Do tree species influence community structure and richness of Ammonia Oxidizing Bacteria at three temperate forest sites?
Malchair, Sandrine ; Carnol, Monique
Poster (2014, July 15)
Introduction: The relationship between biodiversity and ecosystem function remains a controversial subject with numerous open questions. In Europe, the conversion of coniferous monocultures into ... [more ▼]
Introduction: The relationship between biodiversity and ecosystem function remains a controversial subject with numerous open questions. In Europe, the conversion of coniferous monocultures into broadleaved or mixed stand is considered to face ecological and economical risks posed by coniferous monocultures. Belowground effects of such a change in the dominant tree species is however largely unknown, although bacteria regulate many soil processes and some groups, like ammonia oxidizing bacteria (AOB) are highly sensitive to environmental stress. Objectives: The aims of this study were to investigate (i) AOB community structure and richness under several tree species, (ii) microbial/environmental factors related to AOB diversity, (iii) the relationship between AOB diversity and the nitrification process. Materials and methods: Forest floor (Of, Oh) was sampled under European beech, sessile oak, Norway spruce and Douglas fir at three sites. AOB community structure and richness was assessed by PCR-DGGE and sequencing. Samples were analysed for net N mineralization, potential nitrification, basal respiration, microbial biomass, microbial or metabolic quotient, pH, total nitrogen, extractable ammonium, organic matter content and exchangeable cations. Results: AOB community structure and tree species effects on AOB diversity were site-specific. Factors regulating ammonium availability, i.e. net N mineralization or microbial biomass, were related to AOB community structure. AOB richness was not related to nitrification. Conclusions: Our research revealed that, at larger spatial scales, site specific characteristics may be more important that tree species in determining AOB richness and community structure. Within sites, tree species influence AOB diversity. The absence of a relation between AOB richness and nitrification points to a possibly role of AOB abundance, phenotypic plasticity or the implication of ammonia oxidizing archaea in this process. [less ▲]Detailed reference viewed: 37 (2 ULg)
Fifty years of crop residue management have a limited impact on soil heterotrophic respiration.
Buysse, Pauline ; ; Carnol, Monique et al
in Agricultural and Forest Meteorology (2013), 180
The impacts of crop residue management on soil microbial biomass, labile carbon and heterotrophic respiration (HR) were assessed at a long-term experimental site in the Hesbaye region in Belgium. Three ... [more ▼]
The impacts of crop residue management on soil microbial biomass, labile carbon and heterotrophic respiration (HR) were assessed at a long-term experimental site in the Hesbaye region in Belgium. Three treatments, residue export (RE), farmyard manure addition (FYM) and residue restitution after harvest (RR), have been applied continuously since 1959. The soil is a Eutric Cambisol with, in 2010, significantly different total soil organic carbon contents of 4.4, 5.1 and 5.9 kg C m-2 under the RE, RR and FYM treatments, respectively. Manual field HR measurements were carried out during the 2010 and 2012 crop seasons using a dynamic closed chamber system. Microbial biomass, labile C content and metabolic diversity of soil bacteria were assessed in spring 2012. Fifty-one years after the beginning of the treatments, residue management had a limited impact on HR. Based on daily averaged values, the treatment had a significant impact (α = 10%) in 2012 but not in 2010. Based on the individual measurement dates, the treatment impact was less obvious in 2012; with the observation of a significant impact (α = 10%) on HR in only 7% and 36.8% of the measurement dates in 2010 and 2012, respectively. Labile C and microbial biomass were significantly lower in the RE treatment than in FYM and RR. Residue management had no significant effect on cold-water extracted carbon and metabolic diversity of heterotrophic soil bacteria. The limited impact of residue management on HR could be explained by (i) the relatively low amounts of recent above-ground crop inputs, (ii) the large proportion of below-ground residues and other non-exportable above-ground residues reducing the potential differences between treatments and (iii) the relatively large spatial variability of HR. In conclusion, carbon losses due to heterotrophic respiration did not differ between RE, FYM and RR treatments in the studied soil. This contrasts with the different soil organic carbon contents observed in these three treatments after fifty years of experiment. Further investigations regarding the reduction of spatial variability and the potential roles played by organic matter protection within aggregates and biochemical composition of inputs are needed. [less ▲]Detailed reference viewed: 25 (2 ULg)
AOB community structure and richness under European beech, sessile oak, Norway spruce and Douglas-fir at three temperate forest sites
Malchair, Sandrine ; Carnol, Monique
in Plant and Soil (2013), 366(1-2),
Abstract Background and aims The relations between tree species, microbial diversity and activity can alter ecosystem functioning. We investigated ammonia oxidizing bacteria (AOB) community structure and ... [more ▼]
Abstract Background and aims The relations between tree species, microbial diversity and activity can alter ecosystem functioning. We investigated ammonia oxidizing bacteria (AOB) community structure and richness, microbial/environmental factors related to AOB diversity and the relationship between AOB diversity and the nitrification process under several tree species. Methods Forest floor (Of, Oh) was sampled under European beech, sessile oak, Norway spruce and Douglas-fir at three sites. AOB community structure was assessed by PCR-DGGE and sequencing. Samples were analyzed for net N mineralization, potential nitrification, basal respiration, microbial biomass, microbial or metabolic quotient, pH, total nitrogen, extractable ammonium, organic matter content and exchangeable cations. Results AOB community structure and tree species effect on AOB diversity were site-specific. AOB richness was not related to nitrification. Factors regulating ammonium availability, i.e. net N mineralization or microbial biomass, were related to AOB community structure. Conclusion Our research shows that, at larger spatial scales, site specific characteristics may be more important than the nature of tree species in determining AOB diversity (richness and community structure). Within sites, tree species influence AOB diversity. The absence of a relation between AOB richness and nitrification points to a possibly role of AOB abundance, phenotypic plasticity or the implication of ammonia oxidizing archaea. [less ▲]Detailed reference viewed: 44 (18 ULg)
Short-term temperature impact on soil heterotrophic respiration in limed agricultural soil samples
Buysse, Pauline ; Goffin, Stéphanie ; Carnol, Monique et al
in Biogeochemistry (2013), 112(1-3), 441-455
This study sought to investigate the hourly and daily timescale responses of soil CO2 fluxes to temperature in a limed agricultural soil. Observations from different incubation experiments were compared ... [more ▼]
This study sought to investigate the hourly and daily timescale responses of soil CO2 fluxes to temperature in a limed agricultural soil. Observations from different incubation experiments were compared with the results of a model combining biotic (heterotrophic respiration) and abiotic (carbonate weathering) components. Several samples were pre-incubated for 8-9 days at three temperatures (5, 15 and 25°C) and then submitted to short-term temperature cycles (where the temperature was increased from 5 to 35°C in 10°C stages, with each stage being 3 h long). During the temperature cycles (hourly timescale), the soil CO2 fluxes increased significantly with temperature under all pre-incubation temperature treatments. A hysteresis effect and negative fluxes during cooling phases were also systematically observed. At a given hourly timescale temperature, there was a negative relationship of the CO2 fluxes with the pre-incubation temperature. Using the combined model allowed the experimental results to be clearly described, including the negative fluxes and the hysteresis effect, showing the potentially large contribution of abiotic fluxes to total fluxes in limed soils, after short-term temperature changes. The fairly good agreement between the measured and simulated flux results also suggested that the biotic flux temperature sensitivity was probably unaffected by timescale (hourly or daily) or pre-incubation temperature. The negative relationship of the CO2 fluxes with the pre-incubation temperature probably derived from very labile soil carbon depletion, as shown in the simulations. This was not, however, confirmed by soil carbon measurements, which leaves open the possibility of adaptation within the microbial community. [less ▲]Detailed reference viewed: 82 (18 ULg)
Microorganisms in Karsts: a case study in St Anne cave, Belgium
Carnol, Monique ; Willems, Luc ; Malchair, Sandrine
Poster (2011, September 30)
Despite the importance of microorganisms as geochemical agents over geological times, their extended metabolic diversity and their essential role in element cycles (i.e. mineral dissolution, precipitation ... [more ▼]
Despite the importance of microorganisms as geochemical agents over geological times, their extended metabolic diversity and their essential role in element cycles (i.e. mineral dissolution, precipitation, oxido-reduction processes), microbial community composition and processes as well as their ecological role in karst environments are poorly known. While little was published on cave-dwelling microorganisms until the early 1990s, it is now recognized that microorganisms may mediate many important mineral transformations, originally considered to be inorganic in nature. Indeed, recent evidence (Northup & Lavoie, 2001) proved the implication of microorganisms in karstification through precipitation and dissolution processes, resulting in the deposition of carbonate speleothems, silicates, iron or manganese oxides, sulphur compounds and nitrates and in the breakdown of limestone walls. In this poster, we review some potential processes and signs of microbial activity in caves. We present results of a study on the microbial diversity in the ‘St Anne’ cave, Belgium. We focused on ammonia-oxidizing bacteria (AOB), which are responsible for the first, acidifying step of the nitrification process. Chemical composition of the water, numbers of cultivable bacteria (free and particle-associated bacteria) and the diversity of AOB were studied in waters and sediments of the ‘Chawresse’ (underground river in St Anne), on the cave wall and in the soil aboveground. The use of molecular techniques, based on direct ADN extractions, provide more detailed information on the microbial diversity of an environment, as culture-based techniques retrieve only about 1% of bacterial species present in the environment. Bacterial counts showed that most cultivable bacteria were associated with suspended particles and that their numbers decreased underground. Molecular analyses revealed the presence of AOB in the karst system. Comparison of aboveground and belowground diversity also indicated the possibility of a specific endokarst AOB community. Further research perspectives will be discussed. <br /> <br /> <br />Northup, D.E. and Lavoie, K.H. 2001. Geomicrobiology of caves: A review. Geomicrobiology Journal, 18(3):199-220. [less ▲]Detailed reference viewed: 121 (18 ULg)
Microbiological and chemical characterisation of St Anne cave, Belgium
Carnol, Monique ; Malchair, Sandrine
Poster (2011, September)
In Belgium, most drinking water is provided by calcareous karst aquifers. Chemical and microbiological characterisation of these systems focalises mainly on the transfer of pollutants and microbial ... [more ▼]
In Belgium, most drinking water is provided by calcareous karst aquifers. Chemical and microbiological characterisation of these systems focalises mainly on the transfer of pollutants and microbial contaminants, major sources of sanitary risks. These studies are generally based on bacterial cultures, representing however only 1% of bacterial species present in the environment. Molecular techniques allow the study of the global microbial diversity of an environment, as they are based on direct ADN extractions, without previous culturing steps. The objective of this research was the study of the microbial diversity in the ‘St Anne’ cave, Belgium. Chemical composition of the water, cultivable bacteria and the diversity of ammonia-oxydizing bacteria (AOB) were studied in waters and sediments of the ‘Chawresse’ (underground river in St Anne), on the cave’s wall and in soils aboveground. Bacterial counts revealed that most cultivable bacteria were associated with suspended particles and that their numbers decreased underground. Molecular analyses revealed the presence of AOB in the karst system. AOB are responsible for the first, acidifying step of the nitrification process. Further studies will specify and quantify their activity in this karst system. [less ▲]Detailed reference viewed: 130 (18 ULg)
Effects of long term soil organic matter restitution mode on soil heterotrophic respiration and soil biological properties.
Buysse, Pauline ; Carnol, Monique ; Malchair, Sandrine et al
Poster (2011, July)
Soil heterotrophic respiration (SHR) is the process by which CO2 is released during organic matter decomposition. It is generally expected that SHR can act as a positive feedback to global warming ... [more ▼]
Soil heterotrophic respiration (SHR) is the process by which CO2 is released during organic matter decomposition. It is generally expected that SHR can act as a positive feedback to global warming, therefore leading to more CO2 release into the atmosphere. It is thus important to better understand this process. Particularly, agricultural soils may behave as important CO2 sources that are strongly influenced by soil and crop management (e.g. organic matter restitution modes, hereafter “OM-RM”). The present study aimed at determining if, after more than 50 years of application of different OM-RM, (1) significant differences of SHR fluxes can be observed between treatments, (2) SHR responses to temperature and soil moisture content can be affected by the OM-RM and (3) the experimental design is suitable to assess potential differences between treatments. The experimental field is situated in Liroux, near Gembloux in Belgium. At that site, a long term experiment with different OM-RM runs from 1959 onwards. For the present study, three contrasted treatments were considered: (1) exportation of all residues after harvest, (2) addition of manure once every three to four years and (3) restitution of residues after harvest. SHR flux measurements were carried out manually on fourteen occasions from 2 April to 30 July 2010, using a dynamic closed chamber system. Temperature and soil moisture content at 5 cm depth were also measured manually. Results showed that after more than 50 years of OM-RM application, no significant differences could be observed between the three treatments in terms of SHR fluxes and SHR responses to temperature or soil moisture, while the soil organic carbon content did vary significantly between them. The sensitivity to temperature was quite low in all treatments, with a mean Q10 value of 1,36. Besides, SHR fluxes were seen to be more responsive to increases in soil water content than to absolute soil moisture content values. Indeed, when soil moisture content increased between two consecutive measurement dates, the ratio of the corresponding SHR fluxes was larger than 1. Particularly dry conditions in 2010 may actually have caused the fluxes to be very low, making the assessment of differences between treatments more difficult. Moreover, soil dryness is likely to be responsible for the SHR flux increases after rain events, as caused by re-solubilization of organic compounds. Also, an important spatial variability was observed, which may have obscured the assessment of potential differences between treatments. Further investigations will consist in performing a new flux measurement campaign in 2011 that will take the spatial variability issue into account, and in monitoring microbial and soil properties in the different treatments, such as microbial biomass, metabolic activity and labile carbon. [less ▲]Detailed reference viewed: 76 (10 ULg)
Do we need to standardize extraction procedures for community level physiological profiling?
Carnol, Monique ; Bosman, Bernard ; Malchair, Sandrine
Poster (2011, July)
Microorganisms are essential regulators of soil functioning, as they are involved in many crucial processes such as organic matter decomposition, nutrient cycling, soil structure and fertility. Currently ... [more ▼]
Microorganisms are essential regulators of soil functioning, as they are involved in many crucial processes such as organic matter decomposition, nutrient cycling, soil structure and fertility. Currently, there is a growing interest in functional diversity, such as the number and type of substrates used for energy metabolism (CLPP-community level physiological profiling). Such metabolic diversity of heterotroph soil bacteria is frequently investigated through Biolog Ecoplates, containing 31 of the most useful carbon sources for the soil community. The metabolic diversity of soil bacteria might be an interesting biological indicator of soil quality, and also a useful tool for investigating the link between land use change, climate warming, soil carbon, microbial diversity and activity. Methods related to Biolog-CLPP reported in the literature differ in the suspension medium and extraction method, the type and density of inoculums, the inoculation procedures and conditions of incubations. For example, various combinations of extraction methods and suspension media are being used for the first bacterial extraction step. Despite such methodological differences, Biolog-CLPP data are often compared across studies. The development of a standardised method for Biolog-CLPP is however essential improving the relevance and significance of results across studies. In this work, we investigated the influence of extraction procedures on microbial extraction efficiency for further use in CLPP. The microbial extraction efficiency was tested by plate counts for a total of twelve combinations of three suspension media and four extraction methods. The experiment was performed on four soils differing in organic matter content. The aims of this study were to: • Synthesize extraction procedures used for Biolog-CLPP • Measure the effect of extraction procedures on microbial extraction efficiency (plate counts) in four soil types • Investigate a possible interaction between the suspension media and the extraction method used • Evaluate whether a standardized extraction procedure can be recommended across soil types [less ▲]Detailed reference viewed: 70 (7 ULg)
How do climate warming, plant species richness and plant functional group affect ammonia oxidizing bacteria diversity and function in experimental grasslands?
Malchair, Sandrine ; Carnol, Monique
Poster (2011, June 27)
How do climate warming, plant species richness and plant functional group affect ammonia oxidizing bacteria diversity and function in experimental grasslands? Malchair S. and Carnol M. Laboratory of Plant ... [more ▼]
How do climate warming, plant species richness and plant functional group affect ammonia oxidizing bacteria diversity and function in experimental grasslands? Malchair S. and Carnol M. Laboratory of Plant and Microbial Ecology Department of Sciences and Environmental Management University of Liege, Belgium Background: There is increasing evidence of diversity-function relationship and impact of warming for aboveground vegetation. Belowground effects of warming and plant species richness remain however largely unknown, although bacteria regulate many soil processes and some groups, like ammonia oxidizing bacteria (AOB) were, have been suggested highly sensitive to environmental stress. Objectives: 1. Investigation of the response of AOB richness, community composition and function to warming, plant species richness and functional group 2. Exploration of the AOB richness-function link Methods: Soil samples were taken at 2 depths from grassland model ecosystems with different species richness levels (1, 3, 9) and temperature treatments (ambient, ambient+3°C). Selected species belonged to 3 plant functional groups: forbs, legumes and grasses. AOB function: potential nitrification assay (shaken soil slurry method) AOB diversity: polymerase chain reaction followed by denaturing gradient gel electrophoresis (PCR-DGGE) Results: 1. All retrieved AOB sequences were Nitrosospira-like ones 2. Warming had no effect on AOB richness and function 3. Higher plant species richness leads to increased AOB richness and modified community structure. AOB function was increased only at lower depth under warming 4. No difference in AOB richness between the plant functional groups 5. AOB community structure was different and AOB function higher under legumes. 6. The AOB richness-function link was negative under legumes. Conclusions: 1. Plant species influenced AOB richness and community composition. Plant functional group seems to be more important that species richness. 2. Legumes may impact AOB diversity and function through ammonia availability. [less ▲]Detailed reference viewed: 43 (2 ULg)
Effects of long term soil organic matter restitution mode on soil heterotrophic respiration and soil biological properties.
Buysse, Pauline ; Carnol, Monique ; Malchair, Sandrine et al
Conference (2011, May 12)
For more than 50 years, an agricultural site divided in several plots is submitted to different organic matter restitution mode to the soil (crop residues, manure,...). The objectives of this study were ... [more ▼]
For more than 50 years, an agricultural site divided in several plots is submitted to different organic matter restitution mode to the soil (crop residues, manure,...). The objectives of this study were to determine (1) whether these different treatments may cause differences between treatments in terms of soil heterotrophic respiration, that would be of the same order of magnitude than differences in total soil organic carbon, (2) how temperature and soil moisture content affect soil heterotrophic respiration in the different treatments, and (3) how different soil biological properties (microbial biomass, metabolic diversity, labile carbon content) are affected in the different treatments. The results from a first measurement campaign carried out in 2010 are presented, together with the remaining questions at this stage of the study. [less ▲]Detailed reference viewed: 78 (6 ULg)
Appréciation des indicateurs biologiques comme outils d'évaluation de la qualité des sols-rapport final de la convention ULg-SPW
Malchair, Sandrine ; ; et al
Résumé/Abstract Le Laboratoire d’Ecologie Végétale et Microbienne de l’Université de Liège a réalisé une recherche d’intérêt général ayant pour objet l’appréciation d’indicateurs biologiques permettant ... [more ▼]
Résumé/Abstract Le Laboratoire d’Ecologie Végétale et Microbienne de l’Université de Liège a réalisé une recherche d’intérêt général ayant pour objet l’appréciation d’indicateurs biologiques permettant d’évaluer la qualité des sols. Cette étude a été financée par le Service Public de Wallonie (SPW). Les données et les résultats de la présente convention sont la co-propriété du Service Public de Wallonie et du Laboratoire d’Ecologie Végétale et Microbienne (Prof. M. Carnol) de l’Université de Liège. Objet de la recherche : Les objectifs de ce projet sont l'appréciation d'indicateurs biologiques permettant d'évaluer la qualité des sols en réalisant : - Une recherche et synthèse bibliographique des études récentes sur la qualité biologique des sols, des techniques de mesure disponibles et de leurs conditions d'applications. Une attention particulière sera portée sur les indicateurs adaptés aux types de sols wallons, aux pratiques courantes de gestion des sols et aux problèmes environnementaux auxquels la Wallonie est le plus souvent confrontée (pollution par les métaux lourds, les HAP, les hydrocarbures). Cette synthèse permettra d'améliorer nos connaissances sur la pertinence de certaines mesures biologiques comme outil d'évaluation de la qualité des sols. - Un état des lieux des outils d'évaluation de la qualité biologique des sols dans les pays/régions voisins et de leur utilisation dans le cadre de politiques de gestion et/ou de protection des sols. Cet état des lieux a pour but d’explorer et d’analyser le cadre politique ainsi que les objectifs stratégiques poursuivis dans chacun des pays, les caractéristiques générales des différents réseaux existants, les indicateurs mis en œuvre ou suggérés, ainsi que les bases scientifiques justifiant le choix de ces indicateurs. - Une analyse de l'aptitude des outils identifiés aux points 1 et 2 à prédire la capacité des sols à remplir leurs fonctions écologiques, en ciblant trois domaines d'action de ces outils : sols forestiers, sols agricoles et sols potentiellement pollués. - Une évaluation des outils identifiés aux points 1 et 2 selon les critères suivants : sensibilité, reproductibilité, possibilité d'utilisation en routine, facilité d'interprétation, coût. - Des propositions pour la suite des travaux de recherche (liens avec la politique des sols, perspectives de recherche). Méthodes mises en œuvre : Pour la synthèse bibliographique, deux bases de données pertinentes dans le domaine des sciences du vivant et du sol (ISIWeb of Knowlege et ScienceDirect) ont été consultées. Les publications pertinentes dans le cadre de l’étude de la qualité des sols au moyen d’indicateurs biologiques ont été consultées afin de répertorier les indicateurs les plus étudiés et de synthétiser les données concernant la sensibilité de ces indicateurs vis-à-vis des pratiques de gestion agricole et forestière, de l’occupation des sols et de diverses pollutions. D’autres données relatives aux méthodologies employées, à la reproductibilité et l’interprétabilité des mesures on été acquises lors de cette recherche bibliographique. Concernant l’ état des lieux à propos des outils d'évaluation de la qualité biologique des sols existant dans les pays/régions voisin(e)s de la Belgique/Wallonie- réalisé par le bureau d’études RamSes-, le travail s’est effectué par exploration de la documentation technique spécialisée et par enquête. La pré-sélection des indicateurs pertinents pour l’application en Wallonie s’est effectuée sur base d’une approche numérique procédant par itération en considérant à la fois la pertinence et l’applicabilité des indicateurs (critères scientifiques), leur utilisation dans des réseaux existants, ainsi que des critères purement méthodologiques. Résultats : Sur base des définitions de la qualité des sols et des indicateurs biologiques, on peut considérer un indicateur biologique de la qualité d’un sol comme étant un organisme ou un processus biologique qui est l’indice précoce de modifications de l’environnement et dont les valeurs fournissent une information sur la capacité d’un sol à fonctionner comme un système vivant, au sein d’écosystèmes naturels ou gérés, dans le but de maintenir la productivité biologique, de maintenir ou d’augmenter la qualité de l’eau et de l’air et de promouvoir la santé des animaux, des végétaux et humaines. Après un inventaire de la diversité biologique des sols, nous nous sommes intéressés aux caractéristiques et occupations des sols en Wallonie pour aboutir à une sélection de combinaisons type de sol/type d’occupation pertinents dans le cadre d’un réseau de surveillance de la qualité biologique des sols. De plus, en fonction des types d’usage rencontrés en Wallonie, nous avons considéré les services écosystémiques majeurs remplis par le sol afin de pouvoir juger de la pertinence des indicateurs c'est-à-dire de leur capacité à intervenir dans les différents services rendus par le sol au travers de processus ou d’éléments biotiques avec comme bénéfices attendus la production de nourriture ou de fibre ainsi que le maintien d’un environnement sain. L’état des lieux des outils d’évaluation de la qualité biologique des sols dans les pays/régions voisins souligne que plusieurs pays en Europe –parmi lesquels les Pays-Bas, la Suisse, la France, le Royaume-Uni, l’Allemagne, l’Italie, l’Autriche, la Hongrie, la Tchéquie – ont mis en œuvre une démarche globalement similaire pour développer un système d’indicateurs et mettre en place un réseau de surveillance de la qualité biologique et/ou sur la biodiversité des sols de portée nationale. Ces démarches procèdent par étapes successives, à savoir : définition des objectifs du réseau de surveillance, propositions d’indicateurs (relevés bibliographiques), étape de pré-sélection de ces indicateurs, test de ces indicateurs et acquisitions de données de base (valeur de référence). Les réseaux mis en place poursuivent des objectifs stratégiques de surveillance et/ou de prévention mais aussi des objectifs scientifiques d’acquisition de données concernant la composante biologique des sols et ses fonctions spécifiques. Actuellement, seuls les Pays-Bas ont un réseau de surveillance de la qualité biologique des sols déjà en place et fonctionnel au niveau national. Les réseaux dans les autres pays sont soit au stade de test, soit fonctionnels à l’échelle régionale. En intégrant les données acquises au cours de cette recherche bibliographique et au cours de l’état des lieux des outils d’évaluation de la qualité biologique des sols dans les pays/régions voisins, les indicateurs biologiques de la qualité du sol sont majoritairement des paramètres microbiens. Les paramètres faunistiques sont moins fréquemment usités. Il ressort, également, de cet inventaire et de notre recherche bibliographique que les méthodes à développer et à mettre en place en Wallonie doivent se fonder sur une délimitation aussi claire que possible des objectifs poursuivis par les législateurs. En considérant, à l’issue de la recherche bibliographique, les critères de pertinence, d’applicabilité et de méthodologie, combinés à l’utilisation de l’indicateur dans des réseaux existants et à la consultation d’ouvrages de référence, nous avons pu mettre en avant six paramètres microbiens pertinents dans le cadre de la qualité des sols wallons, en tenant compte de l’usage agricole, forestier et urbain. Il s’agit de la biomasse microbienne, de paramètres relatifs à l’activité des micro-organismes du sol à savoir la respiration basale et la minéralisation nette de l’azote, et des indices écophysiologiques. Nous privilégions plutôt l’étude de la diversité fonctionnelle que celle de la diversité structurelle, car le lien entre la structure de la communauté microbienne et la fonction est encore mal établi. Ces différents paramètres sont d’ailleurs couramment employés/ recommandés comme indicateur biologique de la qualité des sols dans différents programmes de suivi des sols existant. Afin de prendre en considération la recommandation de l’union européenne suggérant d’intégrer des paramètres faunistiques dont l’étude de régulateurs biologiques (nématodes ou collemboles) et d’ingénieurs de l’écosystème (vers de terre) au programme de suivi des sols, nous proposons d’étudier le nombre et la biomasse des vers de terre comme paramètre faunistique, en raison de la simplicité d’étude de ce paramètre en comparaison de la complexité d’étude de la faune du sol au niveau taxonomique. L’application et le développement de politiques dans le cadre du décret relatif à la gestion des sols requièreront la mise en place d’indicateurs (notamment biologique) concernant la qualité des sols. Actuellement, aucune étude belge /wallone ne concerne l’étude de la qualité des sols de notre pays/région. D’autres pays européens (Pays-Bas, Allemagne, Italie, Tchéquie, la Hongrie, l’Autriche, ….) ont quant à eux débuté la mise en place du suivi de la qualité des sols faisant intervenir les indicateurs biologiques. Sur le plan opérationnel des perspectives tracées par le Plan d’Environnement pour le Développement Durable de 1994, qui prévoit « d'améliorer la connaissance et le suivi de la qualité des sols », il ressort de la revue d’état des lieux que la mise en œuvre fonctionnelle d’un réseau de mesures biologique cohérent est un processus lent, qui peut s’étaler sur 10 à 15 années. Cependant, les expériences – notamment en Grande-Bretagne - montrent également que les programmes de monitoring peuvent aussi s’initier de façon relativement simple, avec un nombre limité d’indicateurs et de points de mesure, et se complexifier par la suite en intégrant les résultats des efforts de recherche et pour la standardisation des méthodes. Sur base des éléments fournis conjointement à l’issue du travail d’analyse des indicateurs de la littérature et de l’état des lieux dans les pays et régions voisins, il est possible désormais de définir les principes d’un réseau minimum de démarrage et de définir les bases et méthodes de travail à développer par la suite pour consolider et étendre ce premier réseau. The Laboratory of Plant and Microbial Ecology of the University of Liege conducted a research of public interest focusing on the assessment of biological indicators for the evaluation of soil quality. This study was funded by the ’Service Public de Wallonie (SPW)’. Data and results are co-owned by the Service Public de Wallonie and the Laboratory of Plant and Microbial Ecology (Prof. M. Carnol), University of Liege. Research objectives : The objectives of this project were the assessment of biological indicators to estimate soil quality through : - A review and synthesis of recent scientific literature on biological soil quality, available methods and conditions of applicability. Particular attention will be paid on indicators relevant to the type of Walloon soils, to common soil management practices and environmental problems encountered in Wallonia (pollution by heavy metals, PAHs, hydrocarbons). This review will improve our knowledge on the relevance of some biological measures as tools for assessing soil quality. - An inventory of tools used for assessing the biological soil quality in neighbouring countries/regions and their use in management policies and / or soil protection. This inventory aims at exploring and analyzing the political and strategic objectives pursued in each country, the general characteristics of the different existing monitoring networks, the indicators used or suggested, as well as the scientific justification of these indicators. - An analysis of the appropriateness of the tools identified in the two first objectives to predict the capacity of soils to perform their ecological functions, targeting agricultural, forest and potentially polluted soils. - An assessment of the sensitivity, reproducibility, possibility of routine use, ease of understanding and cost of the selected tools. - Suggestions for future research (link to soil policy, research opportunities). Methods : For the literature review, we used two relevant databases for life and soil science (ISIWeb of Knowledge and ScienceDirect). Publications related to the assessment of soil quality through biological indicators were consulted in order to synthesize most frequently used indicators and their sensitivity to farm or forestry management, land use or pollution. Data on methodology, reproducibility and interpretability have also been synthesized. The inventory of tools used for assessing the biological quality soil in neighbouring countries/regions (realised by Ram-Ses), was performed through he exploration of technical and specialized publications and by inquiry. Pertinent indicators for the Walloon region were pre-selected through an iterative numerical approach taking into consideration the relevance and applicability of the indicators, their use in existing monitoring networks, and some methodological criteria. Results : Based on the definitions of soil quality and biological indicators, we can consider biological indicators of soil quality as organisms or biological processes reflecting a modification of the environment and whose values give information about the capacity of soil to function, within natural or managed ecosystem boundaries, to sustain plant and animal productivity, maintain or enhance water and air quality, and support human health and habitation. After an inventory of soil biodiversity, we focused on soil characteristics and land use types to define the most relevant combinations of soil type/land use in the Walloon region. Furthermore, we considered the major soil ecosystem services provided by the most frequent land use types in Wallonia for evaluating the capacity of potential indicators to reflect these services through biota and biotic process (with benefits such as the production of food or fiber as well as maintaining a healthy environment). The inventory of tools used for assessing the biological soil quality in neighbouring countries/regions underlines that several European countries- including the Netherlands, Switzerland, France, the United Kingdom, Germany, Italy, Austria, Hungary, Czech Republic - have followed a broadly similar approach for developing indicators and establishing a monitoring network of the biological soil quality and / or soil biodiversity within a national scope. These approaches proceed by successive stages: definition of the objectives of the monitoring network, suggestion of indicators (literature revue), pre-selection of indicators, test of indicators and data acquisition (reference values). The established networks pursue strategic monitoring and / or prevention objectives, as well as scientific objectives such as data acquisition on the biological component of soils and its specific functions. Currently, only the Netherlands has a functional monitoring network at national level. Networks in other countries are either at the stage of test, or functional at the regional scale. The integration of the literature review and the inventory in neighboring countries/region, revealed that biological indicators of soil quality are mostly microbial parameters. Faunal parameters are less frequently used. Results also highlighted that the framework for developing a soil monitoring network in the Wallonia requires a clear definition of the objectives pursued by the legislator. Taking into account the literature review, the criteria of relevance, applicability and methodology, combined with the use of the indicator in existing networks and the consultation of reference books, we highlight six microbial parameters relevant in the context of soil quality in Wallonia, taking into account three major land use types (agriculture, forestry and urban). They are the microbial biomass, parameters related to the activity of soil microorganisms, namely basal respiration and net nitrogen mineralization, and ecophysiological indices. We recommend the study of functional diversity rather than structural diversity, because the link between microbial community structure and function is not yet well established. These parameters are also commonly used or recommended as biological indicators of soil quality in different soil monitoring networks. In line with the recommendations of the European Union, suggesting the integration of faunal parameters such as biological regulators (nematodes or collembola) and ecosystem engineers (earthworms) in soil monitoring programs, we suggest the number and biomass of earthworms , because of its simplicity in comparison to the study of soil fauna in taxonomic level. The application and policy development under the decree on soil management requires the establishment of indicators (including biological indicators) on soil quality. Currently, no Belgian / Walloon study exist on soil quality in our country / region. Other European countries (The Netherlands, Germany, Italy, Czech Republic, Hungary, Austria, ....) have begun setting up the monitoring of soil quality involving biological indicators. In relation to operational plans outlined by the ‘Plan d’Environnement pour le Développement Durable’ (Environmental Plan for Sustainable Development) in 1995, which intends “to improve the knowledge and the monitoring of soil quality”, it is clear from the inventory in neighboring countries that the establishment of a functional monitoring network is a slow process, spreading out over 10 to 15 years. However, experience- particularly in Great Britain- also reveals that a monitoring network can be initiated realtively easily, with a limited number of indicators and sampling points, and subsequently become more complex by integrating research results and from method standardization. Based on the evidence provided by the outcome of literature review and the inventory of tools used in neighboring countries, it is now possible to define the basic principles of a first monitoring network and define the basis and working methodology to consolidate and extent this first network. [less ▲]Detailed reference viewed: 214 (44 ULg)
Short-term temperature impacts on soil CO2 fluxes: An incubation experiment with agricultural soil samples.
Buysse, Pauline ; Goffin, Stéphanie ; Carnol, Monique et al
in Geophysical Research Abstracts (2010, May 06), 12Detailed reference viewed: 35 (21 ULg)
Biodiversity and activity of soil organisms as indicators of soil quality.
Malchair, Sandrine ; Carnol, Monique ; et al
Scientific conference (2010)Detailed reference viewed: 11 (1 ULg)
Do climate warming and plant species richness affect potential nitrification, basal respiration and ammonia-oxidizing bacteria in experimental grasslands?
Malchair, Sandrine ; ; et al
in Soil Biology & Biochemistry (2010), 42
Ammonia-oxidizing bacteria (AOB) are key organisms in the N cycle, as they control the first, rate-limiting step of the nitrification process. The question whether current environmental disturbances, such ... [more ▼]
Ammonia-oxidizing bacteria (AOB) are key organisms in the N cycle, as they control the first, rate-limiting step of the nitrification process. The question whether current environmental disturbances, such as climate warming and plant diversity losses, select for a particular community structure of AOB and/or influence their activity remains open. The purpose of this research was to study the impact of a 3 °C warming and of plant species richness (S) on microbial activity and diversity in synthesized grasslands, with emphasis on the nitrification process and on the diversity (community structure and richness) of ammonia-oxidizing bacteria (AOB).We measured soil chemical characteristics, basal respiration, potential nitrification and AOB diversity in soils under increasing plant species richness (S ¼ 1, S ¼ 3, S ¼ 9) at ambient and (ambient +3 °C) temperature. Species were drawn from a 9-species pool, belonging to three functional groups: forbs, legumes and grasses. Mixtures comprised species from each of the three functional groups. Warming did not affect AOB diversity and increased potential nitrification at S ¼ 3 only. Under warmed conditions, higher plant species richness resulted in increased potential nitrification rates. AOB richness increased with plant species richness. AOB community structure of monocultures under legumes differed from those under forbs and grasses. Clustering analysis revealed that AOB community structure under legume monocultures and mixtures of three and nine species grouped together. These results indicate that functional group identity rather than plant species richness influenced AOB community structure, especially through the presence of legumes. No clear relationship emerged between AOB richness and potential nitrification whatever plant species richness and temperature treatment. Our findings show a link between aboveground and belowground diversity, namely plant species richness, AOB richness and community structure. AOB richness was not related to soil processes, supporting the idea that increased diversity does not necessarily lead to increased rates of ecosystem processes. [less ▲]Detailed reference viewed: 32 (6 ULg)
Diversity-function relationship of ammonia-oxidizing bacteria in soils among functional groups of grassland species under climate warming
Malchair, Sandrine ; ; et al
in Applied Soil Ecology (2010), 44
Although warming and plant diversity losses have important effects on aboveground ecosystem functioning, their belowground effects remain largely unknown. We studied the impact of a 3 °C warming and of ... [more ▼]
Although warming and plant diversity losses have important effects on aboveground ecosystem functioning, their belowground effects remain largely unknown. We studied the impact of a 3 °C warming and of three plant functional groups (forbs, grasses, legumes) on ammonia-oxidizing bacteria (AOB) diversity (polymerase chain reaction-denaturing gradient gel electrophoresis, PCR-DGGE) and their function (potential nitrification) in artificial grasslands. Warming did not influence AOB diversity and function. Sequencing of 16S rRNA gene fragments retrieved from DGGE gel revealed that they were all related to Nitrosospira-like sequences. Clustering analysis of DGGE profiles resulted in two nodes, separating AOB community structure under legumes from all other samples. Decreased AOB richness (number of DGGE bands) and concurrent increased potential nitrification were also observed under legumes. We hypothesized that ammonium availability was the driving force regulating the link between aboveground and belowground communities, as well as the AOB diversity and function link. The results document that the physiology of AOB might be an important regulator of AOB community structure and function under plant functional groups. This study highlights the major role of the microbial community composition in soil process responses to changes in the functional composition of plant communities. [less ▲]Detailed reference viewed: 102 (13 ULg)
Microbial diversity and activity in temperate forest and grassland ecosystems
Doctoral thesis (2009)
Ecosystems currently face widespread biodiversity losses and other environmental disturbances, such as climate warming, related to increased anthropogenic activities. Within this context, scientists ... [more ▼]
Ecosystems currently face widespread biodiversity losses and other environmental disturbances, such as climate warming, related to increased anthropogenic activities. Within this context, scientists consider the effects of such changes on the biodiversity, and hence on the activity, of soil microorganisms. Indeed, soil microorganisms mediate a wide range of soil processes. Currently, knowledge on soil microbial diversity is still limited, partially due to technical limitations. The advent of molecular-based analyses now allows studying the soil microbial diversity. These advances in the study of soil microbial communities have lead to a growing evidence of the critical role played by the microbial community in ecosystem functioning. This relationship is supposed to be relevant for narrow processes, regulated by a restricted group of microorganisms, such as the nitrification process. This PhD thesis aimed at studying ammonia oxidizing bacteria (AOB) community structure and richness as an integrated part of soil functioning. This research aimed at investigating the effect of aboveground plant diversity on ammonia oxidizing bacteria diversity and function in forest and grassland soils with focus on the influence of (a) functional group identity of grassland plants (legumes, grasses, forbs), (b) grassland plant species richness and (c) tree species, on AOB diversity and function. Another objective of this research was to study the effect of a 3°C increase in air temperature on AOB diversity and function. The link between AOB diversity and function (potential nitrification) is also investigated. For grassland ecosystems, a microcosm experiment was realized. An experimental platform containing 288 assembled grassland communities was established in Wilrijk (Belgium). Grassland species were grown in 12 sunlit, climate controlled chambers. Each chamber contained 24 communities of variable species richness (S) (9 S=1, 9 S=3 and 6 S=9).The grassland species belonged to three functional groups: three species of each grasses (Dactylis glomerata L., Festuca arundinacea SCHREB., Lolium perenne L.), forbs (non-N-fixing dicots; Bellis perennis L., Rumex acetosa L., Plantagolanceolata L.), and legumes (N-fixing dicots; Trifolium repens L., Medicago sativa L., Lotus corniculatus L.). Half of these chambers were exposed to ambient temperature and the other half were exposed to (ambient +3°C) temperature. One ambient and one (ambient+3°C) chambers were destructively harvested 4, 16 and 28 months after the start of the experiment. The influence of plant functional group identity on the nitrification process and on AOB community structure and richness (AOB diversity) was assessed in soils collected from the first two destructive amplings (chapter 2). The effect of plant species richness on AOB diversity and function was considered for soils sampled after 16 and 28 months (chapter 3). AOB function was determined by potential nitrification. AOB community structure and richness were assessed by polymerase chain reaction followed by denaturing gradient gel electrophoresis (DGGE) and sequencing of excised DGGE bands. I found that functional group identity can affect AOB community structure. In particular, the presence of legumes, both in monoculture or in mixture with forbs and grasses, lead to AOB community composition changes towards AOB clusters tolerating higher ammonium concentrations. This change in AOB community structure was only linked to increased potential nitrification under monocultures of legumes, when ammonium was supposed to be not limiting. This study revealed that physiological attributes of AOB and resource availability may be important factors in controlling the nitrification process. This research showed that the impact of plant species richness on the nitrification process could be mediated by the interactions between plants and AOB, through competition for substrate. A 3°C increase in air temperature did not affect AOB community structure, richness or function. In forest ecosystems, we studied the effect of tree species in forest sites located in Belgian and in the Grand-Duchy of Luxembourg covered each by several deciduous or coniferous tree species (Fagus sylvatica L., Quercus petraea (Mattuschka) Lieblein, Picea abies (L.) Karst, Pseudotsuga menziesii (Mirbel) Franco). We investigated the influence of these tree species on microbial processes (chapter 5) related to C and N cycling, particularly with emphasize on the nitrification process and on the diversity of AOB (chapter 6). The results showed that the effect of tree species on net N mineralization was likely to be mediated through their effect on soil microbial biomass, reflecting their influence on organic matter content and carbon availability. Influence of tree species on nitrification (potential and relative) might be related to the presence of ground vegetation through its influence on soil ammonium and labile C availability. AOB community structure was more site-specific than tree specific. However, within sites, AOB community structure under broadleaved trees differed from the one under coniferous trees. The effect on tree species on AOB was likely to be driven by the influence of tree species on net N mineralization, which regulates the substrate availability for AOB. The results also demonstrated that the relationship between AOB diversity and function might be related both to AOB abundance and AOB community structure and richness. This thesis showed no clear relationship between AOB community structure or richness and AOB function. However, we revealed that aboveground grassland plant richness, grassland plant functional groups and tree species influence AOB community structure and richness. [less ▲]Detailed reference viewed: 74 (4 ULg)
Appréciation des indicateurs biologiques comme outils d’évaluation de la qualité des sols-Premier Rapport intermédiaire
Malchair, Sandrine ; Carnol, Monique
Report (2009)Detailed reference viewed: 10 (0 ULg)
Sensitivity of soil heterotrophic respiration to temperature: short-term impacts.
Buysse, Pauline ; Goffin, Stéphanie ; Carnol, Monique et al
Poster (2009, September)
Soil respiration is mostly affected by temperature variations but there is still much debate regarding its temperature sensitivity. Especially the difference between short- and long-term responses driven ... [more ▼]
Soil respiration is mostly affected by temperature variations but there is still much debate regarding its temperature sensitivity. Especially the difference between short- and long-term responses driven by changes in microbial activity and population respectively is addressed here. To this end, an incubation experiment is set up with soil samples taken from the surface layer (0-25cm) of a bare area at the Carboeurope agricultural site of Lonzée in Belgium. After homogenization, they are placed into incubators at three different temperatures, namely 5, 15 and 25°C for 2 weeks. Temperature is regulated by Peltier systems that warm up or cool down a bath containing jars with soil samples. All jars are continuously aerated to prevent CO2 from accumulating inside. Moisture levels in the jars are regularly checked and adjusted to ensure that the soil moisture is optimal for soil respiration. Twice a week, short term temperature response is tested by changing incubation temperatures in the range 5 - 35°C. During these cycles, CO2 fluxes are measured at each temperature step with a closed dynamic chamber system. Microbial biomass and hot water-extractable carbon are determined two times during a temperature cycle, allowing a follow up of the evolution of these two variables through a cycle. A comparison between the respiration rates, microbial biomasses and extractable carbon will be presented and would allow a better understanding of the dynamics of the heterotrophic respiration response to temperature in agricultural soils. In the future, other experiments could be derived from this one to focus on substrate availability or soil moisture impacts on soil respiration. [less ▲]Detailed reference viewed: 70 (4 ULg)
Rapport final de l'AFR. Impact des essences sur la qualité du sol dans les écosystèmes forestiers: nitrification, diversité microbienne et propriétés chimiques
Report (2009)Detailed reference viewed: 18 (7 ULg)
Short-term temperature impacts on soil respiration.
Buysse, Pauline ; Goffin, Stéphanie ; Carnol, Monique et al
Poster (2009, June)
Despite considerable recent work on soil heterotrophic respiration, a mechanistic understanding of this process is still missing. Temperature is one of the most important driving factors. It can influence ... [more ▼]
Despite considerable recent work on soil heterotrophic respiration, a mechanistic understanding of this process is still missing. Temperature is one of the most important driving factors. It can influence the mechanism through multiple ways, whose importance may vary with time. An incubation experiment is set up to study short-term temperature influences on soil microbial respiration and its evolution through time. Soil samples are taken in spring from the surface layer (0-25cm) of a bare agricultural loamy soil situated in Lonzée in Belgium (Hesbaye region) and are homogenized before being placed into incubators at three different temperatures, namely 5, 15 and 25°C. Temperature is regulated by Peltier systems that warm up or cool down a sand bath containing jars with soil samples. Once a week, incubation temperatures are increased and decreased by 5°C-steps, starting from each incubator temperature, to achieve a one-day temperature cycle between 5 and 35°C. CO2 flux measurements are performed at each temperature step by a closed dynamic chamber system, after the temperature has stabilized in the samples. Microbial biomass (C and N) is determined four times during the temperature cycle by the fumigation-extraction technique and soil labile carbon is measured at the beginning of each cycle by the hot-water extraction method. Moisture levels in soil samples are regularly checked and adjusted to keep optimal soil moisture content. Between CO2 flux measurements, jars are left open to ensure that anaerobic conditions do not occur. Further investigations could include an assessment of the importance of substrate availability and depletion on microbial activity, and a model development related to the results provided by this experiment. [less ▲]Detailed reference viewed: 72 (7 ULg)