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Smith, Joanne. "Agri-environment schemes and soil biodiversity: assessing the conservation, biodiversity and functional value of arable field margins for soil macrofauna". Thesis, University of Reading, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.486322.
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Bird, Stephanie. "The impact of native and exotic plants on soil biodiversity and ecosystem function". Thesis, University of Roehampton, 2016. https://pure.roehampton.ac.uk/portal/en/studentthesis/the-impact-of-native-and-exotic-plants-on-soil-biodiversity-and-ecosystem-function(c9707653-095b-4570-83d9-a444585f5b71).html.
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Soil biodiversity is an often overlooked component of global biodiversity, despite being important for supporting soil ecosystem services, notably decomposition processes. As the UK becomes increasingly urbanised, knowledge is required to help gardeners maximise urban green space resources for biodiversity. It is often assumed that non native vegetation has negative impacts on biodiversity, however, this hypothesis has not been tested for soil biodiversity. The overarching aims were to establish whether the geographical origin of vegetation affected soil faunal assemblages and decomposition rates for a UK soil. Traditional taxonomic methods and a molecular phylogenetic approach were used to characterise the Collembola communities of plots planted with vegetation from three geographical regions: ‘Native’, ‘Near native’ and ‘Exotic’. For comparison, additional soil cores were collected from the amenity grassland sites adjacent to the experimental plots, a lowland heath and a semi-natural woodland. No difference was found either in terms of the taxonomic diversity (1-D & H’) or phylogenetic diversity (PD & MPD) for the Collembola, under the different vegetation treatments, although differences in abundance were observed for some taxa (Acari & Collembola). Decomposition rates were assessed for each plot, using both twig (B. pendula) and leaf (Q. robur) litter bags for the soil mesofauna and bait lamina strips for earthworm activity; none of these parameters showed evidence of a vegetation origin effect on decomposition processes. The greatest differences were found when all sites were considered, with distinct Collembola communities found at each of the habitats; the semi-natural habitats had greater Collembola species diversity than the experimental plots, however, the decomposition rates of the latter were significantly higher. The implications of all results have been discussed with regards to the management of gardens for soil biodiversity, reaching the conclusion that vegetation origin is not of paramount importance.
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Godow, Bratt Tora, Mathilda Stigenberg, Andreas Elenborg, Sarah Ågren i Andreas Medhage. "To monitor the microbial biodiversity in soil within Uppsala". Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-444210.
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This is an exploration of the potential for a citizen science project, with the goal to get the general public involved in microbial soil biodiversity around Uppsala, Sweden. Biodiversity serves an important role in how an ecosystem performs and functions. A large part of Earth's biodiversity exists below ground in soil, where microorganisms interact with plants. It would be beneficial to analyse the abundance and spread of some microorganisms in order to gain a better understanding of soil biodiversity. We suggest that one species family to study could be Phytophthora. Phytophthora is a genus of oomycetes that often are pathogenic, causing disease in various trees and other plants. It is unknown exactly how widespread the genus is today, making it extra interesting for the proposed study. For the general public to be able to do this a device needs to be developed that is easy to use and preferably could be used directly in the field. An isothermal amplification method is suitable for identifying the microorganism under these conditions. Many isothermal amplification methods are expensive, perhaps too expensive for a citizen science study, but have great potential for easy field testing. We propose a device utilizing RPA and lateral flow strips. RPA - Recombinase Polymerase Amplification is a method for amplification that might be suitable since it is simple, sensitive, and has a short run time. It is however expensive, which is an issue, but isothermal amplifications are expensive across the board. Lateral flow strips can be used to visualize the results. They utilize antibodies to detect the previously amplified amplicons, and give a positive or negative test answer that would be understandable to even untrained study participants. One of the biggest obstacles identified in this project concerns amplifying DNA from a soil sample, because an extraction step is necessary. The methods we have identified for extraction are not performable in the field, since they require centrifugation. In the proposition for a device a possible work-around for this is proposed, but since it has yet to be tested it is not yet known whether it will work or not.
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Oliveira, Vanessa Bezerra de Menezes. "Soil function and biodiversity: regional variations and climate changes". Doctoral thesis, Universidade de Aveiro, 2013. http://hdl.handle.net/10773/11352.
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Doutoramento em BiologiaEmbora o objetivo principal da proteção internacional dos solos seja proteger tanto as funções quanto a estrutura do solo, a atual abordagem trata principalmente da proteção ao nível estrutural. Há uma carência de estudos que contemplem a ligação das funções do solo com os níveis da comunidade. Além disso, é ainda desconhecido se as variáveis ambientais (ex: tipos de solo, condições climáticas) atuam nas funções do solo da mesma maneira que influenciam sua estrutura biológica. Ademais, as alterações climáticas poderão ter sozinhas ou combinadas com os poluentes, um grande efeito nos ecossistemas terrestres. O presente trabalho propõe estudar as funções e a estrutura biológica do solo quando impactados devido a estresse tóxico (poluição por Cu) e/ou alterações a fatores como a temperatura e abundância de organismos, de maneira a simular possíveis variações regionais ou climáticas. Para alcançar os objetivos principais 3 experiências utilizando diferentes densidades de E. crypticus e 2 gerações foram feitas (Capítulos II e III). Duas experiências com mesocosmos (SMS) decorreram durante 3 meses sob uma gama de diversas temperaturas (10 – 29°C), que representam temperaturas médias para Portugal e Dinamarca (Capítulos IV e V). Duas experiências de campo também foram realizadas com intuito de validar os SMSs (Capítulo VI). Resultados demonstraram que os efeitos do Cu na reprodução dos enquitraídeos dependem da densidade inicial de organismos, especialmente na 2ª geração. Entretanto, nos SMSs expostos a Cu, a densidade inicial é menos importante nos resultados finais. O aumento da temperatura alterou majoritariamente a fase inicial de crescimento populacional. Em períodos mais longos, a abundância estabilizou tornando-se menos influenciada pelas temperaturas. Períodos longos de exposição reforçaram os efeitos da temperatura, como por ex: diversas espécies foram similarmente afetadas a 29 ou 26°C quando expostas durante 28 ou 61 dias respectivamente. De forma geral, o Cu reduziu a abundância da maioria das espécies ao longo do tempo, com poucas exceções. Os resultados da decomposição da matéria orgânica (MO) e atividade alimentar associaram-se com a abundância de organismos em baixas temperaturas (10-23°C). Entretanto, com o aumento das temperaturas (19-29°C), este comportamento não foi claro e a abundância de espécies e atividade alimentar diminuíram enquanto a decomposição da MO aumentou. Além disso, os resultados observados nos SMSs foram confirmados no campo. Mais especificamente, alterações ocorreram na fase de crescimento (correspondente à Primavera) e a exposição ao Cu diminuiu os efeitos da temperatura. Metodologias mais complexas (ex: mais gerações e experiências com múltiplas espécies) apresentam muitos benefícios, mas também proporcionam respostas mais complexas, as quais exigem um maior “peso” de evidências para serem comprovadas.
Although the main aim for international soil protection is to protect both the soil structure and the soil function, the current soil protection approach mainly deals with protecting the soil structure level. There is a lack of studies that link the community level with soil function. Additionally, it is unknown if the environmental variables (e.g. soil type, climate conditions) are acting on function in the same way they influence the biological soil structure. On top of this, climate change will alone and in combination with pollution have a strong effect on the terrestrial ecosystem. In the present work the soil biological structure and function were studied when impacted due to a toxic stress (Cu pollution) and due to changes in factors such as organisms’ abundance, and temperature, simulating ecological aspects, regional and climate changes. To achieve the main goals 3 experiments using different densities of E. crypticus and two generations were performed and culminated in two papers (Chapters II & III). Two multispecies experiments (SMS) were conducted until 3 months and under various temperatures (10-29˚C), representing the span of average temperatures for Denmark and Portugal (Chapters IV & V). Two Field experiments were also performed in order to validate the results of the SMSs (Chapter VI). Results showed that the effect of Cu on reproduction does depend on the density, especially so in the succeeding generation. Nevertheless, in the SMS test with Cu, the initial density is less important for the outcome. Increased temperature in the SMSs caused major changes in the abundance, mainly in the initial phase of population growth. At longer exposures the population abundance stabilized and became less influenced by temperatures. The longer exposure enforced the temperature effects, e.g. for several species effects at 29ºC-28 days were similar to 26ºC-61 days. Copper caused a general depression in abundance over time for most species with a few exceptions. The OM decomposition and feeding activity responses at low temperature (10-23°C) were associated with the increase in species abundance whereas this was less clear at high temperatures (19-29°C), here with a decrease in feeding activity and species abundance but increase in OM decomposition. Additionally, responses observed in the SMSs were confirmed in the field. In specific, changes occurred in the growth phase (corresponding to the late spring exposure) and Cu depressed the temperature responses. More complex approaches (i.e. more generations and multispecies approach) has many benefits, but provides also more complex answers that may require more weight of evidence.
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Visagie, Cobus M. "Biodiversity in the genus Penicillium from coastal fynbos soil". Thesis, Link to the online version, 2008. http://hdl.handle.net/10019/1856.
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Dickens, Helen Elizabeth. "Functional attributes of biodiversity in decomposer communities". Thesis, University of Exeter, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.326955.
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Limer, Laura Michelle Clare. "Biodiversity and ecosystem function : modelling soil biota and carbon cycling". Thesis, University of York, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.442353.
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Pino, Vanessa. "Soil Microbial Diversity Across Different Agroecological Zones in New South Wales". Thesis, The University of Sydney, 2016. http://hdl.handle.net/2123/16705.
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A synergistic relationship between soil diversity (pedodiversity) and soil microbial diversity (biodiversity) seems axiomatic. Soil microbes contribute with biogeochemical cycles on which rely soil services (e.g. food production) and; vice-versa the soil matrix provides the living conditions that structure its microbial communities. A better insight would enable us to quantify/qualify and so sustain, protect, and improve those processes underpinned by soil microorganisms. We hypothesize that the structural patterns of soil microbes rely on multivariate soil units and gradients (e.g. soil horizons) instead of single discrete ‘factors’ (soil pH) and that the microbial patterns can become a well-defined property of determined soils. We began exploring this biotic-abiotic dynamic by modeling soil microbial α-diversity using two orthogonal transects (~900 km each) across NSW. Soils were sampled from paired conserved and disturbed ecosystems. Soil biophysicochemistry was characterized using 16SrDNA/ITS metabarcoding and pedometric approaches. Soil microbial patterns and physicochemical attributes were assessed using linear and non-linear relationships (bootstraped regression trees models) whose output enabled the microbial mapping at 1km across NSW. These maps showed a higher diversity of soil microbes in western than eastern NSW. Despite this gradient, fungi and archaea were respectively lower and higher in Vertosols, whereas bacteria distribution was less clear. Our results suggested that microbial structural patterns relate to most pedological attributes and, the extent of this relationship varies according to the structural parameters analyzed (taxa composition, abundance, diversity metric). Therefore, microbial patterns are more consistent with grouped features defining soil gradients (soil types) rather than on individual soil properties. These conclusions will be supported by analyzing microbial and pedological dissimilarities (β-diversity) in a further research.
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Marí, Marí Teresa. "Changes in soil biodiversity and activity along management and climatic gradients". Doctoral thesis, Universitat de Lleida, 2017. http://hdl.handle.net/10803/457976.
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Els anomenats “rangelands” són àrees sense cultivar, àmpliament pasturades per animals domèstics i salvatges, actualment amenaçats pels canvis climàtic i en l’ús del sòl. Els microorganismes del sòl tenen un paper clau tant en la descomposició com en diversos processos de l’ecosistema, fet pel qual composició i funció de la comunitat microbiana han estat utilitzats durant molt temps com a índexs de fertilitat del sòl.
Els rangelands europeus i africans comparteixen un origen antropogènic comú, però el clima i la gestió del sòl els afecten d’una manera diferent. És per això que aquesta tesi pretén analitzar la comunitat microbiana d’ambdós tipus d’ecosistemes, per tal d’observar els efectes d’algunes de les amenaces comunes des d’una perspectiva més global.
Mentre que la sobrepastura va demostrar tenir l’efecte més perjudicial sobre la funció microbiana en sòls kenyans, es va trobar un efecte més fort del clima sobre els prats europeus. Els fongs i els bacteris van covariar al llarg de gradients altitudinals i climàtics, però la comunitat bacteriana va mostrar una recuperació més ràpida després de les pertorbacions biològiques i físico-químiques del sòl.
Aquest conjunt d’estudis afegeix nous coneixements sobre l’estructura i funció dels rangelands africans i europeus, i convida a explorar noves línies de recerca que incloguin tant bacteris com fongs alhora d’estudiar la comunitat microbiana del sòl.Los llamados "rangelands" son áreas sin cultivar, ampliamente pastoreadas por animales domésticos y salvajes, actualmente amenazados por los cambios climático y de uso del suelo. Los microorganismos del suelo tienen un papel clave tanto en la descomposición como en diversos procesos del ecosistema, por lo que composición y función de la comunidad microbiana han sido utilizados durante mucho tiempo como índices de fertilidad del suelo. Los rangelands europeos y africanos comparten un origen antropogénico común, pero el clima y la gestión del suelo les afectan de una manera diferente. Es por ello que esta tesis pretende analizar la comunidad microbiana de ambos tipos de ecosistemas, a fin de observar los efectos de algunas de las amenazas comunes desde una perspectiva más global. Mientras que el sobrepastoreo demostró tener el efecto más perjudicial sobre la función microbiana en suelos kenianos, se encontró un efecto más fuerte del clima sobre los prados europeos. Los hongos y las bacterias covariaron a lo largo de gradientes altitudinales y climáticos, pero la comunidad bacteriana mostró una recuperación más rápida después de las perturbaciones biológicas y físico-químicas del suelo. Este conjunto de estudios añade nuevos conocimientos sobre la estructura y función de los rangelands africanos y europeos, e invita a explorar nuevas líneas de investigación que incluyan tanto bacterias como hongos en el estudio de la comunidad microbiana del suelo.
Rangelands are uncultivated areas extensively grazed by wild and domestic animals, currently threatened by land use and climatic changes. Soil microorganisms play a key role in decomposition and several ecosystem processes and the composition and function of the microbial community have been long used as indices of soil fertility. African and European rangelands share a common anthropogenic origin, but climate and management affect them in a different way. That is why this thesis aimed to analyze the microbial community of both in order to observe the effects of some common threats from a more global perspective. While overgrazing proved to have the most detrimental effect on the soil microbial function in Kenyan soils, a stronger effect of climate was found to affect European grasslands. Fungi and bacteria co-varied along altitudinal and climatic gradients, but the bacterial community showed a fast recovery after biological and soil physico-chemical disturbances. This group of studies adds new knowledge on the structure and function of the African and European rangelands, and invite to explore new lines of research including both fungal and bacterial consortia when studying the soil microbial community.
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Valentine, Lori Lisa. "The biodiversity of ectomycorrhizal fungi associated with Quercus garryana /". View full-text version online through Southern Oregon Digital Archives, 2002. http://soda.sou.edu/awdata/040226b1.pdf.
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Thesis (M.S.)--Southern Oregon University, 2002.Includes bibliographical references (leaves 37-43). Also available via Internet as PDF file through Southern Oregon Digital Archives: http://soda.sou.edu. Search Bioregion Collection.
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Martinez, Vila, i Martin Alvaro. "Environmental management of soil biodiversity and ecosystems for productive and sustainable agriculture". Thesis, Sumy State University, 2008. http://essuir.sumdu.edu.ua/handle/123456789/11773.
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It is well-known that there is a need for technical assessments to advise farmers, policy-makers and planners
on indicators and methods for the assessment and monitoring of soil health and functions. These should focus on
improving knowledge: on the roles and importance of diverse soil organisms in providing key goods and services;
and on the positive and negative impacts of existing and new agricultural technologies and management practices.
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Marshall, Carolyn Bowers. "Effect of plant functional group removal on the soil microbial community diversity and composition". Thesis, University of British Columbia, 2008. http://hdl.handle.net/2429/2865.
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A major objective of biodiversity-ecosystem functioning (BDEF) research is to determine the consequences of species loss, caused both naturally and anthropogenically, on the functioning of ecosystems. The impact of plant species loss on the soil microbial community has not received much attention even though soil microbes influence many important ecosystem functions such as decomposition and nutrient cycling. The objective of this research was to investigate how the functional group composition of the aboveground plant community influenced the belowground microbial community. Plant functional groups (graminoids, legumes and non-leguminous forbs) were removed from a northern grassland system in the Yukon Territory, Canada. One metre square plots had one of the three functional groups removed or left intact as a control and this was crossed with a fertilizer treatment and a fungicide treatment that targeted mycorrhizal fungi. After five seasons (2003-07) of implementing treatments the soil microbial community was analyzed using substrate-induced respiration (SIR, a measure of metabolic diversity) and phospholipid fatty acid analysis (PLFA, a measure of community composition). Plant functional group removal had almost no effect on the soil microbial community. The only response detected was an increase in stress (indicated by the PLFA stress ratio of cy19:0 to 18:1ω7c) which occurred when legumes were removed and fertilizer was not added, indicating that legumes had a positive effect on the nutrient status of microbes. Likewise, soil properties (total carbon, pH, moisture and nutrients) showed limited response to plant removals. Fertilization decreased the metabolic diversity of the soil microbial community. We detected no soil microbial or plant biomass response to the fungicide indicating that mycorrhizae had little influence in this system. Based on the low-productivity of the grassland, and the lack of response in both the soil properties and the microbial community, we hypothesize that the main determinants of the microbial community may be litter input. When litter decomposition rates are slow, such as in this northern system, five growing seasons may not be sufficient to detect the impact of a changing plant community on the soil microbes.
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Lindberg, Niklas. "Soil fauna and global change : responses to experimental drought, irrigation, fertilisation and soil warming /". Uppsala : Dept. of Ecology and Environmental Research, Swedish Univ. of Agricultural Sciences, 2003. http://epsilon.slu.se/s270.pdf.
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Klinka, Karel. "Forest floor dynamics across a chronosequence in the coastal western hemlock zone". Forest Sciences Department, University of British Columbia, 1997. http://hdl.handle.net/2429/653.
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The forest floor represents the uppermost organic and organicenriched mineral soil horizons. They have been formed by the deposition of organic material and the subsequent biologically mediated
decomposition. The forest floor influences rooting-zone temperature, aeration, moisture, and nutrient conditions, and hence, forest productivity. Considering the importance of the forest floor, and the fact that it is exposed to disturbance (being the surface layer), we need to assess the potential impacts our logging practices may have.
Clearcutting, one of the contentious silvicultural practices used in British Columbia, is imputed to most adversely affect ecosystems and sustainability. We assessed the long-term impact of clearcutting
on the forest floor by documenting changes in the thickness, chemical and biotic properties of the humus form across a chronosequence of forest stands. The study was located in the largest and most representative portion of the coastal rainforest the Very Wet Maritime Coastal Western Hemlock (CWHvm) subzone.
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Murphy, Meaghan Thibault. "Biotic and abiotic controls on soil respiration in a biodiversity plantation in the tropics". Thesis, McGill University, 2005. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=97978.
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The Sardinilla plantation is a long-term facility for studying the links between tree species diversity and ecosystem function. Six native tree species were planted in 2001 in plots containing 1, 3 or 6 species. Soil respiration (SR) measurements were conducted from March to December 2004 on tree pairs. ANOVAs with repeated measure on days were used to test the main effects of species (monocultures), pair (single and two-species pairs), plot (pairs in monoculture, three-, and six-species plots), and season (dry vs. early wet season). ANCOVAs were run for each effect to determine possible biotic and abiotic covariates, including root, tree, and microbial biomass, soil moisture, surface temperature, and bulk density. Significant season and pair effects accounted for 89% and 2% of the variability in SR. Driven by soil moisture, SR increased seven fold during the seasonal transition. In the dry and wet season monocultures had significantly higher SR than two-species pairs.
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ALALI, SUMER. "IMPACT OF AGRICULTURAL PRACTICES ON BIODIVERSITY OF SOIL INVERTEBRATES, ASSESSMENT THROUGH DNA METABARCODING APPROACH". Doctoral thesis, Università degli Studi di Milano, 2019. http://hdl.handle.net/2434/612179.
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In spite of the increase of the organically farmed areas worldwide, it has been always doubted if the organic farming really enhances the soil biodiversity, as the main component in the agroecosystems. This doubt was a target of many studies, trying to reveal the true impact of the applied agricultural practices in the adopted farming strategies, targeting the soil invertebrates as bioindicators of the impact. Unfortunately, the doubt is still, due to the limitations in the sampling and taxonomy of the soil’s invertebrates communities. In the last years, the molecular approaches represent promising methods to overcome these limitations. Thus, the DNA metabarcoding was applied targeting the COI gene in the DNA extracted from soil samples collected in different farming strategies (organic vs non organic), with a different cropping systems (stable meadow vs barley) and different levels in the field from the margin to center, this sampling was performed in three seasons (May, July and October).
In addition, the soil properties (pH, texture, N%, C% and C/N ratio) were determined for the selected samples. The illumine MiSeq run was performed and the obtained reads were processed
bioinformatically to get the OTU table (Operational Taxonomic Unite). This OTU table was used for the statistical and ecological analysis. Finally, the QBS, a soil quality index depends on the soil
inhibiting microarthropods, was calculated by its classic method and estimated based on the obtained molecular data, to check the correlation between the resulted values. Results showed that the DNA metabarcoding approach represents a promising method for the assessment of soil biodiversity in the agroecosystem, but this approach is not able to detect the seasonal changes of the soil invertebrates’ communities. Regarding the farming strategies, the farming management as organic or non organic (conventional) did not affect significantly the community structure of soil invertebrates and the biodiversity indices Shannon and Pielou’s evenness, while the species richness was significantly lower in the conventional farm. Soil invertebrates’ communities were significantly affected by the crop and the position of the field (as margin or field), and the C/N ratio. For Rotifera and Tardigrada communities’ structure were affected by the farming strategy, while insects’ communities were affected by the pH of the soil. The role of the margin of the field as a reservoir is increased in the cultivated fields (barley), while in the stable meadows the interactions between the margin and the center of
the field are lower. Finally, the soil biological quality is decreased from the margin to the center of the field (of the same field), also decreased in the barley field comparing to the stable meadows.
The obtained molecular index mQBS that is developed based on the QBS-ar is a promising approach for the soil biological quality estimation.
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Berkley, Nicholas Alexander James. "Patterns and process : biodiversity and ecosystem function response to changes in the arable landscape". Thesis, University of Plymouth, 2018. http://hdl.handle.net/10026.1/12825.
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Land use change is a major driver of species loss worldwide, the extent and intensity of agricultural land use poses particular pressures for biodiversity and the ecosystem services it provides. In recent years, agroecosystems have seen the introduction of 2nd generation bioenergy crops in order to tackle anthropogenic climate change, providing a renewable alternative to fossil fuels. In this thesis I study the impact of cultivating two commercial perennial energy crops (PECs), Miscanthus x giganteus and willow short-rotation coppice, when compared to the cereal crops they replace. I investigate processes relevant to the provisioning of pollination and decomposition services and explore patterns of soil element bioaccessibility alongside analyses of the similarity and diversity of soil bacterial communities. When compared to cereals, I find a consistent increase in pollinator (hoverfly, bumblebee and butterfly/moth) wildflower visitation in the margins of willow but not Miscanthus. In Miscanthus, opposing trends arose for different pollinator taxa: butterflies/moths were more frequent flower visitors in Miscanthus margins than cereal margins, while hoverfly flower visits were most frequent in cereal margins. Furthermore, the availability of margin wildflowers was enhanced in willow but not Miscanthus and the seed set of margin phytometers was similar between Miscanthus and cereals. Cultivation of willow, in particular, may therefore yield local conservation benefits for both wildflowers and pollinators. However, there was no evidence for enhancement of pollinator activity in cereals adjacent to either PEC, indicating that the strategic cultivation of these crops is unlikely to enhance pollinator service provision in the wider agri-environment. For investigated soil elements, bioaccessibility in PECs did not differ significantly to cereal controls, and denaturing gradient gel electrophoresis (DGGE) revealed no difference in the diversity of bacterial communities. Similarly, DGGE fingerprint patterns did not indicate the development of crop specific assemblages, demonstrating that the mobility of soil elements and structure of bacterial communities were principally determined by factors other than the identity of the crop cultivated. Investigation of meso-microfaunal decomposition rates in Miscanthus using litter bags demonstrated an impact on decomposition processes, with a significant increase in winter decomposition rates in the PEC when compared to cereals.
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Sorkau, Elisabeth [Verfasser], i Yvonne [Akademischer Betreuer] Oelmann. "Land use and biodiversity effects on P-transformation in soil / Elisabeth Sorkau ; Betreuer: Yvonne Oelmann". Tübingen : Universitätsbibliothek Tübingen, 2019. http://d-nb.info/1184271542/34.
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Givaudan, Nicolas. "Adaptation strategies of soil biodiversity (earthworms) to pesticides : mechanisms in play and ecosystemic cost assessment". Thesis, Rennes 1, 2014. http://www.theses.fr/2014REN1S083/document.
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Ce travail de thèse a cherché à déterminer si la contamination résiduelle à long terme des sols agricoles par les pesticides induit le développement de mécanismes d’adaptation aux pesticides chez les vers de terre. Il a aussi visé à identifier les coûts potentiels de l’adaptation de l’échelle de l’individu à celle de la population, et les conséquences pour l’écosystème sol. Une contamination résiduelle du sol par les pesticides est mesurée et comparée dans trois champs cultivés en agriculture conventionnelle (classés en fonction de l’historique cultural comme « haut », « moyen » et « bas » niveaux d’intrants), un champ cultivé en agriculture biologique et une prairie permanente biologique, tous dans ce type de management agricole depuis plus de 20 ans. En utilisant une méthode d’extraction des pesticides en milieu aqueux (représentant la fraction « biodisponible » des pesticides), 6, 8 et 4 résidus de pesticides sont détectés dans les champs à « haut », « moyen », et « bas » niveaux d’applications, respectivement, et un seul pesticide dans le sol du champ biologique (un résidu d’atrazine potentiellement vieux de plus de 20 ans). Les deux espèces endogées Allolobophora chlorotica et Aporrectodea caliginosa , communnes dans les sols des 5 champs,- mis à part A. chlorotica qui est absente du champ cultivé en agriculture biologique-, ont servi de modèles biologiques d’étude. Les stratégies d’adaptation aux pesticides sont étudiées en comparant les réponses de ces populations de vers de terre sur le terrain et après des expositions aux pesticides en laboratoire. Les réponses mesurées s’étendent de l’échelle moléculaire (enzymes de biotransformation et du stress oxidatif), biochimique (ressources énergétiques), métabolique (taux de respiration, métabolomique) à l’échelle de l’individu (biomasse, longueur) et de la population (traits de vie des cocons et des juvéniles), et aux possibles conséquences pour l’écosystème sol en termes de bioturbation (creusement et ingestion de sol) et de dissipation des pesticides comme service ecosystémique. Une capacité de détoxification augmentée et un plus grand potentiel anti-oxidant sont observés le long du gradient de contamination du sol et en laboratoire après exposition des vers de terre des champs conventionnel (population « pré-exposée ») et biologique (« naïve) à des pesticides. Des demandes énergétiques et des réarrangements métaboliques différents sont observés dans les deux populations, et sont plus prononcés chez la population pré-exposée. Une adaptation physiologique est démontrée chez les animaux pré-exposés, qui est associée à une ’augmentation de la bioturbation, et en cascade à une dissipation du pesticide dans le sol. Les conséquences au niveau de la population sont étudiées en termes de traits d’histoire de vie des deux populations pré-exposées et naïves. Le management en conventionnel incluant l’utilisation de pesticides semble diminuer le poids des adultes au champ, et implique potentiellement la réallocation des ressources énergétiques, des mécanismes reproductifs vers les processus métaboliques. Ceci aboutit à une diminution de la fécondité et du pourcentage d’éclosion et pourrait être un facteur participant à la diminution des populations de vers de terre dans les champs cultivés avec utilisation de produits phytosanitairesThis work investigated if long-term residual contamination of agricultural soils leads to adaptation of earthworm populations to pesticides. It also aimed at identifying the costs of adaptation from the individual to the population level, and the consequences for the ecosystem. Residual contamination by pesticides was assessed and compared in three fields under conventional management (classified after evaluation of pesticide applications as ''high-'', ''medium-'', and ''low-''pesticide input), one field under organic agriculture requirements and one organic permanent pasture, all in this type of management for more than 20 years. Using a water extraction method, as indicative of the amount of bioavailable pesticides 6, 8 and 4 residues of pesticides were recovered in the ''high-'', ''medium-'', and ''low-input'' fields, respectively, and almost no pesticides were detected in the soil of the organic field except for low levels of residual (possibly 20 years old) atrazine. The endogeic species Aporrectodea caliginosa and Allolobophora chlorotica were found in common to the five fields, -except A. chlorotica which was absent from the organic field-, and were used as biological models. Adaptation strategies were investigated by comparing the populations of these earthworms between the different fields according to several endpoints in field and laboratory assessments. The endpoints measured ranged from the molecular (biotransformation and anti-oxidant enzymes), biochemical (main energy resources), and metabolic (respiration rate, metabolomics) levels, to individual (weight, length) and population-related parameters (cocoon and juvenile life traits), and to the possible consequences for the ecosystem in terms of bioturbation (earthworm burrowing behaviour) and pesticide disappearance as an crucial ecosystem service. Enhanced detoxification and anti-oxidant potential was demonstrated along the gradient of contamination in the fields, and in particular comparing the response to an experimental pesticide exposure between the pre-exposed, thus possibly adapted earthworms from the ''high-input'' field-, and the naïve population from the organic field. Distinct energetic demands and metabolic rearrangements were observed between the populations, more pronounced in the pre-exposed earthworms. Physiological adaptation was demonstrated in pre-exposed animals, and this was associated with an increase in burrowing behaviour and pesticide disappearance in the soil. Population-level consequences were assessed in life traits of the two populations. The conventional farming including the use of pesticides decreased the weight of adult worms in the field and resulted in reallocation of energy resources, possibly from reproductive to metabolic function. This led to lower fecundity and hatching success and could partly explain lower earthworm densities in pesticide-impacted soils
I dette arbejde blev der forsket i om langsigtet residualforurening af landbrugsjord fører til pesticidadaptation hos regnorme. Forskningen sigtede også efter at identificere adaptations-omkostningerne fra individ- til populationsniveau, og konsekvenserne for økosystemet. Pesticiders residualforurening blev vurderet og sammenlignet i; tre konventionelt styrede marker (klassificeret efter evaluering af pesticid-anvendelser som ”højt-”, ”medium-”, og ”lav-input”), en mark styret ud fra økologiske betingelser, og et økologisk permanent græsningsareal, alle havde været styret på denne måde i mere end 20 år. Ved hjælp af en vand-ekstraktionsmetode blev 6,8 og 4 pesticidresiduums udvundet i henholdsvis ”høj-”, ”medium-”, og ”lav-input” markerne, og næsten ingen pesticider blev detekteret i jorden fra den økologiske mark bortset fra lave niveauer af resterende (højst sandsynligt 20 år gammelt) atrazin. Regnorms-populationerne Aporrectodea caliginosa og Allolobophora chlorotica blev fundet i alle fem marker, bortset fra A. chlorotica som ikke var til stede i den økologiske mark. Adaptationsstrategier blev undersøgt ved at sammenligne populationerne af disse regnorme de forskellige marker imellem ifølge flere parametre i felt- og laboratoriebedømmelserne. De målte parametre rangerede fra molekylære- (biotransformation og antioxiderende enzymer), biokemiske- (primære energiressourcer), og metaboliske- (respirationsrate, metabolomics) niveauer, til individuelle- (vægt, længde) og populations-relaterede parametre (puppe og juvenile livskarakterer), og til de mulige konsekvenser for økosystemet med hensyn til bioturbation (regnormes grave-adfærd) og nedgang i koncentrationen af ekstraherbare pesticider. Forbedret afgiftnings- og antioxiderende potentiale blev demonstreret langs gradienten af pesticid forurening i felten. Forbedret afgiftning i den pre-eksponerede population var særdeles tydeliggjort ved eksponeringen til pesticider i laboratoriet sammenliget med den økologiske population. Der blev observeret distinkte energibehov og metabolisk omgruppering populationerne imellem, dette var mere udtalt hos de pre-eksponerede regnorme. Der blev detekteret fysiologiske adaptationer hos de pre-eksponerede dyr, og dette hang sammen med en kompensatorisk øgning i grave-adfærd og nedgang i koncentrationen af ekstraherbare pesticider i jorden. Konsekvenser, på populationsniveau, blev bedømt ud fra de to populationers livskarakterer. Brug af pesticider resulterede i vægtnedgang hos de voksne orme i felten og omfordeling af energiressourcer, formodentlig fra reproduktiv til metabolisk funktion. Dette førte til lavere frugtbarhed og udklæknings-succes og kunne til dels forklare de lavere regnorme-densiteter i den pesticid-påvirkede jord
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Gadekar, Kumarsukhadeo Prakash. "Analysis of biodiversity and soil C storage in the south Konkan coast of Maharashtra (India)". Thesis, Bangor University, 2012. https://research.bangor.ac.uk/portal/en/theses/analysis-of-biodiversity-and-soil-c-storage-in-the-south-konkan-coast-of-maharashtra-india(a881dcd3-1b20-4199-b211-b3fd04e6712b).html.
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This thesis presents an analysis of floral diversity, soil C carbon storage and bird diversity in the south Konkan coast of the Western Ghats of India. The objectives of the investigation were to study structure, composition, distribution, richness and diversity of vegetation under different land-use types, to determine soil organic carbon content and to determine species composition, richness and diversity of birds under different land-use types. For the investigation, agricultural, forest, casuarina plantation, grassland, mango plantation, homegarden and mangrove sites were selected randomly over a 460 km2 area. At the forest, casuarina, home gardens and mangrove sites quadrate sampling technique was used for phyto-sociological analysis. Soil organic matter was detenTIin~crby the weight loss-on- ignition method on soils collected as selected sites. A point transect survey method based on distance sampling was used to study seasonal variation in bird species richness and diversity in different land-use types. The sample based rarefaction curves were computed using EstimateS 8.2.0 and Eco-sim version free software applications. The bird data was analyzed using Distance 6.2 release 2 software. Floristic analysis revealed that the study area is home for 407 plant species belonging to different 104 families. The most dominating families are Fabaceae, Cucurbitaceae, Euphorbiaceae, Malvaceae, Apocynacaeae, Asteraceae, Caesalpiniaceae, Convolvulaceae, Poaceae, Acanthaceae, Mimosaceae, Rubiaceae, Verbenaceae and Rhizophoraceae. The high species richness was recorded in the forest followed by homegardens and casuarina plantation, while it was lowest in the mangrove vegetation. The highest Shannon-Weaver index of diversity was recorded for the homegardens > forests > casuarina plantation > mangrove vegetation. The highest value of species evenness and Simpson's index of diversity was recorded for the forests and lowest in the casuarina monoculture. The highest total C storage up to 50 cm depth was found in forest soils > mango plantation > mangrove > agricultural land soils > casuarina monoculture soils. The study revealed that the top 30 cm layer contains about 61-69% of the total C stock. SOC content decreased vertically with increase soil depth. SOC content showed significant positive correlation with soil moisture content and soil salinity, and significant negative correlation with soil pH and bulk density. In a total of 4796 encounters, 9348 individual birds belonging to 114 species and 51 families were detected from seven habitats in two seasons during the study period. The highest species richness was observed in the monsoon season. Overall 72% bird species were common in the both seasons. The most dominating families are Accipitridae, Columbidae, Hirundinidae, Muscicapidae, Ardeidae, Corvidae, Cuculidae and Sturnidae. In the dry season the highest species richness and hannon-Weaver diversity index was observed in the forest land. In the monsoon, season the highest species richness and Shannon-Weaver diversity index was observed in the grassland . .The research findings on floral analysis of different land-use types suggest that the ~eg~on IS ecologically and ethno-botanically rich. The wide variety of floral and avian species mdlc~tes the high species richness and diversity in the study area. The region is prone to erratic, anthropogenic land-use changes such as deforestation, conversion to agriculture, industrilalization (especially nuclear power generation), shrimp farming, construction works and chira mining. This study provides a basis for developing measures for the conservation and management of natural resources in south Konkan coast of Maharashtra. Therefore, the study suggests that the nuclear power project should not be started on the site for future environmental health and safety, public health and security and to avoid future hazards of loss of biodiversity in the south Konkan coast of Maharashtra state.
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Smuts, Ian Heinrich. "Influence of Acid Mine Drainage on the soils of Nababeep, Namaqualand with reference to soil chemistry, minerals and metal mobility". Thesis, Stellenbosch : Stellenbosch University, 2015. http://hdl.handle.net/10019.1/96897.
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Thesis (MSc)--Stellenbosch University, 2015.ENGLISH ABSTRACT: The Okiep copper district in the north-western corner of South Africa is a region that has been mined for over 150 years. Most mining operations have ceased, but years of mining has left the area scattered with abandoned mining sites. Acids (as used in ore processing) together with acid mine drainage generated from tailings exposure, collectively referred to as AMD hereafter, are a contamination risk to water resources and the biodiversity of this arid area. This study focused on an abandoned copper processing pond located close to the town of Nababeep. The leaching pond is unlined and has been excavated in the shallow colluvial soils. The natural soils of the area are shallow (60 cm) (WRB – Arenosol; SA – Oakleaf). Formations of corroded granite-gneiss boulders are an indication of the corrosiveness of the AMD collecting in the pond. The AMD was collected from the pond in the dry season at its most concentrated form and the AMD had exceptionally high concentrations of Al (26.9 g/l), Fe (42.9 g/l), Mg (20.5 g/l), Cu (3.8 g/l) and Mn (3.4 g/l). Melanterite (FeSO4·7H2O), a soluble ferrous compound, was found to play an important role in the immediate release of Fe and sulfates. The pristine soils have a sandy texture (2–5.2 %clay). The minerals detected in the clay phase include illite, kaolinite, montmorillonite and quarts. Pristine soils show some degree of contamination with low pH (4.38–4.77) and high Cu and sulfate contents. Soils located in the processing pond, which have been exposed to AMD for an extended period of time, showed poorly crystalline phases to be present (indicated by a broadening of the XRD peaks for clay minerals). Saturation indices (SI) were determined for saturated paste extracts of the pond soils and the obtained SI values support the notion of dissolution of silicate clays, as the obtained SI values ranged between –1.3 and –11.77 for illite and –4.76 to 0.58 for kaolinite. Jarosite, a new phase, formed in the contaminated soil and is a sink for K. Long term weathering experiments of pristine soils exposed to AMD indicated that clay minerals are significantly weathered and altered, which was identified by observing the broadening of the clay XRD peaks. Fourier transform infrared (FTIR) spectra were generated by scanning clay samples of the weathered soil. Amorphous phases were confirmed by structured water bands with wavenumber values of 3700 and 3300 cm−1 for acid treated soil. Micrographs showed a more amorphous and corroded morphology in the acid treated soil. Metal retention experiments were conducted by exposing the pristine soil to AMD repeatedly. Iron was the predominant metal attenuated in the soil. Metals such as Al, Mn, Na, K, Ca and Co were released by the soil into solution. Removal of Si is associated with the dissolution of clay minerals. The pristine soil shows limited capacity to neutralize acidity and low capacity to retain metals when leached with AMD. Metals were predominantly extracted in the water soluble phase of the long term weathering treatments. Aluminium was the most mobile fraction, being extracted predominantly from the water soluble fraction (2035 mg/kg). Exchangeable and acid soluble fractions did not retain significant quantities of metals. In the soil from the processing pond, the reducible fraction had a high concentration of reducible Fe (21175 mg/kg) and Si (3070 mg/kg). The reducible fraction also had the highest concentration of Cr (15.85 mg/kg), Cu (41.53 mg/kg), Pb (8.0 mg/kg) and Zn (10.65 mg/kg) compared to the other fractions of this soil. For the control experiment, the concentration of Cu (77.3 mg/kg), Pb (10.8 mg/kg) and Zn (24.1 mg/kg) were higher than contaminated soil yet lower for Cr (6.05 mg/kg). From these experiments, it can be concluded that the pristine soils studied have a limited ability to retain heavy metals in the non-bioavailable fraction, and, due to the nature of AMD, they are not effective in retaining metals sufficiently. The findings of this study suggest that the capacity of these pristine soils to buffer pH and retain metals is greatly limited. This could be as a result of (1) the low clay content, (2) the low concentration of secondary carbonates and (3) the low pH of the soil. The leaching of AMD from the pond is thus not regulated by the soils and poses a risk for nearby water resources.
AFRIKAANSE OPSOMMING: Die Okiep Koper Distrik, geleë in die noord-westelike hoek van Suid-Afrika, is ‘n streek waar mynbou al vir meer as 150 jaar plaasvind. Die meeste mynbou aktiwiteite is gestaak, maar jare van mynbou het die streek nagelaat met verskeie verlate mynbouterreine. Sure, wat in die prosessering van erts gebruik word, en suurmynwater wat gegenereer word uit die mynuitskot (gesamentlik verwys na as suurmynwater) is ‘n besoedelingsrisiko vir waterbronne en biodiversiteit in hierdie dorre area. Die studie fokus op ‘n verlate koper prosesserings aanleg naby die dorpie Nababeep. Die logingsdam is nie geseël nie en is uitgegrawe in vlak, kolluviale grond. Die natuurlike gronde van hierdie area is vlak (60 cm) (WRB – Arenosol; SA – Oakleaf). Formasies van weggevrete graniet-gneis rotse in die opgaardam is ‘n aanduiding van die bytende potensiaal van hierdie suurmynwater. Suurmynwater was versamel in die dam gedurendie die droë seisoen in die mees gekonsentreerde vorm. Die suurmynwater het besonderse hoë konsentrasies van Al (26.9 g/l), Fe (42.9 g/l), Mg (20.5 g/l), Cu (3.8 g/l) en Mn (3.4 g/l). Melanteriet (FeSO4·7H2O) is ‘n ysterhoudende verbinding en, alhoewel dit oplosbaar is, speel dit ‘n belangrike rol in die onmiddelike vrylating van Fe en sulfate. Die onversteurde grond het ‘n sand tekstuur (2–5.2 % klei). Die minerale wat in die klei fraksie ge-identifiseer is sluit illiet, kaoliniet, montmorilloniet en kwarts in. Die ongerepte gronde dui egter op ‘n mate van besoedeling deurdat dit ‘n lae pH (4.38–4.77) enhoë Cu en sulfaat inhoud het. Die grond wat geleë is naby die prosesseringsaanleg en ook blootgestel is aan suurmynwater vir ‘n verlengde tyd, dui daarop dat swak kristallyne fases teenwoordig is in die grond. Dit word bevestig deur ‘n verbreding van die XRD pieke van kleiminerale. Versadiging indekse (VI), wat bepaal is in versadigde grondekstraksies van die damgrond, ondersteun die oplossing van die silikaatkleie en word gereflekteer deur VI waardes wissel tussen –1.3 en –11.77 vir illiet en –4.76 tot 0.58 vir kaoliniet. Jarosiet is ‘n nuwe fase wat gevorm het in die besoedelde grond en is ‘n sink vir K. Langtermyn verweringseksperimente wat gedoen is deur die onversteurde grond bloot te stel aan suurmynwater wys beduidende verwering en verandering van klei-minerale deur verbreding van die XRD pieke. Fourier transform infrarooi (FTIR) spektra is op kleimonsters van die verweerde grond gegenereer. Amorfe fases is bevestig deur gestruktureerde waterbindings met frekwensies tussen 3700 en 3300 cm−1 vir suurbehandelde grond. Metaal-vasleggings eksperimente is uitgevoer deur herhaaldelik die onversteurde grond aan die suurmynwater bloot te stel. Yster is die metaal wat hoofsaaklik in die grond vasgehou is. Metale soos Al, Mn, Na, K, Ca en Co was vrygestel in oplossing deur die grond. Die vrylating van Si deur die grond word geassosiëer met die oplossing van kleiminerale. Die onversteurde grond toon beperkte vermoë om suur te neutraliseer en metale te bind in die grond wanneer dit met suurmynwater geloog word. Metale was hoofsaaklik ge-ekstraëer in die wateroplosbare fase vir die langtermyn verweringsbehandelings. Aluminium was die mees mobiele fraksie wat ontrek is van die water oplosbare fraksie (2035 mg/kg). Uituilbare en suuroplosbare fraksies het nie ‘n groot hoeveelheid metale vasgehou nie. Gronde wat versamel is naby die prosesseringsdam het die hoë konsentrasies vanFe (21175 mg/kg) en Si (3070 mg/kg) in die gereduseerde fraksie gehad. Die reduserende fraksie het ook die hoogste konsentrasie van Cr (15.85 mg/kg), Cu (41.53 mg/kg), Pb (8.0 mg/kg) en Zn (10.65 mg/kg) gehad in vergelyking met ander fraksies in die grond. Vir die beheer eksperiment was die konsentrasie van Cu (77.3 mg/kg), Pb (10.8 mg/kg) en Zn (24.1 mg/kg) hoër as in die besoedelde grond en laer vir Cr (6.05 mg/kg). Dus kan daar van hierdie eksperimente afgelei word dat die onversteurde grond beperkte kapasiteit het om swaar metale in grond vas te hou in die nie-biobeskikbare fraksie. As gevolg van die aard van die suurmynwater, is die grond nie voldoende om die metale effektief in grond te behou nie. Die bevindinge van hierdie studie dui daarop dat die kapasiteit van die ongerepte grond om pH te buffer en metale in grond te behou baie beperk is. Dit kan toegeskryf word aan die lae kleiinhoud, lae konsentrasie van sekondêre karbonate en die lae pH van die grond. Die loging van suurmynwater van die logingsdam is dus nie gereguleer deur die gronde nie en stel die naasliggende waterbronne in gevaar.
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Sommeria-Klein, Guilhem. "From models to data : understanding biodiversity patterns from environmental DNA data". Thesis, Toulouse 3, 2017. http://www.theses.fr/2017TOU30390/document.
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La distribution de l'abondance des espèces en un site, et la similarité de la composition taxonomique d'un site à l'autre, sont deux mesures de la biodiversité ayant servi de longue date de base empirique aux écologues pour tenter d'établir les règles générales gouvernant l'assemblage des communautés d'organismes. Pour ce type de mesures intégratives, le séquençage haut-débit d'ADN prélevé dans l'environnement (" ADN environnemental ") représente une alternative récente et prometteuse aux observations naturalistes traditionnelles. Cette approche présente l'avantage d'être rapide et standardisée, et donne accès à un large éventail de taxons microbiens jusqu'alors indétectables. Toutefois, ces jeux de données de grande taille à la structure complexe sont difficiles à analyser, et le caractère indirect des observations complique leur interprétation. Le premier objectif de cette thèse est d'identifier les modèles statistiques permettant d'exploiter ce nouveau type de données afin de mieux comprendre l'assemblage des communautés. Le deuxième objectif est de tester les approches retenues sur des données de biodiversité du sol en forêt amazonienne, collectées en Guyane française. Deux grands types de processus sont invoqués pour expliquer l'assemblage des communautés d'organismes : les processus "neutres", indépendants de l'espèce considérée, que sont la naissance, la mort et la dispersion des organismes, et les processus liés à la niche écologique occupée par les organismes, c'est-à-dire les interactions avec l'environnement et entre organismes. Démêler l'importance relative de ces deux types de processus dans l'assemblage des communautés est une question fondamentale en écologie ayant de nombreuses implications, notamment pour l'estimation de la biodiversité et la conservation. Le premier chapitre aborde cette question à travers la comparaison d'échantillons d'ADN environnemental prélevés dans le sol de diverses parcelles forestières en Guyane française, via les outils classiques d'analyse statistique en écologie des communautés. Le deuxième chapitre se concentre sur les processus neutres d'assemblages des communautés.[...]Integrative patterns of biodiversity, such as the distribution of taxa abundances and the spatial turnover of taxonomic composition, have been under scrutiny from ecologists for a long time, as they offer insight into the general rules governing the assembly of organisms into ecological communities. Thank to recent progress in high-throughput DNA sequencing, these patterns can now be measured in a fast and standardized fashion through the sequencing of DNA sampled from the environment (e.g. soil or water), instead of relying on tedious fieldwork and rare naturalist expertise. They can also be measured for the whole tree of life, including the vast and previously unexplored diversity of microorganisms. Taking full advantage of this new type of data is challenging however: DNA-based surveys are indirect, and suffer as such from many potential biases; they also produce large and complex datasets compared to classical censuses. The first goal of this thesis is to investigate how statistical tools and models classically used in ecology or coming from other fields can be adapted to DNA-based data so as to better understand the assembly of ecological communities. The second goal is to apply these approaches to soil DNA data from the Amazonian forest, the Earth's most diverse land ecosystem. Two broad types of mechanisms are classically invoked to explain the assembly of ecological communities: 'neutral' processes, i.e. the random birth, death and dispersal of organisms, and 'niche' processes, i.e. the interaction of the organisms with their environment and with each other according to their phenotype. Disentangling the relative importance of these two types of mechanisms in shaping taxonomic composition is a key ecological question, with many implications from estimating global diversity to conservation issues. In the first chapter, this question is addressed across the tree of life by applying the classical analytic tools of community ecology to soil DNA samples collected from various forest plots in French Guiana. The second chapter focuses on the neutral aspect of community assembly.[...]
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Bateman, Sarah Marie. "Exploring soil erosion and biodiversity in multifunctional landscapes : A case study of the South Downs, UK". Thesis, University of Nottingham, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.523025.
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Lindberg, Niklas. "Impact of climate change on soil fauna diversity : effects of experimental drought, irrigation, soil warming and nutrient addition /". Uppsala : Swedish Univ. of Agricultural Sciences, 2001. http://epsilon.slu.se/avh/2001/99-3576673-X.pdf.
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Rakiep, Adeebah. "Analysis of actinobacterial biodiversity in reservoir sediment and cave soil and screening of isolates for antimycobacterial activity". Master's thesis, Faculty of Science, 2020. http://hdl.handle.net/11427/32941.
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A total of 56 presumptive actinobacterial strains was isolated from three different samples taken from the Silvermine Nature Reserve (Table Mountain National Park, Cape Town), namely, cave soil, the wall of the cave and sediment from the shallow waters of a reservoir. Twenty nine (29) isolates were successfully identified to the genus level by 16S-rRNA gene analysis: one Micrococcus strain, one Streptacidiphilus strain, one Micromonospora strain and 26 Streptomyces strains. The phylogenetic position of each identified strain within its genus was investigated by generating a phylogenetic tree based on its 16S-rRNA gene sequence. Further analysis of the Streptacidiphilus strain was conducted based on the gyrB gene. Metagenomic analysis was used to further analyse the actinobacterial diversity of the freshwater reservoir sediment from the Silvermine Nature Reserve. A total of 97 16S-rRNA gene clones was obtained from the reservoir sediment sample, RS1, using actinobacteriumspecific 16S-rRNA gene primers S-C-Act-0235-a-S-20-F and S-C-Act-0878-a-A-19-R and each clone was identified using the EzBioCloud database. Analysis based on unique phylotypes in the clone library revealed that 80% of the clone library was composed of actinobacterial strains belonging to the orders Acidimicrobiales, Streptomycetales, Streptosporangiales, Corynebacteriales, Sporichthyales and the family Jatrophihabitandaceae (the remaining 20% was identified as non-actinobacterial strains). The percentage composition of the actinobacterial clonal diversity for each order was as follows: Acidimicrobiales, 56%; Streptomycetales, 29%; Streptosporangiales, 9%; Corynebacteriales, 4%; Sporichthyales, 1% and family Jatrophihabitandaceae, 1%. Rarefaction analysis revealed that the total actinobacterial diversity of the sample was not represented in the clone library. Therefore, further sampling and analysis of the sample site would uncover greater actinobacterial diversity. Thirty seven (37) putative actinobacterial isolates of the 56 that were isolated from the Silvermine Nature Reserve were screened for antimycobacterial activity against the non-pathogenic Mycobacterium aurum strain A+ using a standard over-lay method. A total of five identified 2 actinobacterial isolates (Streptomyces strains RS6, RS7, RS9, RS13 and RS15) and an unidentified actinobacterium, strain RS4, demonstrated very strong antimycobacterial activity (zone of growth inhibition of over 3000 mm2 ). In addition, 15 of the 37 strains were active against Staphylococcus aureus ATCC 25923 and three were active against Escherichia coli ATCC 25922. Streptomyces strains CS1, CS3, CS12, CS18, CS19, CW5, RS3, RS6, RS9, RS13 and RS15, displaying varying strengths of antimycobacterial antimicrobial activity, were selected for antibiotic extraction from culture broths. The resulting crude extracts were subjected to spot bioautography to test for antibacterial activity. The organic compounds extracted from the cell mass of Streptomyces strain CS3 and the broth fraction of Streptomyces strain RS3 demonstrated strong activity against M. aurum strain A+. Furthermore, the crude extracts of 15 actinobacterial isolates (Micromonospora strain RS10 and Streptomyces strains CS1, CS3, CS12, CS18, CW2, CW5, RS3, RS6, RS7, RS9, RS13, RS15, RS18 and RS19) were additionally tested for antiplasmodial activity against Plasmodium falciparum strain NF54. Seven of these strains showed activity against Plasmodium namely, Streptomyces strains CW2, CW5, RS3, RS7, RS13, RS15 and RS19. Streptomyces strains CW2, CW5 and RS7 displayed the strongest activity against P. falciparum strain NF54 with IC50 values below the guideline threshold of 1000 ng/mL (strain CW2 culture broth crude extract: IC50 40 ng/mL, strain CW5 culture broth crude extract: IC50 128 ng/mL and strain RS7 culture broth crude extract: IC50 70 ng/mL).
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Nakamura, Akihiro. "Development of Soil and Litter Arthropod Assemblages in Rainforest Restoration". Thesis, Griffith University, 2008. http://hdl.handle.net/10072/367553.
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Broadscale forest clearance is a major human-induced disturbance with devastating consequences for biodiversity. With a rise in public awareness of biodiversity, the last few decades have seen an increasing number of reforestation activities aimed at recreating natural habitat. To date, research on the outcomes of reforestation for biodiversity have mostly focused upon the recovery of vegetation structure and composition, with relatively little attention being paid to the recovery of fauna, especially invertebrates.
Arthropods inhabiting soil and leaf litter constitute a considerable proportion of the biomass and diversity of a given faunal community, and exhibit strong associations with ecological functioning (i.e. soil formation, decomposition). The recovery of soil and litter arthropods in restored landscapes is therefore important, not only for the recovery of biodiversity but also for the re-development of a functioning ecosystem, a goal of most types of reforestation programs. However, we know little about the patterns of development of arthropod assemblages in reforested landscapes or the mechanisms underpinning any such patterns.
The broad objective of this study was to investigate the effects of selected factors on the colonisation patterns of restored rainforest patches by soil and leaf litter arthropods. Criteria for selecting factors for study included their potential influence on the development of arthropod assemblages and their potential for manipulation by restoration practitioners. The study was conducted on the Blackall Range near Maleny, a mid-elevation (250-530 m a.s.l.) basaltic plateau in subtropical eastern Australia (26°S, 152°E). The plateau supported subtropical rainforest until European settlement in the 19th century, when most of the rainforest was cleared for pasture.
The factors selected for study, in relation to the colonisation of restored habitat patches by soil and litter arthropods, were as follows:
1. the isolation of restored habitat patches from remnant forest;
2. the efficacy of inoculation (re-introduction of rainforest soil and litter arthropods) to restored habitat patches;
3. the quality and quantity of substrate (i.e. mulch) used during the initial stages of rainforest restoration;
4. the degree of shading and depth of substrate, and their interaction; and,
5. the short- and longer-term impacts of glyphosate herbicide on arthropod assemblages.
To test explicitly the effects of these factors on arthropod colonisation of restored habitat patches, an experimental approach was adopted in this study. The first four factors were addressed by means of a manipulative field experiment. Small-scale habitat patches were created by adding sterilised mulch to an area previously treated with glyphosate herbicide, and covered with shadecloth, to simulate various conditions of forest restoration which may be experienced by colonising arthropods. In order to test for the impacts of a glyphosate herbicide on rainforest arthropods, I carried out a separate field experiment in which experimental patches were established within remnant rainforests. The experimental approach adopted in this study allowed for the construction of replicated units, while controlling for extraneous factors (e.g. heterogeneity of litter composition, habitat area, age of restoration), to enable robust examination of the effects of selected factors.
To monitor assemblage composition, arthropods were collected using two methods: pitfall traps and extraction from litter. Responses of arthropods were analysed at two main levels of taxonomic resolution: ‘coarse’ arthropods (all arthropods sorted to Order/Class) and ants, identified to species.
Before the field experiments, a survey was carried out to collect reference information on the distribution of soil and litter arthropods in remnant rainforests (undisturbed reference sites) and cleared pasture (disturbed reference sites) in the study region. Regardless of the sampling method (pitfall or litter extraction) or taxonomic resolution employed (coarse arthropods or ant species), the composition of arthropod assemblages clearly differed between rainforest and pasture. The information obtained from this survey generated potential bio-indicators of forested and cleared habitats, assisting interpretation of the data obtained from the field experiments.
The effects of habitat isolation and inoculation were tested using ‘restored’ habitat patches which were established within cleared pasture at increasing distances (0, 15, 100 and ca. 400 m) from the edges of rainforest remnants. After nine months, rainforest-dependent taxa were found to have only colonised the habitat patches closely adjacent to rainforest remnants. Attempts to increase the extent of arthropod establishment by inoculation were unsuccessful: the majority of rainforest arthropods from the raw inoculum failed to persist within the isolated plots. The results indicated that many forest-dependent soil and litter arthropods may have a limited capacity to colonise isolated restoration sites, and/ or small experimental plots in the short term. Inference from the experiment was potentially limited by the relatively small temporal and spatial scales of restoration treatments. Avoiding these limitations in future research may require controlled and replicated efforts in experimental restoration over larger areas, based on collaborations between researchers and practitioners.
To test the effects of quality and quantity of substrate on arthropod colonisation, habitat patches were established by adding either sterilised hay (a conventionally used mulching material in restoration projects) or woodchip mulch (a structurally more complex alternative), each at two depths (3-5 cm, 10-15 cm). Habitat patches were positioned within pasture adjacent to the edges of rainforest remnants to minimise the effect of isolation, and were all unshaded to create conditions similar to those during the initial stages of rainforest restoration. Despite its simple composition, hay performed better than woodchips in facilitating colonisation by arthropods characteristic of rainforest. However, neither hay nor woodchip mulch inhibited arthropods invading from the surrounding pasture. Shallow hay was favoured by ants characteristic of rainforest, but other groups of arthropods (e.g. Coleoptera, Isopoda) were associated with deep hay (10-15 cm). The optimum amount of hay may therefore vary among different groups of arthropods.
The effects of shading and mulch depth, and potential interactions between them, were tested using habitat patches created with varying degrees of shading (none, 50% or 90% shading) and two depths of woodchip mulch (3-5 cm or 10-15 cm deep). The presence of shading, at both 50% and 90%, encouraged colonisation of habitat patches by arthropods characteristic of rainforest. However, only the more complete shading treatment (90%) inhibited re-invasion of restored patches by arthropods from the surrounding pasture habitat. Effects of mulch depth were significant only for rainforest-associated ant species which responded positively to shallow mulch within shaded plots. These results suggest that moderate levels of canopy closure, as produced by tree spacings typical of timber plantations, may be sufficient to facilitate colonisation of reforested land by rainforest arthropods. However, greater canopy shading (90%) is likely to be needed to inhibit re-invasion of arthropods from surrounding pasture habitat. Using deeper woodchip mulch does not necessarily create more suitable conditions for rainforest arthropods or offset the deleterious effects of the lower levels of shading.
Paired herbicide-treated and control plots were created within rainforest remnants to test the short- (approximately three days) and long-term (approximately three months) impacts of herbicide application on soil and litter arthropod assemblages on the floor of the remnant rainforests. The results found no deleterious effects of glyphosate herbicide formulated as Roundup® Biactive™ on rainforest soil and litter arthropods; hence, this herbicide appears suitable for the control of unwanted plants in rainforest restoration projects, from the perspective of arthropod biodiversity.
The outcomes of this study also have a number of important implications for the monitoring of the development of soil and litter arthropod assemblages in restored rainforests. First, pitfall traps (a commonly used sampling technique) can provide sufficient information on the state of arthropod assemblages in the context of subtropical rainforest restoration projects, although samples collected by this method alone do not necessarily represent the whole suite of soil and litter arthropods (e.g. cryptic arthropods that live in soil and litter). Second, a combination of higher-taxon sorting of all arthropods, together with species-level sorting of a significant major taxon (ants), provides a feasible compromise between comprehensiveness and detail in monitoring responses of arthropods. Third, ‘composite habitat indices’, such as those developed in this study to quantify the extent to which a site resembles rainforest or pasture in terms of its arthropod assemblage, can help alleviate problems associated with the patchy distribution of arthropod taxa in monitoring samples.
The experimental approach adopted in this study provided information that would otherwise have been limited by post-hoc empirical studies alone. This study’s results demonstrated that the selected aspects of different restoration techniques and management affect the colonisation of soil and litter arthropod assemblages in rainforest restoration of old fields.Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Griffith School of Environment
Faculty of Science, Environment, Engineering and Technology
Full Text
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Liang, Weiguang, University of Western Sydney, of Science Technology and Environment College i of Science Food and Horticulture School. "Impact of horticultural mineral oil and synthetic pesticides on arboreal and soil fauna biodiversity within citrus orchard ecosystems". THESIS_CSTE_SFH_Liang_W.xml, 2002. http://handle.uws.edu.au:8081/1959.7/121.
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The results of the 3-year project successfully indicated that petroleum-derived spray oils can be used for effective control of a range of citrus pests including citrus leafminer, Asiatic citrus psyllid, chaff scale, red scale, citrus red mite. The results suggested that it should be possible, through use of horticultural and agricultural mineral oils and enhanced natural enemy activity, to reduce the number of pesticide sprays applied annually in China from 14-16 sprays to significantly fewer sprays in most regions. The results are also valuable as references for the implementation of citrus integrated pest management programs in Australia and other citrus-growing countries. However, despite extensive use of PDSOs in citrus and other crops since the late 1800s, few studies have been undertaken to determine their disruptive effects on orchard ecosystems or to compare their effects with those of synthetic pesticides, and these studies are limited in their scDoctor of Philosophy (PhD)
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Liang, Weiguang. "Impact of horticultural mineral oil and synthetic pesticides on arboreal and soil fauna biodiversity within citrus orchard ecosystems". Thesis, View thesis, 2002. http://handle.uws.edu.au:8081/1959.7/121.
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The results of the 3-year project successfully indicated that petroleum-derived spray oils can be used for effective control of a range of citrus pests including citrus leafminer, Asiatic citrus psyllid, chaff scale, red scale, citrus red mite. The results suggested that it should be possible, through use of horticultural and agricultural mineral oils and enhanced natural enemy activity, to reduce the number of pesticide sprays applied annually in China from 14-16 sprays to significantly fewer sprays in most regions. The results are also valuable as references for the implementation of citrus integrated pest management programs in Australia and other citrus-growing countries. However, despite extensive use of PDSOs in citrus and other crops since the late 1800s, few studies have been undertaken to determine their disruptive effects on orchard ecosystems or to compare their effects with those of synthetic pesticides, and these studies are limited in their sc
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Liang, Weiguang. "Impact of horticultural mineral oil and synthetic pesticides on arboreal and soil fauna biodiversity within citrus orchard ecosystems /". View thesis, 2002. http://library.uws.edu.au/adt-NUWS/public/adt-NUWS20030819.153206/index.html.
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Thesis (Ph.D. (Horticulture)) -- University of Western Sydney, 2002."A thesis submitted to the University of Western Sydney for the fulfillment of study for a degree of Doctor of Philosophy in Horticulture" "Principal supervisor: Robert Spooner-Hart, co-supervisor: Andrew Beattie, co-supervisor: Alfie Meats" Bibliography : leaves 231-265.
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Lucas, Shawn T. "MANAGING SOIL MICROBIAL COMMUNITIES WITH ORGANIC AMENDMENTS TO PROMOTE SOIL AGGREGATE FORMATION AND PLANT HEALTH". UKnowledge, 2013. http://uknowledge.uky.edu/pss_etds/24.
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The effects of managing soil with organic amendments were examined with respect to soil microbial community dynamics, macroaggregate formation, and plant physio-genetic responses. The objective was to examine the possibility of managing soil microbial communities via soil management, such that the microbial community would provide agronomic benefits. In part one of this research, effects of three amendments (hairy vetch residue, manure, compost) on soil chemical and microbial properties were examined relative to formation of large macroaggregates in three different soils. Vetch and manure promoted fungal proliferation (measured via two biomarkers: fatty acid methyl ester 18:2ω6c and ergosterol) and also stimulated the greatest macroaggregate formation. In part two of this research, effects of soil management (same amendments as above, inorganic N fertilization, organic production) on soil chemical and microbial properties were examined relative to the expression of nitrogen assimilation and defense response genes in tomato (Solanum lycopersicum L.). Soil management affected expression of a nitrogen assimilation gene (GS1, glutamine synthetase) and several defense-related genes. The GS1 gene was downregulated with inorganic N fertilization, expression of the pathogenesis-related PR1b gene (which codes for the pathogenesis-related PR1b protein) was increased in plants grown in soil amended with compost, vetch, and N fertilizer, and expression of three other defense-related genes coding for chitinase (ChiB), osmotin (Osm), and β-1,3-glucanase (GluA) were decreased in plants from soil amended with manure and in plants from the organically managed soil. Differential expression of defense-related genes was inversely related to the relative abundance of Gram-negative bacteria. The relative abundance of the 18:1ω7c Gram‑negative bacterial biomarker was greatest in manure treated soil and in organically managed soil (which recieves seasonal manure applications). These treatments also had the lowest expression of ChiB, Osm, and GluA, leading to speculation that manure, through increases in Gram-negative bacteria, may have suppressed populations of soil organisms that induce a defense response in plants, possibly allowing for less-stressed plants. Outcomes of this research may be useful for those interested in developing management strategies for maintaining or improving soil structure as well as those interested in understanding management effects plant physio-genetic responses.
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Struckhoff, Garrett Cletus Parkin Gene F. "Plant-assisted bioremediation of perchlorate and the effect of plants on redox conditions and biodiversity in low and high organic carbon soil". [Iowa City, Iowa] : University of Iowa, 2009. http://ir.uiowa.edu/etd/441.
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Vincent, Quentin. "Étude des paramètres abiotiques, biotiques et fonctionnels, et de leurs interactions dans des sols délaissés". Thesis, Université de Lorraine, 2018. http://www.theses.fr/2018LORR0015/document.
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Suite à des usages intensifs d’origines industrielles, des surfaces considérables de sols dégradés, peu fertiles, voire contaminés sont délaissées. Dans un contexte de raréfaction des sols et de pressions foncières et économiques grandissantes, la réhabilitation de ces sols fortement anthropisés et délaissés peut-être un enjeu. Toutefois, pour envisager une réutilisation de ces sols, il est nécessaire de mieux les caractériser. L’étude de la qualité des sols prend rarement en compte la biodiversité et le fonctionnement biologique. Ainsi, l’objectif de ce travail de thèse était de caractériser des sols délaissés, en prenant en compte leurs paramètres abiotiques, biotiques et fonctionnels. Pour cela, six sols fortement anthropisés délaissés du nord-est de la France, correspondant à différentes activités industrielles, ont été étudiés in situ et en laboratoire. Plusieurs groupes biotiques (bactéries, champignons, mésofaune, macrofaune et flore) ont été étudiés afin d’avoir une approche quasi-exhaustive de la biodiversité des sols. Une approche taxonomique et fonctionnelle (basée sur les traits) de la biodiversité a été réalisée pour les champignons, la méso- et la macrofaune. De plus, l’évolution in situ au cours du temps des paramètres abiotiques et biotiques a été prise en compte sur un des six sols délaissés étudiés. Enfin, les interactions biotiques entre une espèce de collembole, de champignon mycorhizien à arbuscules et de plante herbacée ont été étudiées dans deux sols délaissés, en laboratoire. Nous avons montré que les sols délaissés étaient caractérisés par une biodiversité significative, comparable selon les cas, à celles d’autres types de sols, comme les sols forestiers, de prairies ou agricoles. Toutefois, des différences de densité, de richesse et de structures taxonomiques et fonctionnelles entre les sols délaissés existent et dépendent du groupe biotique étudié. Ces différences sont notamment liées aux propriétés physico-chimiques contrastées de ces sols. Ainsi, un sol construit, amendé en compost, était l’écosystème le moins perturbé des sols étudiés, contrairement à un autre sol construit et contaminé en métaux lourds. Nous avons montré que les paramètres physico-chimiques, et surtout biologiques, évoluaient rapidement au cours du temps (environ un an) dans le sol construit contaminé en métaux lourds. Enfin, nous avons mis en évidence, dans les deux sols étudiés en laboratoire, des modifications des interactions biotiques sous l’influence de nombreux paramètres comme le volume de sol, la durée de l’interaction, la présence d’une microflore indigène etc. Finalement, nous avons montré que ces sols pouvaient être le support de services écosystémiques tels que l’habitat pour la biodiversité et qu’ils pouvaient être fonctionnels, permettant ainsi de considérer leur potentielle valorisationDue to industrial activities intensification, large surfaces of degraded soils, with low fertility and sometimes contamination, are derelict. In the context of land depletion and economic pressure, the rehabilitation of these derelict anthropogenic soils could be a key issue. However, these derelict soils needs to be better characterized before to consider their potential use. Soil quality studies rarely take into account the biodiversity and the biological functioning. Thus, the aim of this PhD work was to characterize derelict soils by considering their abiotic, biotic and functional parameters. To this end, six derelict strongly anthropogenic soils from north-eastern France, resulting from different industrial activities, were studied in situ and in laboratory. Several biotic components (bacteria, fungi, mesofauna, macrofauna and flora) were studied to have an almost complete approach of the soil biodiversity. Taxonomical and functional (trait-based approach) study of biodiversity was performed for fungi, meso- and macrofauna. Moreover, the in situ evolution over time of abiotic and biotic parameters was taken into account in one of the six studied derelict soils. Lastly, biotic interactions between a species of Collembola, of arbuscular mycorrhizal fungi and of herbaceous plant were studied in two derelict soils, in a growth chamber. We showed that derelict soils were characterized by a significant biodiversity, comparable case to case with other kinds of soils like forest, grassland or crop. Nevertheless, differences in terms of density, richness and taxonomical and functional structure community were observed between soils and depend on considered biotic group. These differences were notably linked with contrasting physico-chemical parameters between soils. Thus, a compost-amended constructed soil was the less disturbed among the six studied soils, in contrast with a heavy metal-contaminated constructed soil. We showed that abiotic parameters, notably biotic parameters, evolved quickly (within one year) in the metal-contaminated constructed soil. In the two derelict soils where interactions between Collembola and mycorrhizal fungi were studied, biotic interactions were affected by several parameters like soil volume, time of interaction, indigenous microflora presence etc. Finally, we have shown that these derelict soils support ecosystems services such as biodiversity reserve and could be functional, allowing potential re-use
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Franco, André Luiz Custódio. "Soil engineering by macroinvertebrates: controls on soil organic matter storage across land use change". Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/11/11140/tde-26052015-165800/.
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Globally land use change (LUC) with increasing in land use intensity has led to a decrease in soil organic matter (SOM). The reduction of soil C stock across LUC has been accompanied by a destabilization of soil structure and increases the soil erosion susceptibility. The destabilized soil structure is also concomitant with a loss of soil biodiversity and in particular, soil macroinvertebrate community. The focus of this dissertation is the effect of LUC with increasing in land use intensity on soil macrofauna, aggregation and SOM allocation. We hypothesized that LUC reduces soil macrofaunal biodiversity and consequently decreases soil engineering processes, resulting in destabilization of soil structure and impairing the ability of soil to physically protect SOM from decomposition inside stable aggregates, finally leading to depleted SOC stocks across LUC. In order to test these hypotheses, we conducted a field survey in 3 chronosequences of land use comprising native vegetation (NV), pasture (PA), and sugarcane crop (SC) in Central-Southern Brazil. This land use sequence provides a gradient of land use intensity and is projected to add 6.4 Mha of new sugarcane areas in Brazil by 2021. At each sampling point soil blocks of 25 X 25 cm and 5 x 5 cm to 10 cm depth were simultaneously collected from 0-10 cm, 10-20 cm, and 20-30 cm soil layers, for macrofauna isolation and aggregate fractionation, respectively. Within a radius of 6 meters around each sampling point, 12 subsamples were also collected from the same soil layers, and combined for total soil C and N concentration. An average reduction of 89% in the density of the soil macrofaunal community was observed when SC replaces PA, and a loss of 39% in the diversity of macrofauna groups. Our findings showed that, over a range of soil textures (16 - 66% clay), such biodiversity loss was strongly correlated with the destabilization of soil structure across LUC, whereas soil texture was not so. These observations consistently indicate that the abundance of detritivore soil animals, especially earthworms and termites, may be a significant predictor of soil structure transformations across LUC in tropical environments. Moreover, the sharp reduction in the abundance of earthworms was strongly positively correlated with the decrease in intra macroaggregate-associated C. As a result, after more than 20 years of sugarcane crop there were losses of 40 and 35% of C and N stocks, respectively, resulting in a rate of C emission of 1.3 Mg ha-1 yr-1. This C loss primarily occurred in the macroaggregate-associated C, as a result of the faster macroaggregate turnover under SC. In summary, the results presented here provide a mechanistic explanation as to why there is soil C depletion when increasing land use intensity in tropical soils: the huge reduction in the abundance of soil engineering invertebrates after LUC impair the ability of soil to physically protect SOM from decomposition inside stable aggregates, and therefore it is a primary mechanism controlling the soil C stocks\' depletion across LUC.Globalmente mudanças no uso da terra (MUT) com o aumento da intensidade de uso do solo têm levado a uma diminuição da matéria orgânica do solo (MOS). A redução do estoque de C do solo após MUT tem sido acompanhada por uma desestabilização da estrutura do solo e aumento da susceptibilidade a erosão. A desestabilização da estrutura também é concomitante com a perda da biodiversidade do solo e, em particular, da comunidade de macroinvertebrados do solo. O foco deste trabalho é o efeito de MUT com aumento na intensidade de uso do solo sobre a macrofauna do solo, agregação e alocação da MOS. Nossa hipótese é que MUT reduz a diversidade da macrofauna do solo e, conseqüentemente, diminui os processos de engenharia de solo, resultando na desestabilização da estrutura do solo e prejudicando a capacidade do solo para proteger fisicamente a MOS da decomposição dentro de agregados estáveis, finalmente levando a redução dos estoques de C após MUT. Foi realizada uma pesquisa em 3 cronosseqüências de uso da terra que compreendem vegetação nativa (NV), pastagem (PA), e cana-de-açúcar (CA) na região Centro-Sul do Brasil. Esta MUT fornece um gradiente de intensidade de uso do solo e é projetada para adicionar 6,4 Mha de novas áreas de CA no Brasil até 2021. Em cada ponto de amostragem de solo blocos de 25 x 25 cm e 5 x 5 cm a 10 cm de profundidade foram coletados simultaneamente das camadas 0-10 cm, 10-20 cm e 20-30 cm de solo, para isolamento da macrofauna e fracionamento de agregados, respectivamente. Foi observada uma redução média de 89% na densidade da comunidade da macrofauna quando CA substitui PA, e uma perda de 39% da diversidade de grupos. Nossos resultados mostraram que, em um intervalo de texturas do solo (16-66% de argila), tal perda de biodiversidade foi fortemente correlacionada com a desestabilização da estrutura do solo após MUT. Estas observações indicam consistentemente que a abundância de animais detritívoros, especialmente minhocas e cupins, pode ser um preditor significativo de transformações da estrutura do solo em MUT. Além disso, a forte redução na abundância de minhocas foi fortemente e positivamente correlacionada com a diminuição do C alocado intra macroagregados. Como resultado, após mais de 20 anos de cultura de CA houve perdas de 40 e 35% dos estoques de C e N, respectivamente, resultando em uma taxa de emissão de C de 1,3 Mg ha-1 ano-1. Esta perda de C ocorreu principalmente no C associado aos macroagregados, como um resultado da reciclagem mais rápida dos macroagregados sob CA. Em resumo, os resultados aqui apresentados fornecem uma explicação mecanicista a respeito de porque há esgotamento do C do solo quando aumenta-se a intensidade de uso do solo em ambientes tropicais: a enorme redução na abundância de invertebrados \"engenheiros do solo\" após MUT prejudica a capacidade do solo para proteger fisicamente a MOS da decomposição dentro de agregados estáveis, e, portanto, é um mecanismo primário controlando a redução dos estoques de C no solo relacionada a MUT.
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Damaso, Natalie. "Biogeographical Patterns of Soil Microbial Communities: Ecological, Structural, and Functional Diversity and their Application to Soil Provenance". FIU Digital Commons, 2016. http://digitalcommons.fiu.edu/etd/3006.
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The current ecological hypothesis states that the soil type (e.g., chemical and physical properties) determines which microbes occupy a particular soil and provides the foundation for soil provenance studies. As human profiles are used to determine a match between evidence from a crime scene and a suspect, a soil microbial profile can be used to determine a match between soil found on the suspect’s shoes or clothing to the soil at a crime scene. However, for a robust tool to be applied in forensic application, an understanding of the uncertainty associated with any comparisons and the parameters that can significantly influence variability in profiles needs to be determined. This study attempted to address some of the most obvious uncertainties of soil provenance applications such as spatial variability, temporal variability, and marker selection (i.e., taxa discrimination). Pattern analysis was used to validate the ecological theories driving the soil microbial biogeography. Elucidating soil microbial communities’ spatial and temporal variability is critical to improve our understanding of the factors regulating their structure and function. Microbial profiling and bioinformatics analyses of the soil community provided a rapid method for soil provenance that can be informative, easier to perform, and more cost effective than approaches using traditional physico-chemical data. This study also showed that stable profiles may allow comparison between evidence and a possible crime scene despite the time lapse (4 years) between sample collections, however, this is dependent on the analysis method, site, vegetation, and level of disturbance. Marker selection was also an important consideration for profiling. Even though Fungi look promising for single taxon soil discrimination, the additional markers can help discriminate between a wide variety of soil types. As in human identification, the more DNA markers queried the greater the discrimination power. Lastly, this study illustrated a novel method to query the iron relating genes and ability to design a novel marker that can easily be used to profile the functional diversity of a soil community to enhance soil classification. Overall this research demonstrated the potential and effectiveness of using microbial DNA from soil, not just for comparison, but also for intelligence gathering to pinpoint the geographic origin of the soil.
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Majeed, Muhammad Zeeshan. "Emissions of nitrous oxide by tropical soil macrofauna : impact of feeding guilds and licrobial communities involved". Thesis, Montpellier 2, 2012. http://www.theses.fr/2012MON20073/document.
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Les sols représentent environ 63% des émissions de N2O et à eux seuls les sols tropicaux représentent 23% de ce budget soit une contribution bien plus élevé que les sols tempérés. Ces sols sont connus pour abriter une grande biodiversité d'invertébrés dominés par quatre types i.e. termites, vers de terre, fourmis et larves de scarabaeid. Ces groupes macrofaunal sont considérés comme des ingénieurs des sols via notamment leurs actions de régulation de la disponibilité des ressources chimiques, tels que l'azote minéral pour les micro-organismes. Cette régulation est due à leurs capacités de digestion spécifiques de la matière organique ainsi que la création et/ou la modification des habitats des sols. Cette étude est basée sur l'hypothèse suivante (i) l'environnement digestif et les structures biogéniques de ces ingénieurs du sol sont considérées comme des « hot spot » d' émissions de N2O (ii) les taux d'émission de N2O varient en fonction de leurs régimes alimentaires, cette macrofaune ingérant des substrats avec différents C:N (iii) le taux d'émission de N2O de chaque invertébré est corrélé à la densité des communautés bactériennes digestives impliquées dans l'émission de N2O (bactéries nitrifiantes et dénitrifiantes) et à leur teneur en azote minéral dans leur tube digestif. Pour évaluer ces différentes hypothèses, des mesures des taux d'émission de N2O ont été effectuées in vitro en aérobiose pour la macrofaune (30 espèces différentes en provenance d'Afrique, d'Amérique du Sud et d'Europe) et leurs matériels biogéniques associées (nids, turricules). L'abondance des gènes fonctionnelles des bactéries nitrifiantes (AOA et AOB) et dénitrifiantes (nirK, nirS, nosZ) ont été quantifiés par PCR quantitative. Les termites humivores et champignonnistes ainsi que les larves de scarabaeid émettent des quantités significatives de N2O alors que les fourmis n'en émettent pas. Quand aux termites xylophages et litièrivore, ils absorbent le N2O. Les structures biogéniques des vers de terre (turricules) et des fourmis (nid) émettent des quantités importantes de N2O ce qui n'est pas le cas des nids de termites. La faune du sol et leurs structures biogéniques associées, sont donc, dans la majorité des cas étudiés, un lieu d'émission de N2O, confirmant ainsi notre première hypothèse. Ce travail a également démontré qu'il y a avait une étroite corrélation entre régime alimentaire et intensité de l'émission de N2O au sein de chaque type de macrofaune étudié. En revanche, l'abondance des gènes des communautés digestive nitrifiantes et dénitrifiantes et le contenu en N minéral au sein du tube digestif ne semblent pas être des proxies pertinents des émissions de N2O. A partir de ces mesures, des calculs ont été effectuées pour déterminer l'importance de ces émissions à l'échelle des écosystèmes tropicaux étudiés (forêt et savane). Ces calculs suggèrent que la macrofaune du sol dans ces écosystèmes pourrait contribuer entre 0,1 à 11,7% et 0,1 à 8,8% du budget total des émissions de N2O, respectivement. Les résultats de ces travaux devraient contribuer à une meilleure prise en compte de la composante biotique dans la modélisation des émissions de gaz à effet de serre provenant des sols en milieu tropicalSoils account for about 63% of N2O emissions. Tropical soils are estimated to emit 23% of global N2O emission budget which is much higher than temperate soil N2O emissions. These soils also harbor a huge biodiversity of invertebrates dominated by four types of macrofauna i.e. termites, earthworms, ants and scarabaeid grubs. These macrofaunal groups are considered as soil engineers because they regulate the availability of chemical resources, like mineral nitrogen, for the microorganisms via their specific digestion capabilities and/or by creating and modifying soil habitats. This study is based on the following hypothesis (i) the gut environment or biogenic structures of these soil engineers are considered as hotspots of N2O emission (ii) the N2O emission rates will vary according to their feeding behavior as these macrofauna thrive on diverse substrates with different C:N ratio (iii) the rate of N2O emission in each soil fauna will also depend on the gut density of the bacterial communities involved in the N2O emission (nitrifiers and denitrifiers) and on the mineral nitrogen content within the gut. To assess these different hypotheses in-vitro short-term N2O emission rates were assessed for either live macrofauna (30 species collected from Africa, South America and Europe) or their biogenic materials or both under aerobic incubations. Genes abundance of nitrifiers (AOA and AOB) and denitrifiers (nirK, nirS, nosZ) were quantified by real time quantitative PCR. Soil-feeders and fungus-growing termites and scarabaeid grubs emitted in-vivo N2O while ants did not. Surprisingly, wood- and grass-feeding termites revealed an uptake of N2O. Biogenic structures of earthworms and ants emitted substantial amount of N2O while those of termites did not. The emission difference between macrofauna or their biogenic materials and their control materials was significant for most of the macrofaunal groups studied confirming our first hypothesis. We also confirmed that the feeding behavior (total N content and C:N ratio of food material) is the main factor explaining the observed N2O emission pattern of each macrofaunal group investigated whereas genes abundances, particularly of denitrifiers and gut N mineral content did not appear to be relevant proxies of the N2O emissions rates. A back-on-the-envelope data upscaling suggests that soil macrofauna could contribute from 0.1–11.7% and 0.1–8.8% of the total soil N2O emissions, respectively, for the tropical rainforest and dry savanna ecosystems. This work should contribute to a better estimation of the soil biotic compartment in the different models of greenhouse gas emissions from tropical soils
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Malmström, Anna. "Effects of wildfire and prescribed burning on soil fauna in boreal coniferous forests /". Uppsala : Department of Ecology and Environmental Research, Swedish University of Agricultural Sciences, 2006. http://epsilon.slu.se/2006111.pdf.
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Lemenih, Mulugeta. "Effects of land use changes on soil quality and native flora degradation and restoration in the highlands of Ethiopia : implications for sustainable land management /". Uppsala : Dept. of Forest Soils, Swedish Univ. of Agricultural Sciences, 2004. http://epsilon.slu.se/s306.pdf.
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Jones, Isabel L. "Legacies of tropical forest fragmentation and regeneration for biodiversity and carbon storage". Thesis, University of Stirling, 2017. http://hdl.handle.net/1893/26238.
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Expanding anthropogenic development within the tropical forest biome is driving the loss of an irreplaceable global resource. Mega-diverse tropical forests are vital for regulating the global carbon cycle, and are essential for climate change mitigation. Today, over half of the world’s remaining tropical forest is degraded or regenerating secondary forest. Tropical forests are becoming increasingly fragmented through the expansion of agriculture and roads. Landscape-scale flooding of terrestrial habitats caused by dam construction is an emerging driver of habitat loss and fragmentation. Much attention has been paid to the long-term impacts of tropical forest fragmentation for biodiversity, ecosystem functioning, and carbon emissions. Most of our understanding of the impacts associated with habitat fragmentation originates from systems in which the habitat matrix surrounding remnant forest patches is another, albeit low quality, terrestrial habitat. However, dam-induced habitat fragmentation results in remnant terrestrial biological communities becoming isolated on islands within a water matrix. A water matrix presents the worst-case scenario for remnant habitat fragments. In Chapter 2 I synthesise the results of numerous studies reporting the responses of taxonomic groups to isolation on reservoir land-bridge islands, and uncover a globally-applicable pattern of extinction debt acting upon remnant biological communities on reservoir islands. All islands, regardless of taxonomic group, habitat type, or island area lose species as island isolation time increases. Moreover, I show that contrary to existing ecological theory, once terrestrial habitat becomes isolated within a water matrix, it is effectively too isolated for species losses to be buffered by metapopulation dynamics. Dam development is rapidly expanding in the largest remaining tract of intact tropical forest, the Amazon Basin. In Chapters 3 and 4 I study the Balbina mega-dam system in the central Brazilian Amazon. Here, I use detailed field inventories of trees and lianas on islands and in continuous mainland habitat to determine the impact of landscape-scale habitat fragmentation caused by reservoir creation on these taxonomic groups. I find that islands maintain tree communities at significantly lower densities, richness and diversity compared to continuous forest. Furthermore, tree communities on islands exhibit compositional divergence from those found in mainland continuous forest. Island tree assemblages are dominated by low-wood density species, and may be on a trajectory towards communities characteristic of early successional forests with reduced carbon storage capacity. In contrast, liana assemblages remain compositionally intact and are becoming increasingly dominant relative to trees. Thus, lianas appear robust to many of the negative impacts associated with landscape-scale habitat fragmentation. As insular tree communities continue to degrade through area- and edge-effects, lianas may become a key feature of this archipelagic landscape due to their competitive advantage over trees in disturbed forest habitats. Lianas significantly inhibit tree recruitment and carbon storage. Thus, findings from Chapters 3 and 4 provide strong evidence for additional, and currently unaccounted-for biodiversity and carbon impacts associated with tropical dams. As development of tropical forest regions increases, there is an urgent need to reconcile the need for resources with the need for ecosystem service provision, such as carbon storage, particularly as we attempt to mitigate the impacts of rising atmospheric carbon. Recent studies have shown that secondary tropical forests have the potential to rapidly uptake atmospheric carbon, and act as a powerful tool in climate change mitigation policy. Broad-scale estimates of secondary forest carbon uptake are currently based on above-ground biomass alone. In Chapter 5 I present carbon stock estimates of additional tropical forest carbon pools - soil and dead woody biomass - in secondary forests ranging from 40-120 years. I find that soil fertility (nitrogen concentration) is key in determining carbon storage in secondary forests, and that the stability of carbon stocks held in dead woody biomass increases with secondary forest stand age. I highlight the need to integrate detailed site-specific information into broad-scale predictive models of secondary tropical forest carbon sequestration. This thesis links ecological theory and landscape-scale field inventories, to provide new understanding of the long-term costs of tropical forest fragmentation for biodiversity conservation and carbon storage, and provides further evidence of the important role secondary tropical forests may play in carbon sequestration and climate change mitigation.
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Kumpula, Kimmo. "Systematic comparison of the relative accuracy of vegetation surveys and soil DNA metabarcoding : Assessing plant biodiversity at different spatial scales". Thesis, Umeå universitet, Institutionen för ekologi, miljö och geovetenskap, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-172130.
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Analysis of soil-derived DNA has been shown to minimize problems seen during traditional vegetation surveys, e.g. by matching the eDNA to a reference database for taxonomic identification rather than relying solely on taxonomic expertise. However, it has been debated to what extent and how accurately eDNA acts as a proxy for biodiversity. The reliability on eDNA and the awareness on influencing factors is also important for palaeoenvironmental reconstructions where above-ground vegetation cannot be used. This study aimed to investigate how well modern soil-derived eDNA reflects the contemporary vascular vegetation communities in a subarctic environment, and if the efficiency of the taxonomic identification differed between spatial scales. Near-surface soil samples at altitudinal gradients along numerous transects were collected in combination with vegetation surveys. The eDNA was amplified through metabarcoding using the P6 loop region of the chloroplast trnL intron, followed by a high-throughput sequencing. No difference in the number of identified taxa between eDNA and vegetation survey was seen at landscape scale. In contrast, the number of identified taxa was consistently higher in the vegetation survey at smaller spatial scales. The efficiency of identified taxa per scale remained stable for the vegetation survey, whereas for eDNA, a decreasing trend was seen. This study highlights the variations on taxa identification between both methods and which factors might cause it. Combining the methods allows for a more precise modern biodiversity estimation, as well as to minimize wrongful conclusions. This allows for a more accurate palaeoenvironmental reconstructions, which in turn can improve future species conservation decisions.
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Peretti, Emiliano. "Exploring the diversity of a neglected group of soil invertebrates (Chilopoda) across the South-Eastern Prealps". Doctoral thesis, Università degli studi di Padova, 2019. http://hdl.handle.net/11577/3423294.
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Despite their documented importance in maintaining ecosystem functioning, many groups of soildwelling
invertebrates have been inadequately studied with regards to many facets of their biology.
In this thesis, I focussed my attention on two poorly understood aspects of the diversity of soildwelling
invertebrates: (i) local values of species richness and (ii) species boundaries. As a study
system, I used one of the most neglected groups of soil invertebrates, i.e. the centipedes
(Myriapoda: Chilopoda), and I carried out my research in the area of the Southeastern Prealps,
which are known to harbour a large amount of biodiversity.
The present work is in the form of a paper collection and contains a general introduction, two
chapters and a conclusive paragraph. An original research article, dealing with the aforementioned
topics, is presented at the end of each chapter.
In chapter I, I addressed the dearth of knowledge on the local species richness of centipede
communities. I applied statistical models to estimate the actual species richness of 10 centipede
communities in the Southeastern Prealps and to compare richness values between these
communities. I demonstrated that up to 27-28 species of centipedes can coexist in syntopy in
temperate forests of the Southeastern Prealps, and that richness values can vary significantly
among communities.
In chapter II, I addressed the issue of species delimitation in poorly-vagile endogeic invertebrates,
for which traditional morphology-based taxonomy has proven ineffective in identifying species
boundaries. In particular, I applied a rigorous integrative approach, in order to test for the existence
of species boundaries in a set of populations traditionally referred to a single species of endogeic
centipede, i.e., Clinopodes carinthiacus (Chilopoda: Geophilomorpha). Taking advantage of the
integration between different lines of evidence (sequences from three DNA loci and morphological
characters) and different methods for species discovery (ABGD, GMYC, PTP and Expectation
Maximisation cluster analysis with v-fold cross-validation), I found evidence for the existence of at
least two candidate species within the investigated population system.
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Law, Audrey. "EVALUATING THE EFFECTS OF ORGANIC AND CONVENTIONAL INPUTS ON SOIL CHEMICAL AND BIOLOGICAL PROPERTIES IN A FOUR-YEAR VEGETABLE ROTATION AND THE INVESTIGATION OF SOIL MICROBIAL PROPERTIES ON PLANT GENE EXPRESSION". UKnowledge, 2009. http://uknowledge.uky.edu/gradschool_diss/704.
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The objective of this research was to determine the effects of conventional inputs on soil chemical and biological properties compared to organic systems in a four year vegetable rotation. Tillage and cover crops were the same in all treatments to avoid confounding factors often present in similar research. Additional experiments investigated plant gene expression in organic and conventional management systems and in soils with decreased microbial diversity. Experimental plots were prepared in the spring of 2004; four replications of three management treatments, organic, low-input and conventional, were arranged in a randomized complete block design. The rotation consisted of edamame soybean, sweet corn, fallow (pastured poultry in organic plots), and potatoes. Soil samples were taken in the spring and fall of each year, along with data for pest damage, weed control, yield and quality. Soil samples were analyzed for enzyme activity (maximum activity under substrate saturation) and basic soil chemical properties. Treatments were compared over time using 2-Way ANOVA. Multiplex terminal-restriction fragment length polymorphism (M-TRFLP) profiles of the soil microbial community were compared using Multiple Response Permutation Procedures (MRPP). Multi-way ANOVA detected significant treatment effects over time in total carbon, nitrogen, Mehlich III K, Exchangeable K and exchangeable Na (p=0.05). Many significant changes in soil properties over time could not be attributed to treatment effects. All treatments produced similar yields, indicating that successful organic production of these vegetables is possible in Kentucky. Input costs for organic were 37% higher than conventional, due to the cost of organic fertilizer. The organic system required nearly 50% more labor hours than conventional or low-input. The low-input system was the most cost effective, with 58% less input expenses than the conventional system. Microarray analysis of approximately 37,500 Glycine max transcripts did not show significant differences in the gene expression between plants grown organically and conventionally, in plots with significant soil chemical and microbial differences. An experiment in progress is investigating changes in plant gene expression using real time RT-PCR in tomatoes grown in autoclaved soil and native field soil.
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Zewdie, Mulugeta. "Temporal changes of biomass production, soil properties and ground flora in Eucalyptus globulus plantations in the Central highlands of Ethiopia /". Uppsala : Dept. of Forest Soils, Swedish University of Agricultural Sciences, 2008. http://epsilon.slu.se/200818.pdf.
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González-Rivas, Benigno. "Tree species diversity and regeneration of tropical dry forests in Nicaragua /". Umeå : Dept. of Silviculture, Swedish University of Agricultural Sciences, 2005. http://epsilon.slu.se/200558.pdf.
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Adolphson, Honi M. "Acari (Mite) Abundance And Diversity In Soil And Litter Layers Of Eucalyptus Globulus Labill (Tasmanian bluegum) Plantations In Southwest Western Australia". Thesis, Edith Cowan University, Research Online, Perth, Western Australia, 2000. https://ro.ecu.edu.au/theses/1542.
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With the increased planting of E. globulus monoculture plantations, concerns surround the impact these mass plantings will have on the soil environment and wider ecosystem. Soil and litter mites are the dominant saprophages of terrestrial ecosystems, contributing to decomposition processes through their comminution and grazing activities. Despite the importance of mites to decomposition processes, there have been no investigations to date of the litter and soil communities under these plantations within Australia. This study investigated the impact of Eucalyptus globulus subsp. globulus (Tasmanian bluegum) monoculture plantations on the diversity and abundance of the soil and litter acarine (mite) fauna. Mite communities under three 8 year-old E. globulus plantations sited on reclaimed pastureland were compared with an adjacent native E. marginata (jarrah) forest and a grazed pasture in the mediterranean-type region of southwest Western Australia. Sites were sampled in spring 1997 and new sites randomly selected in autumn 1998. Large seasona1 variations in abundance and diversity were found between the sampling periods of spring 1997 and autumn 1998, influenced considerably by soil moisture. Species richness was consistently higher in both the soil and litter layers under native jarrah forest, with the E. globulus plantations intermediate in species richness between the native forest and grazed pasture. A total of 114 mite species/morphospecies was recognized; 16 Mesostigmata, 52 Prostigmata, 45 Oribatida (Cryptostigmata) and 1Astigmata. Species diversity in the surface litter was higher under the native forest, reflecting the greater heterogeneity of the litter. Diversity in the underlying soil was similar for the native forest and E. globulus plantation, although there were considerable differences in species richness. Soil diversity in the pasture was very poor in comparison to the two forest systems, reflecting the absence of a litter layer and reduced niche dimensions. The monospecific E. globulus litter possibly reduced niche variety by simplifying the physical habitat and reducing the variety of resources available for the saprophagous fauna, of which the oribatid mites are a major component. Consequently, the number of families represented in the microphytophagous, phytophagous and predator functional groups under the E. globulus plantation may have been reduced. The most common oribatid families under the plantation were those often reported from disturbed habitats, Oppiidae and Tectocepheidae, and those common in many habitats, Oppiinae and Oppiellinae. An important management implication arising from this study is that these plantations would harbour a more diverse mite fauna if planted as a mixed tree stratum.
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Viketoft, Maria. "Soil nematode communities in grasslands : effects of plant species identity and diversity /". Uppsala : Dept. of Ecology, Swedish University of Agricultural Sciences, 2007. http://epsilon.slu.se/200748.pdf.
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Faugier, Aurélie. "Diversité bactérienne des sols : accès aux populations à effectifs minoritaires "the rare biosphere"". Phd thesis, Ecole Centrale de Lyon, 2010. http://tel.archives-ouvertes.fr/tel-00502105.
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L'exploration complète de la diversité bactérienne reste incomplète, due à des limitations techniques (extraction d'ADN incomplète, limites des techniques de caractérisation...), à la complexité et l'hétérogénéité de la matrice sol (présence de microenvironnements...) et à l'existence de populations numériquement faibles. Bien que ces populations minoritaires jouent probablement un rôle important dans le fonctionnement de la communauté, elles sont rarement détectées par les techniques conventionnelles. Nos objectifs dans le cadre de ce travail de thèse ont été de développer des approches tant conceptuelles que techniques qui permettent d‟accéder à un niveau plus important de la diversité bactérienne présente dans les environnements complexes comme les sols. La première approche a pour but de favoriser le développement de bactéries minoritaires grâce à l'inoculation de communautés bactériennes dans des sols stérilisés avec des propriétés physico-chimiques différentes, afin de confirmer ou d‟infirmer le concept de Baas Becking « tout est partout et l‟environnement sélectionne ». Les changements de structures des communautés bactériennes inoculées, sont analysés à l'aide de puces à ADN taxonomique nouvellement développées. Les résultats confirment clairement l'impact de l'environnement sur la structure des populations bactériennes. De plus l'analyse des puces à ADN révèle des bactéries précédemment non détectées, confirmant la présence de populations minoritaires et la possibilité d‟augmenter leur abondance relative sous différentes conditions. La deuxième approche consiste au développement d'une souche bactérienne capable de capturer in situ des fragments d‟ADN. Elle a pour but d'éviter l'étape d'extraction d‟ADN. Cet outil est basé sur la construction d'un système de contre sélection positive permettant de sélectionner les clones ayant intégré des gènes d'intérêt. Nos travaux montrent clairement qu'il est possible d'améliorer l'accès à cette « rare biosphere » sans toutefois pouvoir répondre entièrement à la question : est-ce que tout est partout?
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MEI, GIACOMO. "Vegetation, Soil and Pedofauna as Proxy to Understand Ecology of Ostrya Carpinifolia Forests in Europe". Doctoral thesis, Università Politecnica delle Marche, 2019. http://hdl.handle.net/11566/263606.
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Identificati i boschi di Ostrya carpinifolia come una delle formazioni forestali più diffuse e caratteristiche della regione biogeografica Appennino-Balcanica e rilevata la carenza di studi e dati nonché la mancata inclusione di queste cenosi tra gli Habitat descritti a livello Europeo, lo scopo principale del progetto di ricerca sviluppato durante il dottorato e riassunto in questo lavoro, è stato quello di fornire dati utili per comprendere il valore ecologico, la dinamica, le potenzialità e le minacce di queste cenosi. Al fine di fornire un quadro il più completo possibile, il progetto è stato articolato in tre punti chiave. (I) L'analisi delle dinamiche relative alla gestione tradizionale del ceduo, la sua modifica e il suo abbandono. Fondamentale per definire la durata ottimale del turno e gli effetti ecologici dell'abbandono, è condotta attraverso lo studio approfondito delle cenosi in diversi momenti del turno e successivamente all’abbandono gestionale, nelle aree appenniniche. (II) Lo studio degli effetti dell'isolamento ecologico su queste cenosi. Utile per delineare il valore ecologico delle cenosi isolate esistenti, le dinamiche attuali e l'individuazione di un'area minima di intervento; condotto mediante uno studio approfondito dei boschi residui di Ostrya carpinifolia presenti nel territorio della regione Marche. (III) Il censimento preliminare di queste formazioni sul territorio Italiano e Balcanico, imperniato sulla raccolta di dati floristico-vegetazionali, pedologici, strutturali e gestionali di queste cenosi a scala di areale. Il risultato principale di questa ampia campagna di raccolta dati è la creazione di set di dati relativi alle caratteristiche ecologiche e gestionali, riguardanti l'intera area di distribuzione e tutte le diverse fasi di gestione. L'interpolazione e la rielaborazione di questi dati permette infatti di migliorare la comprensione delle formazioni forestali in esame, rendendo possibile interpretare le dinamiche e valutare il reale valore ecologico che caratterizza le foreste di Ostrya Carpinifolia. Aspetti questi, difficilmente affrontabili con i dati fino ad oggi disponibili in letteratura, ma che assumono un ruolo chiave nella realizzazione di modelli di previsione dinamici su base ecologica, sostanziali al fine della pianificazione forestale e paesaggistica. Gli studi effettuati e riportati in questa sede, mostrano come queste formazioni, comunemente etichettate come poco interessanti da un punto di vista ecologico, siano invece caratterizzate da una flora particolarmente ricca, un dinamismo molto vivace e da una forte resilienza. Pertanto, queste cenosi non devono essere interpretate come fasi transitorie o di recupero di cenosi più "mature", ma formazioni forestali semi-naturali stabili, molto ricche in termini di biodiversità ed oggi minacciate dal diffuso abbandono, esattamente come gli habitat di prateria secondaria.Having identified the Ostrya carpinifolia forests as one of the most widespread forest types in the Apennines-Balkan bio-geographical region and having highlighted the shortage of studies, and the lack of inclusion of these coenoses in the habitats described at European level, the main purpose of the Ph.D research project, summarized in this work, was to provide useful data to understand the ecological value, the dynamics, the potentiality and the threats of these coenoses. In order to provide an image as complete as possible, the project was articulated into three key points. (I) The analysis of the dynamics related to traditional coppice management, its modification and abandonment, useful to identify the optimum duration of the rotation and the ecological effects of the abandonment, carried out through the in-depth study of coenoses during different moments of the rotations examined and after a decades of abandonment in the Apennines areas. (II) The investigation of the effects of ecological isolation on these coenoses, useful in establishing the ecological value of the existing isolated coenoses, the current dynamics and the identification of a minimal area of intervention, carried out by in-depth study of the residual Ostrya carpinifolia woods present in the territory of the Marche region. (III) A preliminary census of these forest formations along the Italian and Balkan territories, carried out by collecting floristic-vegetational, pedological, structural and management data of these coenoses at the whole geographic distribution range. The main result of this large data collection campaign is the creation of datasets related to the ecological and management characteristics, regarding the entire distribution area and all the different management phases. The interpolation and reworking of these data allow to increase the understanding of these forest formations, making it possible to interpret dynamics and evaluate the real ecological value characterizing the Ostrya carpinifolia forests. These aspects are still difficult to deal with, given the data presently available in literature, but fundamental to build dynamic forecast models. Models necessary for the drafting of real useful management and landscaping plans. The studies carried out and here reported show how these formations, commonly labelled as not very interesting under the ecological point of view, are instead characterized by a particularly rich flora, a very lively dynamism and highlight a strong resilience. Therefore, these coenoses should not be interpreted as transitory or recovery phases of more "mature" coenoses, but real stable semi-natural forest formations very rich in terms of biodiversity, now threatened by widespread abandonment, exactly like the secondary prairies habitats.
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Struckhoff, Garrett Cletus. "Plant-assisted bioremediation of perchlorate and the effect of plants on redox conditions and biodiversity in low and high organic carbon soil". Diss., University of Iowa, 2009. https://ir.uiowa.edu/etd/441.
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Perchlorate is a known inhibitor of the human thyroid gland. Perchlorate is destroyed by ubiquitous perchlorate-reducing bacteria. The bacteria often lack sufficient electron donor. Research was undertaken to evaluate the relationship between plants and perchlorate-reducing bacteria. To what degree can plant-produced electron donors stimulate perchlorate reduction in low organic carbon (LOC) and high organic carbon (HOC) soil? A complication is that plants have been shown to influence redox conditions which may inhibit perchlorate reduction. The removal of perchlorate in a flow-through reactor was monitored with variables of soil organic carbon, hybrid poplar trees, and bioaugmentation. The biodiversity was monitored using denaturing gradient gel electrophoresis.
Low oxidation-reduction potential (ORP) was shown to indicate the capacity for greater perchlorate removal in soil. However, in planted LOC soil systems, evidence suggests that perchlorate reduction may also be possible at higher bulk redox conditions than previously observed. Increased hydraulic retention time was shown to both lower bulk ORP and increase perchlorate removal.
Radiolabeled perchlorate was used to find that in planted systems as much as 11.7% of the influent perchlorate mass was taken up into the tree and 82% of the perchlorate taken up was accumulated in the leaves. The plant contribution to total perchlorate removal in nonbioaugmented LOC soil was 39%, with the balance of the removal being attributed to microbial reduction. In bioaugmented soil the microbial contribution to perchlorate removal was increased.
Just planting poplar trees decreased the diversity of perchlorate reducers in the soil. However, when LOC soil was both planted and bioaugmented, the diversity of perchlorate reducers was not decreased. In HOC soil, the presence of an indigenous population of microorganisms competed with perchlorate reducers. At the increased ORP observed in planted HOC soil, the non-perchlorate-reducing bacteria appear to outcompete the perchlorate reducers and perchlorate removal is decreased.
Engineering implications of this research are that perchlorate remediation in HOC soil does not benefit from planting hybrid poplar trees but that remediation in LOC soil is stimulated by planting and bioaugmentation.
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LOZANO, FONDON Carlos. "MICROARTHROPOD ECOLOGY AND ECOSYSTEM TYPES: LINKING ADAPTATION TO SOIL AND DIVERSITY OF COMMUNITIES TO ENVIRONMENTAL CONDITIONS IN DIFFERENT GEOGRAPHICAL LOCATIONS". Doctoral thesis, Università degli studi di Ferrara, 2021. http://hdl.handle.net/11392/2488070.
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The soil community exhibit high variability in diversity, abundance and structure depending on ecosystems and climate. It is subjected to the integrity of the soil matrix, which constitute their habitat. It is directly involved in the ecosystem functions that constitute the basis for the services that soil provide. Land management often lead to soil degradation, which compromise soil community and ecosystem stability. Soil arthropods are key groups involved in ecosystem processes as decomposition but their role has been neglected in soil organic matter models until recently. Several research questions have been addressed: what are the effects of seasonal microarthropod diversity on ecosystem functions and soil food web stability? Section I focuses on how seasonal changes of arthropods induce changes on carbon cycling and soil food web stability in two beech forests. A modeling process based on the biomass of trophic groups (which includes bacteria, fungi and microarthropods), and environmental characteristics of each study area was implemented by using flow networks. Differences between forests were identified: the soil food web in the area with continental environmental characteristics responded to seasonality by increasing stability, while the soil food web in the area with Mediterranean environmental features increased the resistance and flowing material. Top-predators contributed to enhance the stability of the food webs, whereas fungi and bacteria represented the main groups controlling the cycling of carbon.
Sections II and III focus on the effects of local environmental characteristics on soil arthropods in semi-arid ecosystems. The ecological functioning of semi-arid areas is closely related to the distribution of vegetation, and water cycle. The diversity and functions of soil communities depend on resources and protection provided by vegetation. Pressure exerted by livestock often reduce the capacity of soils to provide their ecosystem functions due to degradation. The main research question was: what are the spatiotemporal patterns of soil arthropods depending on microsites characteristics, livestock pressure, and limiting factors?
Two similar sylvopastoral areas were studied. The first one (section II) is a farmland located in SW Spain. A photo interpretation analysis of an experimental catchment was developed to classify the intensity of livestock pressure. A total of 150 soil samples were collected, half in spring and the other half in autumn. Moreover, half of points were located beneath tree canopies and the other half in open spaces. Soil biological and physicochemical parameters were considered as drivers of arthropod richness, abundance, and adaptation to soil. Results showed higher abundance of arthropods and higher adaptation outside the influence of trees than beneath the tree canopies. Moreover, the classification of livestock pressure revealed by the photo interpretation analysis showed low correlations with community structure, and with the occurrence of well-adapted arthropod groups.
The section III involved the study of arthropods under drought conditions, and how the community changed during a simulated soil rewetting process. Firstly, 9 points were located in a pasture meadow. A total of 24 sampling points were located in sylvopastoral areas (12 grazed and 12 ungrazed). Then, 40 L of water were added to each sampling point 3 days before the sampling to simulate the soil rewetting process. A spatial transposition of samples to one-dimension scale in reference to the nearest trees was used to track changes in abundance and richness of arthropods. Results elucidated that the response of edaphic arthropods to the rewetting of soils was different depending on the closeness to trees: higher abundance and richness were found away from the trees during the rewetting of soil. Conversely, such values were higher as the closeness to trees increased when soil was dry.La comunità del suolo è altamente variabile in diversità e abbondanza a seconda del tipo di ecosistema e clima. È coinvolta nella provvisione di funzioni ecosistemiche che costituiscono la base dei servizi forniti dal suolo. Le pratiche di gestione del suolo portano alla degradazione di esso compromettendo la comunità biotica e la stabilità dell’ecosistema. Gli artropodi del suolo sono coinvolti in processi ecosistemici come la decomposizione della materia organica, nonostante il suo ruolo è stato trascurato fino a tempi recenti. La domanda di ricerca è: quali sono gli effetti dei cambiamenti stagionali nella diversità degli artropodi sulle funzioni ecosistemiche e la stabilità delle reti trofiche del suolo? La sezione I si focalizza su come la variabilità in diversità degli artropodi provoca cambiamenti nei flussi di carbonio in due foreste degli Appennini Italiani (nord e sud). A questo scopo, sono state modellate delle reti trofiche quantitative bassate sulle biomasse dei diversi gruppi di organismi (batteri, funghi e microartropodi). Le differenze climatiche di entrambi posti (continentale nel nord, e mediterraneo nel sud) hanno indotto dei comportamenti antagonisti in base ai cambiamenti stagionali: a nord, la risposta della rete trofica è stata indirizzata sull’incremento della stabilità, mentre a sud si è verificato un incremento della resistenza della rete dovuta all’aumento dell’attività metabolica. Addizionalmente, i predatori contribuirono al miglioramento della stabilità in entrambe le foreste, mentre funghi e batteri costituirono i gruppi principali controllando il flusso di carbonio. Le sezioni II e III si focalizzano sugli effetti delle caratteristiche ambientali locali sugli artropodi del suolo in sistemi semiaridi. Il funzionamento ecologico di queste aree è fortemente relato alla distribuzione della vegetazione e al ciclo idrologico. La diversità e funzioni ecosistemiche del suolo dipendono dalle risorse che la vegetazione provvede. La pressione esercitata dal bestiame riduce la capacità dei suoli di fornire servizi. La domanda di ricerca è: qual è la distribuzione spaziotemporale degli artropodi a seconda delle caratteristiche di ciascun sito, pressione del bestiame e fattori limitanti? Due aree di studio con caratteristiche ambientali simili sono state studiate. La prima (sezione II) è stata individuata nel sudovest della Spagna. Un’analisi di fotointerpretazione in un bacino sperimentale è stata fatta per determinare la pressione del bestiame. In totale, sono stati individuati di 150 punti di campionamento suddivisi in primavera e autunno, e in base alla vicinanza agli alberi (sotto chioma e fuori chioma). Parametri biologici e chimico-fisici del suolo sono stati considerati come fattori incentivanti delle abbondanze, ricchezza e occorrenza di tratti morfologici sugli artropodi. I risultati mostrarono che maggiori abbondanze e adattamento sono correlate con aree fuori chioma. La classificazione delle categorie di pressione del bestiame rilevata dall’analisi delle immagini di satellite mostrò una bassa relazione con i descrittori della comunità. Lo studio degli artropodi sottoposti a siccità estrema e alla simulazione di un processo di umidificazione del terreno si presenta nella sezione III. L’area di studio è localizzata nell’area centrale del Cile. In totale, 33 campioni di suolo sono stati rilevati, e suddivisi in base alla pressione del bestiame fuori chioma e sotto chioma dell’albero. Per lo studio del processo di umidificazione, 40 L di acqua sono stati aggiunti a ciascun punto 3 giorni prima del campionamento. Per tracciare le variazioni di abbondanza e ricchezza della comunità si è sviluppata una trasposizione delle coordinate dei campioni a una dimensione basata sulla distanza dei campioni agli alberi. Valori più alti sono stati trovati lontani dagli alberi durante il processo di umidificazione.
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Pauli, Natasha. "Environmental influences on the spatial and temporal distribution of soil macrofauna in a smallholder agriforestry system of western Honduras". University of Western Australia. School of Earth and Geographical Sciences, 2008. http://theses.library.uwa.edu.au/adt-WU2008.0142.
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This thesis presents the findings of an investigation of the spatial and temporal distribution of soil macrofauna at multiple scales within smallholder agriforestry fields in a remote, mountainous area of western Honduras. Since 1990, smallholder farmers in the study area have switched from traditional slash-and-burn agriculture to a form of slash-and-mulch agriforestry based on cultivating maize, beans and sorghum amongst dispersed trees. The principal objective was to examine the influence of the slash-and-mulch agricultural system on soil macrofauna abundance, biomass and community composition, and relate soil macrofauna distribution patterns to environmental variables. The initial stage of the research comprised transect-based sampling of soil macrofauna and biophysical variables in four common land uses of the study area. All four land uses (secondary forest, young milpa (agriforestry), mature milpa, and pasture) supported abundant, diverse and heterogeneous soil macrofauna communities, with few notable differences in soil macrofauna distribution among land uses. The most abundant soil macrofauna taxa were termites, ants, earthworms and beetles. Of the 'explanatory' environmental variables that were measured (including land use and selected soil properties, vegetation characteristics and topographic variables), those that had the strongest relationships with soil macrofauna abundance were land use, tree density and soil organic matter content. The second stage of the research was spatially-orientated and used stratified sampling based on within-field differences in farmer-defined soil type, as well as grid-based sampling of soil macrofauna surface activity. There was substantial within-field variation in soil type and topography, which was related to distribution patterns of at least one agriculturally-important soil macrofauna taxon. Earthworm activity was higher in areas of fertile soil and lower slope positions. At a finer scale, there was a positive spatial correlation between tree distribution and earthworm casting activity. The final phase situated the biophysical research in the local socio-economic context through participant observation and interviews with farmers. The results of the three phases of the study were incorporated into an original conceptual model of the relationships among soil macrofauna and environmental variables in the study area across multiple spatial scales and along a chronosequence of land use changes. Specific pointers are provided for further research on the role of soil fauna in influencing soil structure, nutrient cycling and pest species abundance, and for further investigating local knowledge and the socio-economic and cultural drivers of land use change.