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Aim Incorporating non-bloat legumes into grass pastures can reduce enteric methane and alter cattle urinary urea-N output by increasing protein intake. Deposition of high urea-N urine influences soil N-cycling microbes and potentially, N2O production. We studied how urea-N concentration affects soil nitrifier and denitrifier abundance and activity and CO2 and N2O production. Methods 15N13C-labelled urea dissolved in cattle urine was added at 3.5 and 7.0 g L− 1 to soils from a grazed, non-bloat legume pasture and incubated under controlled conditions. CO2, N2O, 13CO2, and 15N2O production were quantified over 240 h, along with nitrifer and denitrifier N-cycling genes and mRNA transcripts. Results High urea urine increased total N2O relative to the control; low urea was not significantly different from the control or the high urea treatment. As a result, N2O-N emission factors decreased from 1.25–0.74% in low vs. high urea treatments. Doubling urea concentration doubled urea-derived 13CO2 and 15N2O but not total N2O. Urine addition initially inhibited, but then increased AOB transcription and abundance. nirK and nirS transcript abundances indicated that denitrification by ammonia oxidizers and/or heterotrophic denitrifiers likely dominated N2O production at a lower-than-expected WFPS (47% & 65%). Urine addition increased nosZ-II vs. nosZ-I transcription, improving soil N2O reduction potential. Conclusion Characterizing this interplay between nitrifiers and denitrifiers improves the understanding of urine patch N2O sinks and sources. The smaller emission factor from high urea urine suggests that current inventory methods using N deposition rates could overestimate soil N2O emissions from cattle consuming non-bloat legumes.

Background Continuous application of phosphorus (P) nutrient in association with its low recovery results in large amounts of P being accumulated in soil in different forms. Use of biochar can be a possible means to mobilize soil legacy P and increase its bioavailability. Therefore, the aim of this study was to identify the potential impact of a range of biochar types on P fractions in a long-term cultivated arid soil with high legacy P content. Methodology The soil was treated with biochar produced from four feedstock sources (BFS): sewage sludge (SSB), olive mill pomace (OPB), chicken manure (CMB), and date palm residues (DRB) pyrolyzed at 300, 500, or 700 °C in addition to an untreated control. The soil biochar mixture was incubated for 1 month followed by soil P fractionations using sequential chemical extraction to separate soil P into: labile (Resin-Pi, NaHCO3-Pi, NaHCO3-Po), moderately labile (NaOH-Pi, NaOH-Po), and non-labile (HCl-Pi and Residual-P) pools. Results Biochar addition clearly influenced most of the soil P fractions; however, the extent of this effect greatly varied depending on BFS and pyrolysis temperature (PT). The most evident biochar impact was observed with labile P pool, with the greatest increase being observed in NaHCO3-Pi fraction in most biochar treatments. Irrespective of PT, SSB and CMB were the most effective biochar type in increasing labile inorganic P; the SSB and CMB increased Resin-Pi by 77 and 206% and NaHCO3-Pi by 200 and 188%, respectively. In contrast, DRB made no changes in any P fraction. Differences in effects of biochar types on labile P is presumably related to the higher content of P in biowaste-based biochar compared to plant-based biochar which have much lower P content. The SSB, CMB, and OPB produced at low temperature reduced HCl-Pi content, indicating that these biochars may have stimulated organic matter decomposition and thereby dissolution of non-labile Ca-associated P to labile P forms. Conclusion Overall, biochar addition appeared to be an effective approach in enhancing legacy P availability in arid soil. However, further studies are necessary to verify these findings in the presence of plant and for a longer period. Graphic abstract

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.

Agricultural practices can influence soil microbial communities, which are the primary regulators of soil carbon and nutrient cycling processes. Differences in microbial community composition have the potential to affect the fate of carbon and nutrients during decomposition and may therefore influence the retention of C and provisioning of crop nutrients in agroecosystems. Long term management-induced shifts in microbial communities and resource availability may interact to affect the microbial utilization of fresh inputs of crop residues in the short term, with lasting impacts on soil C accrual and fertility. The objective of this study was to investigate whether long-term organic and conventional management resulted in differences in microbial residue decomposition. Soils under conventional and organic management planted with annual crops or with a mix of annual crops and three years of perennial alfalfa were collected from a long-term (19 y) field study in Saskatchewan, Canada and were incubated in the laboratory with and without 13C-labelled barley residues for 98 d. We measured extracellular enzyme activities (EEAs) and the incorporation of crop residue-derived C within major microbial groups (fungi, actinobacteria, and Gram positive and negative bacteria) during decomposition. Total PLFA biomass and EEAs were highest in soils from the conventional-annual system, similar between the conventional and organic perennial systems, and similar or lowest in the organic-annual system. Crop residue additions alleviated these differences; that is, in residue-amended soils total PLFA biomass, EEAs, and the abundance of the fungal biomarker increased in the organic systems compared to the unamended soils to become similar to the conventional systems. In contrast, residue additions induced small or no changes in biomass and EEAs in the conventional-annual soils. Using 13C-PLFA-SIP we showed that the general pattern of microbial succession during decomposition was similar among soils, but that fungi and especially actinobacteria were relatively more dominant in organic compared to conventionally managed soils during early and later stages of decomposition, respectively. Thus, shifts in the decomposer community composition were greater in soils originating from organic management, possibly as a result of larger changes in resource availability during the incubation that advanced the rate of microbial succession. This may reinforce long term differences in SOC quality and nutrient availability between management regimes. Organically-managed cropping systems are particularly reliant on biological cycling of organic nutrients to support crop growth. This work reinforces the importance of adequate crop residue returns for maintaining soil function, particularly where external organic amendments are not applied to balance nutrients exported as crop products.

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.

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 ıcritical biological processes that underpin soil health.

Zero-tannin (ZT) lentils have been bred for alterations in the phenylpropanoid pathway to reduce tannins from their seed coats. The reduction of seed tannins can alter the chemical composition of roots and rhizodeposits, with unknown consequences for rhizosphere carbon (C) cycling and soil organic matter formation as a result of changes in substrate quality for soil microorganisms. We characterized soil microbial community structure and quantified the fate and distribution of root derived C in rhizosphere soils of ZT and conventional tannin containing genotypes using 13C isotope labelling and phospholipid fatty acid (PLFA) 13C stable isotope probing. We hypothesized that (i) rhizosphere microorganisms would assimilate more root-derived C from ZT vs. conventional tannin (TAN) lentil genotypes due to lower phenolic content, and (ii) the structure of the microbial community would be differentiated between ZT and TAN genotypes, whereby r- and K-strategists would dominate consumption of ZT and TAN rhizodeposits, respectively. Total PLFA and 13C incorporation into PLFAs was consistently higher in TAN than ZT soils indicating that microorganisms in TAN soils assimilated more root derived C, which may lead to a reduction in soil C retention through fewer microbial residues and by-products. Neither the percentage of C derived from rhizodeposition nor root biomass was significantly different between TAN and ZT genotypes. As such, differences in microbial community structure and 13C assimilation reflect differences in the quality (i.e., composition), not quantity, of rhizodeposits between TAN vs. ZT genotypes. Results from our study are in contrast to our hypothesis and suggest that rhizodeposition under ZT genotypes contain less readily available forms of C. Moreover, increased C cycling enzyme activity under ZT genotypes may result in increased decomposition of soil organic matter, exacerbating CO2 emissions and energy losses. Our study highlights that crop breeding for desirable aboveground targets has consequences to belowground soil microorganisms and functions.

Quantifying how cropping systems influence soil C and nutrient turnover is important not only for better understanding the processes that regulate soil functioning, but also for long-term food production goals. We conducted an incubation study on soils collected from adjacent sites with a long-term legacy of annual vegetable, and perennial asparagus, haskap, and apple production. Soils were amended with 13C-labelled vanillin or glucose and incubated for 42 d. Gas and soil samples were collected to measure CO2, N2O, their isotopic signatures, and soil inorganic N and microbial biomass carbon (MBC) dynamics. Throughout the incubation, soil NO3−-N remained highest from vegetable soils, followed by soils from asparagus, haskap, and apple production. In contrast, soils from apple production supported the highest levels of MBC, whereas soil MBC from vegetable production was lowest. In general, glucose-C was utilized more readily than vanillin-C, but differences in glucose-derived CO2-C were more distinct among soils than vanillin-derived CO2-C. Soils from a history of vegetable production had the highest metabolic quotients – indicating poor substrate use efficiency, whereas substrate-C was used most efficiently from soils under apple production. Substrate-C use efficiency inversely corresponded to patterns in denitrifier-N2O production based on 15N2O isotopomers. In general, soils from the intensive vegetable cropping legacy were most susceptible to gaseous losses of both C and N-CO2 by way of soil organic matter priming, and N2O via increased denitrification with additions of labile substrates. Hence, the legacy of past cropping system management had consequences for how C and N was processed in soil.

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&deg, 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&deg, panoramic view, is also presented. The system is tested in the field by imaging canola roots to show the performance advantages over commercial systems.

Belowground N comprises an important component of total residue N, but the N from this pool is often not included in studies that use 15N approaches to trace residue-derived N in succeeding crops. The objective of this greenhouse study was to differentiate between N supplied from aboveground and belowground crop residues, including rhizodeposits, of pea and canola to wheat using 15N labeling. A cross 15N-labeling approach was used in which wheat was grown on 15N-labeled belowground residues and non-labeled aboveground residues and vice versa. On average, the amount of N in wheat derived from belowground residues was almost twice the amount from aboveground residues. The higher input of both aboveground and belowground residue biomass and hence residue N from canola compared to pea tended to increase the residue-derived N in wheat from canola (6.4 %) relative to pea (4.7 %). However, differences in the percent recovery of 15N based on the amount of residue-15N initially applied revealed that a higher proportion of belowground residue N from pea (13.4 %) was recovered in wheat compared to the corresponding aboveground residue N from pea (8.8 %), and both belowground and aboveground residue N from canola (6.5 and 7.3 %, respectively). The total supply of N to wheat from preceding pea and canola crops was relatively low, likely due to wide C/N ratios. This study demonstrates the importance of belowground residue N to the supply of N to succeeding crops as well as differences between species.

Lentil (Lens culinaris) production on the Canadian prairies has increased recently with possible benefits to cropping systems in this region. The yield benefit often observed in cereals grown after a pulse crop can be partially attributed to the supply of nitrogen (N) from decomposing pulse crop residues; however, the contribution of belowground residue (BGR) is poorly documented. The purpose of this greenhouse study was to quantify the N input from BGR (i.e., roots plus rhizodeposits) of lentil and wheat (Triticum aestivum) using shoot 15N-labeling and to trace the 15N from BGR into subsequently grown wheat plants. Belowground N (BGN) comprised 34 and 51 % of total plant N in lentil and wheat, respectively. Whereas wheat produced more root biomass than lentil, total amounts of BGN did not differ between species. However, biomass production and N uptake by wheat grown on lentil BGR were 49 and 14 % higher than wheat grown on wheat BGR. Moreover, a higher proportion of added 15N from lentil BGR (14.4 vs. 8.5 %) was recovered in the succeeding wheat crop, indicating that lentil BGN was more readily mineralized than wheat BGN. The disproportionately high increase in yield vs. N uptake for wheat grown on lentil BGR, however, indicates that non-N factors also contributed to the increase in wheat yield. This study highlights the importance of including estimates of BGN when evaluating the positive effects of including pulse crops in rotation with cereals, although further research is required to identify non-N benefits of lentil.

Crop species grown in a diversified crop rotation can influence soil N dynamics to varying degrees due to differences in the quantity and quality of the residues returned to the soil. The aim of this study was to quantify the contribution of N rhizodeposition by canola (Brassica napus L.) and pea (Pisum sativum L.) to the crop residue N balance and soil inorganic N pool. Canola and pea were grown in a soil-sand mixture and were subject to cotton-wick 15N labeling in a greenhouse experiment. Nitrogen-15 recovered in the soil and roots were used to estimate N rhizodeposition. Belowground N, including root N and N rhizodeposits, comprised 70 % and 61 % of total crop residue N for canola and pea, respectively. Canola released the greatest amount of total root-derived N to the soil, which was related to greater root biomass production by canola. However, root-derived N in the soil inorganic N pool was greater under pea (13 %) than canola (4 %). Our results show a significant belowground N contribution to total crop residue from pea and canola. Further investigation is required to determine whether input of the more labile N rhizodeposits of pea improves soil N supply to succeeding crops or increases the potential for N loss from the soil system relative to canola.

Low soil test phosphorus (P) concentrations are common in organically managed soils in Canada. This field study examined the effect of residues from a buckwheat (Fagopyrum esculentum) green manure (GM) crop grown with an igneous and a sedimentary source of phosphate rock (PR) on in situ soil P supply, Olsen P, and soil microbial biomass P on an organic farm in Ontario, Canada. Phosphate rock application did not increase GM dry matter production, but did increase above-ground tissue P concentration with applications of the sedimentary PR (Calphos). In the following spring, in situ soil P supply and Olsen P were increased in GM residue-applied soils and in soils containing the Calphos PR, while microbial biomass P was largely unaffected. Release of P was detected when GM P concentration was greater than 2.9 g P kg-1. The results suggest the quality of the GM residues had more influence on P availability than the quantity applied to the soil; however, the low changes in available P (P supply and Olsen P) were not agronomically significant. Key words: Phosphate rock, soil phosphate supply, Olsen P, organic agriculture, green manure

During the past decade, soil and geochemists have adopted a variety of novel chemical–analytical methods to explore the chemistry of soil organic N (N org ). This chapter summarizes some of the more recent developments in the use of wet-chemical and instrumental methods to determine total N org concentrations as well as to speciate the N org in soils. A critical evaluation of 15 N nuclear magnetic resonance (NMR) spectroscopy found the technique to be wanting, in terms of its sensitivity and ability to identify classes of N org compounds in soils. Complementary mass spectrometric techniques are described briefly, and improved data evaluations based on broad applications of high-resolution pyrolysis-field ionization mass spectrometry are presented and discussed. A reassessment of older data sets using the new spectral evaluation algorithms provides strong evidence of fire- and management-induced changes in N org speciation. Isotope-ratio mass spectrometry, Fourier transform ion cyclotron resonance mass spectrometry, and nanoscale secondary ion mass spectrometry (Nano-SIMS) also are discussed, with the latter two techniques having potential to (1) identify N org compounds and (2) provide spatially resolved information on the molecular, elemental and isotopic composition of soil N org . The use of 15 N labeling techniques is discussed both from a methodological standpoint and in terms of tracking the fate of plant-derived (residue or rhizodeposit) N in the soil. Indeed, coupling 15 N labeling with analytical techniques such as 15 N NMR, Nano-SIMS and high- or ultrahigh-resolution mass spectrometry can provide information on how N is incorporated into soil organic matter. Analytical and instrumental innovations have resulted in new insights into the chemistry of N org —together with a revised summary of the relative amounts of the different N org compound classes present in soils (e.g. aliphatic amine and amide N, aromatic heterocyclic N), as well as their ecophysiological functions. Particular emphasis is given to the use of multitechnique analyses and the outstanding molecular–chemical diversity of biogenic heterocyclic N org compounds. Examples are given of the new insights obtained using multi-analytical research approaches to explore microbial utilization of heterocyclic N and organic–mineral interactions, as well as the ability of human and environmental intervention to alter the composition of soil N org . Finally, we examine future challenges and propose analytical approaches to tackle open questions regarding the basic chemistry and cycling of N org in soils, as well as the agronomic and environmental consequences associated with N transformations in agro-ecosystems.