Abad Chabbi

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

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.

Evaluation of the ISO Standard 11063 DNA Extraction Procedure for Assessing Soil Microbial Abundance and Community Structure

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.

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

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.

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

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.

The impact of grassland management on biogeochemical cycles involving carbon, nitrogen and phosphorus

Grassland introduction into intensively managed agricultural landscapes may enhance soil organic matter (SOM) content and ecosystem services. However, the magnitude of this effect depends on grassland management practices, and their influence on the soil system. The aim of this paper is to highlight these impacts and their consequences for SOM dynamics and element cycling. We focused in particular on the effect of different grassland management practices in terms of grazing regime, fertilization, and species choice. While carbon, nitrogen and phosphorus cycles are more strongly coupled under grassland as compared to permanent cropping, uncoupling of elemental cycles may occur through management intensification. Grazing regime, fertilization and species choice affect elemental coupling and SOM turnover via organic matter input and rhizosphere activity to different extent, thereby resulting in contrasting SOM storage. Grazing may be more beneficial for SOM contents compared to mowing up to a certain animal density depending on soil type and pedoclimatic context. SOM storage may be increased in some cases through specific fertilizer additions, whereas in others no change was observed. Species choice, e.g. high diversity or introduction of legumes, influence element budgets and soil nutrient availability through plant physiological constraints as well as intra-or interspecific interactions. The effect of different plant species mixtures on soil parameters has rarely been elucidated. We conclude that the impact of grassland management practices on SOM of different soil types and the resulting ecosystem services, such as C and nutrient storage need further research in contrasting pedoclimatic contexts. More studies on the controls of belowground biogeochemical cycling of elements are necessary in order to fully understand and manage belowground processes via aboveground plant communities.

Net carbon storage measured in a mowed and grazed temperate sown grassland shows potential for carbon sequestration under grazed system

Background: Managed temperate grassland has the potential to sequester carbon if management practices are improved. In this study, CO2 flux was measured by the eddy covariance technique in two identical temperate sown grasslands under different managements, viz. mowing and grazing, to estimate and compare net carbon storage under both the management systems. Results: In both mowing and grazing systems, the averaged annual gross plant productivity, ecosystem respiration and net ecosystem exchange were –1720 and –1741, 1244 and 1510, and –476 and –231 g C m–2 year–1, respectively. Although the management practices did not significantly influence gross plant productivity (p > 0.05), grazing system increased Reco significantly by 21% (p < 0.05) but reduced net ecosystem exchange by 52% (p < 0.05) compared to mowing system. However, averaged annual net carbon storage were 23 and 141 g C m–2 year–1 under mowing and grazing, respectively. Conclusion: The results indicate that temperate sown grassland has the potential to sequester carbon under grazing.

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

Abstract 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.

Modelling heat, water and carbon fluxes in mown grassland under multi-objective and multi-criteria constraints

A Monte Carlo-based calibration and uncertainty assessment was performed for heat, water and carbon (C) fluxes, simulated by a soil-plant-atmosphere system model (CoupModel), in mown grassland. Impact of different multi-objective and multi-criteria constraints was investigated on model performance and parameter behaviour. Good agreements between hourly modelled and measurement data were obtained for latent and sensible heat fluxes (R2?=?0.61, ME?=?0.48?MJ?m-2?day-1), soil water contents (R2?=?0.68, ME?=?0.34%) and carbon-dioxide flux (R2?=?0.60, ME?=?-0.18?g?C?m-2?day-1). Multi-objective and multi-criteria constraints were efficient in parameter conditioning, reducing simulation uncertainty and identifying critical parameters. Enforcing multi-constraints separately on heat, water and C processes resulted in the highest model improvement for that specific process, including some improvement too for other processes. Imposing multi-constraints on all groups of variables, associated with heat, water and C fluxes together, resulted in general effective parameters conditioning and model improvement. Uncertainty-based modelling was done for heat, water and carbon flux in grassland.Multi-objective and multi-criteria were enforced to constrain model simulations.Multi-objective and multi-criteria constraints were effective in model calibration.Different multi-constraints conditioned model parameters differently.Different multi-constraints improved the model performance in different way.

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

The DailyDayCent biogeochemical model was used to simulate nitrous oxide (N2O) 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 N2O emissions of 1.97 and 1.24kgNha-1year-1 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 (NH4+), reasonably, but the model significantly underestimated soil nitrate (NO3-) concentration under both systems. In general, the model effectively simulated the dynamics and the magnitude of daily N2O flux over the whole experimental period in grain-cropland (r=0.16, ME=-0.81gNha-1day-1), with reasonable agreement between measured and modelled N2O fluxes for the mown-grassland (r=0.63, ME=-0.65gNha-1day-1). Our results indicate that DailyDayCent has potential for use as a tool for predicting overall N2O emissions in the study region. However, in-depth analysis shows some systematic discrepancies between measured and simulated N2O 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 NO3- concentration, and N2O 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 N2O emissions. Sensitivity estimation also helped to identify critical parameters, which need careful estimation or site-specific calibration for successful modelling of N2O emissions in the study region.

Does grassland introduction into cropping cycles affect carbon dynamics through changes of allocation of soil organic matter within aggregate fractions

Implementation of ley grassland into crop rotation could have positive influence in soil ecosystem services such as C storage. The periodical changes of land-use plus the in situ labelling given by the introduction of maize crops under ley grassland induce differences in soil organic matter (SOM) that could be traced either by stable isotopes or by the characterization of plant biomarkers such as lignin derived phenols. Evaluation of SOM dynamics is often limited by the complexity of soil matrix. To override these limitations, a hierarchical approach to decompose the soil mosaic into aggregates has been proposed in this study. Soil and plant samples were collected from a long-term experimental area in Lusignan (western France). Soils from four different treatments (bare fallow, permanent maize, permanent grassland, and ley grassland based on 6years of grassland followed by 3years of maize) were sampled, fractionated into water stable aggregates, and finally analysed for carbon, nitrogen, and lignin contents, as well as for 13C isotopic signature. Soils under ley and permanent grassland stored higher amount of SOM in larger aggregates and preserved more efficiently the lignin stocks than the corresponding samples under permanent maize. Contemporary, finer fraction of ley grassland showed higher mean residence time of organic carbon, probably due to a legacy effect of the previous years under grassland. Even if maize derived SOM was identified, the grassland footprint was still dominating the ley grassland soils, as described by the principal component analysis. Strong correlation between these results and the quality and stoichiometry of the vegetal litter returned to soil were found, evidencing the needs for a comprehensive evaluation at a molecular level of all the parameters modified by land-use changes, including tillage, to understand the potential for carbon storage of different agroecosystems.