Abstract: Microbial biogeography is the study of the distribution of microbial diversity on large scales of space and time. This science aims at understanding biodiversity regulation and its link with ecosystem biological functioning, goods and services such as maintenance of productivity, of soil and atmospheric quality, and of soil health. Although the initial concept dates from the early 20th century (Beijerinck (1913) De infusies en de ontdekking der backterien, in: Jaarboek van de Knoniklijke Akademie van Wetenschappen, Muller, Amsterdam), only recently an increasing number of studies have investigated the biogeographical patterns of soil microbial diversity. A such delay is due to the constraints of the microbial models, the need to develop relevant molecular and bioinformatic tools to assess microbial diversity, and the non-availability of an adequate sampling strategy. Consequently, the conclusions from microbial ecology studies have rarely been generally applicable and even the fundamental power-laws differ because the taxa-area relationship and the influence of global and distal parameters on the spatial distribution of microbial communities have not been examined. In this article we define and discuss the scientific, technical and operational limits and outcomes resulting from soil microbial biogeography together with the technical and logistical feasibility. The main results are that microbial communities are not stochastically distributed on a wide scale and that biogeographical patterns are more influenced by local parameters such as soil type and land use than by distal ones, e.g. climate and geomorphology, contrary to plants and animals. We then present the European soil biological survey network, focusing on the French national initiative and the "ECOMIC-RMQS" project. The objective of the ECOMIC-RMQS project is to characterise the density and diversity of bacterial communities in all soils in the RMQS library in order to assess, for the first time, not only microbial biogeography across the whole of France but also the impact of land use on soil biodiversity (Reseau de Mesures de la Qualite des Sols = French Soil Quality Monitoring Network, 2200 soils covering all the French territory with a systematic grid of sampling). The scientific, technical and logistical outputs are examined with a view to the future prospects needed to develop this scientific domain and its applications in sustainable land use.
Abstract: The influence of shrubs used as nurse plants was tested on the growth of Cupressus atlantica, on microbial activity and on arbuscular mycorrhizal (AM) soil potential in a Mediterranean environment. An experimental plantation was conducted combining uninoculated, arbuscular mycorrhized Cypress seedlings and an association between Lavandula stoechas planted close to newly planted C. atlantica seedlings. After three years plantation, this association between C. atlantica and L stoechas lead to a higher growth of C atlantica and better soil microbial characteristics compared to the control treatment. AM mycelium network, total microbial activity, dehydrogenase activity, phosphate-solubilizing fluorescent pseudomonads and N. P nutrient uptake by C atlantica, were significantly higher in the presence of L stoechas than those recorded in the other treatments. This pioneer shrubs facilitates the early establishment of Cypress seedlings by improving soil microbial characteristics and AM fungus community development. Given that the facilitative effect of one plant species to another increases with abiotic stress, the benefits of this technique would be useful in reforestation programs undertaken to rehabilitate degraded areas in Mediterranean region. (C) 2011 Elsevier Ltd. All rights reserved.
Abstract: Spatially constrained multivariate analysis methods (MULTISPATI-PCA) and classical principal component analysis are applied for the entire country of France to study the main soil characteristics of topsoil and to assess if their multivariate spatial pattern can provide insight on their extent and origin. The results of the MULTSPATI-PCA provided evidence of strong spatial structures attributed to different natural processes. The first axis was interpreted as an axis of global soil richness in clay content. Axis 2 reflected the influence of some parent materials on the geochemical content of K and Al. Axis 3 showed a very large gradient of relative content in coarse silt. Axis 4 was driven by gradients of maritime influence. We show that MULTISPATI-PCA allows better than classical PCA to detect and map large regional trends in the distribution of topsoil characteristics. The two first axes were expected and the maps obtained by both methods were consistent. Interestingly, the other gradients were not expected and were better shown by MULTISPATI-PCA than by classical PCA. (C) 2010 Elsevier B.V. All rights reserved.
Abstract: The causative agent of legionellosis, Legionella pneumophila, colonizes all natural and human-made water networks, thus constituting the source of contaminated aerosols responsible for airborne human infections. Efficient control of infections, especially during epidemics, necessitates the fastest and most resolutive identification possible of the bacterial source for subsequent disinfection of reservoirs. We thus compared recognized typing approaches for Legionella with a method based on characterization of insertion sequence (IS) content. A total of 86 clinical or environmental isolates of L. pneumophila, including 84 Paris isolates, sampled from 25 clinical investigations in France between 2001 and 2007, were obtained from the Legionella National Reference Center. All strains were typed by monoclonal antibody subgrouping, sequence-based typing, pulsed-field gel electrophoresis, and restriction fragment length polymorphism based on the presence or absence of IS elements. We identified six different types of IS elements in L. pneumophila Paris and used them as genomic markers in hybridization experiments. One IS type, ISLpn11, revealed a high discriminatory power. Simpson's index of discrimination, calculated from the distribution of IS elements, was higher than that obtained with the other typing methods used for L. pneumophila Paris. Moreover, specific ISLpn11 copies were found only in strains isolated from particular cities. In more than half of the cases, each clinical isolate had an ISLpn11 profile that was recovered in at least one environmental isolate from the same geographical location, suggesting that our method could identify the infection source. Phylogenetic analysis suggests a clonal expansion for the L. pneumophila Paris strain.
Abstract: Aim The spatial organization of soil microbial communities on large scales and the identification of environmental factors structuring their distribution have been little investigated. The overall objective of this study was to determine the spatial patterning of microbial biomass in soils over a wide extent and to rank the environmental filters most influencing this distribution. Location French territory using the French Soil Quality Monitoring Network. This network covers the entire French territory and soils were sampled at 2150 sites along a systematic grid. Methods The soil DNA extracted from all these soils was expressed in terms of soil molecular microbial biomass and related to other soil and land-use data over French territory. Results This study provides the first extensive map of microbial biomass and reveals the heterogeneous and spatially structured distribution of this biomass on the scale of France. The main factors driving biomass distribution are the physico-chemical properties of the soil (texture, pH and total organic carbon) as well as land use. Soils from land used for intensive agriculture, especially monoculture and vineyards, exhibited the smallest biomass pools. Interestingly, factors known to influence the large-scale distribution of macroorganisms, such as climatic factors, were not identified as important drivers for microbial communities. Main conclusions Microbial abundance is spatially structured and dependent on local filters such as soil characteristics and land use but is relatively independent of global filters such as climatic factors or the presence of natural barriers. Our study confirms that the biogeography of microorganisms differs fundamentally from the biogeography of 'macroorganisms' and that soil management can have significant large-scale effects.
Abstract: Dermanyssus gallinae is considered to be the most economically significant ectoparasite to affect egg-laying poultry in Europe. This mite can also act as a vector for a number of pathogens. The array of bacteria associated with D. gallinae mites could provide insight into the biology and population dynamics of arthropods, but at the present time little information is available. To understand the intra-and interpopulation diversity of its associated microbiota, we analyzed the whole internal bacterial community of natural populations of D. gallinae originating from two types of poultry farm habitats (standard and free-range) in two regions of France (Brittany and the Rhone-Alpes). Total DNA was extracted from individual or pooled mites, and polymerase chain reaction temporal temperature gradient gel electrophoresis of 16S rRNA was then done to separate bacterial DNA fragments associated with the host arthropod. A large diversity of bacteria was detected, but principally firmicutes and gamma-Proteobacteria. Between-group analyses of temporal temperature gradient gel electrophoresis-banding patterns revealed that bacterial populations clustered into categories according to their geographic origin and the habitat specifics of the farms. Some degree of stability of bacterial populations was observed within a specific time scale. These results suggest that environmental factors either recent (e. g., poultry farming practices) or long-standing (e. g., geographic isolation) may affect the bacterial communities present in D. gallinae. Further knowledge of the microbiota associated with D. gallinae and its variation would indeed offer new perspectives for biological control methods to prevent the establishment, proliferation, and transmission of pathogenic bacteria.
Abstract: Microbial biogeography is the study of the distribution of microbial diversity on large scales of space and time. This science aims at understanding biodiversity regulation and its link with ecosystem biological functioning, goods and services such as maintenance of productivity, of soil and atmospheric quality, and of soil health. Although the initial concept dates from the early 20th century (Beijerinck (1913) De infusies en de ontdekking der backterien, in: Jaarboek van de Knoniklijke Akademie van Wetenschappen, Muller, Amsterdam), only recently have an increasing number of studies have investigated the biogeographical patterns of soil microbial diversity. A such delay is due to the constraints of the microbial models, the need to develop relevant molecular and bioinformatic tools to assess microbial diversity, and the non-availability of an adequate sampling strategy. Consequently, the conclusions from microbial ecology studies have rarely been generally applicable and even the fundamental power-laws differ because the taxa-area relationship and the influence of global and distal parameters on the spatial distribution of microbial communities have not been examined. In this article we define and discuss the scientific, technical and operational limits and outcomes resulting from soil microbial biogeography together with the technical and logistical feasibility. The main results are that microbial communities are not stochastically distributed on a wide scale and that biogeographical patterns are more influenced by local parameters such as soil type and land use than by distal ones, e. g. climate and geomorphology, contrary to plants and animals. We then present the European soil biological survey network, focusing on the French national initiative and the "ECOMIC-RMQS" project. The objective of the ECOMIC-RMQS project is to characterise the density and diversity of bacterial communities in all soils in the RMQS library in order to assess, for the first time, not only microbial biogeography across the whole of France but also the impact of land use on soil biodiversity (Reseau de Mesures de la Qualite des Sols = French Soil Quality Monitoring Network, 2200 soils covering all the French territory with a systematic grid of sampling). The scientific, technical and logistical outputs are examined with a view to the future prospects needed to develop this scientific domain and its applications in sustainable land use.
Abstract: Perception by each individual organism of its environment's parameters is a key factor for survival. In a constantly changing environment, the ability to assess nutrient sources and potentially stressful situations constitutes the main basis for ecological adaptability. Transcription regulators are key decision-making proteins that mediate the communication between environmental conditions and DNA transcription through a multifaceted network. The parallel study of these regulators across microbial organisms adapted to contrasting biotopes constitutes an unexplored approach to understand the evolution of genome plasticity and cell function. We present here a reassessment of bacterial helix-turn-helix regulator diversity in different organisms from a multidisciplinary perspective, on the interface that links metabolism, ecology and phylogeny, further sustained by a statistically based approach. The present revision brought to light evidence of patterns among families of regulators, suggesting that multiple selective forces modulate the number and kind of regulators present in a given genome. Besides being an important step towards understanding the adaptive traits that influence the microbial responses to the varying environment on the very first and most prevalent line of reaction, the transcription of DNA, this approach is a promising tool to extract biological trends from genomic databases.
Abstract: Demanyssus gallinae (Arthropoda, Mesostigmata) is suspected to be involved in the transmission of a wide variety of pathogens, but nothing is known about its associated non-pathogenic bacterial community. To address this question, we examined the composition of bacterial communities in D. gallinae collected from standard poultry farms in Brittany, France. Genetic fingerprints of bacterial communities were generated by temporal temperature gradient gel electrophoresis (TTGE) separation of individual polymerase chain reaction (PCR)-amplified 16S rRNA gene fragments, followed by DNA sequence analysis. Most of the sequences belonged to the Proteobacteria and Firmicute phyla, with a majority of sequences corresponding to the Enterobacteriales order and the Staphylococcus genus. By using statistical analysis, we showed differences in biodiversity between poultry farms. We also determined the major phylotypes that compose the characteristic microbiota associated with D. gallinae. Saprophytes, opportunistic pathogens and pathogenic agents such as Pasteurella multocida, Erysipelothrix rhusiopathiae and sequences close to the genus Aerococcus were identified. Endosymbionts such as Schineria sp., Spiroplasma sp. Anistosticta, "Candidatus Cardinium hertigii" and Rickettsiella sp. were also present in the subdominant bacterial community. Identification of potential targets within the symbiont community may be considered in the future as a means of ectoparasite control. (C) 2008 Elsevier Masson SAS. All rights reserved.
Abstract: In the Mediterranean basin, a millenarian history of overexploitation has lead to the loss of most primeval forests and an increase of the surface area covered by shrublands that represent stages of degradation of mature forests. In this situation, and since environmental characteristics act as barriers to succession, human intervention is usually necessary to improve recovery of woodlands. Reafforestation is a common practice in Mediterranean areas to achieve this aim but its performances are very low with high rates of early mortality making this practice unprofitable in ecological as well as in economic terms. In degraded semiarid ecosystems, shrub and tall-grass species grow following a patchy distribution. Traditionally, shrubs growing near to newly planted trees are considered heavy competitors, and are consequently removed before planting. However, the vegetation patches usually constitute "fertility islands" or "resource islands" which could promote the tree species development. It has previously been assessed that some native plant species could act as "nurse plants" through their positive impacts on soil abiotic characteristics (i.e., soil nutrient contents), but they also exhibit a positive influence on soil microbiota, especially on symbiotic microorganisms including rhizobia and mycorrhizal fungi. In this chapter, an attempt is made to assess the beneficial effects of plant nurses on the growth of Mediterranean tree species like Cupressus species, and on the bio-functioning of soils. Furthermore, the potential benefits of native plant species in the rehabilitation of degraded areas especially in stressful conditions is reviewed and discussed.
Abstract: Many fast growing tree species have been introduced to promote biodiversity rehabilitation on degraded tropical lands. Although it has been shown that plant productivity and stability are dependent on the composition and functionalities of soil microbial communities, more particularly on the abundance and diversity of soil symbiotic micro-organisms (mycorrhizal fungi and rhizobia), the impact of tree introduction on soil microbiota has been scarcely studied. This research has been carried in a field plantation of Acacia holosericea (Australian Acacia species) inoculated or not with an ectomycorrhizal fungus isolate, Pisolithus albus IR100. After 7 year's plantation, the diversity and the symbiotic properties of Bradyrhizobia isolated from the plantation soil or from the surrounding area (Faidherbia albida (Del.) a. Chev. parkland) and able to nodulate E albida, a native Sahelian Acacia species, have been studied. Results clearly showed that A. holosericea modified the structure of Bradyrhizobia populations and their effectiveness on F albida growth. This negative effect was counterbalanced by the introduction of an ectomycorrhizal fungus, P albus, on A. holosericea root systems. In conclusion, this study shows that exotic plant species can drastically affect genotypic and symbiotic effectiveness of native Bradyrhizobia populations that could limit the natural regeneration of endemic plant species such as E albida. This effect could be counterbalanced by controlled ectomycorrhization with P albus. These results have to be considered when exotic tree species are used in afforestation programs that target preservation of native plants and soil ecosystem rehabilitation. (C) 2009 Elsevier Ltd. All rights reserved.
Abstract: Dermanyssus gallinae (Arthropoda, Mesostigmata) is suspected to be involved in the transmission of a wide variety of pathogens, but nothing is known about its associated non-pathogenic bacterial community. To address this question, we examined the composition of bacterial communities in D. gallinae collected from standard poultry farms in Brittany, France. Genetic fingerprints of bacterial communities were generated by temporal temperature gradient gel electrophoresis (TTGE) separation of individual polymerase chain reaction (PCR)-amplified 16S rRNA gene fragments, followed by DNA sequence analysis. Most of the sequences belonged to the Proteobacteria and Firmicute phyla, with a majority of sequences corresponding to the Enterobacteriales order and the Staphylococcus genus. By using statistical analysis, we showed differences in biodiversity between poultry farms. We also determined the major phylotypes that compose the characteristic microbiota associated with D. gallinae. Saprophytes, opportunistic pathogens and pathogenic agents such as Pasteurella multocida, Erysipelothrix rhusiopathiae and sequences close to the genus Aerococcus were identified. Endosymbionts such as Schineria sp., Spiroplasma sp. Anistosticta, "Candidatus Cardinium hertigii" and Rickettsiella sp. were also present in the subdominant bacterial community. Identification of potential targets within the symbiont community may be considered in the future as a means of ectoparasite control.
Abstract: This 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 ('Reseau de Mesures de la Qualite 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.
Abstract: We examined the effects of an ectomycorrhizal (EM) fungus, Pisolithus sp., on of the growth of Pinus halepensis (Allepo pine) seedlings, soil microbial functions and rock phosphate solubilization in a un-disinfected soil amended or not with a Moroccan rock phosphate. Allepo pine seedlings were inoculated with an EM fungus (Pisolithus sp. strain PH4) isolated from a P. halepensis plantation and selected for its high ability to mobilize P from an inorganic form of phosphate. After 4 month's culture in a disinfected substrate, plants were transferred in 10 l-containers filled with a natural forest soil and amended or not with rock phosphate powder. After 12 month's culturing, the growth, needle nutrient concentrations of P. halepensis plants were measured. Soil microbial catabolic diversity was assessed by measuring CO(2) production of substrate induced respiration responses. Fluorescent pseudomonads were isolated from each soil treatment and tested in axenic conditions for their ability to solubilize a source of inorganic phosphate. The results clearly showed that (i) P. halepensis growth was greatly promoted by the presence of the ectomycorrhizal fungus Pisolithus strain PH4 in a disinfected soil/vermiculite mixture and in a non disinfected soil, (ii) ectomycorrhizal inoculation induced significant changes in the functions of soil microbial communities and selected microorganisms potentially beneficial to the plant growth (i.e. phosphate-solubilizing fluorescent pseudomonad) and (iii) rock phosphate solubilisation was mainly dependent on EM inoculation and mycorrhizosphere microorganisms. These results were in accordance with previous studies where it was demonstrated that EM symbiosis has a beneficial effect on plant growth through a direct effect on the host plant but also an indirect effect via a selective pressure on soil microbiota that favours microorganisms potentially beneficial to plant growth.
Abstract: Geostatistical and spatially constrained multivariate analysis methods (MULTISPATI-PCA) have been applied at the scale of France to differentiate the influence of natural background from the pollution due to human activities on the content of 8 trace elements in the topsoil. The results of MULTISPATI-PCA evidence strong spatial structures attributed to different natural and artificial processes. The first axis can be interpreted as an axis of global richness in trace elements. Axis 2 reflects geochemical anomalies in Tl and Pb. Axis 3 exhibits on one hand natural pedogeogenic anomalies and on the other hand, it shows high values attributable to anthropogenic contamination. Finally, axis 4 is driven by anthropogenic copper contamination. At the French territory scale, we show that the main factors controlling trace elements distribution in the topsoil are soil texture. variations in parent material geology and weathering. and various anthropogenic sources. (C) 2009 Elsevier B.V. All rights reserved.
Abstract: Diversity, structure and productivity of above-ground compartment of terrestrial ecosystems have been generally considered as the main drivers of the relationships between diversity and ecosystem functioning. More recently it has been suggested that plant population dynamics may be linked with the development of the below-ground community. The biologically active soil zone where root-root and root-microbe communications occur is named "Rhizosphere" where root exudates play active roles in regulating rhizosphere interactions. Root exudation can regulate the soil microbial community, withstand herbivory, facilitate beneficial symbioses, modify the chemical and physical soil properties and inhibit the growth of competing plant species. In this review, we explore the current knowledge assessing the importance of root exudates in plant interactions, in communications between parasitic plants and their hosts and how some soil microbial components could regulate plant species coexistence and change relationships between plants. This review will be focussed on several well documented biological processes regulating plant-plant communications such as exotic plant species invasions, negative root-root communication (allelopathy) and parasitic plant / host plant interactions and how some soil microbial components can interfere with signal traffic between roots. The reported data show that the overall effect of one plant to another results from multiple interacting mechanisms where soil microbiota can be considered as a key component.
Abstract: The response of microbial functional diversity as well as its resistance to stress or disturbances caused by the introduction of an exotic tree species, Acacia holosericea, ectomycorrhized or not with Pisolithus albus, was examined. The results show that this ectomycorrhizal fungus promotes drastically the growth of this fast-growing tree species in field conditions after 7 years of plantation. Compared to the crop soil surrounding the A. holosericea plantation, this exotic tree species, associated or not with the ectomycorrhizal symbiont, induced strong modifications in soil microbial functionalities (assessed by measuring the patterns of in situ catabolic potential of microbial communities) and reduced soil resistance in response to increasing stress or disturbance (salinity, temperature, and freeze-thaw and wet-dry cycles). In addition, A. holosericea strongly modified the structure of arbuscular mycorrhizal fungus communities. These results show clearly that exotic plants may be responsible for important changes in soil microbiota affecting the structure and functions of microbial communities.
Abstract: The main objectives of this study were (1) to describe the diversity of mycorrhizal fungal communities associated with Uapaca bojeri, an endemic Euphorbiaceae of Madagascar, and (2) to determine the potential benefits of inoculation with mycorrhizal fungi [ectomycorrhizal and/or arbuscular mycorrhizal (AM) fungi] on the growth of this tree species and on the functional diversity of soil microflora. Ninety-four sporophores were collected from three survey sites. They were identified as belonging to the ectomycorrhizal genera Afroboletus, Amanita, Boletus, Cantharellus, Lactarius, Leccinum, Rubinoboletus, Scleroderma, Tricholoma, and Xerocomus. Russula was the most frequent ectomycorrhizal genus recorded under U. bojeri. AM structures (vesicles and hyphae) were detected from the roots in all surveyed sites. In addition, this study showed that this tree species is highly dependent on both types of mycorrhiza, and controlled ectomycorrhization of this Uapaca species strongly influences soil microbial catabolic diversity. These results showed that the complex symbiotic status of U. bojeri could be managed to optimize its development in degraded areas. The use of selected mycorrhizal fungi such the Scleroderma Sc1 isolate in nursery conditions could be of great interest as (1) this fungal strain is very competitive against native symbiotic microflora, and (2) the fungal inoculation improves the catabolic potentialities of the soil microflora.
Abstract: Aims:The study aimed to determine whether inoculation with native arbuscular mycorrhizal (AM) fungi could improve survival and growth of seedlings in degraded soils of Morocco. Methods and Results:Soil samples were collected from the rhizosphere of Cupressus atlantica trees in the N'Fis valley (Haut Atlas, Morocco). AM spores were extracted from the soil, identified and this mixture of native AM fungi was propagated on maize for 12 weeks on a sterilized soil to enrich the fungal inoculum. Then C. atlantica seedlings were inoculated with and without (control) mycorrhizal maize roots, cultured in glasshouse conditions and further, transplanted into the field. The experiment was a randomized block design with one factor and three replication blocks. The results showed that a high AM fungal diversity was associated with C. atlantica; native AM fungi inoculation was very effective on the growth of C. atlantica seedlings in glasshouse conditions and this plant growth stimulation was maintained for 1 year after outplanting. Conclusions:Inoculation of C. atlantica with AM fungi increased growth and survival in greenhouse and field. Significance and Impact of the Study:The data indicate that use of native species of AM fungi may accelerate reforestation of degraded soils. Further studies have to be performed to determine the persistence of these mycorrhizae for a longer period of plantation and to measure the effects of this microbial inoculation on soil biofunctioning.
Abstract: The potential benefits of inoculation with AM (arbuscular mycorrhizal) fungi were investigated on Atlas Cypress (Cupressus atlantica G.), an endemic Cupressacea in Morocco. The parameters under study were (i) the growth of the plant, (ii) the functional diversity of soil microflora and (iii) the rock phosphate (RP) solubilizing activity. C. atlantica growth was measured after 12 months of culture in plastic bags arranged in a randomised complete block design with 10 replicates per treatment. Fungal inoculation consisted of either Glomus intraradices alone or a mixture of native AM fungi. P amendment was supplied under the form of Khouribga Rock Phosphate (KRP) powder. Microbial catabolic diversity was assessed by measuring CO2 production of SIR (substrate induced respiration) responses. Results showed that: (i) the fungal symbionts were effective to improve the growth of C. atlantica, confirming the requirement of mycorrhizal symbiosis for the successful establishment of C. atlantica in a degraded soil; (ii) G. intraradices appeared to be the most effective in promoting growth of C. atlantica, whereas indigenous AM fungi were relatively ineffective. Native AM fungi inoculation strongly modified functional abilities of the soil microflora, and in the treatments with P amendment, growth stimulations of native AM fungi inoculation were significantly higher than those of G. intraradices inoculation for the shoot growth and leaf P content; (iii) C. atlantica plants inoculated with native AM fungi could mobilize P from KRP more efficiently than those mycorrhized with G. intraradices. A strong interaction between KRP amendment and fungus inoculation was detected for the leaf P content results. In conclusion, the use of a mixture of native AM fungi combination may increase the chance of including one very effective fungal isolate, but also, creates a more favourable environment for the development of ecosystems processes. (c) 2007 Elsevier B.V. All rights reserved.
Abstract: The detection in urine of recombinant human erythropoietin (rHuEPO), a hormone misused by endurance athletes as a doping agent, is based on the differentiation of its isoelectric pattern from that of the corresponding natural hormone. Different empirical criteria have been proposed for discriminating the images of the patterns but none of them have been elaborated from a rational statistical approach. Discriminant analysis was applied to a dataset of profiles defined as positive (116 profiles from 26 subjects) (presence of rHuEPO and possibly residual natural endogenous hormone) and negative (131 profiles from 131 subjects) (presence of natural endogenous hormone only). The different bands were numbered according to a template of 16 possible positions and their relative intensities constituted the 16 variables of the statistical analysis. This method was then tested with data from an administration trial of low doses (6.7-10 IU/kg) following high-dose (265 IU/kg) injections (71 profiles from one subject). The analysis of the dataset clearly separated the negative and positive profiles. A cross-validation procedure confirmed that the analysis was extremely stable: with ten-fold cross-validation, no false positives were observed even with 100000 simulations. Furthermore, the detection of rHuEPO in the profiles from the low-dose trial was greatly improved in comparison with a previously validated empirical criterion.
Abstract: The hypothesis of the present study was that bacterial communities would differentiate under Eucalyptus camaldulensis and that an enhancement of arbuscular mycorrhizal (AM) density would minimize this exotic plant species effect. Treatments consisted of control plants, preplanting fertilizer application and AM inoculation. After 4 months of culture in autoclaved soil, E. camaldulensis seedlings were either harvested for growth measurement or transferred into containers filled with the same soil but not sterilized. Other containers were kept without E. camaldulensis seedlings. After 12 months, effects of fertilizer amendment and AM inoculation were measured on the growth of Eucalyptus seedlings and on soil microbial communities. The results clearly show that this plant species significantly modified the soil bacterial community. Both community structure (assessed by denaturing gradient gel electrophoresis profiles) and function (assessed by substrate-induced respiration responses including soil catabolic evenness) were significantly affected. Such changes in the bacterial structure and function were accompanied by disturbances in the composition of the herbaceous plant species layer. These results highlight the role of AM symbiosis in the processes involved in soil bio-functioning and plant coexistence and in afforestation programmes with exotic tree species that target preservation of native plant diversity.
Abstract: Striga hermonthica (Del.) Benth is an obligate root hemi-parasite of several cereals. Its effect on cereal crops is the main constraint for food production in sub-Saharan Africa. Various control methods have been already proposed, but the infestation by these parasitic plants persists. An appropriated method for Striga management adapted for the African farmer is very much needed. In this study, amendment of soil infested by this phytoparasite with Cubitermes mound powder is proposed as chemical amendment and natural microbial inoculum, to promote plant growth and reduce damage by S. hermonthica on sorghum (Sorghum bicolor L.). The influence of Cubitermes mound powder on the development of several microbial groups (arbuscular mycorrhizal fungi, actinomycetes, saprophytic fungi) was investigated in a pot experiment with sorghum cultured in a sandy soil infested by S. hermonthica. In the amended soil, sorghum growth and mycorrhizal colonization of sorghum plants were significantly greater than in the control treatment. Mycorrhizal colonization was negatively correlated with the number of emerged Striga plants per pot and positively correlated with sorghum growth. The relationship with substrate-induced respiration (SIR) responses showed that amended soil was characterized by its response to hydroxybutyric acid (catabolic marker of mycorrhizal colonization) and non-amended soil by its response to phenylalanine. We noted that the number of emerged Striga plants in amended pots was significantly decreased. Since Cubitermes mound suspensions did not affect Striga seed germination under axenic conditions, it suggests that the amendment with Cubitermes powder reduces S. hermonthica infestation indirectly, i.e. via its effect on the indigenous soil microflora. Overall, it appears that management of Cubitermes mounds is a promising strategy to consider for effective protection of sorghum from Striga infestation. (c) 2007 Elsevier B.V. All rights reserved.
Abstract: ade4 is a multivariate data analysis package for the R statistical environment, and ade4TkGUI is a Tcl/Tk graphical user interface for the most essential methods of ade4. Both packages are available on CRAN. An overview of ade4TkGUI is presented, and the pros and cons of this approach are discussed. We conclude that command line interfaces (CLI) and graphical user interfaces (GUI) are complementary. ade4TkGUI can be valuable for biologists and particularly for ecologists who are often occasional users of R. It can spare them having to acquire an in-depth knowledge of R, and it can help first time users in a first approach.
Abstract: The mycorrhizal status of several representative shrub species (Lavandula spp. and Thymus satureioides) in Moroccan semiarid ecosystems, was evaluated as well as their contribution to the mycorrhizal potential of the soil. Furthermore, the rhizosphere soils collected under these target species were tested for their influence on the growth of Cupressus atlantica, a tree species whose natural stands has declined in this area. Soil samples were collected from the rhizosphere of L. stoechas, L. dentata and of C. atlantica existing in the experimental area. Control samples were randomly collected from bare soil sites, away from plant influence. All the target species formed AM symbiosis and the extent of AM fungal colonization was not significantly different between plant species. No significant difference was detected between the total number of AM fungal spores of the bare soil and those recorded in the root zones of target species and C. atlantica. Three genera of AM fungi (Scutellospora, Glomus and Acaulospora) were present in the rhizospheres of the plant species and in the bare soil. The number of mycorrhizal propagules in soil originating from around the four target plant species was significantly higher than the one in the bare soil (Figure 1). The most probable number (MPN) of mycorrhizal propagules per 100 g of dry soil ranged from 7.82 (bare soil) to 179.7 (L. dentata and C. atlantica) and 244.5 (L. stoechas and T. satureioides). As the total number of spores was not different for the soil of different origins, the increase of the mycorrhizal soil infectivity (MSI) mainly resulted from larger AM mycelial networks that constituted the main source of AM fungal inoculum. In addition, this MSI enhancement was linked with changes in the functioning of soil microbial communities. In a glasshouse experiment, the growth of C. atlantica seedlings was significantly higher in the C. atlantica and in the shrub species soils than in the bare soil. Although the AM inoculum potential is not sufficient to ensure the development of forest trees in Mediterranean ecosystems, the use of plant nurses such as T. satureioides or Lavandula spp. could be of great interest to restore a self-sustaining vegetation cover to act against desertification.
Abstract: Bacterial diversity is central to ecosystem sustainability and soil biological function, for which the role of roots is important. The high-throughput analysis potential of taxonomic microarray should match the breadth of bacterial diversity. Here, the power of this technology was evidenced through methodological verifications and analysis of maize rbizosphere effect based on a 16S rRNA-based microarray developed from the prototype of H. Sanguin et al. (Environ. Microbiol. 8:289-307, 2006). The current probe set was composed of 170 probes (41 new probes in this work) that targeted essentially the Proteobacteria. Cloning and sequencing of 16S rRNA amplicons were carried out on maize rhizosphere and bulk soil DNA. All tested clones that had a perfect match with corresponding probes were positive in the hybridization experiment. The hierarchically nested probes were reliable, but the level of taxonomic identification was variable, depending on the probe set specificity. The comparison of experimental and theoretical hybridizations revealed 0.91% false positives and 0.81% false negatives. The microarray detection threshold was estimated at 0.03% of a given DNA type based on DNA spiking experiments. A comparison of the maize rhizosphere and bulk soil hybridization results showed a significant rhizosphere effect, with a higher predominance of Agrobacterium spp. in the rhizosphere, as well as a lower prevalence of Acidobacteria, Bacteroidetes, Verrucomicrobia, and Planctomycetes, a new taxon of interest in soil. In addition, well-known taxonomic groups such as Sphingomonas spp., Rhizobiaceae, and Actinobacteria were identified in both microbial habitats with strong hybridization signals. The taxonomic microarray developed in the present study was able to discriminate and characterize bacterial community composition in related biological samples, offering extensive possibilities for systematic exploration of bacterial diversity in ecosystems.
Abstract: The hypothesis of the present study was that the termite mounds of Macrotermes subhyalinus (MS) (a litter-forager termite) were inhabited by a specific microflora that could enhance with the ectomycorrhizal fungal development. We tested the effect of this feeding group mound material on (i) the ectomycorrhization symbiosis between Acacia holosericea (an Australian Acacia introduced in the sahelian areas) and two ectomycorrhizal fungal isolates of Scleroderma dictyosporum (IR408 and IR412) in greenhouse conditions, (ii) the functional diversity of soil microflora and (iii) the diversity of fluorescent pseudomonads. The results showed that the termite mound amendment significantly increased the ectomycorrhizal expansion. MS mound amendment and ectomycorrhizal inoculation induced strong modifications of the soil functional microbial diversity by promoting the multiplication of carboxylic acid catabolizing microorganisms. The phylogenetic analysis showed that fluorescent pseudomonads mostly belong to the Pseudomonads monteillii species. One of these, P. monteillii isolate KR9, increased the ectomycorrhizal development between S. dictyosporum IR412 and A. holosericea. The occurrence of MS termite mounds could be involved in the expansion of ectomycorrhizal symbiosis and could be implicated in nutrient flow and local diversity.
Abstract: Naturally acquired immunity to Plasmodium falciparum is related to immune system that changes during normal development and ageing. The effects of repeated infections during the early life on the maturation of the immune system are still unknown. Elucidation of these effects is of considerable interest given that malaria originates high mortality, especially during the first years of life. We conducted a cohort study to identify naturally acquired immune responses to P. falciparum. Cellular responses of Cameroonian neonates from birth to 36 months of age were evaluated every 6 months by cell proliferation and cytokines (IFN-gamma, IL-2 and IL-4) production after in vitro culture in the presence of schizont extract and Pf155/RESA peptides. Data were analyzed by a multiple correspondence analysis (MCA) exhibiting three main findings. Firstly, the lack of time-dependant evolution of specific immune pathways recruitment in the response to a given antigen, no antigen inducing a specific mode of response at a given time-point. Secondly, most of the data variability was expressed by IFN-gamma and IL-4 productions, and the major variation of the immune response with age involved this change in IFN-gamma production. Thirdly, the age-related immune response evolution is characterized by the acquisition of the capacity to mount a IFN-gamma response, a transient phase during which children produce a high IL-4 response, and the fast vanishing of the dominance of the IL-2 response. These results suggest that P. falciparum specific immune responses are first oriented towards a Th2-type of response, and later switch to Th1-type of response. (c) 2006 Elsevier B.V. All rights reserved.
Abstract: Gmelina arborea Roxb. (Gmelina, Yemane) is a fast growing tree, native from India and considered as a potentially invasive woody plant in West Africa. Mycorrhizal inoculation of seedlings with Glomus intraradices was performed to study (1) the effect on the growth of G. arborea, (2) the impact on the catabolic diversity of soil microbial communities and (3) the influence on the structure of herbaceous plant species communities in microcosms. Treatments consisted of control plants, pre-planting fertilizer application and arbuscular mycorrhizal (AM) inoculation. After 4 months' culture in autoclaved soil, G. arborea seedlings were either harvested for growth measurement or transferred into containers filled with the same soil but not sterilized. Other containers were kept without G. arborea seedlings. After 12 months' further culture, effects of fertilizer amendment and AM inoculation on the growth of G. arborea seedlings were recorded. AM colonization was significantly and positively correlated with plant diversity. The substrate-induced respiration response to carboxylic acids was significantly higher in the absence of G. arborea and in the presence of G. intraradices as compared to the other treatments. The influence of AM symbiosis on plant coexistence and on allelopathic processes of invasive plants are discussed.
Abstract: The general objective of this study was to measure the mycorrhizal dependencies of Cupressus and Lavandula species, to assess the contribution of Lavandula species to the mycorrhizal soil infectivity (MSI) and to determine the main effects of the association between a Lavandula species (L. multifida) and Cupressus arizonica on the soil microbial activities, on the growth and the mycorrhizal status of each plant species in experimental conditions. Three species of Lavandula (L. stoechas L., L. dentata L. and L. multifida L.) and three species of Cupressus (C. atlantica, C sempervirens and C. arizonica) were tested. Plant species were inoculated with an arbuscular mycorrhizal fungus, Glomus intraradices, to determine their mycorrhizal dependencies in controlled conditions. The results showed that L. multifida and L. dentata were representatives of highly mycorrhizal dependent plant species as well C. arizonica and C sempervirens. The contribution of L. multifida to the MSI was determined by the most probable number (MPN) method. In six different soils, L. multifida enhanced the mycorrhizal soil infectivity, even more if the soil was P deficient. When C arizonica and L. multifida were grown together, the growth and mycorrhizal colonization of each species were higher than those recorded when each plant species grew alone. The impact of this dual cultivation on the growth and mycorrhizal colonization of C arizonica was comparable to those recorded with C arizonica seedlings previously inoculated with G. intraradices. In contrast, the microbial activities of the soil collected from each treatment were different. These results emphasize the role of "resource islands" and "nurse plants" of Lavender plants in the regeneration processes of tree species such as Cupressus spp. In addition, they confirm the role of AM fungi as a major factor contributing to the growth and co-existence of each of the plant species (L multifida and C. arizonica). (c) 2006 Elsevier B.V. All rights reserved.
Abstract: The leaf litter of six tropical tree species (Acacia holosericea, Acacia tortilis, Azadirachta indica, Casuarina equisetifolia, Cordyla pinnata and Faidherbia albida) frequently used in agroforestry plantations in Sahelian and Soudano-Sahelian areas were tested for their influence on soil nitrogen content, microbial biomass and plant growth under controlled greenhouse conditions. Half of the soil was planted with onion (Allium cepa L.) seedlings and the other half was not. Two herbaceous species, Andropogon gayanus and Eragrostis tremula, were also studied. Co-inertia analysis (CIA) and one-way analysis of variance (ANOVA) analysis showed that C. pinnata and F albida leaf powder amendment induced the highest plant growth, whereas leaf powder of E. tremula is associated to higher microbial biomass and NH4+ content. Higher onion seedlings growth is associated with higher concentration of nitrogen and lignin in leaf powders. Conversely, lower plant growth is associated to higher rates of cellulose, hemicellulose and phenols in leaves. Higher rates of cellulose and hemicellulose are associated with higher microbial biomass and NH4+, whereas phenols are associated to lower microbial biomass. The results showed that amendment of A. holoseric a leaf powder (high concentrations of phenol) to the soil resulted in a lower microbial biomass and lower onion seedlings growth. Data showed that the plant residue quality index (PRQI) could be a useful tool to predict the effects of litter materials on root growth in glasshouse conditions. The highest values on soil and plant parameters were recorded with C. pinnata litter. While powdered leaf material increased the accessibility of substrates to microbes, more research with C. pinnata leaf litter (under a wider range of ecological conditions) is needed. It could add deeper on its agronomic impact in the tropics. (c) 2006 Elsevier Masson SAS. All fights reserved.
Abstract: Biovar 1 of the genus Agrobacterium consists of at least nine genomic species that have not yet received accepted species names. However, rapid identification of these organisms in various biotopes is needed to elucidate crown gall epidemiology, as well as Agrobacterium ecology. For this purpose, the AFLP methodology provides rapid and unambiguous determination of the genomic species status of agrobacteria, as confirmed by additional DNA-DNA hybridizations. The AFLP method has been proven to be reliable and to eliminate the need for DNA-DNA hybridization. In addition, AFLP fragments common to all members of the three major genomic species of agrobacteria, genomic species G1 (reference strain, strain TT111), G4 (reference strain, strain B6, the type strain of Agrobacterium tumefaciens), and G8 (reference strain, strain C58), have been identified, and these fragments facilitate analysis and show the applicability of the method. The maximal infraspecies current genome mispairing (CGM) value found for the biovar 1 taxon is 10.8%, while the smallest CGM value found for pairs of genomic species is 15.2%. This emphasizes the gap in the distribution of genome divergence values upon which the genomic species definition is based. The three main genomic species of agrobacteria in biovar 1 displayed high infraspecies current genome mispairing values (9 to 9.7%). The common fragments of a genomic species are thus likely "species-specific" markers tagging the core genomes of the species.
Abstract: Cd-tolerant bacterial strains of fluorescent pseudomonads, mostly belonging to Pseudomonas monteillii, were isolated from termite mound soil (Macrotermes subhyalinus, a litter-forager and fungus-growing termite), in a Sudanese shrubby savanna, Burkina Faso. Such large mounds appeared as sites of great bacterial diversity and could be considered as hot spots of metal-tolerant fluorescent pseudomonads. Microbial isolates were inoculated to Sorghum plants (S. bicolor) in glasshouse experiments with soil amended with CdCl(2) (560 mg Cd kg(-1) soil). Microbial functional diversity was assessed at the end of the experiment by measurement of in situ patterns of catabolic potentials. All the bacteria isolates significantly improved the shoot and total biomass of sorghum plants compared to the control. Results concerning root biomass were not significant with some strains. Arbuscular mycorrhiza (AM) was greatly reduced by CdCl(2) amendment, and fluorescent pseudomonad inoculation significantly increased AM colonisation in the contaminated soil. The bacterial inoculation significantly improved Cd uptake by sorghum plants. Measurement of catabolic potentials on 16 substrates showed that the microbial communities were different according to the soil amendment. Soils samples inoculated with pseudomonad strains presented a higher use of ketoglutaric and hydroxybutiric acids, as opposed to fumaric acid in soil samples not inoculated. It is suggested that fluorescent pseudomonads could act indirectly in such metabolic processes by involving a lower rate of degradation of citric acid, in line with the effect of small organic acid on phytoextraction of heavy metals from soil. This is a first contribution to bioremediation of metal-contaminated sites with soil-to-plant transfer, using termite built structures. Further data are required on the efficiency of the bacterial strains isolated and on the processes involved. (c) 2006 Elsevier B.V. All rights reserved.
Abstract: : Correspondence analysis of codon usage data is a widely used method in sequence analysis, but the variability in amino acid composition between proteins is a confounding factor when one wants to analyse synonymous codon usage variability. A simple and natural way to cope with this problem is to use within-group correspondence analysis. There is, however, no user-friendly implementation of this method available for genomic studies. Our motivation was to provide to the community a Web facility to easily study synonymous codon usage on a subset of data available in public genomic databases.
Abstract: We tested termite mound materials belonging to different feeding groups: Cubitermes (soil-feeder), Trinervitermes (grass-feeder) and Macrotermes (litter-feeder), as natural microbial inoculum to promote plant growth and increase nutrient supplies from soil organic matter and inorganic amendments (rock phosphate), through their effects on soil microoganisms (functional diversity of soil microflora, arbuscular mycorrhizal fungi. rhizobia. fluorescent pseudomonads, actinomycetes and saprophytic fungi). Experiments were made in a pot experiment with Acacia seyal, a leguminous tree abundant in West Africa, with a sandy soil amended or not with rock phosphate. Results indicated a stimulation of plant growth with Cubitermes and Trinervitermes mound powder (plant height and shoot biomass), similar to what was obtained with rock phosphate alone. Leaf content in N was also increased in the termite treatments (except in Macrotermes soil), whereas mycorrhizal colonization was inhibited as compared to the control. The development of saprophytic fungi was significantly higher in the soils amended with rock phosphate and this effect was hypothesized to be related to the production of large quantities of oxalic acid by fungal populations. The fluorescent pseudomonad populations notably increased in the soils dually amended with mound powders and rock phosphate., and this could be due to the fact that some species of this bacterial group are able to dissolve rock phosphate. The organic and inorganic amendments decreased the soil catabolic evenness in all the mound powder treatments. Among the mound materials tested, Cubitermes mound powder had the most promising effect, especially on SIR response to oxalate. It is concluded that soils amended both with rock phosphate and Cubitermes mound soil could promote the development of microbial communities, which could help to metabolize this compound and consequently enhance plant growth. (C) 2004 Elsevier B.V. All rights reserved.
Abstract: MADE4, microarray ade4, is a software package that facilitates multivariate analysis of microarray gene-expression data. MADE4 accepts a wide variety of gene-expression data formats. MADE4 takes advantage of the extensive multivariate statistical and graphical functions in the R package ade4, extending these for application to microarray data. In addition, MADE4 provides new graphical and visualization tools that aid in interpretation of multivariate analysis of microarray data.
Abstract: Before studying the mechanisms by which changes in vegetation influence the nematode community following abandonment of a field, it is necessary to first assess the impact of environmental factors such as soil or climate on these organisms. The study was undertaken on sites of increasing fallow duration located in the same area in the Sudano-Sahelian zone of Senegal: a forest and 10 fallow sites ranging from I to 18 years old. Soil samples were collected over 3 years on 17 occasions, along 21 m fixed transects, located in representative vegetation zones. Plant-parasitic nematodes were extracted. identified and enumerated from soil samples. The statistical analysis showed that the sites could be split in three groups according to the plant-parasitic nematode communities. One group, corresponding to young fallows, was characterised by large populations of Scutellonema cavenessi and Tylenchorhynchus gladiolatus. A second group included most of the older fallows and was characterised by a more diversified nematode community dominated by Helicotylenchus dihystera. The forest hosted a particular community partly similar to both of the other groups. Soil physical and chemical analysis split the sites into two groups, the young fallow sites plus the forest. and the older sites. The study of the annual changes revealed contradictory tendencies, such as a very small increase in T gladiolatus and in the soil clay content, which suggest that the sampling technique had probably slightly influenced the results. If this did occur it did not change the effect of fallow duration on the nematode community. The process of decline of certain nematode populations seemed to be extremely slow and not detectable over three Successive years. Nematode species were apparently able to reproduce for a long time on poor host plants, even if one plant cohort disappeared abruptly, as was the case when the field was not replanted. This study demonstrated that the soil had a greater influence on the nematode community structure than the annual climatic variations. Consequently, the soil effect will have to be mathematically considered in order to identify the mechanisms by which the plant communities progressively transform the nematode communities. (c) 2005 Elsevier B.V. All rights reserved.
Abstract: The hypothesis tested in this present study was that the ectomycorrhizosphere effect on the bacterial community was not root-growth-dependent. The impacts of ectomycorrhizal infection (Pisolithus albus COI007) and a chemical fertilization to reproduce the fungal effect on root growth were examined on (1) the structure of bacterial community and (2) fluorescent pseudomonad and actinomycete populations in the mycorrhizosphere of Acacia auriculiformis using both culture-independent and culture-dependent methods. A. auriculiformis plants were grown in disinfested soil in pots with or without addition of the ectomycorrhizal fungus or N/P/K fertilization (to reproduce the fungal effect on root growth) for 4 months and then transferred to 20-L pots filled with nondisinfested sandy soil. The fungal and fertilizer applications significantly improved the plant growth after 4-month culture in the disinfested soil. In the nondisinfested cultural substrate, these positive effects on plant growth were maintained. The total soil microbiota was significantly different within the treatments as revealed from DNA analysis [denaturing gradient gel electrophoresis (DGGE)]. The structure of fluorescent pseudomonad populations was also affected by fungal and fertilizer applications. In contrast, no qualitative effect was observed for the actinomycete communities within each treatment, but fungal inoculation significantly decreased the number of actinomycetes compared to the fertilizer application treatment. These results show that the mycorrhizosphere effect is not root-growth-dependent but is mainly due to the presence of the ectomycorrhizal fungus and more particularly to the extramatrical mycelium.
Abstract: Plants inoculated with arbuscular mycorrhizal (AM) fungi utilize more soluble phosphorus from soil mineral phosphate than noninoculated plants. However, there is no information on the response of soil microflora to mineral phosphate weathering by AM fungi and, in particular, on the catabolic diversity of soil microbial communities. The AM fungus, Glomus intraradices was examined for (i) its effect on the growth of Acacia holosericea, (ii) plant-available phosphate and (iii) soil microbial activity with and without added rock phosphate. After 4-months culture, AM fungal inoculation significantly increased the plant biomasses (by 1.78 X and 2.23 X for shoot and root biomasses, respectively), while mineral phosphate amendment had no effect in a sterilized soil. After 12-months culture, the biomasses of A. holosericea plants growing in a non-sterilized soil amended with mineral phosphate were significantly higher than those recorded in the control treatment (by 2.5 X and 5 X for shoot and root biomasses, respectively). The fungal inoculation also significantly stimulated plant growth, which was significantly higher than that measured in the mineral phosphate treatment. When G. intraradices and mineral phosphate were added together to the soil, shoot growth were significantly stimulated over the single treatments (inoculation or amendment) (1.45 X). The P leaf mineral content was also higher in the G. intraradices + mineral phosphate treatment than in G. intraradices or rock phosphate amendment. Moreover, the number of fluorescent pseudomonads has been significantly increased when G. intraradices and/or mineral phosphate were added to the soil. By using a specific type of multivariate analysis (co-inertia analysis), it has been shown that plant growth was positively correlated to the metabolization of ketoglutaric acid, and negatively linked to the metabolisation of phenylalanine and other substrates, which shows that microbial activity is also affected. G. intraradices inoculation is highly beneficial to the growth of A. holosericea plants in controlled conditions. This AM symbiosis optimises the P solubilization from the mineral phosphate and affects microbial activity in the hyphosphere of A. holosericea plants. (c) 2005 Elsevier Ltd. All rights reserved.
Abstract: In this paper, we present a statistical method called STATICO that can be used to analyze series of pairs of ecological tables. The objective of this method is to find the stable part in the dynamics of the relationships between the species and their environment. The treateddata are a sequence of pairs of ecological tables. Each pair is made of a species abundance table (species in columns) and an environmental variables table (variables in columns). The sampling sites (in rows) must be the same for the two tables of one pair, but they may be different among the pairs. The environmental variables must be the same in all the environmental tables, and the list of species must be the same in all the species tables too, although some species may be absent from some tables (the corresponding columns will contain all zeros). From a statistical point of view, STATICO is a multitable analysis (partial triadic analysis) performed on the series of cross-tables resulting from the co-inertia analysis of each pair of tables. A small ecological example data set is analyzed and the results are discussed to show how this method can be used to extract the stable part of species-environment relationships. All computations and graphical displays can be performed with free software available on Internet.
Abstract: Numerous methods exist for the analysis of changes applied to time series of satellite images. After a quick review of these methods, a new approach is proposed. This approach is based on residuals computed from PCA (Principal Component Analysis) on a NDVI table. It consists of: computing the NDVI variable for each date; building a space x time table which joins NDVI variables; carrying out a PCA on this table; choosing the number, k , of factors of PCA which explain time invariant landscape structures; and computing residuals between NDVI table and the table computed from the k factors. This method applied to the analysis of a series of three Landsat TM scenes acquired in 1983, 1984 and 1993 on the Camargue region (France) allows separation of the permanent land use structure from its annual variations. The specificity of the so called 'island Camargue' is clearly shown; control of water exchanges by man alters the land use every year.
Abstract: Correspondence discriminant analysis (CDA) is a multivariate statistical method derived from discriminant analysis which can be used on contingency tables. We have used CDA to separate Gram negative bacteria proteins according to their subcellular location. The high resolution of the discrimination obtained makes this method a good tool to predict subcellular location when this information is not known. The main advantage of this technique is its simplicity. Indeed, by computing two linear formulae on amino acid composition, it is possible to classify a protein into one of the three classes of subcellular location we have defined. The CDA itself can be computed with the ADE-4 software package that can be downloaded, as well as the data set used in this study, from the Me Bio-Informatique Lyonnais (PBIL) server at http://pbil.univ-lyonl.fr. (C) 2002 Elsevier Science Ireland Ltd. All rights reserved.
Abstract: Procrustes analysis is a method for fitting a set of points to another. These two sets of points are often defined by the measurements of two sets of variables for the same individuals (e.g., measurements of species abundances and environmental variables at the same sites). We present a solution for graphical representation of the results of procrustes analysis when the number of variables in each of the two datasets exceeds two. This method is named procrustean co-inertia analysis because it is based on the joint use of procrustes analysis and co-inertia analysis, which is a coupling method for finding linear combinations of two sets of variables of maximal covariance. It provides better graphical representation of the concordance between the two datasets than classical co-inertia analysis. Moreover, distance matrices can be introduced in the analysis to improve its ecological meaning. Lastly, a randomization test equivalent to-PROTEST is proposed as an alternative to the Mantel test. An ecological example is presented to illustrate the method.
Abstract: The spatial and genetic unit of bacterial population structure is the clone. Surprisingly, very little is known about the spread of a clone (spatial distance between clonally related bacteria) and the relationship between spatial distance and genetic distance, especially at very short scale (microhabitat scale), where cell division takes place. Agrobacterium spp. Biovar 1 was chosen because it is a soil bacterial taxon easy to isolate. A total of 865 microsamples 500 mum in diameter were sampled with spatial coordinates in 1 cm(3) of undisturbed soil. The 55 isolates obtained yielded 42 ribotypes, covering three genomic species based on amplified ribosomal DNA restriction analysis (ARDRA) of the intergenic spacer 16S-23S, seven of which contained two to six isolates. These clonemates (identical ARDRA patterns) could be found in the same microsample or 1 cm apart. The genetic diversity did not change with distance, indicating the same habitat variability across the cube. The mixing of ribotypes, as assessed by the spatial position of clonemates, corresponded to an overlapping of clones. Although the population probably was in a recession stage in the cube (10(3) agrobacteria g(-1)), a high genetic diversity was maintained. In two independent microsamples (500 mum in diameter) at the invasion stage, the average genetic diversity was at the same level as in the cube. Quantification of the microdiversity landscape will help to estimate the probability of encounter between bacteria under realistic natural conditions and to set appropriate sampling strategies for population genetic analysis.
Abstract: Ecological studies often require studying the common structure of a pair of data tables. Co-inertia analysis is a multivariate method for coupling two tables. It is often neglected,by ecologists who prefer the widely used methods of redundancy analysis and canonical correspondence analysis. We present the co-inertia criterion for measuring the adequacy between two data sets. Co-inertia analysis is based on this criterion as are canonical correspondence analysis or canonical correlation analysis, but the latter two have additional constraints. Co-inertia analysis is very flexible and allows many possibilities for coupling. Co-inertia analysis is suitable for quantitative and/or qualitative or fuzzy environmental variables. Moreover, various weighting of sites and various transformations and/or centering of species data are available for this method. Hence, more ecological considerations can be taken into account in the statistical procedures. Moreover, the principle of this method is very general and can be easily extended to the case of distance matrices or to the case of more than two tables. Simulated ecological data are used to compare the co-inertia approach with other available methods.
Abstract: One hundred and nine soil samples were collected in 69 different localities along two transects, one North-South, about 900 km in length, and the other East-West (750 km in length), across Senegal and Gambia. The first transect followed a rainfall gradient and the second a human density gradient. The relationship between carbon content, C/N ratio and soil type on the abundance and species distribution of the nematodes along the transects was studied. Results showed that short-term fallows did not influence the specific structure of the communities, when compared with the nematode communities of fields located in the immediate vicinity, where Scutellonema cavenessi and Tylenchorhynchus gladiolatus were the dominant species. The expected negative influence of human disturbance on nematode occurrence seemed to be compensated by greater crop diversity, mainly near the towns. Less-disturbed areas also maintained a high diversity, but were characterized by the presence of particular species such as Xiphinema spp. Soil type was the most important factor affecting the species composition of the nematode community. As a result, nematode communities followed a distribution in areas, corresponding to the successive soil types, but did not change in relation to the human or climatic gradients. At a large scale, the study of plant-parasitic nematodes can give both different and complementary information on the ecological trends of an area to that of free-living nematodes.
Abstract: The World Wide Web server of the PBIL (Pole Bioinformatique Lyonnais) provides on-line access to sequence databanks and to many tools of nucleic acid and protein sequence analyses. This server allows to query nucleotide sequence banks in the EMBL and GenBank formats and protein sequence banks in the SWISS-PROT and PIR formats. The query engine on which our data bank access is based is the ACNUC system. It allows the possibility to build complex queries to access functional zones of biological interest and to retrieve large sequence sets. Of special interest are the unique features provided by this system to query the data banks of gene families developed at the PBIL. The server also provides access to a wide range of sequence analysis methods: similarity search programs, multiple alignments, protein structure prediction and multivariate statistics. An originality of this server is the integration of these two aspects: sequence retrieval and sequence analysis. Indeed, thanks to the introduction of re-usable lists, it is possible to perform treatments on large sets of data. The PBIL server can be reached at: http://pbil.univ-lyon1.fr.
Abstract: Numerical analyses of remotely sensed data may valuably contribute to an understanding of the vegetation/land surface interface by pointing out at which scales a given variable displays a high level of spatial variability. Thus, there is a need of methods aimed at classifying many one-dimensional signals, such as airborne laser profiles, on the basis of their spatial structure. The present paper proposes a theoretical framework ensuring a consistent combination of a multi-scale pattern characterization, based on the Haar wavelet variance (also called in ecology Two Terms Local Variance, TTLV), with two multivariate techniques such as principal components analysis (PCA) and hierarchical cluster analysis. We illustrate our approach by comparing and classifying 257 laser profiles, with a length of 64 measurements (448 m), that were collected by the BRGM in French Guiana over three main landscape units with distinct geomorphological and ecological characteristics. We calculate for each profile a scalogram that summarized the multi-scale pattern and analyze the structural variability of profiles via a typology and a classification of one-dimensional patterns. More than 80% of the variability between spatial patterns of laser profiles has been summarized by two PCA axes, while four classes of spatial patterns were identified by cluster analysis. Each landscape unit was associated with one or two dominant classes of spatial patterns. These results confirmed the ability of the method to extract landscape scaling properties from complex and large sets of remotely sensed data. (C) 2003 Elsevier Science Inc. All rights reserved.
Abstract: The expression of most Staphylococcus aureus virulence factors is controlled by the agr locus, which encodes a two-component signaling pathway whose activating ligand is an agr,encoded autoinducing peptide (AIP). A polymorphism in the amino acid sequence of the AIP and of its corresponding receptor divides S. aureus strains into four major groups. Within a given, group, each strain produces a peptide that can activate the agr response in the other member strains, whereas the AIPs belonging to different groups are usually mutually inhibitory. We investigated a possible relationship between agr groups and human S. aureus disease by studying 198 S. aureus strains isolated from 14 asymptomatic carriers, 66 patients with suppurative infection, and 114 patients with acute toxemia. The agr group and the distribution of 24 toxin genes were analyzed by PCR, and the genetic background was determined by means of amplified fragment length polymorphism (AFLP) analysis. The isolates were relatively evenly distributed among the four agr groups, with 61 strains belonging to agr group 1, 49 belonging to group 11, 43 belonging to group 111 and 45 belonging to group IV. Principal coordinate analysis performed on the AFLP distance matrix divided the 198 strains into three main phylogenetic groups, AF1 corresponding to strains of agr group IV, AF2 corresponding to strains of agr groups I and II, and AF3 corresponding to strains of agr group III. This indicated that the agr type was linked to the genetic background. A relationship between genetic background, agr group, and disease type was observed for several toxin-mediated diseases: for instance, agr group IV strains were associated with generalized exfoliative syndromes, and phylogenetic group AF1 strains with bullous impetigo. Among the suppurative infections, endocarditis strains mainly belonged to phylogenetic group AF2 and agr groups I and II. While these results do not show a direct role of the agr type in the type of human disease caused by S. aureus, the agr group may reflect an ancient evolutionary division of S. aureus in terms of this species' fundamental biology.
Abstract: The delineation of bacterial species is presently achieved using direct DNA-DNA relatedness studies of whole genomes. It would be helpful to obtain the same genomically based delineation by indirect methods, provided that descriptions of individual genome composition of bacterial genomes are obtained and included in species descriptions. The amplified fragment length polymorphism (AFLP) technique could provide the necessary data if the nucleotides involved in restriction and amplification are fundamental to the description of genomic divergences. Firstly, in order to verify that AFLP analysis permits a realistic exploration of bacterial genome composition, the strong correspondence between predicted and experimental AFLP data was demonstrated using Agrobacterium strain C58 as a model system. Secondly, a method is proposed for determining current genome mispairing and evolutionary genome divergences between pairs of bacteria, based on arbitrary sampling of genomes by using AFLP. The measure of current genome mispairing was validated by comparison with DNA-DNA relatedness data, which itself correlates with base mispairing. The evolutionary genome divergence is the estimated rate of nucleotide substitution that has occurred since the strains diverged from a common ancestor. Current genome mispairing and evolutionary genome divergence were used to compare members of Agrobacterium, used as a model of closely related genomic species. A strong and highly significant correlation was found between calculated genome mispairing and DNA-DNA relatedness values within genomic species. The canonical 70% DNA-DNA hybridization value used to delineate genomic species was found to correspond to a range of current genome mispairing of 13-13.6%. These limits correspond to 0.097 and 0.104 nucleotide substitutions per site, respectively. in addition, experimental data showed that the large Ti and cryptic plasmids of Agrobacterium had little effect on the estimation of genome divergence. Evolutionary genome divergence was used for phylogenetic inferences. Data showed that members of the same genomic species clustered consistently, as supported by bootstrap resampling. On the basis of these results, it is proposed that the genomic delineation of bacterial species could be based, in future, on phylogenetic groups supported by bootstraps and genome descriptions of individual strains, obtained by AFLP analysis, recorded in accessible databases; this approach might eventually replace DNA-DNA hybridization studies.
Abstract: Correspondence analysis has frequently been used for codon usage studies but this method is often misused. Because amino acid composition exerts constraints on codon usage, it is common to use tables containing relative codon frequencies (or ratios of frequencies) instead of simple codon counts to get rid of these amino acid biases. The problem is that some important properties of correspondence analysis, such as rows weighting, are lost in the process. Moreover, the use of relative measures sometimes introduces other biases and often diminishes the quantity of information to analyse, occasionally resulting in interpretation errors. For instance, in the case of an organism such as Borrelia burgdorferi, the use of relative measures led to the conclusion that there was no translational selection, while analyses based on codon counts show that there is a possibility of a selective effect at that level. In this paper, we expose these problems and we propose alternative strategies to correspondence analysis for studying codon usage biases when amino acid composition effects must be removed.
Abstract: Acacia holosericea seedlings were planted in 1-1 pots filled with a soil collected from an Australian Acacia plantation in Southern Senegal. After 6 months of culture, mycorrhizosphere soil, roots, galls induced by root-knot nematodes and Rhizobium nodules were sampled from each pot. The diversity of this bacterial group was characterized by siderotyping (pyoverdine IsoElectric Focusing (IEF) analysis) and by restriction fragment length polymorphism (RFLP). The effect of these isolates on the establishment of the ectomycorrhizal symbiosis between an Australian Acacia (A. holosericea) and Pisolithus sp. strain IR100 was studied. In the mycorrhizosphere soil, the population of fluorescent pseudomonads was represented by strains of two different siderovars (groups of bacterial strains presenting an identical pyoverdine-IEF pattern): siderovar 1 (74%) and siderovar 2 (26%). The siderotyping of the isolates around galls of the root-knot nematodes revealed three siderovars (40% from siderovar 1, 40% from siderovar 2 and about 15% from siderovar 3), RFLP of 16S rDNA divided the isolates into four different groups with MspI, two with HhaI and two with HaeIII endonucleases. The establishment of the ectomycorrhizal symbiosis with A. holosericea was promoted by 14 bacterial strains isolated from the mycorrhizosphere soil, three isolates from the roots and four from the galls. Shoot biomass of A. holosericea seedlings was stimulated by eight bacterial isolates from soil, six isolates from galls and seven from roots. These mycorrhiza helper bacteria could have a great ecological importance in tropical areas through the reforestation programs. (C) 2002 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.
Abstract: Assessing the impact (direct or indirect) of introduced predator species on native seabird populations is a clear management priority, particularly so in the simple sub-Antarctic ecosystems where these effects may be dramatic. We evaluated the diet of introduced feral cats (Felis catus L.) on the Grande Terre, Kerguelen archipelago, by analysing 149 scats from 5 sites. Overall, rabbits (Oryctolagus cuniculus) were the primary prey (72.6%), followed by house mice (Mus musculus) (11.6%) and birds (all species confounded, 14.9%). However, the proportions of the three prey species varied among sites, reflecting the spreading pattern of cats onto the Grande Terre. Birds were consumed much less frequently in this study (7.3%, all sites pooled but one) compared to a 1976 study in the same area (66.3%), suggesting that cats had a strong impact on the native avifauna.
Abstract: The reliability and the level of taxonomic resolution of the amplified fragment length polymorphism (AFLP) method were evaluated with species of pathogenic bacteria involved in human, animal and plant diseases. The method was found to be very versatile as it can be adapted to the individual genome constraints of all tested species. The calculation of a genetic distance d corresponding to the average dissimilarity between actual overall genome sequences was proposed for comparing AFLP data. Bacterial models showed clearly different patterns between strains belonging to different genomic species, while patterns were clearly similar within a given species. The threshold which distinguishes between inter and infra-specific distances indicates a critical overall genome diversity of about 14% (d = 0.14). AFLP had more resolution power than serology, phage typing, PFGE and restriction analysis of ribosomal intergenic spacers. In the latter case, regression analysis showed that PCR-RFLP of ribosomal intergenic spacers can only be used to differentiate bacteria which have at least 3.4% (d = 0.034) nucleotide differences between their respective genomes. Finally, an improved procedure using newly developed software was also proposed in order to standardize the capture of reliable data and their numeric treatment for the future development of AFLP data bases.
Abstract: This work was carried out to determine the influence of the duration of fallow and of physico-chemical components of soils on the distribution of endomycorrhizal fungal spores and the mycorrhizal soil infectivity. The mycorrhization of indigenous plants from the fallows was examined and it was concluded that, except for Cassia obtusifolia, fungal colonization was poorly developed. No correlation was established between spore populations and duration of fallow or between grazed and fenced areas. The relationships between abundance of mycorrhizal spores and the physico-chemical characteristics of the soils were markedly variable among species of mycorrhizal fungi. The results did not provide evidence of a beneficial effect of increased Length of fallowing on mycorrhizal soil infectivity, but they did demonstrated the positive effect of preventing grazing on the re-establishment of vegetation during the fallow period. (C) 2001 Elsevier Science B.V. All rights reserved.
Abstract: Automated rRNA intergenic spacer analysis (ARISA) was used to characterise bacterial (B-ARISA) and fungal (F-ARISA) communities from different soil types. The 16S-23S intergenic spacer region from the bacterial rRNA operon was amplified from total soil community DNA for B-ARISA. Similarly, the two internal transcribed spacers and the 5.8S rRNA gene (ITS1-5.8S-ITS2) from the fungal rRNA operon were amplified from total soil community DNA for F-ARISA. Universal fluorescence-labeled primers were used for the PCRs, and fragments of between 200 and 1,200 by were resolved on denaturing polyacrylamide gels by use of an automated sequencer with laser detection. Methodological (DNA extraction and PCR amplification) and biological (interand intrasite) variations were evaluated by comparing the number and intensity of peaks (bands) between electrophoregrams (profiles) and by multivariate analysis. Our results showed that ARISA is a high-resolution, highly reproducible technique and is a robust method for discriminating between microbial communities. To evaluate the potential biases in community description provided by ARISA, we also examined databases on length distribution of ribosomal intergenic spacers among bacteria (L. Ranjard, E. Brothier, and S. Nazaret, Appl. Environ. Microbiol. 66:5334-5339, 2000) and fungi.
Abstract: Six provenances of Acacia auriculformis have been tested for their ectomycorrhizal dependency with 2 indigenous strains of Pisolithus sp. Moreover, the endomycorrhizal and rhizobial symbiosis, the multiplication of plant parasitic nematodes have been quantified. The results showed significant variations in plant development between provenances. Both the compatibility with and dependency on the ectomycorrhizal strains were different among the provenances. Three main genera of nematodes have been identified, in particular S. cavenessi, which is one of the most pathogenic nematodes of soudano-sahelian crops. Endomycorrhizal structures were sometimes detected on the root systems. These results suggest that provenances of A. auriculiformis that are well adapted to the indigenous environmental conditions (pedoclimatic, soil borne pathogens) must be selected for their mycorrhizal dependency and for their resistance to plant parasitic nematodes. Moreover, the ectomycorrhizal symbiosis has to be considered as an important component of the cultural system.
Abstract: Pasteuria penetrans isolates sampled from different geographical areas were characterised both for the heterogeneity of the endospore surface using monoclonal antibodies and for the ability of spores to attach to different isolates of Meloidogyne spp. The efficacy of these different Pasteuria isolates as biological control agents was tested in a glasshouse experiment with M. incognita from Senegal on Acacia holosericea. The immunoprofiles divided the P. penetrans isolates broadly differently from the attachment tests. Isolate PP16 from Senegal was associated with better seedling development of M. incognita-inoculated A. holoceria than were other isolates. Substantial variation in root and shoot biomass was not related to the observed variation in spore attachment tests. The difficulties involved in obtaining consistent biological control with Pasteuria are discussed in relation to the high degree of variability of this bacterium.
Abstract: Soil nematode communities in the 0-15 cm soil layer are used as indicators for describing the processes of fallow succession in the semi-arid zone of West Africa (Senegal). Abundance of plant feeding nematodes, non-plant feeding nematodes, plant parasite index (PPI), species richness and Shannon evenness of plant parasitic nematodes were measured at five stages of succession: fields, early (1-3 years), intermediate (8-10 years), old (18-20 years) fallows, and forest stage. These nematological indexes were analyzed simultaneously by multivariate analysis to show the indicative properties of nematode communities. Overall, changes in abundance of nematode groups, PPI and diversity, show continuous trends from early fallow to mature stages of the succession; these trends parallel theoretical trends in secondary succession. In addition, soil nematode parameters were meaningful and expressed interactions of various uncontrolled factors with successional processes, such as environmental conditions or cropping history. During the 3 years of the survey, the structure of nematode communities, described by index analysis, showed little temporal change and supported the use of nematodes as stable indicators. (C) 2000 Elsevier Science B.V. All rights reserved.
Abstract: Thr short term impact of 50 mu M Hg(II) on soil bacterial community structure was evaluated in different microenvironments of a silt loam soil in order to determine the contribution of bacteria located in these microenvironments to the overall bacterial response to mercury spiking. Microenvironments and associated bacteria, designated as bacterial pools, were obtained by successive soil washes to separate the outer fraction, containing loosely associated bacteria; and the inner fraction, containing bacteria retained into aggregates, followed by a physical fractionation of the inner fraction to separate aggregates according to their size (size fractions). Indirect enumerations of viable heterotrophic (VH) and resistant (Hg-R) bacteria were performed before and 30 days after mercury spiking. A ribosomal intergenic spacer analysis (RISA), combined with multivariate analysis, was used to compare modifications at the community level in the unfractionated soil and in the microenvironments. The spatial heterogeneity of the mercury impact was revealed by a higher increase of Hg-R numbers in the outer fraction and in the coarse size fractions. Furthermore, shifts in RISA patterns of total community DNA indicated changes in the composition of the dominant bacterial populations in response to Hg(TT) stress in the outer and in the clay size fractions. The heterogeneity of metal impact on indigenous bacteria, observed at a microscale level, is related to both the physical and chemical characteristics of the soil microenvironments governing mercury bioavailability and to the bacterial composition present before spiking. (C) 2000 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.
Abstract: This article examines the utility of particular bird species and guilds as bioindicators in a complex habitat mosaic, namely that of the tropical city of Cayenne (French Guyana). For this purpose, an urbanization gradient was divided up into nine classes based on 576 standard bird counts (using the point-count method) conducted in and around Cayenne between 1992 and 1995. Each point-count location was characterized by 10 habitat variables. A multiple correspondence analysis of this data set, followed by a cluster analysis, was used to establish a classification of eight habitats, according to level of anthropogenic disturbance and diversity of vegetation. 13667 birds, belonging to 136 species, were recorded. A cc-inertia analysis linking the point-count; and the 72 most common bird species and the urban-rural gradient classes showed that the bird populations were distributed along an anthropogenic gradient extending from second-growth forest to the old city center. The bird species fell into 11 trophic guilds. Six of these guilds, which had a high relative density or were homogenous in distribution, were not used in the characterization of the habitats. The large differences in relative density among the five other guilds allowed them to serve as habitat indicators. The eight dominant species were wide-ranging, and could not be used as biological markers. The co-inertia analysis brought out associations with some habitats of 64 other species. Each omnivorous marker was specific of an anthropogenic step in the gradient, while each insectivorous marker was associated with an increased diversity in vegetation structure. With an investment of just 10 sampling points, it was possible to characterize these habitats using a combination of observations on a maximum of II species. The Cayenne case shows a methodology to understand the relationships between environmental changes and avifaunal responses. The conclusions will be useful for the management of open spaces in growing towns along the tropical belt. (C) 2000 IRD Senegal.
Abstract: The cell density and the genetic structure of bacterial subcommunities (further named pools) present in the various microenvironments of a silt loam soil were investigated. The microenvironments were isolated first using a procedure of soil washes that separated bacteria located outside aggregates (outer part) from those located inside aggregates (inner part). A nondestructive physical fractionation was then applied to the inner part in order to separate bacteria located inside stable aggregates of different size (size fractions, i.e., two macroaggregate fractions, two microaggregate fractions, and the dispersible day fraction). Bacterial densities measured by acridine orange direct counts (AODC) and viable heterotrophic (VH) cell enumerations showed the heterogeneous quantitative distribution of cells in soil. Bacteria were preferentially located in the inner part with 87.6% and 95.4% of the whole AODC and VH bacteria, respectively, and in the microaggregate and dispersible clay fractions of this part with more than 70% and 80% of the whole AODC and VH bacteria, respectively. The rRNA intergenic spacer analysis (RISA) was used to study the genetic structure of the bacterial pools. Different fingerprints and consequently different genetic structures were observed between the unfractionated soil and the microenvironments, and also among the various microenvironments, giving evidence that some populations were specific to a given location in addition to the common populations of all the microenvironments. Cluster and multivariate analysis of RISA profiles showed the weak contribution of the pools located in the macroaggregate fractions to the whole soil community structure, as well as the clear distinction between the pool associated to the macroaggregate fractions and the pools associated to the microaggregate ones. Furthermore, these statistical analyses allowed us to ascertain the influence of the clay and organic matter content of microenvironments on the genetic structure relatedness between pools.
Abstract: Relationships between soil characteristics, various forms of soil organic matter, microbial biomass and the structure of phytoparasitic nematode populations were investigated in six fallow fields aged from 1 to 26 years in the West African Savanna (WAS) belt in southern Senegal. Soil sampling was performed along two transects in each field. Herbaceous biomass and soil physical, chemical and biological characteristics were studied with principal component analysis (PCA) and the relationships between the parameters were extracted with co-inertia analysis. Soil properties (mainly calcium, magnesium and total carbon contents, and cation exchange capacity) slightly improved in the upper soil layer (0-5 cm) during the succession of vegetation. In constrast, in the 0-10 cm soil layer, microbial biomass and total soil organic carbon content showed no clear pattern of change over time, while highest charcoal stocks were found in older fallows where bush fires are frequent. In the 0-40 cm layer, living root biomass increased and herbaceous biomass decreased through the chronosequence. Evidence is presented here for particular relationships between some of the carbon components and the structure of the nematode community. Pratylenchus and Ditylenchus species were associated with the grass vegetation of the youngest fallows. In contrast Helicotylenchus and Scutellonema were present in old fallows. The multiplication of the latter appeared closely related to the presence of woody fine roots, whereas, that of the former seemed to be favoured by the presence of the coarsest roots of trees. Xiphinema had a higher density in soils with higher bulk density. Microbial biomass was not affected by fallow duration and was not correlated with the abundance of non-phytoparasitic nematodes. These results suggested that the management of crop pests such as nematodes in the soils of the WAS could be exerted through stump protection and tree plantation (improved fallow, agroforestry) during the crop-fallow cycle. (C) 2000 Elsevier Science B.V. All rights reserved.
Abstract: Four Acacia species were tested for their susceptibility to the root-knot nematode, Meloidogyne javanica, commonly found in sahelian areas. Faidherbia albida and Acacia senegal were resistant to this nematode. On the contrary, A. raddiana, A. nilotica and A. mangium were susceptible. Among these three species, the growth of A. nilotica and A. mangium was inhibited by M. javanica but A. raddiana was tolerant. The rhizobial symbiosis with F. albida and A. senegal was stimulated by the nematode. The population build-up of the root-knot nematode induced by tree species in agroforestry systems is discussed.
Abstract: A soil and nematode survey of tomato and yam crops was made in Martinique (French West Indies). Each sample was divided into two parts, one for the nematode study and one for the soil analysis. The coupling of the data was made using the coinertia analysis. For tomato plants which were grown from seeds, the nematode-soil relationships were very strong. For the two varieties of yams, Dioscorea cayenensis-rotundata and D. alata, whose infested seed tubers carry nematodes into the field, the relationships were weaker and depended on the yam variety. For D. cayenensis-rotundata, which was attacked by the endemic parasite Pratylenchus coffeae, the relationship between nematode community and soil type was strong. For D. alata, this relationship was weaker because it is mainly parasitised by the exotic species, Scutellonema bradys, which is exclusively introduced into the field with the seed tuber, whatever the soil type. Soil texture was the most important factor explaining the presence of some species. However, Meloidogyne spp. and the ectoparasitic species such as Xiphinema spp. were associated with light andosols; Aorolaimus luci needed, in addition, higher levels of organic matter. P. coffeae preferred any type of soil rich in organic matter and its abundance seemed influenced by calcium and magnesium content or pH. In contrast, P. brachyurus did not appear to be sensitive to any of the measured physico-chemical soil characteristics. (C) 1998 Published by Elsevier Science B.V. All rights reserved.
Abstract: The urban area of Dakar, Senegal, contains >5,000 market-garden wells that provide permanent sites for mosquito larvae, in particular Anopheles arabiensis Patton, the major vector of malaria. A study of the bioecology of mosquito larvae was conducted over 1 yr with a monthly visit to 48 of these wells. Overall, 9,589 larvae were collected of which 80.1% were Culicinae and 11.9% Anophelinae. Larvae from stages III and IV (n = 853) were identified to 10 species. An. arabiensis represented 86% of the anophelines collected and An. ziemanni Grunberg 14%. The most common Culicinae species included Aedeomyia africana Neveu-Lemaire, Culex quinquefasciatus Say, and Mimomyia splendens Theobald. Maximum anopheline abundance was observed at the end of the dry season in June, whereas maximum Culicinae abundance was observed at the end of the rainy season in September. Most wells (67%) did not harbor any An. arabiensis larvae and in the remaining 33% the larval abundance was low, averaging 0.54 larvae in stages III-IV per tray sample. To identify factors that determine the abundance of larvae in these wells, a co-inertia (multivariate) analysis was carried out to account for physicochemical variables (depth, turbidity, temperature, pi-i, conductivity, Na+, Cl-, HCO3-, CO3--, and NO3- concentrations) and biological variables (abundance of mosquito species, predators [e.g., fish, Dytiscidae, Notonectidae, odonates ], molluscs [Bulinus and Biomphalaria], and surface plants [water lettuce, Lemna, and flamentous algae]). The co-inertia analysis indicated that the abundance of An. arabiensis was associated with Cr, quinquefasciatus and Cx. decens for the physiochemical data but was not associated with other mosquito species for floro-faunistic data. The conditions associated with abundant An. arabiensis were warm temperature (28 - 30 degrees C), clear and not too deep water (<0.5 m), elevated concentrations of HCO3- and CO3--, low concentrations of NO3- and NaCl low populations of larvivorous fish and invertebrate predators (notably odonates), the presence of water lettuce, and an absence of Lemna. These results indicate that many contributing factors influence the ecology of the immature stages of An. arabiensis.
Abstract: We present ADE-4, a multivariate analysis and graphical display software. Multivariate analysis methods available in ADE-4 include usual one-table methods like principal component analysis and correspondence analysis, spatial data analysis methods (using a total variance decomposition into local and global components, analogous to Moran and Geary indices), discriminant analysis and within/between groups analyses, many linear regression methods including lowess and polynomial regression, multiple and PLS (partial least squares) regression and orthogonal regression (principal component regression), projection methods like principal component analysis on instrumental variables, canonical correspondence analysis and many other variants, coinertia analysis and the RLQ method, and several three-way table (k-table) analysis methods. Graphical display techniques include an automatic collection of elementary graphics corresponding to groups of rows or to columns in the data table, thus providing a very efficient way for automatic k-table graphics and geographical mapping options. A dynamic graphic module allows interactive operations like searching, zooming, selection of points, and display of data values on factor maps. The user interface is simple and homogeneous among all the programs; this contributes to making the use of ADE-4 very easy for nonspecialists in statistics, data analysis or computer science.
Abstract: The interpretation of the factors computed by multivariate analysis methods is often a difficult task. The main difficulties come from the cluttering of the factor map when the data set is large, and from the need to visualize the data when interpreting the factors. An interactive method based on the representation of the data on the factor maps is presented, with reference to a computer program available on the Internet network. Several techniques offered by this program are demonstrated with the help of a real-size example data set: searching, zooming, and plotting of rows and columns of the data table on the factor map.
Abstract: We have developed a World-Wide-Web server for browsing sequence collections structured under the ACNUC format and for performing multivariate analyses on sequences. General collections (like GenBank or EMBL), as well as specialized data banks (like Hovergen and NRSub) can be accessed. This system allows complex queries to be constructed, and the result of each query, represented by a list of sequences is stored on the server. It is then possible to reuse this list to compute multivariate analyses on the sequences. Two examples of applications are shown. The first one consists in a study of codon usage with correspondence analysis on all the protein genes of Haemophilus influenzae Rd. This study allows the highly expressed genes and the integral membrane proteins of this organism to be identified. The second one consists in an ordering of 70 aligned protein sequences of growth hormone with principal coordinate analysis. With this method, we are able to re-establish the patterns of relationships between the sequences previously determined with tree building programs.
Abstract: This report describes two applications of a multivariate method for studying classes of nucleotide or protein sequences: correspondence discriminant analysis (CDA). The first example is the discrimination between Escherichia coli proteins according to their subcellular location (membrane, cytoplasm and periplasm). The high resolution of the method made it possible to predict the subcellular location of E. coli proteins for whom this information is not known. The second example is discrimination between the coding sequences of leading and lagging strands in four bacteria: Mycoplasma genitalium, Haemophilus influenzae, E.coli and Bacillus subtilis. The programs used for computing the analysis are integrated in a publicly available package that runs on MacOS 7.x or Windows 95 operating systems (http://biomserv.univ-lyon1/.fr/ADE-4.html). These programs are also accessible through our Would Wide Web server (http://biomserv.univ-lyon1.fr/NetMul.html).
Abstract: A multivariate analysis method called co-inertia analysis was used to determine the main relationships between two data tables having identical rows. This method is available in the ADE multivariate analysis package for Macintosh micro-computers. It was applied to two data sets, one containing the amino-acid composition of 999 E. coli proteins, and the other the values of 402 physico-chemical properties for the 20 natural amino-acids. There were strong relationships between amino-acid physico-chemical properties and the composition of proteins. The first common factor was hydrophobicity, it is linked to the biological environment of proteins, either in the cytoplasm (or outside the cell), or in the nonpolar environment of the phospholipid bilayer of biological membranes. The second factor linked the expressivity of protein genes and the propensity of amino-acids to form alpha helix/beta sheets. The third factor showed that heavy, aromatic amino-acids tend to be avoided, except when they are needed for structural or functional reasons. These results are discussed in terms of selective pressure acting on amino-acid composition of proteins.
Abstract: The relationships between the structural variations of a ferrisol and the plant parasitic nematode communities of sugarcane were studied along three transects. These transects, about 20 m long, started in horizon A and ended in a levelled area where horizon C began. Results were analysed with the co-inertia analysis method, which allowed us to study simultaneously the soil and nematode data. Progressive variations of the content of some physico-chemical soil elements (organic matter, phosphorus, pH) appear linked to those of the abundance of some nematode species (Hemicriconemoides and Pratylenchus). This analysis also shows relations that do not vary according to a gradient along the transects. For instance, the abundance of Helicotylenchus can be correlated with the existence of high calcium grades.
Abstract: Systematic sampling designs are widely used in stereology. When an estimator of the total amount, Q, of the sampled variable is evaluated by such a procedure, the coefficient of error can be predicted by applying Matheron's theory of regionalized variables. To evaluate the accuracy of the estimate of Q, it is necessary to study the behaviour of the regionalized variable and to model its covariogram. Histological. data with a low short-range variability and agronomic data with a pronounced nugget effect provided the biological material for extreme case studies. Results show that the short-range variability, if present, cannot be detected when only small samples are available. An underestimation of the coefficient of error is then to be expected. We propose several models of the covariogram, which can be used to test for the presence of a nugget effect. If a nugget effect is present, these models will provide better estimates of the coefficient of error. If there is no nugget effect a simplified method can be used and will provide reliable estimates of the coefficient of error.
Abstract: The method and the associated graphical representations proposed in this paper facilitate the interpretation of the correspondence analysis (CA) of a samples/species data table. By using the "reciprocal discrimination" model of CA, this method introduces directly and on the same graph the notions of niche width and within-sample diversity. We propose two Macintosh programs for computing conditional means, variances, and covariances of factor scores for species and samples, and for drawing ellipses and Gaussian curves from these values. Two examples of ecological interest show how resulting graphics help in understanding the results of multivariate analyses.
