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.     

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 N₂O 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 N₂O production. However, the relative abundance of bacteria possessing the nosZ gene encoding the N₂O reductase in the total bacterial community was a strong predictor of the N₂O/(N₂ + N₂O) 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.     

Biogeographical patterns of soil molecular microbial biomass as influenced by soil characteristics and management

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.     

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.     

Similar Processes but Different Environmental Filters for Soil Bacterial and Fungal Community Composition Turnover on a Broad Spatial Scale

Spatial scaling of microorganisms has been demonstrated over the last decade. However, the processes and environmental filters shaping soil microbial community structure on a broad spatial scale still need to be refined and ranked. Here, we compared bacterial and fungal community composition turnovers through a biogeographical approach on the same soil sampling design at a broad spatial scale (area range: 13300 to 31000 km²): i) to examine their spatial structuring; ii) to investigate the relative importance of environmental selection and spatial autocorrelation in determining their community composition turnover; and iii) to identify and rank the relevant environmental filters and scales involved in their spatial variations. Molecular fingerprinting of soil bacterial and fungal communities was performed on 413 soils from four French regions of contrasting environmental heterogeneity (Landes<Burgundy≤Brittany<<South-East) using the systematic grid of French Soil Quality Monitoring Network to evaluate the communities’ composition turnovers. The relative importance of processes and filters was assessed by distance-based redundancy analysis. This study demonstrates significant community composition turnover rates for soil bacteria and fungi, which were dependent on the region. Bacterial and fungal community composition turnovers were mainly driven by environmental selection explaining from 10% to 20% of community composition variations, but spatial variables also explained 3% to 9% of total variance. These variables highlighted significant spatial autocorrelation of both communities unexplained by the environmental variables measured and could partly be explained by dispersal limitations. Although the identified filters and their hierarchy were dependent on the region and organism, selection was systematically based on a common group of environmental variables: pH, trophic resources, texture and land use. Spatial autocorrelation was also important at coarse (80 to 120 km radius) and/or medium (40 to 65 km radius) spatial scales, suggesting dispersal limitations at these scales.     

Modelling organic carbon turnover in cleared temperate forest soils converted to maize cropping by using 13C natural abundance measurements

In southwest France, thick humic acid loamy soils have developed from Quaternary silty alluvial deposits. On these soils, most forest lands have been converted to continuous intensive maize cropping and the loss of C upon conversion to intensive agriculture has been shown to be significant. The objective of this study was to determine if a study of natural ¹³C abundance in soil organic C makes possible an improved modelling of organic carbon turnover in the cultivated horizons of soils in this landscape in southwest France. A chronosequence study is realized by comparing C pools and C-13 natural abundance of three forest sites and 14 adjacent agricultural sites, whose ages of cultivation ranged from 3 to 32 yr. ¹³C ratio is found to increase with time of cultivation. The fraction of C coming from the maize crop increases during the first decades of cultivation, and reaches a plateau thereafter. This equilibrium level is reached after a few decades of cultivation. The decrease of the initial C pool is fitted by a simple model assuming that about half of this pool is mineralized during the first yr of cultivation whereas the other half decreases at a slower rate. Therefore, a general bi-compartmental model is proposed for describing the soil organic carbon dynamics in these soils after forest clearing and intensive maize cropping.     

Soil organic carbon dynamics in cleared temperate forest spodosols converted to maize cropping

In southwest France, sandy spodosols have developed from Quaternary sandy eolian deposits. On these soils, numerous forest lands have been converted to continuous intensive maize cropping. A chronosequence study is realized by comparing organic C pools and ¹³C natural abundance of one forested and 6 agricultural sites, whose ages of cultivation range from 4 to 32 yr. ¹³C ratio is found to increase with time of cultivation. After 3 decades of intensive maize cropping, about half of the initial organic C content in the forest topsoil layer has disappeared. The fraction of C derived from maize crop increases during the first decades of cultivation, but its level is significantly lower than those observed in other soils, which indicates a high mineralization rate of organic C. In this context, soil characteristics associated to intensive agricultural practices lead to a rapid and large loss of C, whereas inputs from maize seem to have only a very small long-term contribution.