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Selon les projections démographiques de la FAO, la population mondiale atteindra 9 milliards de personnes d'ici 2050. Cette augmentation sera associée à une demande accrue de produits agricoles et à une augmentation de la production de déchets. Par conséquent, des approches alternatives dans les pratiques agricoles, tels que l'utilisation permanente de la couverture végétale et/ou l'application de boues d'épuration, sont envisagées pour répondre aux exigences mondiales et préserver l'environnement. Ces nouvelles pratiques pourraient influencer le fonctionnement et les propriétés du sol et des organismes microbiens présents dans cet environnement. Par conséquent, passer de l'agriculture intensive à une agriculture écologiquement intensive pourrait entraîner des modifications de la biodiversité des sols. En utilisant différents systèmes expérimentaux permettant une comparaison entre différentes pratiques agricoles, des études de la diversité microbienne taxonomique et fonctionnelle du sol (bactéries et champignons) ont été entreprises. La diversité taxonomique des organismes microbiens a été obtenue par séquençage à haut débit des régions hypervariables des gènes codant l'ARN16S et l'ITS1. Nous avons évalué les rôles écologiques des microorganismes du sol en utilisant des identifications taxonomiques, puis des études permettant d'examiner leur physiologie et leurs fonctions par rapport à différentes propriétés physicochimiques du sol. Nous avons constaté que la fertilisation azotée avait une incidence négative sur la diversité microbienne du sol et modifié leur fonctionnalité. Ces effets peuvent être modulés par l'utilisation de PPC ou l'application de boues. Ces travaux indiquent que les pratiques agricoles conventionnelles ont un impact sur la biodiversité microbienne du sol et peuvent être remplacées par des pratiques agricoles plus respectueuses de l'environnement afin de préserver l'écosystème et ses services / According to demographic projections, world population will reach 9 billion people by 2050. This increase will be associated with higher demand of agricultural products and an increase in wastes production. Therefore, alternative approaches in agricultural practices; such as permanent plant cover usage and/or sewage sludge application, are envisaged to meet global demands and preserve the environment. These new practices could therefore influence the properties of the soil and its functioning. Therefore moving from intensive to ecologically intensive agriculture could lead to modifications in soil biodiversity. Using different experimental systems allowing comparison between different agricultural practices, studies of the taxonomic and functional soil microbial diversity (bacteria and fungi) had been undertaken. This was achieved by next generation high-throughput sequencing of the hypervariable regions of the genes encoding RNA16S and ITS1. Sequencing was performed using an Illumina platform and the sequences obtained were analyzed using various bioinformatic tools. We inferred the ecological roles of soil micro-organisms by using taxonomic identifications, moving on to the examination of their physiology and functions in comparison with different soil physiochemical properties. We found that nitrogen fertilization negatively impacted the soil microbial diversity and altered their functionality. These negative effects have been modulated by the PPC usage or SS application. Proving that conventional agricultural practices effects the soil biodiversity and can be replaced by ecofriendly farming applications in order to preserve the ecosystem and its services

The soil organic carbon (C) pool is estimated to contain at least three times as much organic C as is stored in vegetation. However, the processes controlling below-ground C dynamics are poorly understood, representing a key uncertainty in ecosystem models. Soil respiration rate (Rs) is a large component of the forest carbon cycle, however the factors that control it are still poorly understood, and those affecting autotrophic (Ra) and heterotrophic (Rh) respiration rates differ and vary in space and time. A variety of direct (i.e. soil and ingrowth cores) and indirect (i.e. rhizotron and minirhizotron) methods exist for obtaining estimates of fine root (< 2 mm diameter) production, with the consequence that there is a high variability in root biomass estimates between root studies. In this thesis I aim to contribute towards a better understanding of processes governing below-ground C dynamics. In particular I focus on: 1) the spatial and seasonal variability of Rs and drivers; 2) the uncertainty on fine root C pool measurement methods; 3) comparing novel datasets of Rs, fine root biomass and girth increment, with outputs from the SPA v2 model. To determine the dominant controls and spatial heterogeneity of Rs, I measured Rs and key biotic and abiotic drivers seasonally, in a Quercus robur forest in southern England. Measurements were made quarterly in three plots, each with measurement points arranged according to a spatial sampling design, enabling any spatial autocorrelation to be detected. Rs drivers were categorised into plant (i.e. leaf area index, weighted tree proximity (i.e. mean dbh within 4 m of a point), and fine root biomass), physical (i.e. soil moisture, soil temperature and soil bulk density) and substrate (i.e. litter depth and organic layer depth) factors. I explore: 1) what the dominant controls of Rs are and whether they change during the growing season; 2) whether micro-topography and stand structure are correlated with drivers, and influence the spatial variability of Rs, thereby simplifying up-scaling processes; 3) if physical drivers of Rs are spatially more homogeneous than plant drivers and the availability of substrate. I found no clear seasonal difference in drivers, with Rs consistently responding to litter depth, bulk density and soil moisture. The only significant response of Rs to micro-topography and tree factor was in August and September respectively and physical factors were found to be the most spatially homogeneous. Rs measurements were non-normally distributed, with ‘hotspots’ of particularly high fluxes found that remained stable throughout the measurement campaign. These findings suggest that the seasonal and spatial variability and distribution of Rs and its main drivers should be considered at the sampling design stage, to avoid bias for up-scaling non-linear processes. To address the uncertainties associated with determining fine root biomass change, we compared the measurement error for five methodologies (four indirect and one direct) in a Pinus contorta and Quercus robur forest during 2010. Rhizotron and ingrowth measurements were taken during 2010 and fine root standing crop was measured in 2009. Root length against the rhizotron screens was measured using novel software (ORIDIS), developed as part of a collaboration here in Edinburgh. The software was developed to increase precision and reduce the cost and processing time of rhizotron measurements. Differences in final cumulative root ingrowth for each conversion method ranged between 20.7g-2 - 245.0 g m-2 in the oak forest and 89.7 g m-2 - 273.0 g m-2 in the pine forest. The study found that indirect measurements of root length had less operator error than indirect measurements of root diameter. Direct methods of determining root growth using ingrowth cores also showed a seasonal trend; however artefacts may have been introduced into the method, from the affect of severing roots and changing soil conditions. To test the representation of below-ground processes in an ecosystem model, I validate modelled dynamics using default SPA v2 parameters, against independent CO2 flux and C pool datasets. The flux data were of eddy covariance and automatic chamber measurements, partitioned into root (Rroot), mycorhizal (Rmyc) and microbial heterotrophic (Rh) components. The biometric measurements were of foliage, fine root biomass and woody biomass increment. The key findings of this study were that: 1) SPA outputs compare well to ecosystem scale measurements of NEE and GPP. However, model-data mismatch occurs for fine root and wood C allocation; 2) the timing of fine root C allocation is 53 days too late and the turnover rate of fine roots 17 times too high; 3) the timing of modelled below-ground Rh and Ra could be improved by separating above and below-ground Ra and including individual root, mychorrizae and microbial C pools. The thesis concludes by discussing the implications of each chapter for our understanding and capability to model below-ground C dynamics. I find that the key challenge for measuring individual below-ground C pools and fluxes is ensuring that the measurements are spatially representative and avoid bias. The key challenge for modelling below-ground C dynamics is ensuring processes sufficiently reflect reality, when the sparse data that exist for corroboration, capture multiple processes. I explore the possibilities of further research that could be conducted, as a result of this work.

The application of crop residues is one of the most common agricultural practices used to maintain soil ecosystems and crop productivity. This thesis focuses on the oil palm (Elaeis guineensis) agroecosystem, an important tropical crop that has expanded rapidly over the past four decades. Both land conversion and business-as-usual practices within the plantations have contributed to soil degradation. The application of oil palm residues, such as empty fruit bunches (EFB) and oil palm fronds, are thought to have positive effects on the soil ecosystem; yet there is currently a deficit of knowledge on their effectiveness. This thesis aims to examine the effects of oil palm residue application on soil physicochemical properties, soil biota, and ecosystem functions. It reports the results of extensive field trials, sample collection, and statistical analysis of crop residue applications in oil palm plantations in Central Sumatra, Indonesia. Four key results emerged from the thesis. First, in this study site land conversion from secondary forest to oil palm does not affect litter decomposition rate, but positively influences soil fauna activity. Second, there is greater soil fauna activity following EFB application than oil palm fronds or chemical fertilizers, and the fauna activity is highly associated with changes in soil chemical properties and soil moisture conditions. Third, EFB application enhances soil ecosystem functions, through the direct provision of organic matter, and by influencing soil biota. Finally, over 15 years of application, EFB appears to be effective in maintaining or increasing annual crop yield in comparison to chemical fertiliser treatment. Temporal changes in crop yield under EFB application appear to be associated with climatic conditions and soil organic carbon. Overall, these findings improve our understanding of the potential of oil palm residue applications to increase soil quality, soil biota, and ecosystem functions. They also provide useful information for a wider audience of soil ecologists, agricultural managers, and policy makers to improve sustainable management of the oil palm ecosystem.

No description available.

Områden som antas vara förorenade utreds idag med hjälp av Naturvårdsverkets vägledning för förorenade områden. Vägledningsmaterialet baseras till stor del på miljömålet giftfri miljö och vilka risker ett förorenat område kan utgöra för människor och ekosystem. Soil Security-konceptet är relativt nytt och är främst utvecklat för att bedöma jordbruksmarker och bygger på att jordförvaltningen ska leda till att jordresursen bevaras eller förbättras. I detta projekt har en utvärdering utförts om Soil Security-konceptet skulle kunna användas för att arbetet med förorenade områden ska leda mot hållbarhet. Nio indikatorer som alla indikerar att biomassaproduktion fungerar har tagits fram och sedan använts som underlag för jämförelsen mellan Naturvårdsverkets vägledning och Soil Security-konceptet. Dessa indikatorer har även använts för att utreda vad som utförs i det praktiska arbetet med förorenade områden. En analys av hur markmiljön värderas i det praktiska arbetet och om de åtgärder som utförs leder till fungerande markekosystem har också genomförts. Slutligen har Magdalena Gleisner på Naturvårdsverket intervjuats eftersom projektet har en koppling till den utvärdering de utför av vägledningsmaterialet. Vid jämförelse av utgångspunkterna bakom Soil Security-konceptet och Naturvårdsverkets vägledning hittades både skillnader och likheter. I stora drag är Naturvårdsverkets vägledning främst inriktad på vilka risker en förorenad jord kan utgöra och ser inte jorden som ett skyddsobjekt som behöver skyddas eftersom den kan utföra funktioner som är till nytta för människor och ekosystem. I Soil Security- konceptet är utgångspunkten att skydda markfunktioner för att de senare ska kunna bidra till att lösa globala samhällsutmaningar som exempelvis säker tillgång på livsmedel och vatten. När ramverken jämfördes med avseende på indikatorerna för biomassaproduktion fanns de flesta av indikatorerna med i Naturvårdsverkets vägledning, antingen direkt eller indirekt. Hur indikatorerna sedan analyserades för att bedöma jordens tillstånd var den största skillnaden mellan ramverken. I Soil Security- konceptet används indikatorerna för att avgöra om växtetablering kan ske och även jordens status, medan i Naturvårdsverkets vägledning bedöms istället vilka risker föroreningarna kan utgöra. Tre praktiska fall har också utvärderats och i dessa har Naturvårdsverkets vägledning följts till största delen. Markmiljön har bedömts skyddas av åtgärderna i två av tre fall, dock är det enda kravet på återfyllnadsmaterialet att det inte bidrar till ökade föroreningshalter. För att markfunktioner ska fungera och åtgärderna ska leda mot hållbarhet krävs även att markmaterialet exempelvis har en god jordtextur, ett gynnsamt pH-värde och innehåller näring. För att arbetet med förorenade områden ska leda mot hållbarhet behövs en ny vägledning där Soil Security-konceptet beaktas, nya studier tas fram och delar av den gamla vägledningen används. / In this project, today’s work with contaminated sites was evaluated. In Sweden when assessing sites that probably are contaminated, a guideline made by the Swedish EPA is used. This guideline was compared with the soil security concept both by comparing the foundations, and which indicators that differs between the frameworks. The differences in the foundations were that in the Swedish EPA guideline focus is on the risks contaminated sites could have on humans and ecosystems. The soil security concept on the other hand focuses in functioning soil functions to contribute in global societal challenges. In the comparison evaluating the indicators, nine indicators for the soil function production of biomass were formulated. All of the indicators are mentioned in the soil security concept and even in the Swedish EPA guidelines most of them are mentioned either direct or indirect. The biggest differ between the frameworks is how the indicators are analyzed. In the Swedish EPA guidelines, the risks the indicators could provide are analyzed, while in the soil security concept the indicators are analyzed to know if plants can be established in the area. The practical work with contaminated sites was also evaluated in the project. The same indicators where used to see if differences could be found between the actual work and the Swedish EPA guidelines. Three studies were evaluated and they followed most of guidelines. The soil ecosystem was assessed to be protected in two of the three studies, even though the filling material that could be used only has one requirement that it not contributes to increasing contamination levels. This could lead to non-sustainability due to soil material that is incapable of plant establishment and other important soil functions. If the work with contaminated sites should reach sustainability a new framework needs to be produced which has parts from the Swedish EPA guidelines, the soil security concept and even new research.

Les Streptomyces sont des bactéries communes des écosystèmes forestiers tempérés. Elles sont présentes au sein de différentes niches écologiques telles que la rhizosphère des plantes, la mycorhizosphère ou encore la minéralosphère. Dans ces niches, elles interagissent avec de nombreux autres genres bactériens et différents champignons symbiotiques, pathogènes et saprophytes. Nous avons entrepris une étude sur l'interaction entre deux souches bactériennes modèles du sol Streptomyces ambofaciens ATCC23877 et Pseudomonas fluorescens BBc6R8. Des expériences de cocultures sur différents milieux gélosés ont révélé que chaque souche bactérienne affecte la production de métabolites secondaires chez l'autre partenaire. Ainsi, P. fluorescens inhibe la capacité de S. ambofaciens à produire la kinamycine, un « effet ping-pong » a été mis en évidence. D'autre part, sur un milieu déficient en fer, P. fluorescens est capable d'utiliser les desferrioxamines et la coelicheline produites par S. ambofaciens en tant que xénosiderophores et ne produit alors plus ses propres sidérophores, la pyoverdine et l’énantio-pyochéline. Enfin, au cours des études d’interactions, P. fluorescens BBc6R8 s’est révélée capable d’inhiber la production du pigment bleu diffusible γ-actinorhodine chez Streptomyces coelicolor A3(2) M145 en acidifiant le milieu par la production d’acide gluconique. L’ensemble de ces résultats nous permet de proposer différentes hypothèses sur l’importance écologique de ces trois interactions en les replaçant au sein du contexte de l’écosystème sol / Streptomyces are common bacteria in temperate forest ecosystems, which inhabit various ecological niches such as plant rhizosphere and mycorrhizosphere, as well as mineralosphere. In these niches, they interact with many other bacterial genera and different symbiotic, pathogenic and saprotrophic fungi. We have initiated a study on interaction between two soil model bacteria strains Streptomyces ambofaciens ATCC23877 and Pseudomonas fluorescens BBc6R8. Cocultures experiments on different agar media have revealed that each bacteria affects the production of secondary metabolites in the other partner. Thus, P. fluorescens inhibits the ability of S. ambofaciens to produce kanamycin, a "ping-pong effect" was highlighted. On the other hand, on iron deficient medium, P. fluorescens is able to use the desferrioxamines and coelichelin produced by S. ambofaciens as xenosiderophores and does no longer produce its own siderophores, pyoverdin and enantio-pyochelin. In another way, during pairwise co-culture experiments, Pseudomonas fluorescens BBc6R8 was shown to prevent the production of the diffusible blue pigment antibiotic γ-actinorhodin by Streptomyces coelicolor A3(2) M145 by acidifying the medium through the production of gluconic acid. Other fluorescent Pseudomonas strains and the opportunistic pathogen Pseudomonas aeruginosa PAO1 also prevented the γ-actinorhodin production in a similar way. Altogether these results prompt us to propose some hypotheses on the ecological significance of these three interactions by replacing them in the soil ecosystem context

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