Variable selection in near infrared spectra for the biological characterization of soil and earthworm casts

International audienceNear infrared reflectance spectroscopy (NIRS) was used to predict six biological properties of soil and earthworm casts including extracellular soil enzymes, microbial carbon, potential nitrification and denitrification. Partial least squares regression (PLSR) models were developed with a selection of the most important near infrared wavelengths. They reached coefficients of determination ranging from 0.81 to 0.91 and ratios of performance-to-deviation above 2.3. Variable selection with the variable importance in the projection (VIP) method increased dramatically the prediction performance of all models with an important contribution from the 1750–2500 nm region. We discuss whether selected wavelengths can be attributed to macronutrient availability or to microbial biomass. Wavelength selection in NIR spectra is recommended for improving PLSR models in soil research

Outbreak of Corynebacterium pseudodiphtheriticum Infection in Cystic Fibrosis Patients, France

Respiratory tract colonization with these bacteria may be common in this population

Evolution de la flore, des humus et de la pédofaune associée sous l'effet de perturbations sylvicoles

TOULOUSE3-BU Sciences (315552104) / SudocBRUNOY-Bib. d'ecologie generale (911145101) / SudocSudocFranceF

Le pommier en agroforesterie : Dynamique des ravageurs et de leurs ennemis naturels

La culture de pommier (Malus domestica) est l’une des principales productions fruitières en climat tempéré. En production fruitière, la gestion des ravageurs repose sur un usage intensif des pesticides afin d’assurer l’absence de défaut visuel sur les fruits. Ces systèmes conventionnels sont désormais remis en question de par leurs impacts négatifs sur la biodiversité, la santé humaine et la qualité des sols, de l’air et de l’eau. Le développement de la biodiversité à l’intérieur des parcelles agricoles est une alternative potentielle pour répondre à ces enjeux environnementaux, sanitaires et agronomiques. Les mécanismes de régulation biologique peuvent permettre un contrôle des populations de ravageurs phytophages grâce à leurs ennemis-naturels. Ces ennemis-naturels sont des prédateurs ou des parasitoïdes qui détruisent les ravageurs. Les ennemis naturels sont nombreux et leur diversité est importante pour la régulation biologique, car ils sont complémentaires (dans l’espace, le temps et les fonctions). Pour bénéficier naturellement de ces ennemis-naturels, les parcelles doivent être aménagées afin de leur offrir une continuité de ressources et d’habitats. Pour ce faire, on peut intégrer des infrastructures agroécologiques afin de pérenniser les ennemis-naturels : c’est la lutte biologique par conservation. Cependant il existe de nombreuses infrastructures agroécologiques et leurs effets ne sont pas tous bien renseignés. Dans le contexte méditerranéen, on sait que l’agroforesterie apporte des bénéfices agronomiques aux vergers de pommiers. L’objectif de l’étude est d’évaluer l’effet de l’agroforesterie sur les arthropodes et les mécanismes de régulation biologique de trois ravageurs : le puceron cendré (Dysaphis plantaginea), le puceron vert (Aphis pomi) et le carpocapse (Cydia pomonella). L’expérimentation a lieu sur une parcelle associant des noyers à bois et des pommes (variété Dalinette). Elle est située dans un environnement semi-naturel et conduite en agriculture biologique. En fonction de leur distance des noyers, les pommiers sont agencés selon trois modalités d’un gradient agroforestier. Sur les pommiers, on réalise des suivis dynamiques approfondis des arthropodes et/ou de leurs dégâts. Les résultats sont analysés en fonction du gradient agroforestier et des différents blocs de la parcelle afin d’évaluer la présence d’un gradient parcellaire. La proximité de noyers diminue la présence du carpocapse dans les pommiers. Le pourcentage de fruits infestés par le carpocapse est plus faible à proximité de noyers. Les hypothèses explicatives sont : 1/ La partie aérienne des noyers forme un effet barrière, qui limite la propagation du carpocapse. 2/ Les rangs de noyers forment des couloirs de chasse pour les chiroptères, qui régulent le carpocapse au stade adulte. 3/ La compétition des noyers (racinaire et aérienne) diminue le nombre de fruits des pommiers proches, réduisant leur attractivité pour la ponte des femelles adultes. En revanche, la proximité des noyers favorise la présence de fourmis, de pucerons verts et de certains arthropodes détritivores dans les pommiers. Les hypothèses explicatives sont : 1/ Les fourmis, favorisées par l’agroforesterie, diminuent la régulation biologique, en protégeant les pucerons. En effet la survie et la longévité des foyers de pucerons verts sont étroitement liées à la présence de fourmis dans ces foyers. 2/ Le microclimat généré par les noyers est favorable au puceron vert pendant la période chaude et sèche de la saison. L’effet de l’agroforesterie sur le puceron cendré n’a pas pu être évalué. Un effet parcellaire est mis en évidence. Il est provoqué principalement par une haie de bordure, qui constitue un corridor écologique pour certains arthropodes, notamment les fourmis. Cette haie favorise la présence du puceron vert dans la parcelle

Predicting soil quality indices with near infrared analysis in a wildfire chronosequence

International audienceWe investigated the power of near infrared (NIR) analysis for the quantitative assessment of soil quality in a wildfire chronosequence. The effect of wildfire disturbance and soil engineering activity of earthworms on soil organic matter quality was first assessed with principal component analysis of NIR spectra. Three soil quality indices were further calculated using an adaptation of the method proposed by Velasquez et al. [Velasquez, E., Lavelle, P., Andrade, M. GISQ, a multifunctional indicator of soil quality. Soil Biol Biochem 2007; 39: 3066–3080.], each one addressing an ecosystem service provided by soils: organic matter storage, nutrient supply and biological activity. Partial least squares regression models were developed to test the predicting ability of NIR analysis for these soil quality indices. All models reached coefficients of determination above 0.90 and ratios of performance to deviation above 2.8. This finding provides new opportunities for the monitoring of soil quality, using NIR scanning of soil samples

Les Collemboles endémiques, des indicateurs privilégiés dans l'aménagement durable des forêts

International audienceOur study compared the soil collembolan community at three semi-natural sites (a beech forest, a beechfir forest and a fir stand) and three managed sites (Norway spruce, beechfir and fir). Collembola were extracted from a total of 60 samples with a BerleseTullgren funnel, counted and identified to species level. A total of 7187 specimens, representing 51 species and 37 genera, were collected. There were significant differences between managed and natural forests (t-test, P=0.000). The communities and their population densities were significantly lower in the managed site: 51 species with 708,498 ind m−2 in the semi-natural forests to 36 species and 306,042 ind m−2 in the managed stands. The endemic component suffered a particularly severe decrease in species richness and abundance (57% and 71% lower in the managed forests, respectively). These species with narrow distribution and small local populations are doubly vulnerable to alterations of environmental conditions. They are very sensitive to loss of their natural habitat owing to human intervention and thus represent useful indicators of tolerance to environmental stress. We highlight the need to take endemic species into consideration in studies on the conservation of biodiversity because they are most at risk of extinction. Semi-natural forests are refuges for endemic species and should be protected

Effets directs et combinés des stress liés aux sécheresses et incendies sur les communautés de vers de terre dans un écosystème méditerranéen

International audienceWe studied the dynamics of earthworm populations in a fire prone forest environment in Mediterranean France from 2005 to 2011. Species diversity, worm number, size and biomass and worm casts size, number and spatial distribution were measured in an experimental design including 33 plots, with various fire regimes combining 2 fire frequencies (few fires vs many fires in 50 years) and 3 dates for the last fire (1, 4 and 15 years ago) and unburnt control plots. The follow up included a period of repeated drought (2003-2007) followed by a period of normal climate (2008-spring 2011). The two last fires (2003 and 2007 occurred respectively at the beginning and at the end of the dry period, which allowed assessing the drought-fire stress interaction. Worm populations, diversity and activity were reduced by fire as well by repeated drought. The reduction was higher in case of repeated fires. Fire and drought mutually increased their respective impact, showing a strong interaction. Worm activity, size and spatial distribution gradually recovered in 4 years after the end of drought but remained lower than normal in recently or frequently burned plots. Population spreading from refugees was studied too and proved to be slow (2-3 m/year)

The combined effects of faba bean and endogeic earthworms on soil microbial activity in intercrops

The rhizosphere is a hotspot of interactions between plants and soil organisms that affect the soil functioning and nutrient cycling. The drilosphere is a hotspot of interactions between earthworms and soil microbial communities affecting plant growth, soil aggregation, and porosity. Central to these interactions are microorganisms, which are affected by both plant species diversity and earthworm activity. Little is known about the effects of earthworms on the microbial community activity under the influence of root-trait diversity in cases of multispecies plant covers. We investigated the impact of plant composition and the presence of endogeic earthworms on the metabolic response of microorganisms to the addition of 10 carbon substrates relevant as rhizodeposition components. A greenhouse experiment was conducted with mesocosms filled with 10 kg of soil, sown with two plants of either the same or different species, chosen based on their contrasting root traits. Five modalities were investigated: 1 faba bean (Vicia faba L. ssp. Minor) intercropped with either 1 rapeseed (Brassica napus L.) or 1 wheat (Triticum aestivum L.) plant, as well as crops of the same species: either 2 rapeseeds, 2 wheats, or 2 faba beans. For each modality, 10 mesocosms were set up, and half of them were inoculated with 5 endogeic earthworms (Aporrectodea caliginosa Savigny). After 91 days, the plants' dry weight, N content, and 15N:14N ratio were measured. The rhizosphere microbial respiration was assessed using the MicroRespTM method. The results showed that the level of metabolic activity depends on the plant species composition. Faba bean had the highest positive effect on microbial growth and metabolic activity. Microbial activity was also significantly increased by earthworms, but with no specific effect between plant treatments. Our findings suggest that plant traits are the main driver of the metabolic activity of soil microorganisms that is stimulated by earthworms