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Original Paper in PNAS • Goulet Lab 2022 • A flavin-dependent monooxygenase produces nitrogenous tomato aroma volatiles using cysteine as a nitrogen source

Original Paper in PNAS • Goulet Lab 2022 • A flavin-dependent monooxygenase produces nitrogenous tomato aroma volatiles using cysteine as a nitrogen source | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

Tomato (Solanum lycopersicum) produces a wide range of volatile chemicals during fruit ripening, generating a distinct aroma and contributing to the overall flavor. Among these volatiles are several aromatic and aliphatic nitrogen-containing compounds for which the biosynthetic pathways are not known. While nitrogenous volatiles are abundant in tomato fruit, their content in fruits of the closely related species of the tomato clade is highly variable. For example, the green-fruited species Solanum pennellii are nearly devoid, while the red-fruited species S. lycopersicum and Solanum pimpinellifolium accumulate high amounts. Using an introgression population derived from S. pennellii, we identified a locus essential for the production of all the detectable nitrogenous volatiles in tomato fruit. Silencing of the underlying gene (SlTNH1;Solyc12g013690) in transgenic plants abolished production of aliphatic and aromatic nitrogenous volatiles in ripe fruit, and metabolomic analysis of these fruit revealed the accumulation of 2-isobutyl-tetrahydrothiazolidine-4-carboxylic acid, a known conjugate of cysteine and 3-methylbutanal. Biosynthetic incorporation of stable isotope-labeled precursors into 2-isobutylthiazole and 2-phenylacetonitrile confirmed that cysteine provides the nitrogen atom for all nitrogenous volatiles in tomato fruit. Nicotiana benthamiana plants expressing SlTNH1 readily transformed synthetic 2-substituted tetrahydrothiazolidine-4-carboxylic acid substrates into a mixture of the corresponding 2-substituted oxime, nitro, and nitrile volatiles. Distinct from other known flavin-dependent monooxygenase enzymes in plants, this tetrahydrothiazolidine-4-carboxylic acid N-hydroxylase catalyzes sequential hydroxylations. Elucidation of this pathway is a major step forward in understanding and ultimately improving tomato flavor quality.

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Original Paper in Sci Total Environ • Grégoire Lab 2022 • Contribution of grass clippings to turfgrass fertilization and soil water content under four nitrogen levels

Original Paper in Sci Total Environ • Grégoire Lab 2022 • Contribution of grass clippings to turfgrass fertilization and soil water content under four nitrogen levels | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

Returning turfgrass clippings to soil (i.e., mulching) has been shown to yield many benefits, such as reducing fertilizer requirements. However, previous reports on the contribution of clippings to turfgrass fertilization varies widely, making it difficult for turfgrass managers to adjust their fertilization practices. Other potential benefits of this practice, such as soil water conservation, still need to be quantified. The objectives of this project were to measure the contribution of Kentucky bluegrass clippings to N, P and K fertilization under four different N levels and to measure the impact of clippings management on turfgrass color (NDVI), soil nutrient and water content as well as thatch accumulation. A field experiment was conducted over three years, with treatments consisting of two clipping management strategies (returned or removed) and four nitrogen levels (0, 48, 96 and 144 kg N ha −1 yr −1). Clippings were collected on every mowing date and were analyzed for N, P and K foliar content. Soil volumetric water content and NDVI were measured weekly, while thatch accumulation and soil chemical content (Mehlich-3) were assessed twice per year. Increasing N fertilization resulted in an increase in both clippings dry matter yield (DMY) and foliar N concentration. Returning grass clippings was equivalent to doubling the amount of N applied through the fertilizer and resulted in an increase in turfgrass color and soil P and K levels. For P and K, clippings contribution was more affected by their DMY than by foliar concentrations. Grass clippings did not contribute to thatch accumulation, but resulted in a consistent increase (3.9% on average) in soil volumetric water content.

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Original Paper in Genome Biol Evol • Leducq Lab 2022 • Comprehensive phylogenomics of Methylobacterium reveals four evolutionary distinct groups and underappreciated phyllosphere diversity

Original Paper in Genome Biol Evol • Leducq Lab 2022 • Comprehensive phylogenomics of Methylobacterium reveals four evolutionary distinct groups and underappreciated phyllosphere diversity | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

Methylobacterium is a group of methylotrophic microbes associated with soil, fresh water, and particularly the phyllosphere, the aerial part of plants that has been well-studied in terms of physiology but whose evolutionary history and taxonomy are unclear. Recent work has suggested that Methylobacterium is much more diverse than thought previously, questioning its status as an ecologically and phylogenetically coherent taxonomic genus. However, taxonomic and evolutionary studies of Methylobacterium have mostly been restricted to model species, often isolated from habitats other than the phyllosphere, and have yet to utilize comprehensive phylogenomic methods to examine gene trees, gene content, or synteny. By analyzing 189 Methylobacterium genomes from a wide range of habitats, including the phyllosphere, we inferred a robust phylogenetic tree while explicitly accounting for the impact of horizontal gene transfer. We showed that Methylobacterium contains four evolutionarily distinct groups of bacteria (namely A, B, C, D), characterized by different genome size, GC content, gene content and genome architecture, revealing the dynamic nature of Methylobacterium genomes. In addition to recovering 59 described species, we identified 45 candidate species, mostly phyllosphere-associated, stressing the significance of plants as a reservoir of Methylobacterium diversity. We inferred an ancient transition from a free-living lifestyle to association with plant roots in Methylobacteriaceae ancestor, followed by phyllosphere association of three of the major groups (A, B, D), whose early branching in Methylobacterium history has been heavily obscured by HGT. Together, our work lays the foundations for a thorough redefinition of Methylobacterium taxonomy, beginning with the abandonment of Methylorubrum.

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Original Paper in Agronomy • Dorais Lab 2022 • Drench Application of Soy Protein Hydrolysates Increases Tomato Plant Fitness, Fruit Yield, and Resistance to a Hemibiotrophic Pathogen

Original Paper in Agronomy • Dorais Lab 2022 • Drench Application of Soy Protein Hydrolysates Increases Tomato Plant Fitness, Fruit Yield, and Resistance to a Hemibiotrophic Pathogen | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it
At a time when growers have to increase food production, while facing many environmental challenges, biostimulants and plant defence stimulators (PDS) may help reduce the use of chemical fertilizers and pesticides and to promote agriculture that is more respectful of the environment. For organic farming, they may contribute to increasing plant resilience and crop productivity. Several studies have shown that plant-derived protein hydrolysates may increase nutrient use efficiency and promote plant resistance to abiotic or biotic stresses. We therefore hypothesized that soy protein hydrolysates increase tomato growth and productivity, while promoting plant disease resistance. Our results showed that one or two drench applications of soy protein hydrolysates (SPH13 and SPH18 at 10 g L−1) to the growing medium increased tomato (‘Micro Tom’) plant growth and fruit production, while one studied hydrolysate enriched in glycine (SPH18) increased the expression levels of PR1 and PR8, two defence-related genes. Although no significant effect was observed on Botrytis cinerea resistance of Micro Tom plants, SPHs significantly increased ‘M82’ plant resistance to foliar inoculation with Pseudomonas syringae pv. tomato DC3000, which further confirmed the systemic activation of plant defence mechanisms by SPHs in tomatoes.
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Original Paper in J Ecol • Maire Collaboration 2022 • Leaf nitrogen from the perspective of optimal plant function

Original Paper in J Ecol • Maire Collaboration 2022 • Leaf nitrogen from the perspective of optimal plant function | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it
  1. Leaf dry mass per unit area (LMA), carboxylation capacity (Vcmax) and leaf nitrogen per unit area (Narea) and mass (Nmass) are key traits for plant functional ecology and ecosystem modelling. There is however no consensus about how these traits are regulated, or how they should be modelled. Here we confirm that observed leaf nitrogen across species and sites can be estimated well from observed LMA and Vcmax at 25˚C (Vcmax25). We then test the hypothesis that global variations of both quantities depend on climate variables in specific ways that are predicted by leaf-level optimality theory, thus allowing both Narea to be predicted as functions of the growth environment.
  2. A new global compilation of field measurements was used to quantify the empirical relationships of leaf N to Vcmax25 and LMA. Relationships of observed Vcmax25 and LMA to climate variables were estimated, and compared to independent theoretical predictions of these relationships. Soil effects were assessed by analysing biases in the theoretical predictions.
  3. LMA was the most important predictor of Narea (increasing) and Nmass (decreasing). About 60% of global variation across species and sites in observed Narea, and 31% in Nmass, could be explained by observed LMA and Vcmax25. These traits in turn were quantitatively related to climate variables, with significant partial relationships similar or indistinguishable from those predicted by optimality theory. Predicted trait values explained 21% of global variation in observed site-mean Vcmax25, 43% in LMA, and 31% in Narea. Predicted Vcmax25 was biased low on clay-rich soils but predicted LMA was biased high, with compensating effects on Narea. Narea was overpredicted on organic soils.
  4. Synthesis. Global patterns of variation in observed site-mean Narea can be explained by climate-induced variations in optimal Vcmax25 and LMA. Leaf nitrogen should accordingly be modelled as a consequence (not a cause) of Vcmax25 and LMA, both being optimized to the environment. Nitrogen limitation of plant growth would then be modelled principally via whole-plant carbon allocation, rather than via leaf-level traits. Further research is required to better understand and model the terrestrial nitrogen and carbon cycles and their coupling.
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Original paper in Nitrogen • Dessureault-Rompré Lab 2022 • Impact of Plant-Based Amendments on Water-Soluble Nitrogen Release Dynamics in Cultivated Peatlands

Original paper in Nitrogen • Dessureault-Rompré Lab 2022 • Impact of Plant-Based Amendments on Water-Soluble Nitrogen Release Dynamics in Cultivated Peatlands | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

Drained cultivated peatlands have been an essential agricultural resource for many years. To slow and reduce the degradation of these soils, which increases with drainage, the use of plant-based amendments (straw, wood chips, and biochar) has been proposed. Literature on the effects of such amendments in cultivated peatlands is scarce, and questions have been raised regarding the impact of this practice on nutrient cycling, particularly nitrogen (N) dynamics. By means of a six-month incubation experiment, this study assessed the effects of four plant-based amendments (biochar, a forest mix, willow, and miscanthus) on the release kinetics of water-soluble N pools (mineral and organic) in two histosols of differing degrees of decomposition (Haplosaprist and Haplohemist). The amendment rate was set at 15 Mg ha−1 on a dry weight basis. The N release kinetics were significantly impacted by soil type and amendment. Miscanthus and willow were the amendments that most reduced the release of soluble organic N (SON) and mineral N (minN). The addition of plant-based amendments reduced the total amount of released N pools during the incubation (cumulative N pools) by 50.3 to 355.2 mg kg−1, depending on the soil type, the N pool, and the type of amendment. A significant relationship was found between microbial biomass N, urease activity, and the cumulative N at the end of the incubation. The results showed that the input of plant-based amendments in cultivated peatland decreases N release, which could have a beneficial impact by decreasing N leaching; however, it could also restrict crop growth. Further research is needed to fully assess the impact of such amendments used in cultivated peatlands on N and on C fluxes at the soil–plant and soil–atmosphere interfaces to determine if they constitute a long-term solution for more sustainable agriculture.

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Review in Biomolecules • Desgagné-Penix Lab 2022 • Biotechnological Approaches to Optimize the Production of Amaryllidaceae Alkaloids

Review in Biomolecules • Desgagné-Penix Lab 2022 • Biotechnological Approaches to Optimize the Production of Amaryllidaceae Alkaloids | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it
Amaryllidaceae alkaloids (AAs) are plant specialized metabolites with therapeutic properties exclusively produced by the Amaryllidaceae plant family. The two most studied representatives of the family are galanthamine, an acetylcholinesterase inhibitor used as a treatment of Alzheimer’s disease, and lycorine, displaying potent in vitro and in vivo cytotoxic and antiviral properties. Unfortunately, the variable level of AAs’ production in planta restricts most of the pharmaceutical applications. Several biotechnological alternatives, such as in vitro culture or synthetic biology, are being developed to enhance the production and fulfil the increasing demand for these AAs plant-derived drugs. In this review, current biotechnological approaches to produce different types of bioactive AAs are discussed.
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Review in Curr Opin Environ Sci Health • Duarte-Sierra Lab 2022 • Postharvest hormesis in produce

Review in Curr Opin Environ Sci Health • Duarte-Sierra Lab 2022 • Postharvest hormesis in produce | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

The evolutionary fitness of plants to changing environments has been a continuous effort of stimulatory or adaptive responses to stress-induced hormesis; it is somewhat considered transgenerational. Recently, stress-induced hormesis in produce has recently drawn much attention, and various abiotic stressors have been tested successfully. The beneficial effects of hormesis in harvested crops include delayed senescence, disease resistance and enhanced abundance of secondary metabolites. This review attempts to give an overview of the importance of postharvest hormesis, the possible existence of such phenomenon in various stressors, possible underlying mechanisms involved, and finally provide some perspectives for its future application.

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Review in Front Soil Sci • Dessureault-Rompré Lab 2022 • Restoring Soil Functions and Agroecosystem Services Through Phytotechnologies

Review in Front Soil Sci • Dessureault-Rompré Lab 2022 • Restoring Soil Functions and Agroecosystem Services Through Phytotechnologies | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

Phytotechnology has traditionally been considered as a tool to remediate contaminated soils. While phytotechnology has been generally defined as the application of science and engineering to study problems and provide solutions involving plants, the practical applications go far beyond restoring contaminated land. This review aims to broaden the way we think about phytotechnologies while highlighting how these living technologies can restore, conserve and regenerate the multiple functions and ecosystem services provided by the soil, particularly in the context of agroecosystems. At first, the main problems of soil degradation in agroecosystems are shortly underlined. Subsequently, the importance of plants and their living roots as engines of restoration are reviewed. This paper demonstrates the importance of root traits and functions for soil restoration. It also demonstrates that plant and root diversity together with perenniality are key component of an efficient soil restoration process. Then, a phytotechnology toolbox which includes three pillars for agroecosystems restoration is presented. The three pillars are agricultural practices and land management (1), rhizosphere engineering (2) and ecological intensification (3). This paper also highlights the importance of developing targeted phytotechnology-based restoration strategies developed from root functions and knowledge of rhizosphere processes. More work is needed to evaluate the potential benefits of incorporating phytotechnology-based restoration strategies in the context of grain or vegetable crop productions as most of the studies for agroecosystem restoration strategies were intended to mimic natural prairies.

 

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Disease report in Plant Dis• Pérez-López/Bélanger Collaboration 2022 • First Report of Powdery Mildew Caused by Golovinomyces ambrosiae on Cannabis sativa L. (marijuana) in Quebec, Canada

Disease report in Plant Dis• Pérez-López/Bélanger Collaboration 2022 • First Report of Powdery Mildew Caused by Golovinomyces ambrosiae on Cannabis sativa L. (marijuana) in Quebec, Canada | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

Marijuana (Cannabis sativa L.) is legal in Canada for medical and recreational purposes and is currently 23 a multi-million-dollar industry. The province of Quebec follows British Columbia and Ontario in 24 production acreage (Government of Canada 2018). During the growing season 2020-2021, five 25 greenhouse growers throughout Quebec reported the presence of signs and symptoms reminiscent of 26 powdery mildew including the presence of white powdery patches on the adaxial sides of leaves of 27 several C. sativa cultivars. From one commercial facility, infected leaves of three cannabis cultivars 28 (Sour Diesel, Orange Krush, and Lemon Sour) were photographed and the fungal mycelium was 29 collected for identification in the laboratory.

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Original Paper in ncRNA • Bélanger Collaboration 2022 • An Expanded Landscape of Unusually Short RNAs in 11 Samples from Six Eukaryotic Organisms

Original Paper in ncRNA • Bélanger Collaboration 2022 • An Expanded Landscape of Unusually Short RNAs in 11 Samples from Six Eukaryotic Organisms | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it
Small RNA sequencing (sRNA-Seq) approaches unveiled sequences derived from longer non-coding RNAs, such as transfer RNA (tRNA) and ribosomal RNA (rRNA) fragments, known as tRFs and rRFs, respectively. However, rRNAs and RNAs shorter than 16 nt are often depleted from library preparations/sequencing analyses, although they may be functional. Here, we sought to obtain a complete repertoire of small RNAs by sequencing the total RNA from 11 samples of 6 different eukaryotic organisms, from yeasts to human, in an extended 8- to 30-nt window of RNA length. The 8- to 15-nt window essentially contained fragments of longer non-coding RNAs, such as microRNAs, PIWI-associated RNAs (piRNAs), small nucleolar RNAs (snoRNAs), tRNAs and rRNAs. Notably, unusually short RNAs < 16 nt were more abundant than those >16 nt in bilaterian organisms. A new RT-qPCR method confirmed that two unusually short rRFs of 12 and 13 nt were more overly abundant (~3-log difference) than two microRNAs. We propose to not deplete rRNA and to reduce the lower threshold of RNA length to include unusually short RNAs in sRNA-Seq analyses and datasets, as their abundance and diversity support their potential role and importance as biomarkers of disease and/or mediators of cellular function.
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Original Paper in Agronomy •Menchari Collaboration 2022 • Approach to Demography of ALS-Resistant Glebionis coronaria as Influenced by Management Factors: Tillage, Allelopathic Crops and Herbicides

Original Paper in Agronomy •Menchari Collaboration 2022 • Approach to Demography of ALS-Resistant Glebionis coronaria as Influenced by Management Factors: Tillage, Allelopathic Crops and Herbicides | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it
Glebionis coronaria (L.) Cass. ex Spach is one of the most serious weeds in cereal crops in Northern Tunisia. Our previous studies have confirmed the presence of resistance to ALS-inhibiting herbicides in G. coronaria, showing the evolution of cross-resistance through TS and NTS mechanisms. The purpose of this study was to evaluate the effects of (i) two tillage practices (conventional tillage and reduced tillage), (ii) three known allelopathic crops: Hordeum vulgare L. (Barley), Brassica napus L. (Rapeseed) and Triticum durum (Wheat) and (iii) herbicides belonging to different modes of action on the density, the cohort numbers and the growth of an ALS-inhibiting cross-resistant population of G. coronaria. Field experiments were conducted in two consecutive years (2017–2018 and 2018–2019) in the Fritissa-Mateur-Bizerte region. Our results revealed that barley considerably contributed to the decrease in G. coronaria’s density, cohort number, total biomass accumulation and plant height. The effect of rapeseed is likely dependent on the tillage practice and the timing of herbicide application, while G. coronaria could be successfully controlled in wheat using auxin herbicides. It is suggested that the management of resistant population of G. coronaria could be achieved by combining barely or rapeseed with right tillage practice and auxin herbicides’ application.
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Original Paper in Atmosphere • Rochefort/ Maire Collaboration 2022 • N/P Addition Is More Likely Than N Addition Alone to Promote a Transition from Moss-Dominated to Graminoid-Dominated Tundra in t...

Original Paper in Atmosphere • Rochefort/ Maire Collaboration 2022 • N/P Addition Is More Likely Than N Addition Alone to Promote a Transition from Moss-Dominated to Graminoid-Dominated Tundra in t... | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it
Nutrient availability for tundra vegetation could change drastically due to increasing temperatures and frequency of nitrogen deposition in the Arctic. Few studies have simultaneously examined the response of plant communities to these two pressures over a long period. This study aims to assess which driver between increasing nitrogen (N) and phosphorus (P) availability through global warming and increasing N availability alone via N deposition is more likely to transform arctic wetland vegetation and whether there is a time lag in this response. An annual fertilization experiment simulating these nutrient inputs was conducted for 17 years in the Canadian High-Arctic to assess the impact on aboveground net primary productivity, floristic composition, and plant nutrient concentration. While the primary productivity of mosses remains unchanged by fertilization after 17 years, productivity of graminoids was increased slightly by N addition (36% increase at the highest dose). In contrast, the primary productivity of graminoids increased strongly with N/P addition (over 227% increase). We noted no difference in graminoid productivity between the 2nd and 5th year of the experiment, but we observed a 203% increase between the 5th and 17th year in the N/P addition treatments. We also noted a 49% decrease in the total moss cover and an 155% increase in the total graminoid cover between the 2nd and 17th year of N/P addition. These results indicate that the impact of warming through increased N/P availability was greater than those of N deposition alone (N addition) and promoted the transition from a moss-dominated tundra to a graminoid-dominated tundra. However, this transition was subject to a time lag of up to 17 years, suggesting that increased productivity of graminoids resulted from a release of nutrients via the decomposition of lower parts of the moss mat.
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Original Paper in J Appl Phycol • Goulet Collaboration 2022 • Impact of temperature and cooking time on the physicochemical properties and sensory potential of seaweed water extracts of Palmaria pa...

Original Paper in J Appl Phycol • Goulet Collaboration 2022 • Impact of temperature and cooking time on the physicochemical properties and sensory potential of seaweed water extracts of Palmaria pa... | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it
The growing world population, global ecological awareness, and the desire to have alternatives to animal proteins, as well as the need for a diet that is tasty, promote gastronomic innovation in connection with science and technology engineering. This study evaluated the chemical composition and the sensory potential of water extracts made with two Quebec coast edible seaweeds (Saccharina longicruris and Palmaria palmata) and measured the influence of extraction parameters (seaweed species, temperature, and cooking time) on these aspects, in order to assess the culinary interest of these local resources and promote them as a food in phycogastronomy. Chemical composition (minerals, proteins, lipids, and carbohydrates) was determined for the crude seaweeds and different water extracts. Extract viscosity, color, and composition in umami (free amino acids, nucleotides) and volatile compounds were also determined. The results show that water extraction preserves the nutrients from crude seaweed. The effect of temperature and cooking time is variable depending on the component and the seaweed. Saccharina longicruris water extracts are more colorful, richer in minerals, uridine monophosphate (UMP), and have salty, marine-sea, and green aromas. Palmaria palmata water extracts are more viscous, with a higher amount of carbohydrates, inosine monophosphate (IMP), sweet and herbaceous-fruity aromas, and good umami flavor potential. To produce a broth richer in umami flavor and aromas, P. palmata should be selected.
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Original Paper in Front Soil Sci • Gumiere Collaboration 2022 • A Computational Method for Modeling Spatiotemporal Variability of Hydrodynamic Properties in Sandy Soil Under Drainage and Recharge

Original Paper in Front Soil Sci • Gumiere Collaboration 2022 • A Computational Method for Modeling Spatiotemporal Variability of Hydrodynamic Properties in Sandy Soil Under Drainage and Recharge | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

This article proposes an analytical strategy that combines X-ray Computed Tomography (CT) and Continuous Wavelet Transform (CWT) analysis as an alternative solution to long-term experiments that seek to investigate spatiotemporal variations in soil hydraulic properties induced by drainage and recharge cycles. We conducted CT scanning on 100-cm-high column filled with two types of sandy soil in a laboratory environment to simulate, over the period of a month, the equivalent of nearly 40 years of drainage/recharge cycles akin to agricultural fields adopting subirrigation as water management practices. We also monitored soil matric potential, water inflow and outflow, as well as movement of tracers. This later consists in zirconium oxide (ZrO2) that we added to the top 20 cm of each soil column. The results revealed that drainage and recharge cycles greatly affect the evolution of soil hydraulic properties at different locations along the soil profile by reducing drainage and capillary capacities. The approach also allowed us to identify each periodic component of drainage and recharge cycles, and thereby calculate the periodic drift over time. The proposed method can be applied to predict soil evolution according to soil texture, drainage system design and water management, thereby offering a potential basis for proposing mitigation measures related to soil hydrodynamics. It may find its application in agricultural farms adopting subirrigation and surface (e.g., drip) irrigation approaches and, in mining and civil engineering.

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Original Paper in Agronomy • Dorais Collaboration 2022 • Diet Composition Influences Growth Performance, Bioconversion of Black Soldier Fly Larvae: Agronomic Value and In Vitro Biofungicidal Activi...

Original Paper in Agronomy • Dorais Collaboration 2022 • Diet Composition Influences Growth Performance, Bioconversion of Black Soldier Fly Larvae: Agronomic Value and In Vitro Biofungicidal Activi... | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it
In recent years, the larval stage of Hermetia illucens, commonly known as the black soldier fly (BSFL), has been used to promote the circularity of the agri-food sector by bioconverting organic waste into larval biomass which has been used as a livestock feed. A secondary byproduct of this process is frass that can be used as an organic fertilizer. This study compared two different plant-based diets on frass characteristics as well as larval performance, nutritional composition, and waste reduction efficiency. A fruit/vegetable/bakery waste-based diet supplemented with brewery waste (FVBB) was compared to a control Gainesville (GV) reference diet and fed to BSFL under standard conditions. The results demonstrated that NPK and some of the macro and micronutrients in both frasses are comparable to commercially available organic fertilizers. It was shown that microorganisms present in frass from the two diets inhibit the mycelial growth of several plant pathogens through the production of antifungal and/or anti-oomycetes compound(s) (antibiosis). This diet also had a positive effect on individual larval mass (162.11 mg), bioconversion rate (13.32%), and larval crude lipid (35.99% of dry matter) content. The BSFL reared on this diet reduced feedstock dry matter by 67.76% in a very short time (10 days), which is a promising solution for food waste management.
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Original Paper in Front Plant Sci • Dorais Collaboration 2022 • Different Temperature and UV Patterns Modulate Berry Maturation and Volatile Compounds Accumulation in Vitis sp.

Original Paper in Front Plant Sci • Dorais Collaboration 2022 • Different Temperature and UV Patterns Modulate Berry Maturation and Volatile Compounds Accumulation in Vitis sp. | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

Volatile compounds (VCs) in grapevine berries play an important role in wine quality; however, such compounds and vine development can be sensitive to environmental conditions. Due to this sensitivity, changes in temperature patterns due to global warming are likely to further impact grape production and berry composition. The aim of this study was to determine the possible effects of different growing-degree day accumulation patterns on berry ripening and composition at harvest. An experimental field was conducted using Vitis sp. L'Acadie blanc, in Nova Scotia, Canada. Using on-the-row mini-greenhouses, moderate temperature increase and reduced ultraviolet (UV) exposure were triggered in grapevines during pre-veraison (inflorescence to the beginning of berry softening), post-veraison (berry softening to full maturity), and whole season (inflorescence to full maturity), while controls were left without treatment. Free and bound VCs were extracted from berries sampled at three different phenological stages between veraison and maturity before analysis by gas chromatography–mass spectrometry (GC-MS). Berries from grapevines exposed to higher temperatures during early berry development (pre-veraison and whole) accumulated significantly higher concentrations of benzene derivatives 2-phenylethanol and benzyl alcohol at harvest, but lower concentrations of hydroxy-methoxy-substituted volatile phenols, terpenes, and C13-norisoprenoids than the control berries. These results illustrate the importance of different environmental interactions in berry composition and suggest that temperature could potentially modulate phenylpropanoid and mevalonate metabolism in developing berries. This study provides insights into the relationships between abiotic conditions and secondary metabolism in grapevine and highlights the significance of early developmental stages on berry quality at harvest.

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Original Paper in Agronomy • Dorais Lab 2022 • Biostimulants Promote Plant Development, Crop Productivity, and Fruit Quality of Protected Strawberries

Original Paper in Agronomy • Dorais Lab 2022 • Biostimulants Promote Plant Development, Crop Productivity, and Fruit Quality of Protected Strawberries | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it
Berries such as strawberries are recognized as a significant constituent of healthy human diets owing to their bioactive secondary metabolites. To improve crop sustainability, yield and berry quality, alternative production systems should be proposed such as organic farming and the use of biostimulants. Thus, we have compared within a complete randomized block design seven biostimulant treatments: 1-control, 2-seaweed extract, 3-Trichoderma, 4-mycorrhiza, 5-mixture of three bacteria, 6-combination of mycorrhiza + bacteria, and 7-citric acid. Strawberry plants were grown in conventional high tunnel (CH), conventional greenhouse (CG) and organic greenhouse (OG). Our results showed that biostimulants did not impact the soil microbial activity (FDA) when compared with the control. Leaf chlorophyll content and photosynthetic leaf performance were not affected by any studied biostimulants. Bacteria, citric acid, and the combination of mycorrhiza + bacteria increased the number of flowering stalks compared with the control in CH, while bacteria increased the crown diameter and all biostimulants increased fresh and dry shoot plant biomass. Citric acid increased leaf Ca content in CG, when all biostimulants increased leaf N content in CH. Studied biostimulants increased berry productivity in CH, while citric acid treatment had the highest yield in CG. The anthocyanins content increased with the use of biostimulants in CH, whereas Trichoderma (CG) and the combination of mycorrhiza + bacteria (OG) increased the Brix, total polyphenols, and anthocyanin contents of the berries compared with the control.
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Original Paper in Agriculture • Grégoire Lab 2022 • Novel Hybrid Statistical Learning Framework Coupled with Random Forest and Grasshopper Optimization Algorithm to Forecast Pesticide Use on Golf C...

Original Paper in Agriculture • Grégoire Lab 2022 • Novel Hybrid Statistical Learning Framework Coupled with Random Forest and Grasshopper Optimization Algorithm to Forecast Pesticide Use on Golf C... | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it
Golf course maintenance requires the use of several inputs, such as pesticides and fertilizers, that can be harmful to human health or the environment. Understanding the factors associated with pesticide use on golf courses may help golf-course managers reduce their reliance on these products. In this study, we used a database of about 14,000 pesticide applications in the province of Québec, Canada, to develop a novel hybrid machine learning approach to predict pesticide use on golf courses. We created this proposed model, called RF-SVM-GOA, by coupling a support vector machine (SVM) with random forest (RF) and the grasshopper optimization algorithm (GOA). We applied RF to handle the wide range of datasets and GOA to find the optimal SVM settings. We considered five different dependent variables—region, golf course ID, number of holes, year, and treated area—as input variables. The experimental results confirmed that the developed hybrid RF-SVM-GOA approach was able to estimate the active ingredient total (AIT) with a high level of accuracy (R = 0.99; MAE = 0.84; RMSE = 0.84; NRMSE = 0.04). We compared the results produced by the developed RF-SVM-GOA model with those of four tree-based techniques including M5P, random tree, reduced error pruning tree (REP tree), and RF, as well as with those of two non-tree-based techniques including the generalized structure of group method of data handling (GSGMDH) and evolutionary polynomial regression (EPR). The computational results showed that the accuracy of the proposed RF-SVM-GOA approach was higher, outperforming the other methods. We analyzed sensitivity to find the most effective variables in AIT forecasting. The results indicated that the treated area is the most effective variable in AIT forecasting. The results of the current study provide a method for increasing the sustainability of golf course management.
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Original Paper in Theor Appl Genet • Torkamaneh Collaboration 2022 • Identification of quantitative trait loci associated with seed quality traits between Canadian and Ukrainian mega-environments u...

Original Paper in Theor Appl Genet • Torkamaneh Collaboration 2022 • Identification of quantitative trait loci associated with seed quality traits between Canadian and Ukrainian mega-environments u... | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it
Key Message Identifying QTL associated with soybean seed quality traits from a diverse GWAS panel cultivated in Canadian and Ukrainian mega-environments may facilitate future cultivar development for foreign markets. Abstract Understanding the complex genetic basis of seed quality traits for soybean in the mega-environments (MEs) is critical for developing a marker-assisted selection program that will lead to breeding superior cultivars adapted to specific regions. This study aimed to analyze the accumulation of 14 soybean seed quality traits in Canadian ME and two seed quality traits in Ukrainian ME and identify associated ME specific quantitative trait loci (QTLSP) and ME universal QTL (QTLU) for protein and oil using a genome-wide association study (GWAS) panel consisting of 184 soybean genotypes. The panel was planted in three locations in Canada and two locations in Ukraine in 2018 and 2019. Genotype plus genotype-by-environment biplot analysis was conducted to assess the accumulation of individual seed compounds across different locations. The protein accumulation was high in the Canadian ME and low in the Ukrainian ME, whereas the oil concentration showed the opposite trends between the two MEs. No QTLU were identified across the MEs for protein and oil concentrations. In contrast, nine Canadian QTLSP for protein were identified on various chromosomes, which were co-located with QTL controlling other traits identified in the Canadian ME. The lack of common QTLU for protein and oil suggests that it may be necessary to use QTLSP associated with these traits separately for the Canadian and Ukrainian ME. Additional Ukrainian data for seed compounds other than oil and protein are required to identify novel QTLSP and QTLU for such traits for the individual or combined Canadian and Ukrainian MEs.
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Book Chapter in Methods Mol Biol • Pérez-López Collaboration 2022 • Rapid Molecular Diagnostics in the Field and Laboratory to Detect Plant Pathogen DNA in Potential Insect Vectors

Book Chapter in Methods Mol Biol • Pérez-López Collaboration 2022 • Rapid Molecular Diagnostics in the Field and Laboratory to Detect Plant Pathogen DNA in Potential Insect Vectors | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

A variety of sensitive and specific molecular diagnostic assays has been described for detecting nucleic acids in biological samples that may harbor pathogens of interest. These methods include very rapid, isothermal nucleic acid amplification methods that can be deployed outside of the laboratory environment, such as loop-mediated isothermal DNA amplification (LAMP) and recombinase-polymerase amplification (RPA). However, all molecular diagnostic assays must be preceded by nucleic acid extraction from the biological samples of interest, which provides suitable template molecules for the assays. To exploit the features of the amplification assays and be utilized outside of the lab, these methods must be rapid and avoid the need for typical laboratory chemicals and equipment. We describe a protocol for the extraction of DNA from field-collected insects that can be implemented at the point of collection and used to detect the presence of DNA sequences from potential plant pathogens that may be vectored by the insects. This protocol provides template DNA that is suitable for PCR, LAMP, and RPA. The FTA PlantSaver card-based DNA extraction product was also confirmed to amplify the mitochondrial cytochrome oxidase 1 (CO1) universal barcode that could later be sequenced to identify any insect. Lastly, we provide an example using field-collected insects, Neokolla (Graphocephala) heiroglyphica, and demonstrate the detection of the plant pathogen Xylella fastidiosa in carrier insects using PCR, RPA, and LAMP.

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Original Paper in Front Soil Sci • Dessureault-Rompré Collaboration 2022 • Carbon, Nitrogen, Phosphorus, and Extracellular Soil Enzyme Responses to Different Land Use

Original Paper in Front Soil Sci • Dessureault-Rompré Collaboration 2022 • Carbon, Nitrogen, Phosphorus, and Extracellular Soil Enzyme Responses to Different Land Use | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

Extracellular soil enzymes play a key role in soil organic matter decomposition and nutrient cycling. However, it is not fully understood how these enzymes respond to different land use. Long-term research studies were used to evaluate how diversified management practices affect extracellular enzymes driving C cycling [phenol oxidases (PO), peroxidases (PP), α-glucosidase (AG), β-glucosidase (BG), cellobiohydrolase (CB), β-1,-4-Nacetylglucosaminidase (NAG)], N cycling [leucine aminopeptidase (LAP)], and P cycling [phosphomonoesterase (PME)]. The soil pH, contents of total organic C, total N, mehlich-3 P, soil respiration and soil nitrogen supply capacity were also measured. Different land use included tillage frequency, tillage regimes, mineral N fertilization, crop rotations and liquid dairy manure. Compared to medium or high tillage frequency, low tillage frequency increased total organic C and total N and soil respiration as well as NAG and PME activities, whereas it decreased soil nitrogen supply, mehlich-3 P, and soil pH, as well as PO, PP, AG, BG, CB, and LAP activities. Non till was associated with lower PP and PO activities than moldboard plow. Nitrogen fertilization decreased soil pH and PO activity but increased PME activity. Barley (Hordeum vulgare) in rotation with forage increased total organic C, total N, soil nitrogen supply and soil respiration by 31, 21, 44, and 33%, respectively, in comparison with barley in monoculture. The application of liquid dairy manure increased soil pH, total N and soil nitrogen supply and soil enzyme activities (AG, BG, NAG) in comparison to the mineral N fertilizer. When principal component analysis was performed, soil pH, PO, PP, CB, LAP, and PME were grouped in the first component, which explained the highest variance. This is the core group controlling the C, N, and P cycling. The activities of C, N, and P acquiring enzymes, soil nitrogen supply and soil respiration were related to changes in soil total C and N, and extractable P contents across a broad range of management practices. Increased PO and PP activities reflect total C decline.

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Original Paper in Genome • Belzile Lab 2022 • The Construction of a High-Density Consensus Genetic Map for Soybean Based on SNP Markers Derived from Genotyping-by-Sequencing (GBS)

Original Paper in Genome • Belzile Lab 2022 • The Construction of a High-Density Consensus Genetic Map for Soybean Based on SNP Markers Derived from Genotyping-by-Sequencing (GBS) | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it
Genetic linkage maps are used to localize markers on the genome based on the recombination frequency. Most often, these maps are based on the segregation observed within a single biparental population of limited size (n<300) where relatively few recombination events are sampled and in which some genomic regions are monomorphic because both parents carry the same alleles. Together, these two limitations affect both the resolution and extent of genome coverage of such maps. Consensus genetic maps overcome the limitations of individual genetic maps by merging the information from multiple segregating populations derived from a greater diversity of parental combinations, thus increasing the number of recombination events and reducing the number of monomorphic regions. The aim of this study was to construct a high-density consensus genetic map for SNP markers obtained through a genotyping-by-sequencing (GBS) approach. Individual genetic maps were generated from six F4:5 mapping populations (n=278-365), totaling 1857 individuals. The six linkage maps were then merged to produce a consensus map comprising a total of 16,311 mapped SNPs that jointly cover 99.5% of the soybean genome with only two gaps larger than 10 cM. Compared to previous soybean consensus maps, it offers a more extensive and uniform coverage.
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Review in Appl Microbiol Biotechnol • Torkamaneh Lab 2022 • Machine learning: its challenges and opportunities in plant system biology

Review in Appl Microbiol Biotechnol • Torkamaneh Lab 2022 • Machine learning: its challenges and opportunities in plant system biology | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

Sequencing technologies are evolving at a rapid pace, enabling the generation of massive amounts of data in multiple dimensions (e.g., genomics, epigenomics, transcriptomic, metabolomics, proteomics, and single-cell omics) in plants. To provide comprehensive insights into the complexity of plant biological systems, it is important to integrate diferent omics datasets. Although recent advances in computational analytical pipelines have enabled efcient and high-quality exploration and exploitation of single omics data, the integration of multidimensional, heterogenous, and large datasets (i.e., multi-omics) remains a challenge. In this regard, machine learning (ML) ofers promising approaches to integrate large datasets and to recognize fne-grained patterns and relationships. Nevertheless, they require rigorous optimizations to process multi-omicsderived datasets. In this review, we discuss the main concepts of machine learning as well as the key challenges and solutions related to the big data derived from plant system biology. We also provide in-depth insight into the principles of data integration using ML, as well as challenges and opportunities in diferent contexts including multi-omics, single-cell omics, protein function, and protein–protein interaction.

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Original Paper in Restor Ecol • Rochefort Lab 2022 • Reestablishment of peatland vegetation following surface levelling of decommissioned in situ oil mining infrastructures

Original Paper in Restor Ecol • Rochefort Lab 2022 • Reestablishment of peatland vegetation following surface levelling of decommissioned in situ oil mining infrastructures | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

Peatland ecosystem restoration following oil mining activities in Alberta, Canada, aims at reestablishing crucial peatland functions, such as wildlife habitat, water storage and filtration, peat accumulation and carbon sequestration. To reinstate peatland functions, characteristic hydrological conditions are necessary to support the establishment and growth of characteristic wetland vegetation. Following in situ oil sands well pad disturbances in the Peace River and Cold Lake Oil Sands regions in Alberta, we evaluated the efficiency of peatland restoration approaches including different groundwork and revegetation techniques. Groundwork techniques included the complete removal (CR) or partial removal (PR) of the former in situ well pads’ mineral fill and revegetation included the spontaneous revegetation via natural ingress of diaspores from nearby peatlands, or managed revegetation via planting of Carex aquatilis, Larix laricina, and Salix lutea. We assessed the plant species composition, biochemical and hydrological properties of all study areas, including restored peatland areas, an unrestored area and reference areas (REF) for comparison. Ten years post-restoration, in the restored areas the mean total plant cover was 57% with an average of 35 vascular plant and bryophyte species, while in REF 68% mean total plant cover and an average of 64 plant species were recorded. Respectively, characteristic peatland species contributed to 61 and 100% to the species composition. PR and hydrological connection to the adjacent peatland resulted in near surface water table and the highest peatland plant species diversity, while CR promoted the formation of a shallow open water area.

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Review In Front Plant Sci • Belzile/Bélanger/Torkamaneh Labs 2022 • The SoyaGen Project: Putting Genomics to Work for Soybean Breeders

Review In Front Plant Sci • Belzile/Bélanger/Torkamaneh Labs 2022 • The SoyaGen Project: Putting Genomics to Work for Soybean Breeders | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it
The SoyaGen project was a collaborative endeavor involving Canadian soybean researchers and breeders from academia and the private sector as well as international collaborators. Its aims were to develop genomics-derived solutions to real-world challenges faced by breeders. Based on the needs expressed by the stakeholders, the research efforts were focused on maximizing realized yield through optimization of maturity and improved disease resistance. The main deliverables related to molecular breeding in soybean will be reviewed here. These include: (1) SNP datasets capturing the genetic diversity within cultivated soybean (both within a worldwide collection of > 1,000 soybean accessions and a subset of 102 short-season accessions (MG0 and earlier) directly relevant to this group); (2) SNP markers for selecting favorable alleles at key maturity genes as well as loci associated with increased resistance to key pathogens and pests (Phytophthora sojae, Heterodera glycines, Sclerotinia sclerotiorum); (3) diagnostic tools to facilitate the identification and mapping of specific pathotypes of P. sojae; and (4) a genomic prediction approach to identify the most promising combinations of parents. As a result of this fruitful collaboration, breeders have gained new tools and approaches to implement molecular, genomics-informed breeding strategies. We believe these tools and approaches are broadly applicable to soybean breeding efforts around the world.
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