Publications by authors named "Abad Chabbi"

16 Publications

  • Page 1 of 1

Legacy effects of temporary grassland in annual crop rotation on soil ecosystem services.

Sci Total Environ 2021 Aug 10;780:146140. Epub 2021 Mar 10.

UMR SAS, INRAE, INSTITUT AGRO AGROCAMPUS OUEST, 35000 Rennes, France.

The introduction of temporary grassland into an annual crop rotation is recognized to improve soil ecosystem services, and resulting legacies can be beneficial for the following crops. In this context, the aim of the present study was to evaluate legacy effects of introducing temporary grassland into an annual crop rotation on five ecosystem services (i) soil structure maintenance (aggregate stability), (ii) water regulation (saturated hydraulic conductivity), (iii) biodiversity conservation (microbial biomass and microbial metabolic activity, as well as microorganism, enchytraeid, springtail and earthworm communities), (iv) pathogen regulation (soil suppressiveness to Verticillium dahliae), and (v) forage production and quality. Three crop rotation schemes, maintained for twelve years, were compared in four random blocks, one being an annual crop rotation without grassland (0%), another with a medium percentage of grassland (50%, corresponding to 3 years of continuous grassland in the crop rotation), and a third one with a high percentage of grassland in the crop rotation (75%, corresponding to 6 years of continuous grassland in the crop rotation). The results showed that the grassland introduction into an annual crop rotation improved, whatever the duration of the grassland, soil structure maintenance and biodiversity conservation, while it decreased pathogen regulation and did not modify water regulation. Comparing the two crop rotations that included grassland, indicated a stronger beneficial grassland legacy effect for the higher proportion of grassland concerning soil structure maintenance and biodiversity conservation. By contrast, water regulation, pathogen regulation and forage production were not affected by the legacy of the 75% grassland during the rotation. Overall, our findings demonstrated the extent to which grassland legacies are affecting the current state of soil properties and possible ecosystem services provided. To improve ecosystem services, soil management should take legacy effects into account and consider longer timeframes to apply beneficial practices.
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http://dx.doi.org/10.1016/j.scitotenv.2021.146140DOI Listing
August 2021

Does the higher root carbon contribution to soil under cropping cycles following grassland conversion also increase shoot biomass?

Authors:
Teng Hu Abad Chabbi

Sci Total Environ 2021 Jan 12;752:141684. Epub 2020 Aug 12.

French National Research Institute for Agriculture, Food and Environment (INRAE), INRAE Nouvelle-Aquitaine-Poitiers, URP3F 86600 Lusignan, France; French National Research Institute for Agriculture, Food and Environment (INRAE), Versailles-Grignon, UMR-ECOSYS, AgroParisTech, 78850 Thiverval-Grignan, France. Electronic address:

This study tested the possible root biomass improvements in crop rotations after the conversion of grasslands, and crop samples from maize, winter wheat, and winter barley were collected during 2011-2013 from a long-term experimental site in Lusignan, France (http://www.soere-acbb). Root biomass C quantification was performed using δC isotopic signatures to determine the presence of both C3 and C4 plants. We also calculated the recovery rate of maize root biomass C. The results showed that after crop rotations, 0-60 cm root biomass C values were 44.1, 34.2, and 18.7 g C m for maize, winter wheat, and winter barley respectively. The Root biomass C of crops after conversion to grassland was approximately 2-3 times those observed after crop rotations. However, incorporating ley grassland duration into crop rotations showed limited improvements in shoot biomass C and grain yield of the crops, regardless of the decreased rate of N fertilizer for maize. Moreover, root biomass C had a significant relationship with N supply from residues (P < .05). Nevertheless, shoot biomass C of only maize showed significance in its relationships with N supply and root biomass C. In addition, in each 30 cm soil layer (0-30 cm, 30-60 cm, and 60-90 cm), the recovery rate of maize roots decreased to approximately 15% when root biomass C increased to 10 g C m. However, further increases in root biomass C had little impact on the recovery rate. In conclusion, compared with continuous cropland, incorporating ley grassland duration into crop rotations increases root biomass C of crops, but this change may not be a significant increase of the shoot biomass C or grain yield. This finding simply indicates the improved C input from crops and the potential to increase soil organic C, as well as providing a model for the sustainability of crop rotations.
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http://dx.doi.org/10.1016/j.scitotenv.2020.141684DOI Listing
January 2021

Combining eddy covariance measurements with process-based modelling to enhance understanding of carbon exchange rates of dairy pastures.

Sci Total Environ 2020 Nov 15;745:140917. Epub 2020 Jul 15.

UMR ECOSYS, Centre INRA, Versailles-Grignon, Bâtiment EGER, 78850 Thiverval-Grignon, France; French National Research Institute for Agriculture, Food and Environment (INRAE), Poitou-Charentes, URP3Fm, 86600 Lusignan, France.

Many temperate grasslands are used for dairying, and ongoing research aims to better understand these systems in order to increase animal production and soil organic carbon (SOC) stocks. However, it is difficult to fully understand management effects on SOC because most changes are slow and difficult to distinguish from natural variability, even if changes are important over years to decades. Eddy covariance (EC) measurements can overcome this problem by continuously measuring net carbon exchange from pastures, but net balances are very sensitive to even small systematic measurement errors. Combining EC measurements with detailed process-based modelling can reduce the risks inherent in total reliance on EC measurements. Modelling can also reveal information about the underlying processes that drive observed fluxes. Here, we describe carbon exchange patterns of five paddocks situated at four different locations in New Zealand and France where EC data and detailed physiological modelling were available. The work showed that respiration by grazing animals was often only incompletely captured in EC measurements. This was most problematic when fluxes were based on gap-filling, which could have estimated incorrect fluxes during grazing periods based on observations from periods without grazing. We then aimed to extract plant physiological insights from these studies. We found appreciable carbon uptake rates even at temperatures below 0 °C. After grazing, carbon uptake was reduced for up to 2 weeks. This reduction was larger than expected from reduced leaf area after grazing, but the factors contributing to that difference have not yet been identified. Detailed physiological models can also extrapolate findings to new management regimes, environmental conditions or plant attributes. This overcomes the limitation of experimental studies, which are necessarily restricted to actual site and weather conditions allowing models to make further progress on predicting management effects on SOC.
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http://dx.doi.org/10.1016/j.scitotenv.2020.140917DOI Listing
November 2020

Temperature sensitivity of decomposition decreases with increasing soil organic matter stability.

Sci Total Environ 2020 Feb 21;704:135460. Epub 2019 Nov 21.

Manaaki Whenua - Landcare Research, PO Box 69040, Lincoln 7640, New Zealand.

Evaluation of the temperature sensitivity of soil organic matter (SOM) decomposition is critical for forecasting whether soils in a warming world will lose or gain carbon and, therefore, accelerate or mitigate climate warming. It is usually described, using Arrhenius kinetics, as increasing with the stability of the substrate in laboratory conditions, where substrate availability is non-limiting and where chemical recalcitrance, therefore, predominantly regulates stability. However, conditions of non-limiting subtrate availability are rare in the undisturbed soil, where physicochemical protection of substrates may control their stability. The aim of this study was to assess the temperature sensitivity of decomposition of SOM with contrasting stability in the field. Our conceptual approach was based on in situ measurements of soil CO efflux at a range of temperatures from root exclusion plots of increasing age (1 month and three decades) and, therefore, with SOM of increasing stability. From a set of short-term measurements in spring, using diurnal temperature variation, the relative temperature sensitivity of SOM decomposition decreased significantly (p < 0.0001) with increasing SOM stability, and was weak (Q < 1.3) in long-term root exclusion plots. This result was confirmed in a similar set of short-term measurements repeated later in the year, in summer, as well as from an analysis perfomed at the seasonal timscale. We provide direct field evidence that the temperature sensitivity of SOM decomposition decreases with increasing stability, in direct contrast with Arrhenius kinetics prediction, and therefore show that stability of SOM in the field cannot be the sole result of chemical recalcitrance. We conclude that the physicochemical protection of SOM, which controls SOM stability in the field, constrains the temperature sensitivity of SOM decomposition under field conditions.
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http://dx.doi.org/10.1016/j.scitotenv.2019.135460DOI Listing
February 2020

High Microbial Diversity Promotes Soil Ecosystem Functioning.

Appl Environ Microbiol 2018 05 16;84(9). Epub 2018 Apr 16.

UMR 1347 Agroécologie, AgroSup Dijon, INRA, Université de Bourgogne Franche-Comté, Dijon, France.

In soil, the link between microbial diversity and carbon transformations is challenged by the concept of functional redundancy. Here, we hypothesized that functional redundancy may decrease with increasing carbon source recalcitrance and that coupling of diversity with C cycling may change accordingly. We manipulated microbial diversity to examine how diversity decrease affects the decomposition of easily degradable (i.e., allochthonous plant residues) versus recalcitrant (i.e., autochthonous organic matter) C sources. We found that a decrease in microbial diversity (i) affected the decomposition of both autochthonous and allochthonous carbon sources, thereby reducing global CO emission by up to 40%, and (ii) shaped the source of CO emission toward preferential decomposition of most degradable C sources. Our results also revealed that the significance of the diversity effect increases with nutrient availability. Altogether, these findings show that C cycling in soil may be more vulnerable to microbial diversity changes than expected from previous studies, particularly in ecosystems exposed to nutrient inputs. Thus, concern about the preservation of microbial diversity may be highly relevant in the current global-change context assumed to impact soil biodiversity and the pulse inputs of plant residues and rhizodeposits into the soil. With hundreds of thousands of taxa per gram of soil, microbial diversity dominates soil biodiversity. While numerous studies have established that microbial communities respond rapidly to environmental changes, the relationship between microbial diversity and soil functioning remains controversial. Using a well-controlled laboratory approach, we provide empirical evidence that microbial diversity may be of high significance for organic matter decomposition, a major process on which rely many of the ecosystem services provided by the soil ecosystem. These new findings should be taken into account in future studies aimed at understanding and predicting the functional consequences of changes in microbial diversity on soil ecosystem services and carbon storage in soil.
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http://dx.doi.org/10.1128/AEM.02738-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5930326PMC
May 2018

Ozone flux in plant ecosystems: new opportunities for long-term monitoring networks to deliver ozone-risk assessments.

Environ Sci Pollut Res Int 2018 Mar 2;25(9):8240-8248. Epub 2017 Oct 2.

Institut National de la Recherche Agronomique (INRA), URP3F, 86600, Lusignan, France.

Ozone (O) is a photochemically formed reactive gas responsible for a decreasing carbon assimilation in plant ecosystems. Present in the atmosphere in trace concentrations (less than 100 ppbv), this molecule is capable of inhibiting carbon assimilation in agricultural and forest ecosystems. Ozone-risk assessments are typically based on manipulative experiments. Present regulations regarding critical ozone levels are mostly based on an estimated accumulated exposure over a given threshold concentration. There is however a scientific consensus over flux estimates being more accurate, because they include plant physiology analyses and different environmental parameters that control the uptake-that is, not just the exposure-of O. While O is a lot more difficult to measure than other non-reactive greenhouse gases, UV-based and chemiluminescence sensors enable precise and fast measurements and are therefore highly desirable for eddy covariance studies. Using micrometeorological techniques in association with latent heat flux measurements in the field allows for the partition of ozone fluxes into the stomatal and non-stomatal sinks along the soil-plant continuum. Long-term eddy covariance measurements represent a key opportunity in estimating carbon assimilation at high-temporal resolutions, in an effort to study the effect of climate change on photosynthetic mechanisms. Our aim in this work is to describe potential of O flux measurement at the canopy level for ozone-risk assessment in established long-term monitoring networks.
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http://dx.doi.org/10.1007/s11356-017-0352-0DOI Listing
March 2018

Modelling nitrous oxide emissions from mown-grass and grain-cropping systems: Testing and sensitivity analysis of DailyDayCent using high frequency measurements.

Sci Total Environ 2016 Dec 18;572:955-977. Epub 2016 Aug 18.

Institute of Biological and Environmental Sciences, University of Aberdeen, 23 St Machar Drive, Aberdeen AB24 3UU, UK. Electronic address:

The DailyDayCent biogeochemical model was used to simulate nitrous oxide (NO) emissions from two contrasting agro-ecosystems viz. a mown-grassland and a grain-cropping system in France. Model performance was tested using high frequency measurements over three years; additionally a local sensitivity analysis was performed. Annual NO emissions of 1.97 and 1.24kgNhayear were simulated from mown-grassland and grain-cropland, respectively. Measured and simulated water filled pore space (r=0.86, ME=-2.5%) and soil temperature (r=0.96, ME=-0.63°C) at 10cm soil depth matched well in mown-grassland. The model predicted cumulative hay and crop production effectively. The model simulated soil mineral nitrogen (N) concentrations, particularly ammonium (NH), reasonably, but the model significantly underestimated soil nitrate (NO) concentration under both systems. In general, the model effectively simulated the dynamics and the magnitude of daily NO flux over the whole experimental period in grain-cropland (r=0.16, ME=-0.81gNhaday), with reasonable agreement between measured and modelled NO fluxes for the mown-grassland (r=0.63, ME=-0.65gNhaday). Our results indicate that DailyDayCent has potential for use as a tool for predicting overall NO emissions in the study region. However, in-depth analysis shows some systematic discrepancies between measured and simulated NO fluxes on a daily basis. The current exercise suggests that the DailyDayCent may need improvement, particularly the sub-module responsible for N transformations, for better simulating soil mineral N, especially soil NO concentration, and NO flux on a daily basis. The sensitivity analysis shows that many factors such as climate change, N-fertilizer use, input uncertainty and parameter value could influence the simulation of NO emissions. Sensitivity estimation also helped to identify critical parameters, which need careful estimation or site-specific calibration for successful modelling of NO emissions in the study region.
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http://dx.doi.org/10.1016/j.scitotenv.2016.07.226DOI Listing
December 2016

Land Use History Shifts In Situ Fungal and Bacterial Successions following Wheat Straw Input into the Soil.

PLoS One 2015 23;10(6):e0130672. Epub 2015 Jun 23.

INRA, UMR 1347 Agroecology, Dijon, France; INRA, Plateforme GenoSol, UMR1347 Agroecology, Dijon, France.

Soil microbial communities undergo rapid shifts following modifications in environmental conditions. Although microbial diversity changes may alter soil functioning, the in situ temporal dynamics of microbial diversity is poorly documented. Here, we investigated the response of fungal and bacterial diversity to wheat straw input in a 12-months field experiment and explored whether this response depended on the soil management history (grassland vs. cropland). Seasonal climatic fluctuations had no effect on the diversity of soil communities. Contrastingly fungi and bacteria responded strongly to wheat regardless of the soil history. After straw incorporation, diversity decreased due to the temporary dominance of a subset of copiotrophic populations. While fungi responded as quickly as bacteria, the resilience of fungal diversity lasted much longer, indicating that the relative involvement of each community might change as decomposition progressed. Soil history did not affect the response patterns, but determined the identity of some of the populations stimulated. Most strikingly, the bacteria Burkholderia, Lysobacter and fungi Rhizopus, Fusarium were selectively stimulated. Given the ecological importance of these microbial groups as decomposers and/or plant pathogens, such regulation of the composition of microbial successions by soil history may have important consequences in terms of soil carbon turnover and crop health.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130672PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4478037PMC
April 2016

Grassland-Cropping Rotations: An Avenue for Agricultural Diversification to Reconcile High Production with Environmental Quality.

Environ Manage 2015 Nov 13;56(5):1065-77. Epub 2015 Jun 13.

INRA UR4, P3F, 86600, Lusignan, France.

A need to increase agricultural production across the world to ensure continued food security appears to be at odds with the urgency to reduce the negative environmental impacts of intensive agriculture. Around the world, intensification has been associated with massive simplification and uniformity at all levels of organization, i.e., field, farm, landscape, and region. Therefore, we postulate that negative environmental impacts of modern agriculture are due more to production simplification than to inherent characteristics of agricultural productivity. Thus by enhancing diversity within agricultural systems, it should be possible to reconcile high quantity and quality of food production with environmental quality. Intensification of livestock and cropping systems separately within different specialized regions inevitably leads to unacceptable environmental impacts because of the overly uniform land use system in intensive cereal areas and excessive N-P loads in intensive animal areas. The capacity of grassland ecosystems to couple C and N cycles through microbial-soil-plant interactions as a way for mitigating the environmental impacts of intensive arable cropping system was analyzed in different management options: grazing, cutting, and ley duration, in order to minimize trade-offs between production and the environment. We suggest that integrated crop-livestock systems are an appropriate strategy to enhance diversity. Sod-based rotations can temporally and spatially capture the benefits of leys for minimizing environmental impacts, while still maintaining periods and areas of intensive cropping. Long-term experimental results illustrate the potential of such systems to sequester C in soil and to reduce and control N emissions to the atmosphere and hydrosphere.
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http://dx.doi.org/10.1007/s00267-015-0561-6DOI Listing
November 2015

Meta-barcoded evaluation of the ISO standard 11063 DNA extraction procedure to characterize soil bacterial and fungal community diversity and composition.

Microb Biotechnol 2015 Jan 4;8(1):131-42. Epub 2014 Sep 4.

INRA, UMR1347 Agroécologie, Plateforme GenoSol, Dijon, France.

This study was designed to assess the influence of three soil DNA extraction procedures, namely the International Organization for Standardization (ISO-11063, GnS-GII and modified ISO procedure (ISOm), on the taxonomic diversity and composition of soil bacterial and fungal communities. The efficacy of each soil DNA extraction method was assessed on five soils, differing in their physico-chemical characteristics and land use. A meta-barcoded pyrosequencing approach targeting 16S and 18S rRNA genes was applied to characterize soil microbial communities. We first observed that the GnS-GII introduced some heterogeneity in bacterial composition between replicates. Then, although no major difference was observed between extraction procedures for soil bacterial diversity, we saw that the number of fungal genera could be underestimated by the ISO-11063. In particular, this procedure underestimated the detection in several soils of the genera Cryptococcus, Pseudallescheria, Hypocrea and Plectosphaerella, which are of ecological interest. Based on these results, we recommend using the ISOm method for studies focusing on both the bacterial and fungal communities. Indeed, the ISOm procedure provides a better evaluation of bacterial and fungal communities and is limited to the modification of the mechanical lysis step of the existing ISO-11063 standard.
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http://dx.doi.org/10.1111/1751-7915.12162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4321379PMC
January 2015

Stability of soil microbial structure and activity depends on microbial diversity.

Environ Microbiol Rep 2014 Apr 2;6(2):173-83. Epub 2013 Dec 2.

UMR 1347 Agroecology, INRA, Dijon, France.

Despite the central role of microbes in soil processes, empirical evidence concerning the effect of their diversity on soil stability remains controversial. Here, we addressed the ecological insurance hypothesis by examining the stability of microbial communities along a gradient of soil microbial diversity in response to mercury pollution and heat stress. Diversity was manipulated by dilution extinction approach. Structural and functional stabilities of microbial communities were assessed from patterns of genetic structure and soil respiration after the stress. Dilution led to the establishment of a consistent diversity gradient, as revealed by 454 sequencing of ribosomal genes. Diversity stability was enhanced in species-rich communities whatever the stress whereas functional stability was improved with increasing diversity after heat stress, but not after mercury pollution. This discrepancy implies that the relevance of ecological insurance for soil microbial communities might depend on the type of stress. Our results also suggest that the significance of microbial diversity for soil functional stability might increase with available soil resources. This could have strong repercussions in the current 'global changes' context because it suggests that the combined increased frequencies of extreme climatic events, nutrient loading and biotic exploitation may amplify the functional consequences of diversity decrease.
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http://dx.doi.org/10.1111/1758-2229.12126DOI Listing
April 2014

Current status, uncertainty and future needs in soil organic carbon monitoring.

Sci Total Environ 2014 Jan 13;468-469:376-83. Epub 2013 Sep 13.

Forest Research Center (BFW), Seckendorff Gudent Weg 8, A-1131 Vienna, Austria. Electronic address:

Increasing human demands on soil-derived ecosystem services requires reliable data on global soil resources for sustainable development. The soil organic carbon (SOC) pool is a key indicator of soil quality as it affects essential biological, chemical and physical soil functions such as nutrient cycling, pesticide and water retention, and soil structure maintenance. However, information on the SOC pool, and its temporal and spatial dynamics is unbalanced. Even in well-studied regions with a pronounced interest in environmental issues information on soil carbon (C) is inconsistent. Several activities for the compilation of global soil C data are under way. However, different approaches for soil sampling and chemical analyses make even regional comparisons highly uncertain. Often, the procedures used so far have not allowed the reliable estimation of the total SOC pool, partly because the available knowledge is focused on not clearly defined upper soil horizons and the contribution of subsoil to SOC stocks has been less considered. Even more difficult is quantifying SOC pool changes over time. SOC consists of variable amounts of labile and recalcitrant molecules of plant, and microbial and animal origin that are often operationally defined. A comprehensively active soil expert community needs to agree on protocols of soil surveying and lab procedures towards reliable SOC pool estimates. Already established long-term ecological research sites, where SOC changes are quantified and the underlying mechanisms are investigated, are potentially the backbones for regional, national, and international SOC monitoring programs.
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http://dx.doi.org/10.1016/j.scitotenv.2013.08.026DOI Listing
January 2014

Evaluation of the ISO standard 11063 DNA extraction procedure for assessing soil microbial abundance and community structure.

PLoS One 2012 11;7(9):e44279. Epub 2012 Sep 11.

INRA, UMR1347 Agroécologie, Dijon, France.

Soil DNA extraction has become a critical step in describing microbial biodiversity. Historically, ascertaining overarching microbial ecological theories has been hindered as independent studies have used numerous custom and commercial DNA extraction procedures. For that reason, a standardized soil DNA extraction method (ISO-11063) was previously published. However, although this ISO method is suited for molecular tools such as quantitative PCR and community fingerprinting techniques, it has only been optimized for examining soil bacteria. Therefore, the aim of this study was to assess an appropriate soil DNA extraction procedure for examining bacterial, archaeal and fungal diversity in soils of contrasting land-use and physico-chemical properties. Three different procedures were tested: the ISO-11063 standard; a custom procedure (GnS-GII); and a modified ISO procedure (ISOm) which includes a different mechanical lysis step (a FastPrep ®-24 lysis step instead of the recommended bead-beating). The efficacy of each method was first assessed by estimating microbial biomass through total DNA quantification. Then, the abundances and community structure of bacteria, archaea and fungi were determined using real-time PCR and terminal restriction fragment length polymorphism approaches. Results showed that DNA yield was improved with the GnS-GII and ISOm procedures, and fungal community patterns were found to be strongly dependent on the extraction method. The main methodological factor responsible for differences between extraction procedure efficiencies was found to be the soil homogenization step. For integrative studies which aim to examine bacteria, archaea and fungi simultaneously, the ISOm procedure results in higher DNA recovery and better represents microbial communities.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0044279PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439486PMC
March 2013

Origin of nitrogen in reforested lignite-rich mine soils revealed by stable isotope analysis.

Environ Sci Technol 2008 Apr;42(8):2787-92

Department of Soil Protection and Recultivation, Brandenburg University of Technology, P.O. Box 101344, D-03013 Cottbus, Germany,

Restoration of the nitrogen cycle is an important step in the recovery of an ecosystem after mining. Carbon and nitrogen in rehabilitated lignite containing mine soils can be derived from plant material as well as from lignite inherent to the parent substrate. We assessed the use elemental and stable carbon and nitrogen isotope measurements to trace the orgin of soil nitrogen and applied these techniques to elucidate the origin of mineral N in the soil and the soil solution. The conceptual approach of this study included physical fractionation in addition to sampling of vegetation and soil from a lignite-containing mine site rehabilitated in 1985 with Pinus Nigra. We studied the elemental and isotopic composition of bulk samples as well as isolated fractions and soil solution. Our data indicate that the stable carbon and nitrogen isotopic composition of the soil samples are the result of mixing between plant material and substrate inherent lignite. delta15N isotopes may be used as indicators of nitrogen contribution from plants to solid samples as well as soil solution. N-isotope composition of ammonia shows low spatial and interannual variability, despite strong concentration changes. Plant-derived nitrogen contributes in higher amounts to the soil solution compared to the bulk mineral soil.
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http://dx.doi.org/10.1021/es702377kDOI Listing
April 2008
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