Dissertations / Theses on the topic 'Soil ecology'

Thesis (Ph.D.)--University of Delaware, 2006.
Principal faculty advisors: Karl E. Wommack, Dept. of Plant & Soil Sciences, University of Delaware; Mark Radosevich, Dept. of Biosystems Engineering and Soil Science, University of Tennessee. Includes bibliographical references.

Microbial communities in soil are among the most diverse and species-rich of any habitat, but we know surprisingly little about the factors that structure them. Geothermal soils present unique and relatively unexplored model systems in which to address ecological questions using soil microbial communities, since harsh conditions in these soils exert strong filters on most organisms. This work represents two very different approaches to studying soil ecology in geothermal soils in Yellowstone National Park: 1) Arbuscular mycorrhizal fungal (AMF) communities living in the roots of Mimulus gutattus in contrasting plant community types were compared to assess a link in community structure between plants and their AMF symbionts; and 2) soil microbial communities were surveyed across multiple spatial scales in an unstudied diatomaceous biological soil crust in alkaline siliceous geothermal soils, using bar-coded 454 pyrosequencing of 18S and 16S rDNA. Mycorrhizal communities living in plant roots from contrasting community types showed a striking difference in taxon richness and diversity that appears to transcend soil-chemical differences, though robust conclusions are difficult since plant and fungal communities are structured by some of the same confounding soil conditions. Cluster and discriminant analyses were employed to compare drivers of AMF community structure. Eukaryotic and prokaryotic communities in a diatomaceous biological soil crust differ significantly from that of an adjacent sinter soil, and along a photic depth gradient. Along with a description of this unique system, extensive multivariate community analyses were used to address outstanding questions of soil microbial community spatial heterogeneity and the methodologies best suited to the unique assumptions of these datasets. Depending on the intended scope of inference, much detail can be gained by investigation of microbial communities at the aggregate or soil particle scale, rather than through composite sampling. Additionally, beta-diversity patterns are apparent with relatively few sequences per sample. 'Co-authored by Catherine A. Zabinski.'

A series of three experiments were conducted to determine the diversity of indigenous chlorobenzoate (CB) degraders in soil and to investigate the use of different methods of bioaugmentation for remediation of contaminated soil. In the first study, soil was amended with either 500 or 1000 μg of 3-CB g⁻¹ and was either uninoculated or inoculated with the 3-CB degrader Comamonas testosteroni BR60. Bioaugmentation with C. testosteroni BR60 increased 3-CB degradation at both contaminant levels, and the increase was more pronounced at the higher level due to contaminant inhibition of indigenous 3-CB degraders. Bioaugmentation also appeared to reduce the deleterious effects that 3-CB contamination had on indigenous soil microbial populations as evidenced by changes in culturable heterotrophic bacterial populations. In the second study, two similar pristine soils were contaminated with 500 μg of 2-, 3-, or 4-CB g⁻¹ . The two soils differed in their ability to degrade the compounds with one degrading 2- and 4-CB and the other degrading 3- and 4-CB. Several hundred degraders were isolated, grouped according to DNA fingerprints, and selected degraders were identified by 16S rDNA sequences. The identity of the CB degraders differed between the two soils. The results indicated that the development of 2-, 3-, and 4-CB degrader populations was site-specific even for the soils that developed under similar soil-forming conditions. The third study also used the two soils from the second study. This project investigated the potential for use of activated soil, which contained an indigenous degrader population, as a bioaugmentation inoculant. An aliquot of a given soil that contained an indigenous 2-, 3-, or 4-CB degrader population was added to a soil that did not have an indigenous degrader population for the same contaminant. The study found that bioaugmentation with activated soil increased degradation of each 2-, 3-, and 4-CB but only if the activated soil was pre-exposed to the contaminant prior to use for bioaugmentation. The results from these three studies indicate that CB degrader populations are diverse and variable in pristine soils and, if not present in contaminated soils, appropriate degrader populations may be established via different bioaugmentation strategies.

Thesis (doctoral)--Swedish University of Agricultural Sciences, 2002.
Abstract inserted. Appendix reprints four papers and manuscripts co-authored with others. Includes bibliographical references. Also partially issued electronically via World Wide Web in PDF format; online version lacks appendix.

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.

Antibiotic resistance is ubiquitous due to high usage of antibiotics and the capability of bacteria to transfer genes both horizontally and vertically. While this has dire implications for human health, the potential to disturb microbial communities and ecosystem functions they regulate is under appreciated. Antibiotics are commonly used in the livestock sector, accounting for 80% of antibiotic use domestically. This dissertation addresses three facets of this problem. Chapter 2 is a nation-wide survey of antibiotic resistance at dairy operations, aimed at understanding how ecosystem function is affected in situ. Chapter 3 describes a field-experiment, seeking to determine whether antibiotics have effects beyond soil through impacts on plant-microbe-soil feedbacks, thus potentially altering terrestrial ecosystem function. Chapter 4 investigates how rising global temperature interacts with antibiotic exposure through a microcosm-incubation experiment. These multiple stressors (i.e. temperature and antibiotics) could alter microbial community composition or physiology with repercussions on function. Additionally, chapter 4 seeks to determine whether microbes acclimate to continued antibiotic exposure. In chapter 2 I present evidence that increased antibiotic resistant gene (ARG) abundance with exposure to antibiotics and manure, and a correlation between ARGs and microbial stress. This increase in microbial stress results in elevated soil carbon loss. Chapter 3 shows that antibiotic exposure can change plant function – presumably through impacts on rhizospheric microbial community composition. Plants assimilate more nitrogen, but more carbon is lost from the system overall seemingly due to plant-soil-microbe tradeoffs. Chapter 4 shows a temporally dependent temperature–antibiotic interactive effect. Initially, pirlimycin increased microbial respiration at high temperatures, however this diminishes with time. Additional studies of microbial respiration at a range of temperatures show that microbial acclimation to antibiotic exposure may be taking place. However, interactive effects of high temperature and antibiotics appear to inhibit active microbial biomass production. Possible explanations to both of these patterns are the underlying differences in microbial community composition, specifically the fungal:bacterial. My results show that antibiotics not only lead to increased ARG abundance, but also have wide ranging effects on communities and ecosystem processes that are likely to be compounded in the face of global change.
Ph. D.

Upland soils are a significant sink of atmospheric methane, but the organisms responsible for methane consumption have yet to be identified. The ecology of methanotrophs was investigated in a beech forest soil which exhibited atmospheric-methane-uptake. Maximal methane-oxidation was observed in the upper mineral layer between the organic and inorganic horizons at a rate of 3.1 +/- 0.3 nmoles CH 4 g [fresh wt soil]-1 d-1. A clone bank of the methanotroph pmoA gene was constructed by PCR amplification from soil DNA extracts. The PCR primers used coamplify the related amoA gene of ammonia-oxidizers. The clones recovered grouped into three clusters: Nitrosospira-like sequences, a group somewhat related to alpha-Proteobacteria methanotrophs and previously referred to as the RA14 group, and a cluster which could not be characterized as either amoA or pmoA sequences. No pmoA genes closely related to genera of cultured methanotrophs were obtained. The 16S rDNA was also targeted using eubacterial and methanotroph-specific primers. 16S rDNA sequence analysis revealed the presence of organisms distantly related to known methanotrophs. Methanotroph enrichment cultures were established by inoculating mineral salts medium with soil and incubating under an atmosphere of 10% methane in air. Gene sequencing from the enrichments indicated the presence of organisms belonging to the genera Methylosinus and Methylocystis. The results suggest that the dominant methanotrophs in the forest soil are not related to known organisms and do not grow under conditions typically used to isolate methanotrophs.

Tropical ecosystems are some of the most diverse and productive ecosystems on the planet. These ecosystems are also some of the most threatened worldwide and this is largely driven by agricultural expansion. Predicting biotic responses to such forms of environmental change is a challenge that requires an increased understanding of the factors structuring these communities in both pristine environments as well as environments that are undergoing environmental change. Studying patterns in the spatial structure of communities can provide important insights into ecological and evolutionary processes structuring communities. Combining such approaches with analyses of the distribution of activity and the genomic content of communities can help us better understand relationships between community structure and function. I explore the topics of microbial spatial scaling, activity, and gene content in both pristine tropical rainforest environments as well as tropical regions undergoing agricultural conversion. I first pose a fundamental question in microbial spatial ecology, i.e. why do microorganisms tend to show weaker spatial patterns than macro-organisms? I show that trees and soil microorganisms differ in the rates at which their communities change over space. I test the hypothesis that low rates of spatial turnover in microbial communities are an artifact of how we assess the community structure of microbial communities and show that sampling extent is likely the main driver of these differences. Next, I examine a Central Africa ecosystem that is undergoing conversion to agriculture. I show that there are numerous indications of biotic homogenization in these soil microbial communities and that the active fraction of the community shows a more pronounced response to environmental change. Finally, I examine two microbial processes in the Amazon Basin that have been reported to change following conversion to agriculture: methane production and methane consumption. I investigate changes to the genes and taxa involved in these processes and propose a new conceptual framework for how these processes might be changing. Work in this thesis contributes to a broader understanding of the spatial and functional ecology of tropical microorganisms and offers perspectives useful for those interested in predicting and mitigating the impacts of environmental change on these communities.
2019-02-17

Viruses have been shown to be responsible for considerable bacterial mortality and nutrient cycling in aquatic systems. As yet no detailed studies have been published on the role of viruses in natural soil bacterial communities despite common knowledge that viruses exist in the soil. This thesis sought to address some key questions on the ecology of soil bacterial viruses and their hosts. Disturbance through soil desiccation, nutrient inputs, rhizosphere effects and protozoan predation pressure were investigated. The first study of lysogeny in natural soil systems was also undertaken. The work presented here utilised tools and techniques commonplace in aquatic systems research and applied them to soil. A novel protocol was developed based on physical extraction of bacteria and viruses from soil and direct counting with epifluorescence microscopy. Physical extraction was achieved using shaking, ultrasound sonication and low speed centrifugation. The fluorochrome SYBR Gold was used to stain nucleic acid of extracted bacteria and viruses, and image analysis software used to determine bacterial cell volumes. Bacterial and viral abundances were in the region of 107-109 per gram of soil over a range of soil types. Significant fluctuations in viral and bacterial abundances were recorded at timescales of less than 24 h. Glucose and nitrogen addition led to substantial increases in bacterial and viral abundance. Loss of soil moisture resulted in peaks of viral abundance in sandy soils but not in a clay soil. A six-week microcosm study demonstrated that phage were not a significant regulator of bacterial abundance. Low levels of lysogeny were recorded over a range of soils when measured explicitly with Mitomycin C. The implication from that study was that viruses in soil behave differently to those in aquatic systems. Bacterial and viral abundances were highly coupled in most instances, irrespective of the potential activity of bacteria. Further fundamental studies are recommended.

Landfills are a major anthropogenic source of methane and understanding the factors influencing the activity and diversity of methane oxidizing bacteria (methanotrophs) in landfill cover soil is critical to devise better landfill cover soil management strategies. A detailed study was carried out to investigate the effect of earthworms on soil methane oxidation potential and community structure of active methanotrophs in a landfill cover soil. Earthworms were found increase soil methane oxidation potential by 15% ± 7%. However, no substantial shifts in the community structure of active methanotrophs were observed. A Bacteroidetes-related bacterium was identified only in active bacterial community of earthworm-incubated landfill cover soil. However, its role in methane cycling is uncertain. In a subsequent study, a larger experimental system was used to simulate in situ landfill conditions and also to mimic the in situ environmental heterogeneity. A mRNA-based microarray analysis revealed that earthworm activity in landfill cover soil stimulates activity and diversity of Type I methanotrophs compared to Type II methanotrophs. Understanding spatio-temporal distribution pattern of microorganisms and the factors influencing their distribution pattern are integral for a better understanding of microbial functions in ecosystems. A pmoA-based microarray analysis of methanotroph community structure in a landfill cover soil revealed a temporal shift in methanotroph populations across different seasons. In the case of spatial distribution, only minor differences in methanotroph community structure were observed with no recognizable patterns. Correlation analysis between soil abiotic parameters (total C, N, NH4 +, NO3 - and water content) and distribution of methanotrophs revealed a lack of conclusive evidence for any distinct correlation pattern between measured abiotic parameters and methanotroph community structure, suggesting that complex interactions of several physic-chemical parameters shape methanotroph diversity and activity in landfill cover soils. A study was designed to investigate the shift in functional diversity of methanotrophs when microniches created by soil aggregates are physically altered. mRNA-based analysis of the bacterial transcription activity revealed an effect of physical disruption on active methanotrophs. The result emphasized that a change in a particular microbial niche need not be accompanied by an immediate change to the bacterial functional diversity and it depends on the ability of the bacterial communities to respond to the perturbation and perform the ecosystem function. DNA-SIP and mRNA based microarray techniques were compared for the assessment of active methanotroph community structure. Results from this study indicated that assessment of active methanotroph community structure by both the techniques were congruent. This suggested that the mRNA based microarray technique could be used to study active methanotroph community structure in situations where SIP experiments are not practical. However, both DNA-SIP and mRNA-microarray have their advantages and limitations and the selection of appropriate technique to assess active community structure depends on the nature of the study.

Master of Science
Department of Agronomy
Charles W. Rice
Declining soil health is the underlying cause of decreasing agricultural productivity and environmental degradation. To address this challenge, research was conducted to determine how: (1) cover crops affect soil health in Kansas, USA and (2) direct seeding mulch–based cropping (DMC) systems affect soil health in Nyankpala, Ghana. Soil health indicators assessed include: biomass yield (kg ha[superscript]-1), soil microbial respiration (SMR), soil microbial C and N (MBC & MBN), potentially mineralizable N (PMN), dissolved organic carbon (DOC), soil organic C (SOC), soil total nitrogen (TN), phospholipid fatty acid analysis (PLFA), water stable aggregate (WSA), bulk density, pH, N, P, K, Ca and Mg. DMC systems from Ghana yielded significantly greater biomass compared to the control. High biomass produced by DMC systems did not increase SOC and PMN relative to the control. Fertilizer application had a significant impact on biomass production, which resulted in a significant increase in SOC and PMN in the 0-5 cm soil layer. Soil pH was significantly reduced by cropping systems and fertilizer in the 0-5 cm soil layer. Microbial biomass N, TN, SMR, N, P, Ca and Mg were not affected by the DMC cropping systems. Application of mineral fertilizer increased SMR, MBN, TN, N, and P. Soil K was also significantly affected by cropping systems and mineral fertilizer. The combination of mineral fertilizer and plant residues would be needed to improve soil health and increase crop productivity in the Guinea Savanna Zone of Ghana. Liming would be required to address low soil pH. In the USA, of all the soil health indicators examined, actinomycetes, gram-positive bacteria, fungi-bacteria ratio (F:B), SMR, MBN and WSA, were those significantly influenced by cover crops. The interactive effect of cover cops and N fertilizer also affected gram-positive bacteria, total PLFA, MBN, F:B ratio and WSA. Cover crop residues contributed to the observed differences in these indicators. The low response of soil health indicators suggest further evaluations are needed to determine the effectiveness of the indicators.

The variations of ecosystem and soil respiration are mainly driven by temperature and precipitation, but the importance of temperature and precipitation could vary across temporal and spatial. At diurnal to annual temporal scales, ecosystem and soil respiration generally increase with average annual temperature, but very low or very high soil moisture has been shown to diminish the temperature response of respiration. Therefore, in water-limited ecosystem, such as the Mediterranean region where the seasonal pattern is characterized with significant summer drought, precipitation patterns are likely to play a particularly important role in regulating ecosystem and soil respiration inter annual whereas temperature may be much less factor. In this dissertation, I try to reduce the uncertainties of terrestrial net ecosystem exchange in Mediterranean region by measuring the interaction between environmental factors and soil respiration at short (i.e., diurnal) and medium (i.e., seasonal-years) temporal scales. Three in situ experiments were employed to investigate how soil respiration responds to environmental variations and management. Together, these three studies gave a consistent picture on how soil moisture strongly affects the dynamic and magnitude of soil respiration in Mediterranean forests. Results elucidated a clear soil moisture threshold; when soil moisture is above this threshold, soil temperature is the main driver of soil respiration, meanwhile, when soil moisture is below this threshold, soil respiration decoupled from soil temperature and is controlled by soil moisture. This suggests that soil moisture modified, at least in Mediterranean ecosystems, the temperature sensitivity of respiration through threshold-like response.
Las variaciones de la respiración del ecosistema y del suelo son principalmente impulsadas por la temperatura y la precipitación, pero la importancia de la temperatura y la precipitación puede variar a lo largo del tiempo y el espacio. En las escalas temporales diurnas a anuales, la respiración del ecosistema y del suelo generalmente aumenta con la temperatura media anual, pero se ha demostrado que la humedad del suelo muy baja o muy alta disminuye la respuesta a la temperatura de la respiración. Por lo tanto, en ecosistemas con escasez de agua, como la región mediterránea, donde el patrón estacional se caracteriza por sequías significativas en verano, es probable que los patrones de precipitación jueguen un papel particularmente importante en la regulación de la respiración del ecosistema y del suelo. En esta tesis, intento reducir las incertidumbres del intercambio de ecosistemas netos terrestres en la región mediterránea midiendo la interacción entre los factores ambientales y la respiración del suelo a escalas temporales cortas (diurnas) y medias (estacionales). Se utilizaron tres experimentos in situ para investigar cómo la respiración del suelo responde a las variaciones y manejo del ambiente. En conjunto, estos tres estudios dieron una imagen consistente de cómo la humedad del suelo afecta fuertemente la dinámica y la magnitud de la respiración del suelo en los bosques mediterráneos. Los resultados dilucidaron un umbral claro de humedad del suelo; Cuando la humedad del suelo está por encima de este umbral, la temperatura del suelo es el principal impulsor de la respiración del suelo, mientras que la humedad del suelo está por debajo de este umbral, la respiración del suelo está desacoplada de la temperatura del suelo y controlada por la humedad del suelo. Esto sugiere que la humedad del suelo modificó, al menos en los ecosistemas mediterráneos, la sensibilidad a la temperatura de la respiración a través de la respuesta tipo umbral.

Thesis (Ph.D.) -- La Trobe University, 2006.
Research. "A thesis submitted in total fulfilment of the requirements for the degree of Doctor of Philosophy, [to the] Centre for Applied Alpine Ecology, Department of Agricultural Sciences, School of Life Sciences, Faculty of Science, Technology and Engineering, La Trobe University, Bundoora". Includes bibliographical references (leaves 172-186). Also available via the World Wide Web.

Antarctica provides some of the most extreme environments on earth. Low temperatures, low water availability and nutrient deficiency are contributing factors to the limited colonisation of Antarctic biotopes, particularly in the continental Dry Valleys. The survival of microorganisms in this harsh continent provides the basis for the significance of this study. This study aimed to explore microbial phylotypic diversity across a 500 m altitudinal transect in the Miers Dry Valley, Ross Desert, East Antarctica. The study also attempted to infer from phylogenetic data, the possible presence of indicative phenotypes which might contribute to a functional microbial community.

Thesis (MScAgric)--Stellenbosch University, 2013.
ENGLISH ABSTRACT: The effect of long-term tillage on basic soil properties with respect to sustainability was investigated in this dissertation. Over the last three decades soil conservation has become an important prerequisite for sustainable agriculture. The primary aim of this study was to evaluate the effect of different tillage practices on the physical and some of the chemical properties of soil after 37 years of continuous application. This study was conducted on the Langgewens experimental farm, 18 km north of Malmesbury in the Western Cape. The experiment was initiated in 1975 on a Glenrosa (Haploxeralf) soil form with a gravelly sandy-loam texture. It was treated with four main tillage methods, namely conventional, tine, minimum and no-tillage. Important basic soil properties studied were the electrical conductivity (EC) and total carbon percentage, water stable aggregate percentage, bulk density and hydraulic conductivity. Most of the properties were analysed for the 0-100 mm and 100-200 mm depths. Seasonal bulk density variation for the 0-100 mm soil depth was determined by a Troxler surface gamma-neutron meter for in situ measurement. ANOVA’s and Tukey’s LSD posthoc tests were computed to assess whether significant statistical differences existed between tillage treatments. No-tillage proved to be beneficial in terms of salinity and had the lowest electrical conductivity, indicating that salts leeched out of the profile. Total carbon content was in general very low and in the 0-100 mm soil depth it decreased in the order of: no (0.92%), minimum (0.86%), tine (0.83%) and conventional tillage (0.51%). Aggregate stability was significantly the lowest under conventional (47.82%) and tine tillage (45.02%) compared to minimum (61.43%) and no-tillage (78.40%) at 0-100 mm depth. This can be explained by the relatively low amount of total carbon in the soil combined with the tillage intensity. The same trend was observed for the 100-200 mm depth. Significant correlation between total carbon content and aggregate stability for the 0-100 mm confirmed that an increase in total carbon in the soil would lead to an increase in aggregate stability. Significant, increased aggregate stability under the no-tillage treatment would therefore indicate that there may be some stable structure present in the soil. Seasonal bulk density variation was the lowest in no-tillage, which supports the manifestations of stable soil structure. More intensive tillage treatments such as conventional and tine tillage initially showed lower bulk densities, but only for the first month. Thereafter it increased to significantly higher values as the season progressed. This was mainly as a result of hardsetting of the soil which is driven by natural processes and rainfall. It is also due to the sandy loam texture that is particularly prone to compaction. Hydraulic conductivity studied for conventional and no-tillage showed significant differences. No-tillage (41 mm.h-1) showed a noticeably higher conductivity, which remained constant compared to conventional tillage (20 mm.h-1) that decreased over time. The main reasons for this increased hydraulic conductivity under no-tillage was higher water stable aggregates and lower bulk density. In the long term no-tillage thus stimulated structure formation of a Glenrosa soil form that significantly improved soil properties studied. These properties may influence processes such as water infiltration, water storage, run-off and drainage positively, due to soil property interaction. No-tillage, in terms of sustainability, quantified by the soil properties studied, thus proved to be superior compared to conventional and tine tillage but to a lesser extent if compared to minimum tillage.
AFRIKAANSE OPSOMMING: In hierdie tesis word die effek van langtermynbewerking op basiese grondeienskappe met betrekking tot volhoubaarheid ondersoek. Oor die afgelope drie dekades het grondbewaring ‘n belangrike aspek in landbou geword, ten einde volhoubaarheid te verseker. Die primêre doel van hierdie studie was om die effek van verskillende bewerkingspraktyke op die fisiese en chemiese eienskappe van grond na 37 jaar van deurlopende bewerking te ondersoek. Die studie is uitgevoer op die Langgewens eksperimentele plaas, 18 km noord van Malmesbury in die Wes-Kaap. Die eksperiment is in 1975 geïnisieer op 'n Glenrosa (Haploxeralf) grondvorm met ʼn klipperige sandleem-tekstuur. Dit bestaan uit vier hoof-bewerkingsbehandelings, naamlik konvensionele, tand-, minimum en geenbewerking. Belangrike basiese grondeienskappe wat bestudeer is, is die elektriese geleidingsvermoë (EG) en die totale persentasie koolstof, persentasie waterstabiele aggregate, bulkdigtheid en hidrouliese geleiding. Die meeste van die eienskappe is ontleed op die 0-100 mm en 100-200 mm diepte. Seisoenale bulkdigtheidsvariasie vir die 0-100 mm gronddiepte is bepaal deur 'n Troxler oppervlak gamma-neutron meter deur middel van in situ meting. ANOVA en Tukey se LSD posthoc-toetse is bereken om te bepaal of daar statisties-beduidende verskille tussen die bewerkingsmetodes is. Geenbewerking het geblyk voordelig te wees in terme van die soutgehalte en het die laagste elektriese geleidingsvermoë gehad, wat daarop dui dat die soute uit die profiel loog. Die totale koolstofinhoud was oor die algemeen baie laag en in die 0-100 mm gronddiepte het dit afgeneem in die volgorde geen- (0.92%), minimum- (0.86%), tand- (0.83%) en konvensionele bewerking (0.51%). Aggregaatstabiliteit was betekenisvol die laagste onder konvensionele (47.82%) en tandbewerking (45.02%) in vergelyking met die minimum (61.43%) en geenbewerking (78.40%) by die 0-100 mm diepte en kan verduidelik word deur die relatief lae totale koolstofinhoud in die grond gekombineer met die bewerkings-intensiteit. Dieselfde tendens is waargeneem vir die 100-200 mm diepte. ‘n Beduidende korrelasie tussen totale koolstofinhoud en aggregaatstabiliteit is vir die 0-100 mm diepte gevind en dit bevestig dat 'n toename in totale koolstof in die grond sal lei tot 'n toename in aggregaatstabiliteit. Betekenisvolle verhoogde aggregaatstabiliteit onder die geenbewerking-behandeling sal dus aandui dat die grond 'n meer stabiele struktuur vertoon. Seisoenale bulkdigtsheidsvariasie was die laagste in geenbewerking en ondersteun die manifestasies van 'n stabiele grondstruktuur. Meer intensiewe bewerkingsbehandelings, konvensionele en tandbewerking het vir die eerste maand ‘n laer bulkdigtheid getoon, waarna dit tot aansienlik hoër waardes gestyg het soos die seisoen verloop het. Dit was hoofsaaklik as gevolg van grondkonsolidering wat gedryf word deur natuurlike prosesse soos reënval en ook as gevolg van die sandleemtekstuur wat veral geneig is tot verdigting. Hidrouliese geleiding is bestudeer vir konvensionele en geenbewerking en het beduidende verskille getoon. Geenbewerking (41 mm.h-1) het 'n merkbare hoër geleidingsvermoë gehad wat konstant gebly het, in vergelyking met konvensionele bewerking (20 mm.h-1) wat met die verloop van tyd afgeneem het. Die vernaamste redes vir hierdie verhoogde hidrouliese geleiding onder geenbewerking is hoër waterstabiele aggregate en ‘n laer bulkdigtheid. Op die langtermyn het geenbewerking dus struktuurvorming van 'n Glenrosa-grondvorm gestimuleer, wat die grondeienskappe wat bestudeer is, aansienlik verbeter het. Hierdie eienskappe kan prosesse soos waterinfiltrasie, waterretensie, -afloop en -dreinering positief beïnvloed as gevolg van grondeienskapinteraksie. Geenbewerking, in terme van volhoubaarheid, gekwantifiseer deur die grondeienskappe wat bestudeer is, is dus bewys as superieur in vergelyking met konvensionele en tandbewerking, maar tot 'n mindere mate in vergelyking met minimumbewerking.
Water Research Commission

An understanding of the movement of bacteria in soil is of importance in many areas of microbial ecology. The study of bacterial dispersal is of fundamental importance in understanding the dissemination of soil-borne plant pathogens and symbionts as well as human pathogens introduced into soil. In addition, the increasing interest in the use of bacterial inocula for improved plant nutrition, biological control of plant pathogens and bioremediation of contaminated soils, necessitates the study of movement of such inocula, both to optimise their function and determine their fate in the environment. The fate of inocula is of particular interest when such inocula are non-indigenous (genetically-modified or otherwise), where their impact on the environment outwith the target site is uncertain. Intact soil microcosms were used in the study of factors affecting the movement of bacterial inocula through soils in the presence of percolating water. Two ecophysiologically contrasting bacterial species (Pseudomonas fluorescens and Bacillus subtilis) were used as inocula. The strains were genetically marked with lux genes encoding bioluminescence and with antibiotic resistance markers (chromosomal integrations), these traits were used in the selective enumeration of the introduced bacteria against the indigenous soil populations. The effect of soil type on the leaching of P. fluorescens inocula was investigated using intact soil microcosms sampled from contrasting soils: Craibstone (loamy sand), Insch (sandy loam) and Cruden Bay (clay loam). It was found that cells of the inoculum were leached more rapidly, in greater numbers and over a longer period from the clay loam, than the two lighter textured soils. These differences were attributed to the interaction of the inocula with percolating water, as determined by the respective soil characteristics. Leaching of B. subtilis differed from that of P. fluorescens, in that the rate of movement through soil was slower and the number of colony forming units leached was less. It was found that the colony forming units of B. subtilis leached were predominantly in the form of spores. The differences in leaching of B. subtilis and P. fluorescens were attributed to the greater adsorption of vegetative cells of B. subtilis to the soils and the requirement for formation of spores prior to leaching.

In this dissertation, I asked how soil biota, abiotic stress, and plant provenance influence plant communities and interactions between plants. Soil biota can have positive or negative effects on individual plants, and also influence the diversity and productivity of plant communities through their net effects on individuals and by mediating plant-plant interactions. However, the level of abiotic stress experienced by plants is likely to drive plant responses to soil mutualists and antagonists. Additionally, plant provenance (e.g. population origin) can influence responses to abiotic soil conditions as well as to soil organisms. Understanding how these three interacting components shape plant interactions may improve success of restoration and invasive plant management. During restoration, the goal is typically to create conditions conducive to native plant reestablishment. However, amelioration of disturbed areas by reducing abiotic stress or by adding beneficial soil organisms may unintentionally increase colonization and growth of non-native plants. Using the applied context of mine restoration, I examined how soil biota, abiotic stress, and plant provenance affected plant communities and interactions in four studies.

In Chapter 1, I found that both a native grass (Bouteloua gracilis ) and an invasive grass (Bromus tectorum) responded positively to soil biota when grown alone in the greenhouse. However, when grown together, the presence of soil biota increased the competitive ability of Bromus, while the removal of soil biota increased competition by Bouteloua. Results supported the hypothesis that invasive species such as Bromus often have positive responses to soil biota in the invaded range, but I also found that Bromus response to soil biota removal varied considerably by site.

In Chapters 2 and 3, I examined how methods used during restoration (application of stockpiled soil and inoculation with soil biota) affected native and non-native plant growth in field plots. I found that native plant biomass and non-native plant biomass both tended to increase when soil abiotic stress was ameliorated through the addition of deeper stockpiled soil. In addition, both native and non-native grasses responded positively to the use of local soil an as inoculant, while non-native forbs responded negatively to local soil inoculum. However, native plants only received significant benefits from inoculation when targeted application to native seedling transplants was used. Commercial mycorrhizal fungal inoculum did not affect plant growth. In studies of both stockpiled soil addition and soil inoculation, year was an important factor in determining plant responses. Variation in effects by year may reflect differences in precipitation timing or amount, or changes associated with plant and soil biota growth over time.

In Chapter 4, I used a greenhouse experiment to examine how one type of soil biota, arbuscular mycorrhizal fungi (AMF), influenced plant-plant interactions. I also manipulated abiotic stress (soil phosphorus availability) and plant provenance (stress-tolerant ecotype versus competitive ecotype) to assess whether these factors influenced AMF-mediated interactions among plants. I found that allowing or denying AMF hyphal access between neighboring pots altered plant reproduction. Inflorescence production was substantially decreased when hyphal access was allowed between two stress-tolerant plants. In addition, when hyphal access was permitted from a stress-tolerant plant to a competitive plant, the competitive plant flowered slightly sooner, whereas allowing hyphal access between two stress-tolerant plants led to slightly slower flowering. These results did not appear to be driven by abiotic stress or plant nutrition. It is possible that AMF transmission of infochemicals may play a role in regulating plant phenology and reproduction; however, further research in this area is needed.

Les comunitats fúngiques dels sòls juguen un paper vital en molts processos ecosistèmics forestals, així com en el manteniment de les poblacions d'espècies vegetals. Amb l'aparició de noves tècniques moleculars és possible estimar la diversitat i composició d'aquestes comunitats de forma més precisa i conèixer la seva resposta a pertorbacions com la gestió forestal o els canvis en el clima. L'objectiu principal d'aquesta tesi va ser descriure l'efecte de dos factors en les comunitats fúngiques de sòls forestals: la gestió forestal (concretament les aclarides) i el clima. A més, hem desenvolupat un mètode per analitzar la diversitat i composició d'espores de fongs a l'aire, així com els seus canvis en el temps i en l’espai. Aquesta tesi doctoral es va realitzar sobre un dispositiu experimental consistent en 28 parcel·les forestals localitzades en el Paratge Natural d’Interès Nacional de Poblet i dominades per Pinus pinaster de 60 anys, on es van aplicar aclarides de diverses intensitats. Mitjançant l'ús de diverses tècniques moleculars com la PCR en temps real (qPCR), seqüenciació massiva d'ADN (PacBio RS II, Illumina MiSeq) i l'extracció d'ergosterol, hem descrit les dinàmiques de biomassa i composició fúngica d'aquests sòls forestals, així com de la comunitat aèria (espores). Les dades obtingudes s'han analitzat en un gradient d'humitat i temperatura del sòl, així com també en les aclarides realitzades l’any 2009. Pel que fa a la part metodològica d'aquesta tesi, observem com liofilitzant els sòls es va recuperar el màxim d'ADN i es va evitar el creixement de floridures. Un cop establert el millor tractament d'assecat, es va observar com la sequera d'estiu afectava negativament la biomassa fúngica del sòl i causava importants canvis funcionals i estructurals en les comunitats de fongs. Entre les espècies més resistents a la sequera figuraven els fongs ectomicorízics, probablement per la seva relació simbiòtica amb arbres hoste. Els màxims valors de biomassa fúngica en sòl es van observar a la tardor, coincidint amb majors abundàncies de fongs ectomicorízics, molt probablement a causa d'una redistribució del carboni al sòl per part de la planta hoste. D'altra banda, la majoria de fongs sapròfits es van veure afavorits sota condicions d’alta humitat i baixes temperatures al sòl. A diferència dels factors climàtics, les aclarides realitzades l’any 2009 no van afectar a la composició de fongs als sòls, possiblement degut a que es va deixat un nombre d’arbres suficients per mantenir la comunitat. Finalment, les comunitats d'espores en l'aire variaven a escala espaial però sobretot a escala temporal. Les variacions temporals d'aquesta comunitat es veien condicionades en gran part per la fenologia de la comunitat de bolets. Moltes espècies que produïen cossos fructífers van poder ser detectades a les trampes d'espores, i per tant aquesta tècnica es podria utilitzar per detectar l'emergència de bolets. En base a aquests resultats es pot concloure que 1.- La liofilització és el mètode d'assecat que millor preserva l'ADN de fongs específics i evita el creixement de floridures. 2.- El cicle anual de certes espècies de fongs es pot veure modificat en un context de canvi climàtic, amb menor biomassa fúngica a l'estiu però major biomassa durant l’hivern i primavera. 3.- Les condicions climàtiques afecten les comunitats de fongs segons els seus trets funcionals, essent els fongs ectomicorrízics els que suporten millor les condicions de sequera estiuenca. 4.- Increments d'humitat afavoreixen la proliferació de sapròfits i fongs degradadors de miceli. 5.- Les aclarides no afecten de manera significativa les poblacions de fongs del sòl si es deixen en peu el nombre suficient d'arbres. 6.- Mitjançant l'ús de tècniques moleculars i trampes d'espores, és possible estudiar la comunitat d'espores a l'aire, essent aquesta altament afectada per la fenologia dels cossos fructífers de fongs i mostrant variabilitat espaial i temporal.
Las comunidades fúngicas de los suelos juegan un papel vital en muchos procesos ecosistémicos forestales, así como en el mantenimiento de las poblaciones de especies vegetales. Con la aparición de nuevas técnicas moleculares es posible estimar la diversidad y composición de estas comunidades de forma más precisa y conocer su respuesta a perturbaciones como la gestión forestal o los cambios en el clima. El objetivo principal de esta tesis fue describir el efecto de dos factores en las comunidades fúngicas de suelos forestales: la gestión forestal (concretamente las claras forestales) y el clima. Además, hemos desarrollado un método para analizar la diversidad y composición de esporas de hongos en el aire, así como sus cambios espacio-temporales. Esta tesis doctoral se realizó sobre un dispositivo experimental consistente en 28 parcelas forestales localizadas en el Paraje Natural de Interés Nacional de Poblet y dominadas por Pinus pinaster de 60 años, en las que se aplicaron diferentes intensidades de claras. Mediante el uso de varias técnicas moleculares como la PCR en tiempo real (qPCR), secuenciación masiva de ADN (PacBio RS II, Illumina MiSeq) y la extracción de ergosterol, hemos descrito las dinámicas de biomasa y composición fúngica de estos suelos forestales, así como de la comunidad aérea (esporas). Los datos obtenidos se han analizado en un gradiente de humedad y temperatura del suelo, así como también en las claras realizadas el año 2009. En cuanto a la parte metodológica de esta tesis, observamos como liofilizando los suelos se recuperó el máximo de ADN y se evitó el crecimiento de mohos. Una vez establecido el mejor tratamiento de secado, se observó como la sequía de verano afectaba negativamente la biomasa fúngica del suelo y causaba importantes cambios funcionales y estructurales en las comunidades de hongos. Entre las especies más resistentes a la sequía figuraban los hongos ectomicorrízicos, probablemente por su relación simbiótica con los árboles huésped. Los máximos valores de biomasa fúngica en suelo se observaron en otoño, coincidiendo con mayores abundancias de hongos ectomicorrízicos, muy probablemente debido a una redistribución del carbono en el suelo por parte de la planta huésped. Por otro lado, la mayoría de hongos saprófitos se vieron favorecidos en condiciones de alta humedad y bajas temperaturas en suelo. A diferencia de los factores climáticos, las claras realizadas en 2009 no afectaron a la composición de hongos en suelos, posiblemente debido a que se dejó un número de árboles suficiente para mantener la comunidad. Finalmente, las comunidades de esporas en el aire variaban a escala espacial, pero sobre todo a escala temporal. Asimismo, comprobamos como las variaciones temporales de estas comunidades se veían condicionadas en gran parte por la fenología de la comunidad de setas. Muchas de las especies que producían cuerpos fructíferos pudieron ser detectadas en las trampas de esporas, y por lo tanto creemos que esta técnica podría ser utilizada para detectar la emergencia de setas. En base a estos resultados se puede concluir que 1.- La liofilización es el método de secado de muestras de suelo que mejor preserva el ADN de hongos específicos y previene el crecimiento de mohos. 2.- El ciclo anual de ciertas especies de hongos se puede ver modificada en un contexto de cambio climático, con menor biomasa fúngica en verano, pero mayor durante invierno-primavera. 3.- Las condiciones climáticas afectan a las comunidades de hongos según sus rasgos funcionales, siendo los hongos ectomicorrízicos los que soportan mejor las condiciones de sequía estival. 4.- Incrementos de humedad favorecen la proliferación de saprófitos y hongos degradadores de micelio. 5.- Las claras no afectan de manera significativa las poblaciones de hongos del suelo si se dejan en pie el número suficiente de árboles. 6.- Mediante el uso de técnicas moleculares y trampas de esporas, es posible estudiar la comunidad de esporas en el aire, siendo esta altamente afectada por la fenología de los cuerpos fructíferos de hongos y mostrando una elevada variabilidad espacio-temporal.
Fungal communities inhabiting soils play a vital role in many forest ecosystem processes, as well as in the maintenance of plant species. With the emergence of new molecular techniques, it is possible to estimate the diversity and composition of these communities more precisely and study their responses to disturbances such as forest management or changes in climate. The main objective of this thesis was to describe the effect of two factors in the soil fungal communities: forest management (specifically forest thinnings) and climate. In addition, we have developed a method to study the diversity and composition of airborne fungal spores, as well as their spatio-temporal changes. This doctoral thesis was carried out in an experimental set-up consisting of 28 forest plots located in the Natural Park of Poblet, dominated by 60-year-old Pinus pinaster trees, where thinnings were applied under different intensities. Using several molecular techniques such as real-time PCR (qPCR), high-throughput DNA sequencing (PacBio RS II, Illumina MiSeq) and ergosterol extraction, we have described the fungal biomass dynamics and fungal composition of these forest soils, as well as from the airborne community (spores). The data obtained have been analyzed in a gradient of soil moisture and temperature, as well as in the forest thinnings made in 2009. Regarding the methodological part of this thesis, we observed how maximum DNA recovery and lowest growth of molds occurs under freeze-drying treatments. Once the best drying treatment was established, we observed how summer drought negatively affected the soil fungal biomass and caused important functional and structural changes in the fungal community. Ectomycorrhizal fungi were the most resistant species to drought, probably because of their symbiotic relationship with host trees. The maximum soil fungal biomass was observed in autumn, coinciding with higher abundances of ectomycorrhizal fungi, most likely due to a redistribution of soil carbon by the host plant. On the other hand, most saprotrophic fungi were promoted under conditions of high soil moisture and low temperatures. Unlike climatic factors, the forest thinnings made in 2009 did not affect the soil fungal community, likely because a sufficient number of trees were left to support the community. Finally, the airborne spore community changed at spatial scale, but especially at temporal scale. We verified how the temporal variations of these communities were largely determined by fruiting body emergence. Many of the species that produced fruiting bodies could be detected in the spore traps, and therefore this technique could be used to detect fruiting body emergence Based on these results, it can be concluded that 1.- Freeze-drying is the method that best preserves the DNA of specific fungi and prevents the growth of molds. 2.- The annual cycle of specific fungal species can be modified in a context of climate change, with predicted lower fungal biomass in summer, but higher biomass during winter-spring. 3.- Micro-climatic soil conditions affect fungal communities according to their functional traits, with ectomycorrhizal fungi being the ones that better resist summer drought conditions. 4.- High soil moisture promote the proliferation of saprotrophs. 5.- Forest thinnings does not affect significantly the soil fungal communities if enough trees are left standing. 6.- It is possible to study the airborne spore community using spore traps and molecular techniques, being these communities highly affected by the phenology of the fruiting bodies and showing spatio-temporal variability.

Soils formed from ultramafic rocks are normally by pH values close to neutrality, a high base status and are usually rich in Mg, Fe and heavy metals. The low Ca/Mg ratio and the high heavy metal content could cause toxic effects in the biological communities. Plant communities, in particular, are usually different from nearby areas with different substrates and rich in endemisms and adapted species and subspecies. Despite their great environmental and ecological interest, pedological and ecological properties of mountain or boreal soils developed on similar substrates have seldom been studied worldwide. 198 soil pits (associated with phytosociological surveys) have been opened and analyzed in the ophiolitic area of Mont Avic Natural Park (Val d’Aosta, Western Alps, Italy), beween 900 and 2900 m above see level. Soils formed from ultramafic, mafic rocks and calcschists have been observed, in order to recognize the most ecologically important soil factors. The results show that soil properties are related with altitude and slope aspect in forest habitats, while the effect of substrate becomes important above timberline. Strong leaching in forest soils, related to high acidity and to the podzolization process, decrease the total and bioavailable heavy metal contents, above the treeline pedogenic and geomorphic processes release and accumulate large quantities of potentially hazardous trace elements. The plant communities strictly depend on the edaphic properties above the treeline, while in the forest habitats the differences caused by substrate are less discernible. Microbial and microarthropodal communities suffer stress caused by heavy metals in forest soils, while at the alpine level non significant statistical or ecological correlation are visible. Heavy metals (Ni, in particular) are the most important edaphic properties in differentiating plant communities on different substrata, while the Ca/Mg ratio (usually considered the most influencing soil properties on ultramafic soils) has no particular ecological effect.

Earthworms are well known for their casting and burrowing activities which improve soil structure and soil fertility. However, earthworm populations in temperate regions exhibit patchy distribution in space and time. This makes it difficult to predict how earthworm activities may influence paedogenesis and nutrient cycling processes at the ecosystem level. The main objective of this study was to determine the spatiotemporal dynamic of surface cast production of two earthworm species, Aporrectodea turgida and Lumbricus terrestris, on the row-interrow scale in a temperate soybean agroecosystem. Our observations demonstrated that casting activity was synchronous with plant growth. More casts were also found in the row intercepts compared to the interrow ones. Both the spatial and temporal variations are thought to be caused by the microclimate found under the plant canopy, verifying results from controlled laboratory studies that show casting activity to be controlled by soil temperature and moisture. These results suggest a possible mutualism between earthworm and plants in cultivated temperate soybean agroecosystems, but this remained to be confirmed.