil coverage, lowest ET rates, and shallow root colonization.

Project description:The dataset presented here supports the research paper entitled "A calculator to quantify cover crop effects on soil health and productivity". Soil health (sometimes used synonymously with soil quality) is a concept that describes soil as a living system to sustain plants, animals, and human. Soil physical, chemical, and biological properties, along with their interactions, are required to quantify soil health. The use of cover crops in agricultural rotations may enhance soil health, yet there has been little progress in understanding how external factors such as climate, soil type, and agronomic practices affect soil and cash crop responses. In response, this dataset compiles measurements from 281 studies and provides an analysis of field-measured changes in 38 soil health indicators due to cover crop usage. Environmental and background indicators were also compiled to assess how climatic and management practices affect soil and cash crop responses to cover crops, with specific categories including climate type (tropical, arid, temperate, and continental), soil texture (coarse, medium, and fine), cover crop type (legume, grass, multi-species mixture, and other), and cash crop type (corn, soybean, wheat, vegetable, corn-soybean rotation, corn-soybean-wheat rotation, and other). An unbalanced analysis of variation was used to determine the hierarchy of most to least important factors that affected responsiveness of each soil health indicator. Based on the hierarchy structure, a soil health calculator was then developed to quantify the response of 13 parameters - erosion, runoff, weed suppression, soil aggregate stability, leaching, infiltration, microbial biomass carbon, soil bulk density, soil organic carbon, soil nitrogen, microbial biomass nitrogen, cash crop yield, and saturated hydraulic conductivity - to cover crops. The presented data in the calculator report the mean change in parameter values based on all combinations of climate, soil texture, cover crop type, and cash crop type.

Dataset Information

Characterization of Cover Crop Rooting Types from Integration of Rhizobox Imaging and Root Atlas Information.

Publications

Characterization of Cover Crop Rooting Types from Integration of Rhizobox Imaging and Root Atlas Information.

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