Quentin A.G.,CSIRO |
Rodemann T.,University of Tasmania |
Doutreleau M.-F.,AgriTerr Unit |
Moreau M.,AgriTerr Unit |
Davies N.W.,University of Tasmania
Tree Physiology | Year: 2017
Near-infrared reflectance spectroscopy (NIRS) is frequently used for the assessment of key nutrients of forage or crops but remains underused in ecological and physiological studies, especially to quantify non-structural carbohydrates. The aim of this study was to develop calibration models to assess the content in soluble sugars (fructose, glucose, sucrose) and starch in foliar material of Eucalyptus globulus. A partial least squares (PLS) regression was used on the sample spectral data and was compared to the contents measured using standard wet chemistry methods. The calibration models were validated using a completely independent set of samples. We used key indicators such as the ratio of prediction to deviation (RPD) and the range error ratio to give an assessment of the performance of the calibration models. Accurate calibration models were obtained for fructose and sucrose content (R2 > 0.85, root mean square error of prediction (RMSEP) of 0.95%-1.26% in the validation models), followed by sucrose and total soluble sugar content (R2 ∼ 0.70 and RMSEP > 2.3%). In comparison to the others, calibration of the starch model performed very poorly with RPD = 1.70. This study establishes the ability of the NIRS calibration model to infer soluble sugar content in foliar samples of E. globulus in a rapid and cost-effective way. We suggest a complete redevelopment of the starch analysis using more specific quantification such as an HPLC-based technique to reach higher performance in the starch model. Overall, NIRS could serve as a high-throughput phenotyping tool to study plant response to stress factors. © The Author 2016.
Merlin C.,University of Rouen |
Merlin C.,French National Institute for Agricultural Research |
Besaury L.,University of Rouen |
Niepceron M.,University of Rouen |
And 5 more authors.
Letters in Applied Microbiology | Year: 2014
Cellulose is the main structural component of the cell walls of higher plants, representing c. 35-50% of a plant's dry weight; after decomposition and transformation, and constituting a large part of soil organic matter. Telluric micro-organisms able to use cellulose as carbon and energy sources for growth are widely distributed in the environment, but the factors controlling the rate of cellulose degradation are not well understood. In this study, we have developed a quantitative real-time PCR (qPCR) primer set to quantify the glycoside hydrolase family 6 (GH6 family) cellulase genes in soil samples. The qPCR assays were linear over 8 orders of magnitude and sensitive down to 10 copies per assay. qPCR analysis of contrasted soil samples showed densities between 2·47 × 107 and 1·48 × 1010 copies per gram of soil. Cloning and sequencing of the PCR products from environmental DNA confirmed both specific amplification (more than 96%) and the wide diversity targeted by the primer set, throughout nearly all the GH6 family, including sequences of bacteria and fungi. © 2014 The Society for Applied Microbiology.
Lebrun J.D.,IRSTEA |
Lebrun J.D.,Agriterr Unit |
Lebrun J.D.,French National Institute for Agricultural Research |
Demont-Caulet N.,French National Institute for Agricultural Research |
And 6 more authors.
Environmental Science and Pollution Research | Year: 2016
The present study investigates the effect of metals on the secretion of enzymes from12 fungal strains maintained in liquid cultures. Hydrolases (acid phosphatase, β-glucosidase, β-galactosidase, and N-acetyl-β-glucosaminidase) and ligninolytic oxidoreductases (laccase, Mn, and lignin peroxidases) activities, as well as biomass production, were measured in culture fluids from fungi exposed to Cu or Cd. Our results showed that all fungi secreted most of the selected hydrolases and that about 50 % of them produced a partial oxidative system in the absence of metals. Then, exposure of fungi to metals led to the decrease in biomass production. At the enzymatic level, Cu and Cd modified the secretion profiles of soil fungi. The response of hydrolases to metals was contrasted and complex and depended on metal, enzyme, and fungal strain considered. By contrast, the metals always stimulated the activity of ligninolytic oxidoreductases in fungal strains. In some of them, oxidoreductases were specifically produced following metal exposure. Fungal oxidoreductases provide a more generic response than hydrolases, constituting thus a physiological basis for their use as biomarkers of metal exposure in soils. © 2015, Springer-Verlag Berlin Heidelberg.
PubMed | AgriTerr Unit, University of Tasmania and CSIRO
Type: | Journal: Tree physiology | Year: 2016
Near-infrared reflectance spectroscopy (NIRS) is frequently used for the assessment of key nutrients of forage or crops but remains underused in ecological and physiological studies, especially to quantify non-structural carbohydrates. The aim of this study was to develop calibration models to assess the content in soluble sugars (fructose, glucose, sucrose) and starch in foliar material of Eucalyptus globulus A partial least squares (PLS) regression was used on the sample spectral data and was compared to the contents measured using standard wet chemistry methods. The calibration models were validated using a completely independent set of samples. We used key indicators such as the ratio of prediction to deviation (RPD) and the range error ratioto give an assessment of the performance of the calibration models. Accurate calibration models were obtained for fructose and sucrose content (R
Bressan M.,AgriTerr Unit |
Trinsoutrot Gattin I.,AgriTerr Unit |
Desaire S.,AgriTerr Unit |
Castel L.,AgriTerr Unit |
And 2 more authors.
Applied Soil Ecology | Year: 2015
Soil microorganisms play key roles in ecosystem functioning. Finding tools to accurately measure, quantify and understand this component of soil is crucial to establish relevant indicators of the state of soil. This study proposes an optimized methodology using flow cytometry (FCM) for the quantification of bacteria in soil. This rapid and reproducible methodology was validated in two steps: (a) the recovery of spiked cells from sterilized soil matrix backgrounds and (b) the determination of the total number of bacteria from silty native soils (grassland and crop field). The ratio of counted SYBR Green-stained cells versus expected values amounted to 0.83 on average by FCM, compared to 0.64 by plate counts. We used this FCM method to compare bacterial abundance measured in four types of crop management systems: organic, integrated with (TRC) or without tillage (RTRC) and conventional. The FCM count ranged from 3.91×108 to 5.69×108cellsg-1 soil for crop field and was 6.69×108cellsg-1 soil for grassland. Similarly, two other frequently used descriptors of the bacterial community (quantification of the 16S rRNA gene by real-time PCR and total culturable heterotrophic bacteria by plate count analysis) were analyzed for all soils and compared with the FCM data. FCM counts were relevant enough to report significant differences between the four crop management systems. Higher bacterial counts were observed in conventional and integrated RTRC systems in comparison with organic and integrated TRC. The same tendency was observed when considering 16S rRNA gene abundance. As expected, a slight but significant correlation was observed between FCM counts and 16S rRNA gene quantification when considering all soil samples. No difference between crop management systems was noticed if we considered only colony forming unit (CFU) count. A calculated ratio between culturable and total bacterial counts (CFU/FCM) suggests some differences in the culturable proportion according to soil management.In the context of evaluating the state of soil, our FCM method offers a quick and simple assessment of total bacterial abundance in numerous samples. Combined with other biological indicators, FCM contributes to understanding soil bacterial biomass and could represent a useful complement in a larger panel of indicators to evaluate and detect changes in the structure of the soil microbial community. © 2015 Elsevier B.V.
Bressan M.,AgriTerr unit |
Blum A.,AgriTerr unit |
Castel L.,AgriTerr unit |
Trinsoutrot-Gattin I.,AgriTerr unit |
And 2 more authors.
Applied Soil Ecology | Year: 2016
Verticillium wilt, due to the soilborne fungus Verticillium dahliae, is a persistent disease affecting flax culture in Upper Normandy. This pathology has increased since the last decade, leading to yield losses for flax producers. In part due to the long survival of V. dahliae in soil and the difficulty of early diagnosis in affected plant, Verticillium flax wilt management remains problematic in the absence of efficient phytosanitary treatment. Pathogen avoidance and the reduction of soil inoculum through adapted cultural practices are the best alternatives to fight against Verticillium wilt. Therefore, the objective was here to optimize and validate a rapid and specific real-time PCR assay targeting the ribosomal DNA Internal Transcribed Spacers (ITS) to measure V. dahliae density in soil. This method was then used to assess and compare the pathogen density in fields from four diverse management systems: conventional, integrated with or without tillage, and organic. First, the real-time PCR assay provided sensitive and reliable quantification of V. dahliae in a range of artificially inoculated soils with known inoculum density. Then, this method was successfully applied in crop fields. Measured V. dahliae densities presented an intra-parcel heterogeneity, emphasizing the importance of an adapted sampling strategy to assess pathogen load in crop field. Furthermore, these densities appeared to be impacted by agricultural practices, particularly tillage. The influence of the previous crop on pathogen load had also to be considered with attention to manage efficiently this disease through crop rotation. Such knowledge of pathogen density in soils could provide critical information for stakeholders to identify infested fields and predict disease development. Molecular approach should be considered as a useful tool for Verticillium wilt management in flax culture. © 2016 Elsevier B.V.