Nitrogen Use Efficiency in Parent vs. Hybrid Canola under Varying Nitrogen Availabilities.

Improving nitrogen use efficiency (NUE) is essential for sustainable agriculture, especially in high-N-demanding crops such as canola (Brassica napus). While advancements in above-ground agronomic practices have improved NUE, research on soil and below-ground processes are limited. Plant NUE-and its components, N uptake efficiency (NUpE), and N utilization efficiency (NUtE)-can be further improved by exploring crop variety and soil N cycling. Canola parental genotypes (NAM-0 and NAM-17) and hybrids (H151857 and H151816) were grown on a dark brown chernozem in Saskatchewan, Canada. Soil and plant samples were collected at the 5-6 leaf stage and flowering, and seeds were collected at harvest maturity. Soil N cycling varied with phenotypic stage, with higher potential ammonium oxidation rates at the 5-6 leaf stage and higher urease activity at flowering. Seed N uptake was higher under higher urea-N rates, while the converse was true for NUE metrics. Hybrids had higher yield, seed N uptake, NUtE, and NUE, with higher NUE potentially owing to higher NUtE at flowering, which led to higher yield and seed N allocation. Soil N cycling and soil N concentrations correlated for improved canola NUE, revealing below-ground breeding targets. Future studies should consider multiple root characteristics, including rhizosphere microbial N cycling, root exudates, and root system architecture, to determine the below-ground dynamics of plant NUE.

Nitrogen Use Efficiency Definitions of Today and Tomorrow.

Crop production has a large impact on the nitrogen (N) cycle, with consequences to climate, environment, and public health. Designing better N management will require indicators that accurately reflect the complexities of N cycling and provide biological meaning. Nitrogen use efficiency (NUE) is an established metric used to benchmark N management. There are numerous approaches to calculate NUE, but it is difficult to find an authoritative resource that collates the various NUE indices and systematically identifies their assets and shortcomings. Furthermore, there is reason to question the usefulness of many traditional NUE formulations, and to consider factors to improve the conceptualization of NUE for future use. As a resource for agricultural researchers and students, here we present a comprehensive list of NUE indices and discuss their functions, strengths, and limitations. We also suggest several factors-which are currently ignored in traditional NUE indices-that will improve the conceptualization of NUE, such as: accounting for a wider range of soil N forms, considering how plants mediate their response to the soil N status, including the below-ground/root N pools, capturing the synchrony between available N and plant N demand, blending agronomic performance with ecosystem functioning, and affirming the biological meaning of NUE.

An intensive multilocation temporal dataset of fungal and bacterial communities in the root and rhizosphere of Brassica napus.

The plant microbiome has been recently recognized as a plant phenotype to help in the food security of the future population. However, global plant microbiome datasets are insufficient to be used effectively for breeding this new generation of crop plants. We surveyed the diversity and temporal composition of bacterial and fungal communities in the root and rhizosphere of Brassica napus, the world's second largest oilseed crop, weekly in eight diverse lines at one site and every three weeks in sixteen lines, at three sites in 2016 and 2017 in the Canadian Prairies. We sequenced the bacterial 16S ribosomal RNA gene generating a total of 127.7 million reads and the fungal internal transcribed spacer (ITS) region generating 113.4 million reads. 14,944 unique fungal amplicon sequence variants (ASV) were detected, with an average of 43 ASVs per root and 105 ASVs per rhizosphere sample. We detected 10,882 unique bacterial ASVs with an average of 249 ASVs per sample. Temporal, site-to-site, and line-driven variability were key determinants of microbial community structure. This dataset is a valuable resource to systematically extract information on the belowground microbiome of diverse B. napus lines in different environments, at different times in the growing season, in order to adapt effective varieties for sustainable crop production systems.

An intensive multilocation temporal dataset of fungal communities in the root and rhizosphere of Brassica napus.

The plant microbiome has been recently recognized as a plant phenotype to help in the food security of the future population. However, global plant microbiome datasets are insufficient to be used effectively for breeding this new generation of crop plants. We surveyed the diversity and temporal composition of fungal communities in the root and rhizosphere of Brassica napus, the world's second largest oilseed crop, weekly in eight diverse lines at one site and every three weeks in sixteen lines, at three sites in 2016 and 2017 in the Canadian Prairies. 14,944 unique amplicon sequence variants (ASV) were detected based on the internal transcribed spacer region, with an average of 43 ASVs per root and 105 ASVs per rhizosphere sample. Temporal, site-to-site, and line-driven variability were key determinants of fungal community structure. This dataset is a valuable resource to systematically extract information on the belowground microbiome of diverse B. napus lines in different environments, at different times in the growing season, in order to adapt effective varieties for sustainable crop production systems.

SoilCam: A Fully Automated Minirhizotron using Multispectral Imaging for Root Activity Monitoring.

A minirhizotron is an in situ root imaging system that captures components of root system architecture dynamics over time. Commercial minirhizotrons are expensive, limited to white-light imaging, and often need human intervention. The implementation of a minirhizotron needs to be low cost, automated, and customizable to be effective and widely adopted. We present a newly designed root imaging system called SoilCam that addresses the above mentioned limitations. The imaging system is multi-modal, i.e., it supports both conventional white-light and multispectral imaging, with fully automated operations for long-term in-situ monitoring using wireless control and access. The system is capable of taking 360° images covering the entire area surrounding the tube. The image sensor can be customized depending on the spectral imaging requirements. The maximum achievable image quality of the system is 8 MP (Mega Pixel)/picture, which is equivalent to a 2500 DPI (dots per inch) image resolution. The length of time in the field can be extended with a rechargeable battery and solar panel connectivity. Offline image-processing software, with several image enhancement algorithms to eliminate motion blur and geometric distortion and to reconstruct the 360° panoramic view, is also presented. The system is tested in the field by imaging canola roots to show the performance advantages over commercial systems.

Core and Differentially Abundant Bacterial Taxa in the Rhizosphere of Field Grown Brassica napus Genotypes: Implications for Canola Breeding.

Modifying the rhizosphere microbiome through targeted plant breeding is key to harnessing positive plant-microbial interrelationships in cropping agroecosystems. Here, we examine the composition of rhizosphere bacterial communities of diverse Brassica napus genotypes to identify: (1) taxa that preferentially associate with genotypes, (2) core bacterial microbiota associated with B. napus, (3) heritable alpha diversity measures at flowering and whole growing season, and (4) correlation between microbial and plant genetic distance among canola genotypes at different growth stages. Our aim is to identify and describe signature microbiota with potential positive benefits that could be integrated in B. napus breeding and management strategies. Rhizosphere soils of 16 diverse genotypes sampled weekly over a 10-week period at single location as well as at three time points at two additional locations were analyzed using 16S rRNA gene amplicon sequencing. The B. napus rhizosphere microbiome was characterized by diverse bacterial communities with 32 named bacterial phyla. The most abundant phyla were Proteobacteria, Actinobacteria, and Acidobacteria. Overall microbial and plant genetic distances were highly correlated (R = 0.65). Alpha diversity heritability estimates were between 0.16 and 0.41 when evaluated across growth stage and between 0.24 and 0.59 at flowering. Compared with a reference B. napus genotype, a total of 81 genera were significantly more abundant and 71 were significantly less abundant in at least one B. napus genotype out of the total 558 bacterial genera. Most differentially abundant genera were Proteobacteria and Actinobacteria followed by Bacteroidetes and Firmicutes. Here, we also show that B. napus genotypes select an overall core bacterial microbiome with growth-stage-related patterns as to how taxa joined the core membership. In addition, we report that sets of B. napus core taxa were consistent across our three sites and 2 years. Both differential abundance and core analysis implicate numerous bacteria that have been reported to have beneficial effects on plant growth including disease suppression, antifungal properties, and plant growth promotion. Using a multi-site year, temporally intensive field sampling approach, we showed that small plant genetic differences cause predictable changes in canola microbiome and are potential target for direct and indirect selection within breeding programs.

Resource Legacies of Organic and Conventional Management Differentiate Soil Microbial Carbon Use.

Long-term contrasts in agricultural management can shift soil resource availability with potential consequences to microbial carbon (C) use efficiency (CUE) and the fate of C in soils. Isothermal calorimetry was combined with 13C-labeled glucose stable isotope probing (SIP) of 16S rRNA genes to test the hypothesis that organically managed soils would support microbial communities with greater thermodynamic efficiency compared to conventional soils due to a legacy of lower resource availability and a resultant shift toward communities supportive of more oligotrophic taxa. Resource availability was greater in conventionally managed soils, with 3.5 times higher available phosphorus, 5% more nitrate, and 36% more dissolved organic C. The two management systems harbored distinct glucose-utilizing populations of Proteobacteria and Actinobacteria, with a higher Proteobacteria:Actinobacteria ratio (2.4 vs. 0.7) in conventional soils. Organically managed soils also harbored notable activity of Firmicutes. Thermodynamic efficiency indices were similar between soils, indicating that glucose was metabolized at similar energetic cost. However, differentially abundant glucose utilizers in organically managed soils were positively correlated with soil organic matter (SOM) priming and negatively correlated to soil nutrient and carbon availability, respiration, and heat production. These correlation patterns were strongly reversed in the conventionally managed soils indicating clear differentiation of microbial functioning related to soil resource availability. Fresh C addition caused proportionally more priming of SOM decomposition (57 vs. 51%) in organically managed soils likely due to mineralization of organic nutrients to satisfy microbial demands during glucose utilization in these more resource deprived soils. The additional heat released from SOM oxidation may explain the similar community level thermodynamic efficiencies between management systems. Restoring fertility to soils with a legacy of nutrient limitation requires a balanced supply of both nutrients and energy to protect stable SOM from microbial degradation. These results highlight the need to consider managing C for the energy it provides to icritical biological processes that underpin soil health.

Plant- and microbial-based mechanisms to improve the agronomic effectiveness of phosphate rock: a review.

Deficiency in plant-available phosphorus is considered to be a major limiting factor to food production in many agricultural soils. Mineral resources are necessary to restore soil phosphorus content. In regions where conventional fertilizers are not used due to cost limitations or to mitigate adverse environmental effects, local sources of phosphate rock are being increasingly recognized for potential use as alternative phosphorus fertilizers. The main obstacle associated with using directly applied ground phosphate rock is that the phosphate released is often unable to supply sufficient plant-available phosphorus for crop uptake. Plantand microbial-based mechanisms are low-cost, appropriate technologies to enhance the solubilization and increase the agronomic effectiveness of phosphate rock. Common mechanisms of phosphate rock dissolution including proton and organic acid production will be reviewed for both plants and microorganisms. This review will also address possibilities for future research directions and applications to agriculture, as well as highlight ongoing research at the University of Guelph, Guelph, Canada.

Plant- and microbial-based mechanisms to improve the agronomic effectiveness of phosphate rock: a review

Deficiency in plant-available phosphorus is considered to be a major limiting factor to food production in many agricultural soils. Mineral resources are necessary to restore soil phosphorus content. In regions where conventional fertilizers are not used due to cost limitations or to mitigate adverse environmental effects, local sources of phosphate rock are being increasingly recognized for potential use as alternative phosphorus fertilizers. The main obstacle associated with using directly applied ground phosphate rock is that the phosphate released is often unable to supply sufficient plant-available phosphorus for crop uptake. Plantand microbial-based mechanisms are low-cost, appropriate technologies to enhance the solubilization and increase the agronomic effectiveness of phosphate rock. Common mechanisms of phosphate rock dissolution including proton and organic acid production will be reviewed for both plants and microorganisms. This review will also address possibilities for future research directions and applications to agriculture, as well as highlight ongoing research at the University of Guelph, Guelph, Canada.

A deficiência de fósforo disponível nas plantas é considerada o maior fator de limitação na produção de alimentos em diversos solos agrícolas. São necessários recursos minerais para restaurar o conteúdo de fósforo no solo. Em regiões onde fertilizantes convencionais nãosão utilizados devido às limitações de custo ou de seus efeitos ambientais adversos, fontes locais de rocha fosfática estão sendo crescentemente reconhecidas por seu uso potencial como alternativa aos fertilizantes solúveis de fósforo. O principal obstáculo associado ao uso daaplicação direta da rocha fosfática no solo é que o fósforo liberado é, muitas vezes, incapaz de suprir as necessidades das plantas de forma a aumentar a produção. Mecanismos baseados no uso de plantas e micro-organismos são consideradas tecnologias apropriadas de baixo custo, para ativar a solubilização e aumentar a efetividade agronômica das rochas fosfáticas. Mecanismos comuns de dissolução da rocha fosfática, incluindo a produção de prótons e ácidos orgânicos serão revisados tanto para plantas quanto para microorganismos. Esta revisão também tratará das possibilidades para futuras pesquisas com rochas fosfáticas e suas aplicações na agricultura, assim como destaca pesquisas em andamento na Universidade de Guelph, Canadá.