Soil parameters, land use, and geographical distance drive soil bacterial communities along a European transect

To better understand the relationship between soil bacterial communities, soil physicochemical properties, land use and geographical distance, we considered for the first time ever a European transect running from Sweden down to Portugal and from France to Slovenia. We investigated 71 sites based on their range of variation in soil properties (pH, texture and organic matter), climatic conditions (Atlantic, alpine, boreal, continental, Mediterranean) and land uses (arable, forest and grassland). 16S rRNA gene amplicon pyrosequencing revealed that bacterial communities highly varied in diversity, richness, and structure according to environmental factors. At the European scale, taxa area relationship (TAR) was significant, supporting spatial structuration of bacterial communities. Spatial variations in community diversity and structure were mainly driven by soil physicochemical parameters. Within soil clusters (k-means approach) corresponding to similar edaphic and climatic properties, but to multiple land uses, land use was a major driver of the bacterial communities. Our analyses identified specific indicators of land use (arable, forest, grasslands) or soil conditions (pH, organic C, texture). These findings provide unprecedented information on soil bacterial communities at the European scale and on the drivers involved; possible applications for sustainable soil management are discussed

Associations between infant fungal and bacterial dysbiosis and childhood atopic wheeze in a nonindustrialized setting.

BACKGROUND: Asthma is the most prevalent chronic disease of childhood. Recently, we identified a critical window early in the life of both mice and Canadian infants during which gut microbial changes (dysbiosis) affect asthma development. Given geographic differences in human gut microbiota worldwide, we studied the effects of gut microbial dysbiosis on atopic wheeze in a population living in a distinct developing world environment. OBJECTIVE: We sought to determine whether microbial alterations in early infancy are associated with the development of atopic wheeze in a nonindustrialized setting. METHODS: We conducted a case-control study nested within a birth cohort from rural Ecuador in which we identified 27 children with atopic wheeze and 70 healthy control subjects at 5 years of age. We analyzed bacterial and eukaryotic gut microbiota in stool samples collected at 3 months of age using 16S and 18S sequencing. Bacterial metagenomes were predicted from 16S rRNA data by using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States and categorized by function with Kyoto Encyclopedia of Genes and Genomes ontology. Concentrations of fecal short-chain fatty acids were determined by using gas chromatography. RESULTS: As previously observed in Canadian infants, microbial dysbiosis at 3 months of age was associated with later development of atopic wheeze. However, the dysbiosis in Ecuadorian babies involved different bacterial taxa, was more pronounced, and also involved several fungal taxa. Predicted metagenomic analysis emphasized significant dysbiosis-associated differences in genes involved in carbohydrate and taurine metabolism. Levels of the fecal short-chain fatty acids acetate and caproate were reduced and increased, respectively, in the 3-month stool samples of children who went on to have atopic wheeze. CONCLUSIONS: Our findings support the importance of fungal and bacterial microbiota during the first 100 days of life on the development of atopic wheeze and provide additional support for considering modulation of the gut microbiome as a primary asthma prevention strategy

In Situ Identification of Intracellular Bacteria Related to Paenibacillus spp. in the Mycelium of the Ectomycorrhizal Fungus Laccaria bicolor S238N

Bacterial proliferations have recurrently been observed for the past 15 years in fermentor cultures of the ectomycorrhizal fungus Laccaria bicolor S238N, suggesting the presence of cryptic bacteria in the collection culture of this fungus. In this study, intracellular bacteria were detected by fluorescence in situ hybridization in combination with confocal laser scanning microscopy in several collection subcultures of L. bicolor S238N. They were small (0.5 μm in diameter), rare, and heterogeneously distributed in the mycelium and were identified as Paenibacillus spp. by using a 16S rRNA-directed oligonucleotide probe initially designed for bacteria isolated from a fermentor culture of L. bicolor S238N

Land-use and other biogeochemical constraints modulate priming effect at the landscape scale: a fingerprinting approach using analytical pyrolysis

International audienceSoil has the potential to sequester or to emit great amounts of CO2, since soil carbon stocks constitute the largest terrestrial reservoir of carbon. Land-use is among the main factors affecting the net storage or the net mineralization of soil organic carbon (SOC) and land-use policies are currently aiming to increase soil organic carbon stocks.However, adding labile sources of carbon to soil (e.g. more crop residues or manure) may alter the carbon cycle, increasing the microbial degradation of the existing SOC pools, a process called “priming effect” (PE). PE could significantly reduce the net storage of carbon and taking into account this effect into carbon storage models may alter their predictions.Land-use is one of the numerous constraints that influence PE, together with soil chemical, biological and physical properties, all of them are contributing to shape the chemical composition of the SOC pools. The objectives of this study are:- to conduct a fingerprint characterization of the chemical composition of soil organic matter using analytical pyrolysis coupled to gas chromatography and mass spectrometry;- to use pyrograms to decipher which soil chemical markers are the most relevant descriptors of the PE;- to relate those chemical markers to the different types of crop rotations.This approach will help to decipher the complex interactions of the PE descriptors and to relate PE intensity to specific land-uses for a determined area, identifying which land management is capable to reduce soil susceptibility to priming effect and to be more efficient in term of net SOC storage.With this purpose, soil samples from 88 agricultural farms within a 12 km2 water catchment in Brittany (France) were incubated in presence of a 13C labelled wheat litter to measure the PE. Data regarding soil chemistry, soil microbial diversity, crop rotation, land-use, and manuring obtained for the studied farms were coupled to pyrograms to select the most relevant descriptors of the priming effect.Our results showed that:- the inclusion of grassland into crop rotation reduce the susceptibility of soils to PE, but only if grassland is maintained for an adequate period of the rotation time;- although PE is a microbial process, only a marginal part of its total variance is assigned to both richness and evenness of microbial communities;- the intensity of PE is correlated with the concentration of condensed aromatic compounds in soil water extracts, identified with excitation-emission fluorescence spectroscopy;- the intensity of the PE decreases with the molecular complexity of the soil organic matter assessed with pyrolysis coupled to gas chromatography and mass spectrometry.Disclosure of Interest: None declare

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

Root exclusion through trenching does not affect the isotopic composition of soil CO2 efflux

Disentangling the autotrophic and heterotrophic components of soil CO 2 efflux is critical to understanding the role of soil system in terrestrial carbon (C) cycling. In this study, we combined a stable C-isotope natural abundance approach with the trenched plot method to determine if root exclusion significantly affected the isotopic composition (δ 13C) of soil CO2 efflux (RS). This study was performed in different forest ecosystems: a tropical rainforest and two temperate broadleaved forests, where trenched plots had previously been installed. At each site, RS and its δ13C (δ13CRs) tended to be lower in trenched plots than in control plots. Contrary to RS, δ13CRs differences were not significant. This observation is consistent with the small differences in δ13C measured on organic matter from root, litter and soil. The lack of an effect on δ13CRs by root exclusion could be from the small difference in δ13C between autotrophic and heterotrophic soil respirations, but further investigations are needed because of potential artefacts associated with the root exclusion technique. © 2008 Springer Science+Business Media B.V

Land-use and other biogeochemical constraints modulate priming effect at the landscape scale: a fingerprinting approach using analytical pyrolysis

International audienceSoil has the potential to sequester or to emit great amounts of CO2, since soil carbon stocks constitute the largest terrestrial reservoir of carbon. Land-use is among the main factors affecting the net storage or the net mineralization of soil organic carbon (SOC) and land-use policies are currently aiming to increase soil organic carbon stocks.However, adding labile sources of carbon to soil (e.g. more crop residues or manure) may alter the carbon cycle, increasing the microbial degradation of the existing SOC pools, a process called “priming effect” (PE). PE could significantly reduce the net storage of carbon and taking into account this effect into carbon storage models may alter their predictions.Land-use is one of the numerous constraints that influence PE, together with soil chemical, biological and physical properties, all of them are contributing to shape the chemical composition of the SOC pools. The objectives of this study are:- to conduct a fingerprint characterization of the chemical composition of soil organic matter using analytical pyrolysis coupled to gas chromatography and mass spectrometry;- to use pyrograms to decipher which soil chemical markers are the most relevant descriptors of the PE;- to relate those chemical markers to the different types of crop rotations.This approach will help to decipher the complex interactions of the PE descriptors and to relate PE intensity to specific land-uses for a determined area, identifying which land management is capable to reduce soil susceptibility to priming effect and to be more efficient in term of net SOC storage.With this purpose, soil samples from 88 agricultural farms within a 12 km2 water catchment in Brittany (France) were incubated in presence of a 13C labelled wheat litter to measure the PE. Data regarding soil chemistry, soil microbial diversity, crop rotation, land-use, and manuring obtained for the studied farms were coupled to pyrograms to select the most relevant descriptors of the priming effect.Our results showed that:- the inclusion of grassland into crop rotation reduce the susceptibility of soils to PE, but only if grassland is maintained for an adequate period of the rotation time;- although PE is a microbial process, only a marginal part of its total variance is assigned to both richness and evenness of microbial communities;- the intensity of PE is correlated with the concentration of condensed aromatic compounds in soil water extracts, identified with excitation-emission fluorescence spectroscopy;- the intensity of the PE decreases with the molecular complexity of the soil organic matter assessed with pyrolysis coupled to gas chromatography and mass spectrometry.Disclosure of Interest: None declare

ECOMIC-RMQS : biogéographie microbienne à l’échelle de la France. Etat d’avancement et premiers résultats

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