Vignette d'image

Verrecchia, Eric

Nom
Verrecchia, Eric
Affiliation principale
Fonction
Professeur.e associé.e
Identifiants
https://libra.unine.ch/handle/123456789/143

Résultat de la recherche

Filtres

4122
374
401
Réinitialiser les filtres

Paramètres

Voici les éléments 1 - 10 sur 41
  • Publication
    Accès libre
    Composition and superposition of alluvial deposits drive macro-biological soil engineering and organic matter dynamics in floodplains
    (2019-8)
    Schomburg, Andreas Cédric 
    ;
    Sebag, D.
    ;
    Turberg, P.
    ;
    Verrecchia, Eric 
    ;
    Guenat, C.
    ;
    Brunner, Philip 
    ;
    Adatte, T.
    ;
    Schlaepfer, R.
    ;
    Le Bayon, Renée-Claire 
    Soil structure formation in alluvial soils is a fundamental process in near-natural floodplains. A stable soil structure is essential for many ecosystem services and helps to prevent river bank erosion. Plants and earthworms are successful soil engineering organisms that improve the soil structural stability through the incorporation of mineral and organic matter into soil aggregates. However, the heterogeneous succession of different textured mineral and buried organic matter layers could impede the development of a stable soil structure. Our study aims at improving the current understanding of soil structure formation and organic matter dynamics in near natural alluvial soils. We investigate the effects of soil engineering organisms, the composition, and the superimposition of different alluvial deposits on the structuration patterns, the aggregate stability, and organic matter dynamics in in vitro soil columns, representing sediment deposition processes in alluvial soils. Two successions of three different deposits, silt–buried litter–sand, and the inverse, were set up in mesocosms and allocated to four different treatments, i.e. plants, earthworms, plants+earthworms, and a control. X-ray computed tomography was used to identify structuration patterns generated by ecosystem engineers, i.e. plant root galleries and earthworm tunnels. Organic matter dynamics in macro-aggregates were investigated by Rock- Eval pyrolysis. Plant roots only extended in the top layers, whereas earthworms preferentially selected the buried litter and the silt layers. Soil structural stability measured via water stable aggregates (%WSA) increased in the presence of plants and in aggregates recovered from the buried litter layer. Organic matter dynamics were controlled by a complex interplay between the type of engineer, the composition (silt, sand, buried litter) and the succession of the deposits in the mesocosm. Our results indicate that the progress and efficiency of soil structure formation in alluvial soils strongly depends on the textural sequences of alluvial deposits.
  • Publication
    Accès libre
    Rock-Eval pyrolysis discriminates soil macro-aggregates formed by plants and earthworms
    (2018)
    Schomburg, Andreas Cédric 
    ;
    Verrecchia, Eric 
    ;
    Guenat, C.
    ;
    Brunner, Philip 
    ;
    Sebag, D.
    ;
    Le Bayon, Renée-Claire 
    Plants and earthworms, as soil ecosystem engineers, play a crucial role during stabilisation of organic matter in soil through its incorporation into soil aggregates. It is therefore essential to better understand the mechanisms and interactions of soil engineering organisms regarding soil organic matter stabilisation. Several methods have already been successfully applied to differentiate soil aggregates by their origin, but they cannot specify the degree of organic matter stability within soil aggregates. Rock-Eval pyrolysis has already been proved to be pertinent for analyses of soil organic matter bulk chemistry and thermal stability, but it has not yet been directly applied to identify biogenic organic matter signatures within soil aggregates. In this study, Rock-Eval pyrolysis was used for the identification of the soil aggregate origin as well as for the determination of the soil organic matter bulk chemistry and thermal stability in a controlled experiment. Mesocosms were set up, containing treatments with a plant, an earthworm species, or both. Water stable soil macro-aggregates > 250 μm were sampled and tested with Rock-Eval pyrolysis after a two-month incubation period. Rock-Eval pyrolysis was able to differentiate soil macro-aggregates by their origin, and to identify a specific signature for each treatment. Macro-aggregates from the plant and earthworm treatment were characterized by a mixed signature incoming from the two soil engineers, indicating that both engineers contribute concomitantly to soil aggregate formation. Organic matter thermal stability was not positively affected by earthworms and even tends to decrease for the plant treatment, emphasising that organic matter was mainly physically protected during the incubation period, but not stabilised. However, future research is required to test if signatures for the tested organisms are species-specific or generally assignable to other plant and earthworm species.
  • Publication
    Accès libre
    Rock-Eval pyrolysis discriminates soil macro-aggregates formed by plants and earthworms
    (2018)
    Schomburg, Andreas
    ;
    Verrecchia, Eric 
    ;
    Guenat, Claire
    ;
    Brunner, Philip 
    ;
    Sebag, David
    ;
    Le Bayon, Renée Claire
    Plants and earthworms, as soil ecosystem engineers, play a crucial role during stabilisation of organic matter in soil through its incorporation into soil aggregates. It is therefore essential to better understand the mechanisms and interactions of soil engineering organisms regarding soil organic matter stabilisation. Several methods have already been successfully applied to differentiate soil aggregates by their origin, but they cannot specify the degree of organic matter stability within soil aggregates. Rock-Eval pyrolysis has already been proved to be pertinent for analyses of soil organic matter bulk chemistry and thermal stability, but it has not yet been directly applied to identify biogenic organic matter signatures within soil aggregates. In this study, Rock-Eval pyrolysis was used for the identification of the soil aggregate origin as well as for the determination of the soil organic matter bulk chemistry and thermal stability in a controlled experiment. Mesocosms were set up, containing treatments with a plant, an earthworm species, or both. Water stable soil macro-aggregates > 250 μm were sampled and tested with Rock-Eval pyrolysis after a two-month incubation period. Rock-Eval pyrolysis was able to differentiate soil macro-aggregates by their origin, and to identify a specific signature for each treatment. Macro-aggregates from the plant and earthworm treatment were characterized by a mixed signature incoming from the two soil engineers, indicating that both engineers contribute concomitantly to soil aggregate formation. Organic matter thermal stability was not positively affected by earthworms and even tends to decrease for the plant treatment, emphasising that organic matter was mainly physically protected during the incubation period, but not stabilised. However, future research is required to test if signatures for the tested organisms are species-specific or generally assignable to other plant and earthworm species.
  • Publication
    Accès libre
    Exploiting the fungal highway: development of a novel tool for the in situ isolation of bacteria migrating along fungal mycelium
    (2015)
    Simon, Anaele 
    ;
    Bindschedler, Saskia 
    ;
    Job, Daniel 
    ;
    Wick, Lukas Y.
    ;
    Filippidou, Sevasti 
    ;
    Kooli, Wafa M.
    ;
    Verrecchia, Eric 
    ;
    Junier, Pilar 
    Fungi and bacteria form various associations that are central to numerous environmental processes. In the so-called fungal highway, bacteria disperse along fungal mycelium. We developed a novel tool for the in situ isolation of bacteria moving along fungal hyphae as well as for the recovery of fungi potentially involved in dispersal, both of which are attracted towards a target culture medium. We present the validation and the results of the first in situ test. Couples of fungi and bacteria were isolated from soil. Amongst the enriched organisms, we identified several species of fast-growing fungi (Fusarium sp. and Chaetomium sp.), as well as various potentially associated bacterial groups, including Variovorax soli, Olivibacter soli, Acinetobacter calcoaceticus, and several species of the genera Stenotrophomonas, Achromobacter and Ochrobactrum. Migration of bacteria along fungal hyphae across a discontinuous medium was confirmed in most of the cases. Although the majority of the bacteria for which migration was confirmed were also positive for flagellar motility, not all motile bacteria dispersed using their potential fungal partner. In addition, the importance of hydrophobicity of the fungal mycelial surface was confirmed. Future applications of the columns include targeting different types of microorganisms and their interactions, either by enrichment or by state of the art molecular biological methods.
  • Publication
    Accès libre
    Isolation and characterization of oxalotrophic bacteria from tropical soils
    (2015)
    Bravo, Daniel 
    ;
    Braissant, Olivier
    ;
    Cailleau, Guillaume 
    ;
    Verrecchia, Eric 
    ;
    Junier, Pilar 
    The oxalate–carbonate pathway (OCP) is a biogeochemical set of reactions that involves the conversion of atmospheric CO2 fixed by plants into biomass and, after the biological recycling of calcium oxalate by fungi and bacteria, into calcium carbonate in terrestrial environments. Oxalotrophic bacteria are a key element of this process because of their ability to oxidize calcium oxalate. However, the diversity and alternative carbon sources of oxalotrophs participating to this pathway are unknown. Therefore, the aim of this study was to characterize oxalotrophic bacteria in tropical OCP systems from Bolivia, India, and Cameroon. Ninety-five oxalotrophic strains were isolated and identified by sequencing of the 16S rRNA gene. Four genera corresponded to newly reported oxalotrophs (Afipia, Polaromonas, Humihabitans, and Psychrobacillus). Ten strains were selected to perform a more detailed characterization. Kinetic curves and microcalorimetry analyses showed that Variovorax soli C18 has the highest oxalate consumption rate with 0.240 μM h-1. Moreover, Streptomyces achromogenes A9 displays the highest metabolic plasticity. This study highlights the phylogenetic and physiological diversity of oxalotrophic bacteria in tropical soils under the influence of the oxalate–carbonate pathway.
  • Publication
    Accès libre
    Fungi, bacteria and soil pH: the oxalate–carbonate pathway as a model for metabolic interaction
    (2012)
    Martin, Gaëtan
    ;
    Guggiari, Matteo
    ;
    Bravo, Daniel 
    ;
    Zopfi, Jakob 
    ;
    Cailleau, Guillaume 
    ;
    Aragno, Michel 
    ;
    Job, Daniel 
    ;
    Verrecchia, Eric 
    ;
    Junier, Pilar 
    The oxalate–carbonate pathway involves the oxidation of calcium oxalate to low-magnesium calcite and represents a potential long-term terrestrial sink for atmospheric CO2. In this pathway, bacterial oxalate degradation is associated with a strong local alkalinization and subsequent carbonate precipitation. In order to test whether this process occurs in soil, the role of bacteria, fungi and calcium oxalate amendments was studied using microcosms. In a model system with sterile soil amended with laboratory cultures of oxalotrophic bacteria and fungi, the addition of calcium oxalate induced a distinct pH shift and led to the final precipitation of calcite. However, the simultaneous presence of bacteria and fungi was essential to drive this pH shift. Growth of both oxalotrophic bacteria and fungi was confirmed by qPCR on the frc (oxalotrophic bacteria) and 16S rRNA genes, and the quantification of ergosterol (active fungal biomass) respectively. The experiment was replicated in microcosms with non-sterilized soil. In this case, the bacterial and fungal contribution to oxalate degradation was evaluated by treatments with specific biocides (cycloheximide and bronopol). Results showed that the autochthonous microflora oxidized calcium oxalate and induced a significant soil alkalinization. Moreover, data confirmed the results from the model soil showing that bacteria are essentially responsible for the pH shift, but require the presence of fungi for their oxalotrophic activity. The combined results highlight that the interaction between bacteria and fungi is essential to drive metabolic processes in complex environments such as soil.
  • Publication
    Accès libre
    Use of an isothermal microcalorimetry assay to characterize microbial oxalotrophic activity
    (2011)
    Bravo, Daniel 
    ;
    Braissant, Olivier
    ;
    Solokhina, Anna
    ;
    Clerc, Martin
    ;
    Daniels, Alma U.
    ;
    Verrecchia, Eric 
    ;
    Junier, Pilar 
    Isothermal microcalorimetry (IMC) has been used in the past to monitor metabolic activities in living systems. A few studies have used it on ecological research. In this study, IMC was used to monitor oxalotrophic activity, a widespread bacterial metabolism found in the environment, and particularly in soils. Six model strains were inoculated in solid angle media with K-oxalate as the sole carbon source. Cupriavidus oxalaticus, Cupriavidus necator, and Streptomyces violaceoruber presented the highest activity (91, 40, and 55 μW, respectively) and a maximum growth rate (μmax h−1) of 0.264, 0.185, and 0.199, respectively, among the strains tested. These three strains were selected to test the incidence of different oxalate sources (Ca, Cu, and Fe-oxalate salts) in the metabolic activity. The highest activity was obtained in Ca-oxalate for C. oxalaticus. Similar experiments were carried out with a model soil to test whether this approach can be used to measure oxalotrophic activity in field samples. Although measuring oxalotrophic activity in a soil was challenging, there was a clear effect of the amendment with oxalate on the metabolic activity measured in soil. The correlation between heat flow and growth suggests that IMC analysis is a powerful method to monitor bacterial oxalotrophic activity.