Agnès Robin

Agnès Robin
Cirad - La recherche agronomique pour le développement | CIRAD · Unité Mixte de Recherche Ecologie Fonctionnelle et Biogéochimie des Sols et des Agro-Écosystèmes (Eco et Sols)

PhD - Researcher

About

70
Publications
15,823
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
1,560
Citations

Publications

Publications (70)
Article
Eucalyptus is the tree most widely planted in tropical countries to satisfy growing demand for wood products, but high yields require high fertilizer inputs. Introducing N2-fixing trees (NFT), such as Acacia mangium, has been proposed to improve soil fertility and aboveground tree biomass in Eucalyptus plantations. In addition to N inputs, NFT spec...
Article
Ecosystem restoration is a global priority, currently promoted by several ambitious commitments. Most of the research to guide restoration practices was so far put on the recovery of aboveground functions and services, although soil health is increasingly recognized as a fundamental condition to restoration success. Soil restoration is particularly...
Article
Mycorrhizal colonization of roots is traditionally evaluated by empirical methods, such as root microscopy. We compared this method with data from using a real time PCR technique, and determined the correlation between methods, indicating particularities of a promising system for a quick and accurate molecular diagnostic of arbuscular mycorrhizatio...
Article
Full-text available
Arbuscular mycorrhizal fungi (AMF) are important symbionts of many plant species, facilitating the acquisition of soil nutrients by roots. We hypothesized that AMF root colonization is strongly influenced by the composition of the soil microbiome. Here, we evaluated mycorrhizal colonization of two plants, the grass Urochloa brizantha (Brachiaria) a...
Article
Fertilization is commonly used to increase growth in forest plantations, but it may also affect tree water relations and responses to drought. Here, we measured changes in biomass, transpiration, sapwood-to-leaf area ratio (As:Al) and sap flow driving force (ΔΨ) during the 6-year rotation of tropical plantations of Eucalyptus grandis under controll...
Article
Full-text available
Aims Belowground interactions are still poorly understood in mixed-species forests. We investigated the effects of soil fertility on belowground processes in mixed planted forests. Methods The dynamics and traits of Eucalyptus and Acacia mangium fine roots (diameter < 2 mm) in plantations with 50% of each species were studied in a randomized bloc...
Article
Full-text available
The soil is a complex, heterogeneous and dynamic environment, it is there that various and essential biogeochemical processes take place for the functionning of plants and their ecosystems. The study of soil-roots interactions in the different soil horizons is crucial to understand the dynamics of nutriments and carbon as well as the role played by...
Article
While the number of studies dealing with fine root dynamics in deep soils layers (depth > 1 m) has increased sharply recently, the phenology, the morphology, the anatomy and the role of deep fine roots are still poorly known in forest ecosystems. This review summarizes the current knowledge on fine root production, mortality and longevity in deep s...
Article
Many studies have shown that introducing N2-fixing trees (e.g. Acacia mangium) in eucalypt plantations can increase soil N availability as a result of biological N2 fixation and faster N cycling. Some studies have also shown improved eucalypt P nutrition. However, the effects of N2-fixing trees on P cycling in tropical soils remain poorly understoo...
Chapter
Full-text available
Mycorrhiza is a mutualistic symbiosis found in about 90% of the terrestrial plants. The arbuscular mycorrhiza (AM) and ectomycorrhiza (ECM), present in Eucalypt and Acacia, are the most studied in forests due to their importance in ecosystem productivity and sustainability in forestry. Here, our focus is to show recent results regarding their incid...
Article
Full-text available
Le sol est un environnement complexe, hétérogène et dynamique, lieu de multiples processus biogéochimiques essentiels au fonctionnement des plantes et des écosystèmes. L'étude des interactions sol-racine dans les différents horizons du sol est cruciale pour appréhender la dynamique des nutriments et du carbone, ainsi que le rôle joué par les microo...
Article
Full-text available
Despite the strong ecological importance of ectomycorrhizal (ECM) fungi, their vertical distribution remains poorly understood. To our knowledge, ECM structures associated with trees have never been reported in depths below 2 meters. In this study, fine roots and ECM root tips were sampled down to 4-m depth during the digging of two independent pit...
Article
Biochar is a potential tool to mitigate climate change by enhancing C sequestration in soils, but its use as a soil amendment to improve soil fertility and crop yields is still a contentious subject. In North East (NE) Thailand, biochar has been promoted to restore soil fertility in rubber tree plantations. Despite this, there is scarce information...
Article
Functional specialization of fine roots was found for Eucalyptus grandis trees at harvesting age (6 years) on tropical soils. Aiming to elucidate whether functional specialization is a ubiquitous feature of eucalypts, we focused on its changes with ontogeny, tree nutrient status and soil depth. We studied the potential uptake of N, K and Ca by 2-ye...
Article
Harvest residue management is a key issue for the sustainability of Eucalyptus plantations established on poor soils. Soil microbial communities contribute to soil fertility by the decomposition of the organic matter (OM), but little is known about the effect of whole-tree harvesting (WTH) in comparison to stem only harvesting (SOH) on soil microbi...
Article
Mixed plantations of Eucalyptus and N 2-fixing trees are ecologically beneficial because they stimulate organic matter cycling and increase carbon (C) and nitrogen (N) pools in the soil. However, the microbial mechanisms that contribute to the improvement of C and N dynamics remain poorly understood in managed forest ecosystems. Here, we evaluated...
Presentation
Full-text available
The major factors driving greenhouse gas exchanges in forest soils (substrate supply, temperature, water content) vary with soil depth. Our study aimed to assess the effects of clear-cutting and drought on the temporal variability of CO2, CH4 and N2O fluxes throughout very deep soil profiles in Brazilian eucalypt plantations conducted in coppice. S...
Article
Full-text available
Background and aims While the role of deep roots in major ecosystem services has been shown for tropical forests, there have been few direct measurements of fine root dynamics at depths of more than 2 m. The factors influencing root phenology remain poorly understood, creating a gap in the knowledge required for predicting the effects of climate ch...
Article
In agricultural studies, estimating and testing differences between treatment regimes in a designed experiment usually determines the subsequent success or failure of inputs or management practices. Fine-scale soil variability of the experimental site can reduce statistical power and should be determined in order to optimize the experiment design....
Article
Full-text available
Our knowledge of the rhizosphere bacterial communities in deep soils and the role of Eucalyptus and Acacia on the structure of these communities remains very limited. In this study, we targeted the bacterial community along a depth profile (0 to 800 cm) and compared community structure in monospecific or mixed plantations of Acacia mangium and Euca...
Data
Chemical and physical properties of soil at various depths and in the different plantation systems. (DOCX)
Data
Average abundance (n = 3) of bacterial phyla across treatments. 100A (A. mangium in a monospecific plantation system); A(A+E) (mixed plantation of A. mangium and E. grandis, with sampling at the Acacia base; 100E (E. grandis in a monospecific plantation system); and E(A+E) (plantation of A. mangium and E. grandis, with sampling at the Eucalyptus ba...
Data
Average abundance (n = 3) of bacterial phyla in the soil layer. 100A (A. mangium in a monospecific plantation system); A(A+E) (mixed plantation of A. mangium and E. grandis, with sampling at the Acacia base; 100E (E. grandis in a monospecific plantation system); and E(A+E) (plantation of A. mangium and E. grandis, with sampling at the Eucalyptus ba...
Data
Relative abundance (n = 3) of bacterial classes across treatments. 100A (A. mangium in a monospecific plantation system); A(A+E) (mixed plantation of A. mangium and E. grandis, with sampling at the Acacia base); 100E (E. grandis in a monospecific plantation system); and E(A+E) (plantation of A. mangium and E. grandis, with sampling at the Eucalyptu...
Data
Average abundance (n = 3) of bacterial classes across treatments. 100A (A. mangium in a monospecific plantation system); A(A+E) (mixed plantation of A. mangium and E. grandis, with sampling at the Acacia base; 100E (E. grandis in a monospecific plantation system); and E(A+E) (plantation of A. mangium and E. grandis, with sampling at the Eucalyptus...
Data
Average abundance (n = 3) of bacterial classes in the soil layer. 100A (A. mangium in a monospecific plantation system); A(A+E) (mixed plantation of A. mangium and E. grandis, with sampling at the Acacia base; 100E (E. grandis in a monospecific plantation system); and E(A+E) (plantation of A. mangium and E. grandis, with sampling at the Eucalyptus...
Data
Relative abundance (n = 3) of bacterial phyla across treatments. 100A (A. mangium in a monospecific plantation system); A(A+E) (mixed plantation of A. mangium and E. grandis, with sampling at the Acacia base); 100E (E. grandis in a monospecific plantation system); and E(A+E) (plantation of A. mangium and E. grandis, with sampling at the Eucalyptus...
Poster
Full-text available
Tropical forests strongly influence the concentrations of carbon dioxide (CO2), nitrous oxide (N2O) and methane (CH4) in the atmosphere. Silvicultural practices in planted forests affect the fluxes of greenhouse gases at the soil surface and the major factors driving greenhouse gas production in forest soils (substrate supply, temperature, water co...
Article
Full-text available
Rubber tree (Hevea brasiliensis) is of major economic importance in Southeast Asia and for small land holders in Thailand in particular. Due to the high value of latex, plantations are expanding into unsuitable areas, such as the northeast province of Thailand where soil fertility is very low and therefore appropriate management practices are of pr...
Article
Full-text available
Background and aims Positive below-ground interactions (facilitation) should be more pronounced when resources limit crop growth, according to the stress-gradient hypothesis. Our aim was to test this hypothesis for intercropped durum wheat and faba bean along a P-fertilizer gradient. Methods A field experiment was conducted in a long-term P-fertili...
Article
We examined changes in morphological and genomic diversities of viruses by means of transmission electronic microscopy and pulsed field gel electrophoresis (PFGE) over a nine-month period (April–December 2005) at four different depths in the oligomesotrophic Lac Pavin. We found that the majority of viruses in this lake belonged to the family of Sip...
Article
Rubber tree is a very important crop in Thailand, representing an essential source of income for farmers. In the past two decades, rubber tree plantations have been greatly expanding in unfavorable areas, where climate conditions are difficult and soil fertility is very poor. To optimize latex yields, mineral fertilizers have been widely used. A be...
Article
Full-text available
Unlike Eucalyptus monocultures, nitrogen fixing trees are likely to improve the soil nutrient status through the decomposition of N-enriched litter. The Home Field Advantage (HFA) hypothesis states that plants can create conditions that increase the decomposition rates of their own litter. However, there may not be any HFA when most of the decompos...
Chapter
Full-text available
Phosphorus (P) occurs at low concentrations in soils because of the numerous processes responsible for P sorption or immobilisation. Soil P is also characterised by its restricted mobility, and thus the most limiting step of P acquisition is not its absorption by plant roots, but rather the many processes that determine the fate of soil P in the rh...
Article
Full-text available
An optimized method, based on the coupling of two commercial kits, is described for the extraction of soil nucleic acids, with simultaneous extraction and purification of DNA and RNA following a cascade scheme and avoiding the use of harmful solvents. The protocol canmonitor the variations in the recovery yield of DNA and RNA from soils of various...
Article
Full-text available
Les ions orthophosphates (Pi) représentent les seules formes de phosphore (P) utilisable par les cultures. Dans les sols, ils sont généralement présents à de faibles concentrations dans la solution, en raison des nombreux processus géochimiques contraignant leur mobilité et disponibilité. Les plantes et les micro-organismes associés, au travers de...
Book
Phosphorus (P) occurs at low concentrations in soils because of the numerous processes responsible for P sorption or immobilisation. Soil P is also characterised by its restricted mobility, and thus the most limiting step of P acquisition is not its absorption by plant roots, but rather the many processes that determine the fate of soil P in the rh...
Conference Paper
Full-text available
Many field observations suggest that ECM contribute to a number of key ecosystem functions such as carbon cycling, nutrient mobilization from soil organic matter and soil minerals, providing a link between trees through common mycorrhizal networks. In Brazil, the ECM form symbiotic associations with species of great economic importance, belonging t...
Chapter
Iron is an essential element for living organisms. However, in most cultivated soils, iron availability is low despite its abundance due to soil physicochemical properties, including relative oxygen pressure and pH. Therefore, there is a strong competition for this element, required for plant and microorganism physiology, but showing a low availabi...
Article
Full-text available
Morphological diversity, abundance and community structure of viruses were examined in the deep and anoxic sediments of the volcanic Lake Pavin (France). The sediment core, encompassing 130 years of sedimentation, was subsampled every centimeter. High viral abundances were recorded and correlated to prokaryotic densities. Abundances of viruses and...
Article
Full-text available
Transitions between saline and fresh waters have been shown to be infrequent for microorganisms. Based on host-specific interactions, the presence of specific clades among hosts suggests the existence of freshwater-specific viral clades. Yet, little is known about the composition and diversity of the temperate freshwater viral communities, and even...
Data
Rarefaction curves based on whole viromes. Each virome was clusterized at 75% identity, and the curve presents the number of different clusters as a function of the number of input sequences. (PDF)
Data
Full-text available
Maximum-likelihood tree for T4-like phages (G20). The main reference groups are indicated on the tree (near-T4 in red, T4-like cyanophages in blue), and the Far-T4 group is highlighted in yellow. Leaf labels corresponding to virome sequences are colored (red for Lake Pavin and blue for Lake Bourget). The number of reads assembled is given in bracke...
Data
Full-text available
Maximum-likelihood tree for T4-like phage (G20). A phylogenetic tree has been drawn for the T4-like phage group, and the two main reference groups are indicated (near-T4 in red and T4-like cyanophages in blue). The Far-T4 group is highlighted in yellow. Leaf labels are colored according to their sample (red for Lake Pavin and blue for Lake Bourget)...
Data
Schematic representation of the phylogenetic tree creation pipeline. (PDF)
Data
Main functions retrieved in the viromes. In the first table, the 30 most retrieved PFAM domains in the viromes are listed, with the number of sequences for each virome alongside informations about their description in viral genomes, or the fact that most of the sequences from this domain are of viral origin (identified as «viral» domains). In the s...
Data
Full-text available
Maximum-likelihood tree for T4-like phages (GP23). The main reference groups are indicated on the tree (near-T4 in red, T4-like cyanophages in blue), and leaf labels corresponding to virome sequences are colored (red for Lake Pavin and blue for Lake Bourget). The Far-T4 group is highlighted in yellow. The number of reads assembled is given in brack...
Data
Bacterial taxonomic composition as deduced from virome reads best BLAST hits, compared with previously published data. These previous data are from a metagenome for Lake Bourget, and from 16SrRNA PCR amplification for Lake Pavin. (DOC)
Data
Characteristics of the two lakes studied. (DOC)
Data
Main characteristics of viromes included in the different comparisons. Extraction methodology is indicated where available. Peg = polyethylene glycol; CsCl = Cesium Chloride. The BLAST hit ratio is the percentage of reads significantly similar to a protein of the database the non-redundant database (threshold of 10-3 on e-value and 50 on scores). A...
Article
Full-text available
Remarkable morphological diversity of virus-like particles was observed by transmission electron microscopy in a hypersaline water sample from Lake Retba, Senegal. The majority of particles morphologically resembled hyperthermophilic archaeal DNA viruses isolated from extreme geothermal environments. Some hypersaline viral morphotypes have not been...
Article
Virus-prokaryote interactions were investigated in four natural sites in Senegal (West Africa) covering a salinity gradient ranging from brackish (10‰) to near salt saturation (360‰). Both the viral and the prokaryote communities exhibited remarkable differences in their physiological, ecological and morphological traits along the gradient. Above 2...
Article
Type III secretion systems (T3SSs) of Gram-negative bacteria mediate direct interactions with eukaryotic cells. Pseudomonas spp. harboring T3SS genes (T3SS+) were previously shown to be more abundant in the rhizosphere than in bulk soil. To discriminate the contribution of roots and associated arbuscular mycorrhizal fungi (AMF) on the enrichment of...
Article
PurposeSurface runoff and erosion are major drivers of pesticide transport from soils to rivers draining vineyard watersheds. A recent study showed that applications of diuron on vineyards and diuron dispersal could lead to microbial adaptation to diuron biodegradation from treated soils to the receiving hydrosystem. Given the limited knowledge on...
Article
This study presents a depth-related survey of virioplankton abundance in Lake Pavin (Massif Central, France), in relation to the abundances of heterotrophic prokaryotes, picocyanobacteria (Pcy), autotrophic picoeukaryotes (Peu), and of autotrophic (ANF) and heterotrophic (HNF) nanoflagellates. The sampling strategy was designed to be representative...
Article
Iron is an essential micronutrient for most organisms due to its role in fundamental metabolic processes. In cultivated soils, soil solution iron is mostly oxidized [Fe(III) species] unless local anoxic conditions develop. The concentration of these Fe(III) species is small in soil solution due to the low solubility of ferric oxides, oxyhydroxides,...
Article
Full-text available
Iron is an essential micronutrient for most organisms due to its role in fundamental metabolic processes. In cultivated soils, soil solution iron is mostly oxidized [Fe(III) species] unless local anoxic conditions develop. The concentration of these Fe(III) species is small in soil solution due to the low solubility of ferric oxides, oxyhydroxides,...
Article
Full-text available
We have described the use of Polyethylene glycol (PEG) for the precipitation of natural communities of aquatic viruses, and its comparison with the usual concentration method based on ultracentrifugation. Experimental samples were obtained from different freshwater ecosystems whose trophic status varied. Based on transmission electron microscope ob...
Article
Full-text available
A transgenic tobacco overexpressing ferritin (P6) was recently shown to accumulate more iron than the wild type (WT), leading to a reduced availability of iron in the rhizosphere and shifts in the pseudomonad community. The impact of the transgenic line on the community of fluorescent pseudomonads was assessed. The diversity of 635 isolates from rh...
Article
Full-text available
Taking into account the strong iron competition in the rhizosphere and the high affinity of pyoverdines for Fe(III), these molecules are expected to interfere with the iron nutrition of plants, as they do with rhizospheric microbes. The impact of Fe-pyoverdine on iron content of Arabidopsis thaliana was compared with that of Fe-EDTA. Iron chelated...