Dominique Arrouays

Mapping field‐scale spatial patterns of size and activity of the denitrifier community

There is ample evidence that microbial processes can exhibit large variations in activity on a field scale. However, very little is known about the spatial distribution of the microbial communities mediating these processes. Here we used geostatistical modelling to explore spatial patterns of size and activity of the denitrifying community, a functional guild involved in N-cycling, in a grassland field subjected to different cattle grazing regimes. We observed a non-random distribution pattern of the size of the denitrifier community estimated by quantification of the denitrification genes copy numbers with a macro-scale spatial dependence (6-16 m) and mapped the distribution of this functional guild in the field. The spatial patterns of soil properties, which were strongly affected by presence of cattle, imposed significant control on potential denitrification activity, potential N(2)O production and relative abundance of some denitrification genes but not on the size of the denitrifier community. Absolute abundance of most denitrification genes was not correlated with the distribution patterns of potential denitrification activity or potential N(2)O production. However, the relative abundance of bacteria possessing the nosZ gene encoding the N(2)O reductase in the total bacterial community was a strong predictor of the N(2)O/(N(2) + N(2)O) ratio, which provides evidence for a relationship between bacterial community composition based on the relative abundance of denitrifiers in the total bacterial community and ecosystem processes. More generally, the presented geostatistical approach allows integrated mapping of microbial communities, and hence can facilitate our understanding of relationships between the ecology of microbial communities and microbial processes along environmental gradients.

Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale

Little information is available regarding the landscape-scale distribution of microbial communities and its environmental determinants. However, a landscape perspective is needed to understand the relative importance of local and regional factors and land management for the microbial communities and the ecosystem services they provide. In the most comprehensive analysis of spatial patterns of microbial communities to date, we investigated the distribution of functional microbial communities involved in N-cycling and of the total bacterial and crenarchaeal communities over 107 sites in Burgundy, a 31 500 km2 region of France, using a 16 × 16 km2 sampling grid. At each sampling site, the abundance of total bacteria, crenarchaea, nitrate reducers, denitrifiers- and ammonia oxidizers were estimated by quantitative PCR and 42 soil physico-chemical properties were measured. The relative contributions of land use, spatial distance, climatic conditions, time, and soil physico-chemical properties to the spatial distribution of the different communities were analyzed by canonical variation partitioning. Our results indicate that 43–85% of the spatial variation in community abundances could be explained by the measured environmental parameters, with soil chemical properties (mostly pH) being the main driver. We found spatial autocorrelation up to 739 km and used geostatistical modelling to generate predictive maps of the distribution of microbial communities at the landscape scale. The present study highlights the potential of a spatially explicit approach for microbial ecology to identify the overarching factors driving the spatial heterogeneity of microbial communities even at the landscape scale.

The dynamics of carbon in particle-size fractions of soil in a forest-cultivation sequence

Cultivation of forest and grassland soils induces heavy changes in soil organic matter (SOM) dynamics. To better predict the effect of cultivation, there is a need to describe which organic pools are affected and to which extent. We used a chronosequence of thick humic forest soils converted to maize cultivation for 40 yr in southwest France. The dynamics of soil carbon was investigated through particle-size fractionation and the use of 13C allowed to distinguish forest-derived organic matter and new crop-derived organic matter. This partitioning of soil carbon by size on one hand and by age on the other provided a precise description of carbon turnover. The level towards which tend the organic pools under cultivation showed that the decay rates of soil carbon were one order of magnitude higher under cultivation than under forest. SOM can thus be considered as deprotected under cultivation. All size fractions appeared to be deprotected to the same extent. A progressive transfer of silt-sized C to clay-sized C was nevertheless suspected and attributed to the decreasing stability of fine silt-sized microaggregates with cultivation. SOM furthermore contained some very stable C present as silt-sized and possibly clay-sized particles. The turnover times of maize-derived organic matter was the same as that observed in similar soils cultivated for centuries. This indicated that the new conditions induced by cultivation were reached in the very first years after forest clearing and that the high initial SOM content and high mineralization rate of initial organic matter did not affect the dynamics of newly incorporated carbon.

Validation and Application of a PCR Primer Set to Quantify Fungal Communities in the Soil Environment by Real-Time Quantitative PCR

Fungi constitute an important group in soil biological diversity and functioning. However, characterization and knowledge of fungal communities is hampered because few primer sets are available to quantify fungal abundance by real-time quantitative PCR (real-time Q-PCR). The aim in this study was to quantify fungal abundance in soils by incorporating, into a real-time Q-PCR using the SYBRGreen® method, a primer set already used to study the genetic structure of soil fungal communities. To satisfy the real-time Q-PCR requirements to enhance the accuracy and reproducibility of the detection technique, this study focused on the 18S rRNA gene conserved regions. These regions are little affected by length polymorphism and may provide sufficiently small targets, a crucial criterion for enhancing accuracy and reproducibility of the detection technique. An in silico analysis of 33 primer sets targeting the 18S rRNA gene was performed to select the primer set with the best potential for real-time Q-PCR: short amplicon length; good fungal specificity and coverage. The best consensus between specificity, coverage and amplicon length among the 33 sets tested was the primer set FR1 / FF390. This in silico analysis of the specificity of FR1 / FF390 also provided additional information to the previously published analysis on this primer set. The specificity of the primer set FR1 / FF390 for Fungi was validated in vitro by cloning - sequencing the amplicons obtained from a real time Q-PCR assay performed on five independent soil samples. This assay was also used to evaluate the sensitivity and reproducibility of the method. Finally, fungal abundance in samples from 24 soils with contrasting physico-chemical and environmental characteristics was examined and ranked to determine the importance of soil texture, organic carbon content, C∶N ratio and land use in determining fungal abundance in soils.

Spatial patterns of bacterial taxa in nature reflect ecological traits of deep branches of the 16S rRNA bacterial tree

Whether bacteria display spatial patterns of distribution and at which level of taxonomic organization such patterns can be observed are central questions in microbial ecology. Here we investigated how the total and relative abundances of eight bacterial taxa at the phylum or class level were spatially distributed in a pasture by using quantitative PCR and geostatistical modelling. The distributions of the relative abundance of most taxa varied by a factor of 2.5-6.5 and displayed strong spatial patterns at the field scale. These spatial patterns were taxon-specific and correlated to soil properties, which indicates that members of a bacterial clade defined at high taxonomical levels shared specific ecological traits in the pasture. Ecologically meaningful assemblages of bacteria at the phylum or class level in the environment provides evidence that deep branching patterns of the 16S rRNA bacterial tree are actually mirrored in nature.

GlobalSoilMap: Toward a Fine-Resolution Global Grid of Soil Properties

Abstract Soil scientists are being challenged to provide assessments of soil condition from local through to global scales. A particular issue is the need for estimates of the stores and fluxes in soils of water, carbon, nutrients, and solutes. This review outlines progress in the development and testing of GlobalSoilMap —a digital soil map that aims to provide a fine-resolution global grid of soil functional properties with estimates of their associated uncertainties. A range of methods can be used to generate the fine-resolution spatial estimates depending on the availability of existing soil surveys, environmental data, and point observations. The system has an explicit geometry for estimating point and block estimates of soil properties continuously down the soil profile. This geometry is necessary to ensure mass balance when stores and fluxes are computed. It also overcomes some limitations with existing systems for characterizing soil variation with depth. GlobalSoilMap has been designed to enable delivery of soil data via Web services. This review provides an overview of the systems technical specifications including the minimum data set. Examples from contrasting countries and environments are then presented to demonstrate the robustness of the technical specifications. GlobalSoilMap provides the means for supplying soil information in a format and resolution compatible with other fundamental data sets from remote sensing, terrain analysis, and other systems for mapping, monitoring, and forecasting biophysical processes. The initial research phase of the core project is nearing completion and attention is now shifting toward establishing the institutional and governance arrangements necessary to complete a full global coverage and maintaining the operational version of the GlobalSoilMap . This will be a grand and rewarding challenge for the soil science profession in the coming years.

Changes in carbon storage in temperate humic loamy soils after forest clearing and continuous corn cropping in France

Soil samples from forest and agricultural sites in three areas of southwest France were collected to determine the effect of forest conversion to continuous intensive corn cropping with no organic matter management on soil organic carbon (C) content. Soils were humic loamy soils and site characteristics that may affect soil C were as uniform as possible (slope, elevation, texture, soil type, vegetation).Three areas were selected, with adjacent sites of various ages of cultivation (3 to 35 yr), and paired control forest sites. The ploughed horizon (0-Dt cm) and the Dt-50 cm layer were collected at each agricultural site. In forest sites, each 10 cm layer was collected systematically down to 1 meter depth. Carbon concentrations were converted to total content to a given depth as the product of concentration, depth of sample and bulk density, and expressed in units of kg m-2. For each site and each sampled layer, the mineral mass of soil was calculated, in order to base comparisons on the same soil mass rather than the same depth.The pattern of C accumulation in forest soils showed an exponential decrease with depth. Results suggested that soil organic carbon declined rapidly during the first years of cultivation, and at a slower rate thereafter. This pattern of decrease can be fitted by a bi-exponential model assuming that initial soil organic carbon can be separated into two parts, a very labile pool reduced during the first rapid decline and more refractory fractions oxidizing at a slower rate. Sampling to shallow depths (0-Dt cm) resulted in over-estimation of the rate of carbon release in proportion to the initial amount of C, and in under-estimation of the total loss of C with age. The results for the 0–50 cm horizon indicated that losses of total carbon average about 50% in these soils, ranging in initial carbon content from 19 to 32.5 kg m-2. Carbon release to the atmosphere averaged 0.8 kg m-2 yr-1 to 50 cm depth during the first 10 years of cultivation. The results demonstrate that temperate soils may also be an important source of atmospheric carbon, when they are initially high in carbon content and then cultivated intensively with no organic matter management.

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

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

Modeling Vertical Distribution Of Carbon In Oxisols Of The Western Brazilian Amazon (rondonia)

Oxisols have great ecological significance in tropical soils because they are the dominant soil type of the Brazilian Amazon ecosystem, comprising more than 40% of its total. To estimate carbon (C) stocks and changes requires knowledge of the vertical distribution of C in profiles. The objective of this study was to determine if specific patterns occur in C profiles of Oxisols in the Western Brazilian Amazon so that total C storage can be assessed down to any given depth by simple models with low input data requirements. Two models, a power-based model and an exponential-based model, were tested using nonlinear regression analysis on a soil database made up of 129 Oxisol profiles corresponding to 519 soil horizons. These models, as judged by the coefficient of determination (R 2 ) value, explained more than 55% of the total variance for all of the horizons, whether or not segregated by taxonomic unit. The models were then tested with individual profiles. The power model exhibited a tendency to overestimate C stocks when integration was done for the 0-20-cm and the 0-100-cm layers. Results from the exponential model were better than those from the power model. The R 2 values were greater than 0.82, and the associated standard error was reduced. In a validation procedure, the mean error (ME) was close to zero for the exponential model, with a systematic ME of only 0.06 kg C.m -2 for the 0-100-cm layer.

Modeling carbon storage profiles in temperate forest humic loamy soils of France

In southwest France, thick humic acid soils have developed from Quaternary silty alluvial deposits. The objective of this study was to determine if specific patterns of carbon profiles occurred in these soils in order to evaluate total carbon storage using mathematical modeling and laboratory analysis on a small number of samples. Soil samples were collected from an oceanic zone of the French Pyrenean piedmont, ancient terraces of Pyrenean streams (southwest France), and from seven mature forests. The results demonstrated that these soils have accumulated large amounts of organic carbon. The pattern of C accumulation showed an exponential decrease with depth and appeared to be characteristic of these soils. This typical pattern allowed modeling of the carbon storage profile and reduction of the number of samples from 10 to 3 without modifying significantly the fitted model and the evaluation of the total amounts of C. This study also demonstrated that sampling to shallow depths fails to include a large proportion of the total C content in these soils. Therefore, studies restricted to shallow depths appear not to be relevant for studying the role of these soils in carbon storage. A regression predicting bulk density from organic carbon was used to calculate total C amounts down to a depth of 1 meter. The analysis used simple determinations of C concentration in three specific horizons.