Water-extractable organic matter linked to soil physico-chemistry and microbiology at the regional scale.

10 pagesInternational audienceA better understanding of the links between dissolved organic matter and biogeochemical processes in soil could help in evaluating global soil dynamics. To assess the effects of land cover and parental material on soil biogeochemistry, we studied 120 soil samples collected from various ecosystems in Burgundy, France. The potential solubility and aromaticity of dissolved organic matter was characterised by pressurised hot-water extraction of organic carbon (PH-WEOC). Soil physico-chemical characteristics (pH, texture, soil carbon and nitrogen) were measured, as was the δ13C signature both in soils and in PH-WEOC. We also determined bacterial and fungal abundance and the genetic structure of bacterial communities. Our results show that the potential solubility of soil organic carbon is correlated to carbon and clay content in the soil. The aromaticity of PH-WEOC and its δ13C signature reflect differences in the decomposition pathways of soil organic matter and in the production of water-extractable organic compounds, in relation to land cover. The genetic structure of bacterial communities is related to soil texture and pH, and to PH-WEOC, revealing that water-extractable organic matter is closely related to the dynamics of bacterial communities. This comprehensive study, at the regional scale, thus provides better definition of the relationships between water-extractable organic matter and soil biogeochemical properties

Purification of Fungal High Molecular Weight Genomic DNA from Environmental Samples

Sequencing of a high number of fungal genomes has become possible due to the development of next generation sequencing techniques (NGS).The most recent developments aim to sequence single-molecule long-reads in order to improve genome assemblies, but consequently needs higher quality (minimum >20 kbp) DNA as starting material.However, environmental-derived samples from soil, wood, or litter often contain phenolic compounds, pigments, and other molecules that can be inhibitors for reactions during sequencing library construction.In this chapter, we propose an optimized protocol allowing the preparation of high quality and long fragment DNA from different samples (mycelium, fruiting body, soil) compatible with the current sequencing requirements

Turnover of soil bacterial diversity driven by wide-scale environmental heterogeneity.

International audienceSpatial scaling and determinism of the wide-scale distribution of macroorganism diversity has been largely demonstrated over a century. For microorganisms, and especially for soil bacteria, this fundamental question requires more thorough investigation, as little information has been reported to date. Here by applying the taxa-area relationship to the largest spatially explicit soil sampling available in France (2,085 soils, area covered ~5.3 × 10(5) km(2)) and developing an innovative evaluation of the habitat-area relationship, we show that the turnover rate of bacterial diversity in soils on a wide scale is highly significant and strongly correlated with the turnover rate of soil habitat. As the diversity of micro- and macroorganisms appears to be driven by similar processes (dispersal and selection), maintaining diverse and spatially structured habitats is essential for soil biological patrimony and the resulting ecosystem services

Biogeographical patterns of soil bacterial communities

International audienceThis study provides the first maps of variations in bacterial community structure on a broad scale based on genotyping of DNA extracts from 593 soils from four different regions of France (North, Brittany, South-East and Landes). Soils were obtained from the soil library of RMQS (Réseau de Mesures de la Qualité des Sols = French soil quality monitoring network). The relevance of a biogeographic approach for studying bacterial communities was demonstrated by the great variability in community structure and specific geographical patterns within and between the four regions. The data indicated that the distribution of bacterial community composition might be more related to local factors such as soil type and land cover than to more global factors such as climatic and geomorphologic characteristics. Furthermore, the regional pools of biodiversity could be ordered: South-East >=North > Brittany > Landes, according to the observed regional variability of the bacterial communities, which could be helpful for improving land use in accordance with soil biodiversity management

Validation d’un tableau de bord d’indicateurs sur un réseau national de fermes en grande culture et en viticulture pour diagnostiquer la qualité biologique des sols agricoles

Ce numéro comprend les articles correspondant aux présentations du Colloque Casdar 2017.National audienceWithin a context of agroecological transition, the Agrinnov project validated a set of indicators of the biological quality of agricultural soils to enable farmers to grasp the impact of their practices. AgrInnov project brought researchers and farmers to work together. To accompany the set of indicators of soil fauna, microbiology and agronomy, training sessions on soil biology have also been implemented together with an appropriate transfer procedure. The training sessions and the set of indicators were spread on a national network of more than 250 field-crop and viticulture farms. From an operational viewpoint, more than 97% of the farmers invested heavily in the project and stayed involved throughout Cannavacciulo M. et al. 42 Innovations Agronomiques 55 (2017), 41-54 the project. From a scientific viewpoint, less than 10% of the tested plots were assessed to be in a critical state in terms of soil biology, which is encouraging on agricultural soil quality, even though the monitoring should be developed on a broader number of farms and production systems in order to have a more exhaustive and representative diagnosis. Thus the AgrInnov project demonstrated the application and adoption by the farmers of new research-based tools for diagnosing soil quality.Dans un contexte de transition agroécologique, le projet Agrinnov a permis de valider un tableau de bord d’indicateurs analytiques de la qualité biologique des sols agricoles permettant aux agriculteurs d’appréhender l’impact de leurs pratiques. Le projet AgrInnov a amené des chercheurs et des agriculteurs à collaborer. En parallèle du tableau de bord (comprenant des indicateurs de faune du sol, de microbiologie et agronomiques), des formations sur la biologie des sols ont été élaborées ainsi qu’un mode opératoire de transfert. Les formations et le tableau de bord ont été déployés sur un réseau national de plus de 250 fermes en grande culture et en viticulture. D’un point de vue scientifique, il a été démontré que moins de 10% des parcelles testées étaient dans un état critique en termes de biologie du sol ce qui est encourageant sur la qualité des sols agricoles, même si il faudrait développer leur surveillance sur un plus grand nombre de fermes et de systèmes de production afin d’avoir un diagnostic plus exhaustif et représentatif. D’un point de vue opérationnel, plus de 97% des agriculteurs ont suivi le projet jusqu’au bout avec un fort investissement de leur part. Par conséquent, le projet AgrInnov a fait la démonstration opérationnelle de l’application et de l’appropriation par les agriculteurs des nouveaux outils de diagnostic de la qualité des sols émanant directement de la recherche

Improving soil bacterial taxa–area relationships assessment using DNA meta-barcoding

EA SPE GENOSOL ECOLDUR IPM CT3 EJ3 BDD Sol Infosols Autres projets nationauxInternational audienceThe evaluation of the taxa-area relationship (TAR) with molecular fingerprinting data demonstrated the spatial structuration of soil microorganisms and provided insights into the processes shaping their diversity. The increasing use of massive sequencing technologies in biodiversity investigations has now raised the question of the advantages of such technologies over the fingerprinting approach for elucidation of the determinism of soil microbial community assembly in broad-scale biogeographic studies. Our objectives in this study were to compare DNA fingerprinting and meta-barcoding approaches for evaluating soil bacterial TAR and the determinism of soil bacterial community assembly on a broad scale. This comparison was performed on 392 soil samples from four French geographic regions with different levels of environmental heterogeneity. Both molecular approaches demonstrated a TAR with a significant slope but, because of its more sensitive description of soil bacterial community richness, meta-barcoding provided significantly higher and more accurate estimates of turnover rates. Both approaches were useful in evidencing the processes shaping bacterial diversity variations on a broad scale. When different taxonomic resolutions were considered for meta-barcoding data, they significantly influenced the estimation of turnover rates but not the relative importance of each component process. Altogether, DNA meta-barcoding provides a more accurate evaluation of the TAR and may lead to re-examination of the processes shaping soil bacterial community assembly. This should provide new insights into soil microbial ecology in the context of sustainable use of soil resources