First steps on asynchronous lattice-gas models with an application to a swarming rule

International audienceLattice-gas cellular automata are often considered as a particular case of cellular automata in which additional constraints apply, such as conservation of particles or spatial exclusion. But what about their updating? How to deal with non-perfect synchrony? Novel definitions of asynchronism are proposed that respect the specific hypotheses of lattice-gas models. These definitions are then applied to a swarming rule in order to explore the robustness of the global emergent behaviour. In particular, we compare the synchronous and asynchronous case, and remark that anti-alignment of particles is no longer observed when a small critical amount of asynchronism is added

A guided tour of asynchronous cellular automata

Research on asynchronous cellular automata has received a great amount of attention these last years and has turned to a thriving field. We survey the recent research that has been carried out on this topic and present a wide state of the art where computing and modelling issues are both represented.Comment: To appear in the Journal of Cellular Automat

Asynchronous cellular automata

This text has been proposed for the Encyclopedia of Complexity and Systems Science edited by Springer Nature and should appear in 2018.International audienceThis text is intended as an introduction to the topic of asynchronous cellular automata. We start from the simple example of the Game of Life and examine what happens to this model when it is made asynchronous (Sec. 1). We then formulate our definitions and objectives to give a mathematical description of our topic (Sec. 2). Our journey starts with the examination of the shift rule with fully asynchronous updating and from this simple example, we will progressively explore more and more rules and gain insights on the behaviour of the simplest rules (Sec. 3). As we will meet some obstacles in having a full analytical description of the asynchronous behaviour of these rules, we will turn our attention to the descriptions offered by statistical physics, and more specifically to the phase transition phenomena that occur in a wide range of rules (Sec. 4). To finish this journey, we will discuss the various problems linked to the question of asynchrony (Sec. 5) and present some openings for the readers who wish to go further (Sec. 6)

Water-extractable organic matter linked to soil physico-chemistry and microbiology at the regional scale.

10 pagesInternational audienceA better understanding of the links between dissolved organic matter and biogeochemical processes in soil could help in evaluating global soil dynamics. To assess the effects of land cover and parental material on soil biogeochemistry, we studied 120 soil samples collected from various ecosystems in Burgundy, France. The potential solubility and aromaticity of dissolved organic matter was characterised by pressurised hot-water extraction of organic carbon (PH-WEOC). Soil physico-chemical characteristics (pH, texture, soil carbon and nitrogen) were measured, as was the δ13C signature both in soils and in PH-WEOC. We also determined bacterial and fungal abundance and the genetic structure of bacterial communities. Our results show that the potential solubility of soil organic carbon is correlated to carbon and clay content in the soil. The aromaticity of PH-WEOC and its δ13C signature reflect differences in the decomposition pathways of soil organic matter and in the production of water-extractable organic compounds, in relation to land cover. The genetic structure of bacterial communities is related to soil texture and pH, and to PH-WEOC, revealing that water-extractable organic matter is closely related to the dynamics of bacterial communities. This comprehensive study, at the regional scale, thus provides better definition of the relationships between water-extractable organic matter and soil biogeochemical properties

Land-use and other biogeochemical constraints modulate priming effect at the landscape scale: a fingerprinting approach using analytical pyrolysis

International audienceSoil has the potential to sequester or to emit great amounts of CO2, since soil carbon stocks constitute the largest terrestrial reservoir of carbon. Land-use is among the main factors affecting the net storage or the net mineralization of soil organic carbon (SOC) and land-use policies are currently aiming to increase soil organic carbon stocks.However, adding labile sources of carbon to soil (e.g. more crop residues or manure) may alter the carbon cycle, increasing the microbial degradation of the existing SOC pools, a process called “priming effect” (PE). PE could significantly reduce the net storage of carbon and taking into account this effect into carbon storage models may alter their predictions.Land-use is one of the numerous constraints that influence PE, together with soil chemical, biological and physical properties, all of them are contributing to shape the chemical composition of the SOC pools. The objectives of this study are:- to conduct a fingerprint characterization of the chemical composition of soil organic matter using analytical pyrolysis coupled to gas chromatography and mass spectrometry;- to use pyrograms to decipher which soil chemical markers are the most relevant descriptors of the PE;- to relate those chemical markers to the different types of crop rotations.This approach will help to decipher the complex interactions of the PE descriptors and to relate PE intensity to specific land-uses for a determined area, identifying which land management is capable to reduce soil susceptibility to priming effect and to be more efficient in term of net SOC storage.With this purpose, soil samples from 88 agricultural farms within a 12 km2 water catchment in Brittany (France) were incubated in presence of a 13C labelled wheat litter to measure the PE. Data regarding soil chemistry, soil microbial diversity, crop rotation, land-use, and manuring obtained for the studied farms were coupled to pyrograms to select the most relevant descriptors of the priming effect.Our results showed that:- the inclusion of grassland into crop rotation reduce the susceptibility of soils to PE, but only if grassland is maintained for an adequate period of the rotation time;- although PE is a microbial process, only a marginal part of its total variance is assigned to both richness and evenness of microbial communities;- the intensity of PE is correlated with the concentration of condensed aromatic compounds in soil water extracts, identified with excitation-emission fluorescence spectroscopy;- the intensity of the PE decreases with the molecular complexity of the soil organic matter assessed with pyrolysis coupled to gas chromatography and mass spectrometry.Disclosure of Interest: None declare

Land-use and other biogeochemical constraints modulate priming effect at the landscape scale: a fingerprinting approach using analytical pyrolysis

International audienceSoil has the potential to sequester or to emit great amounts of CO2, since soil carbon stocks constitute the largest terrestrial reservoir of carbon. Land-use is among the main factors affecting the net storage or the net mineralization of soil organic carbon (SOC) and land-use policies are currently aiming to increase soil organic carbon stocks.However, adding labile sources of carbon to soil (e.g. more crop residues or manure) may alter the carbon cycle, increasing the microbial degradation of the existing SOC pools, a process called “priming effect” (PE). PE could significantly reduce the net storage of carbon and taking into account this effect into carbon storage models may alter their predictions.Land-use is one of the numerous constraints that influence PE, together with soil chemical, biological and physical properties, all of them are contributing to shape the chemical composition of the SOC pools. The objectives of this study are:- to conduct a fingerprint characterization of the chemical composition of soil organic matter using analytical pyrolysis coupled to gas chromatography and mass spectrometry;- to use pyrograms to decipher which soil chemical markers are the most relevant descriptors of the PE;- to relate those chemical markers to the different types of crop rotations.This approach will help to decipher the complex interactions of the PE descriptors and to relate PE intensity to specific land-uses for a determined area, identifying which land management is capable to reduce soil susceptibility to priming effect and to be more efficient in term of net SOC storage.With this purpose, soil samples from 88 agricultural farms within a 12 km2 water catchment in Brittany (France) were incubated in presence of a 13C labelled wheat litter to measure the PE. Data regarding soil chemistry, soil microbial diversity, crop rotation, land-use, and manuring obtained for the studied farms were coupled to pyrograms to select the most relevant descriptors of the priming effect.Our results showed that:- the inclusion of grassland into crop rotation reduce the susceptibility of soils to PE, but only if grassland is maintained for an adequate period of the rotation time;- although PE is a microbial process, only a marginal part of its total variance is assigned to both richness and evenness of microbial communities;- the intensity of PE is correlated with the concentration of condensed aromatic compounds in soil water extracts, identified with excitation-emission fluorescence spectroscopy;- the intensity of the PE decreases with the molecular complexity of the soil organic matter assessed with pyrolysis coupled to gas chromatography and mass spectrometry.Disclosure of Interest: None declare

Purification of Fungal High Molecular Weight Genomic DNA from Environmental Samples

Sequencing of a high number of fungal genomes has become possible due to the development of next generation sequencing techniques (NGS).The most recent developments aim to sequence single-molecule long-reads in order to improve genome assemblies, but consequently needs higher quality (minimum >20 kbp) DNA as starting material.However, environmental-derived samples from soil, wood, or litter often contain phenolic compounds, pigments, and other molecules that can be inhibitors for reactions during sequencing library construction.In this chapter, we propose an optimized protocol allowing the preparation of high quality and long fragment DNA from different samples (mycelium, fruiting body, soil) compatible with the current sequencing requirements