Structure and function of soil microbial communities in montane spruce forest Martina Štursová Abstract Coniferous forests are spatially heterogeneous environments and represent an important ecosystem that acts as carbon sink under current climate storing large amounts of carbon in standing biomass or as soil organic matter. The formation of organic matter via decomposition of dead biomass and transformation of rhizodeposited organic compounds is primarily mediated by microbial community of forest topsoil. Despite growing insight into the composition of these soil communities, little is known about the microbes actually responsible for those transformation processes, about the drivers shaping these communities or their response to increasing numbers of severe disturbances. Studies presented in this thesis contribute to filling the information. The studies were carried out in unmanaged spruce forests in the highest elevations of Bohemian Forest, in both, the undisturbed areas as well as those affected by bark beetle outbreaks at different time periods. Combination of methods including culturing of fungi, enzymatic activity measurements or high throughput sequencing were used to describe the microbial communities, their distribution in space and time, and factors involved in shaping these communities in those...

A study was conducted at the Savannah River Site near Aiken, SC to: 1) characterize the spatial patterns of soil and forest floor variables (moisture, pH, soil phosphate, forest floor and soil carbon and nitrogen, and soil available nitrogen), 2) assess the spatial patterns of the plant community, and 3) investigate spatial relationships among the variables and between the variables and woody vegetation. Spatial soil and litter samples were collected on five 0.25 hectare plots, and relationships were explored using Pearson's correlation tests, canonical correlation analysis, variogram modeling and kriging. The average range of spatial autocorrelation for the forest floor variables was >45 m, while that for soil variables was 12 m. Woody stem basal area exhibited spatial autocorrelation at ranges of less than 12 m, and was only weakly correlated with forest floor and soil resource patterns. Few strong spatial correlations among the forest floor and soil variables were observed. The means and variances of the variables were low, and differences in resource levels probably had little impact on the spatial pattern of vegetation. Results indicate a weak, differential effect of species group on litter quality, a weak relationship between large pine trees and soil nitrogen patterns, and a general homogeneity of the stands. / Master of Science

This thesis provides an overview of mercury distribution in the forest soils located in vicinity of historical and current mercury emission sources. The sites were chosen around Bohemian Karst due to presence of emission source, i.e. iron production processes, cement plants, lime processing plants. The chosen sites were near municipalities of Králův Dvůr, Radotín and Hrádek u Rokycan. From these sites the soils samples were collected from organic and mineral horizons. Average mercury concentration in organic horizons was 288 µg.kg-1, organo-mineral horizons A contained 241 µg.kg-1, anthropogenic horizons M 287 µg.kg-1 and horizons B 56 µg.kg-1 only. The relations among mercury and soil components were tested. Strong link between mercury, soil organic matter (SOM) and sulfur was found. The result indicated that the origin of mercury in soil samples was atmospheric deposition rather than bedrock. High concentrations of oxalate extractable aluminum, iron and manganese in mineral horizons have been explained as the cause of bedrock weathering. Powered by TCPDF (www.tcpdf.org)

<p>Inorganic chlorine (Clinorg) is generally considered to be inert and has been used as a tracer for groundwater movements. This assumption is thereby fundamental for current knowledge about soil biogeochemistry. However, recent work showed that Clinorg can be retained, i.e. immobilised, in soil, which contradicts the previous assumptions. The aim of this laboratory study was to investigate if the processes that immobilise Clinorg in soil are affected by molecular oxygen (O2), and if the immobilisation occurs in the top soil layer only or also further down were the soil structure is different from the upper soil layer. Two experimental set-ups have been established. In the first experiment regarding the O2 regime (OXANIS), the immobilisation of Clinorg was studied in soil under oxic and anoxic conditions, respectively. In a second incubation study (SOLIS) the immobilisation was studied under oxic conditions in different layers of a coniferous forest soil. To investigate the immobilisation of Clinorg, a method using radiolabelled chloride 36 (36Clinorg) was applied. The use of radiolabelled chloride is an excellent and reliable method for studying transformation processes in soil systems. The results of the laboratory study showed that Clinorg retention rates under oxic conditions were much higher than retention rates under anoxic conditions, indicating an important role of O2. Furthermore, the immobilisation of Clinorg occurred in all soil layers were oxygen is provided, but rates were highest in the top soil layer (organic layer, O-horizon). Clearly, O2 influenced the net Clinorg retention, but additional studies are required to identify the processes behind this result. The calculated immobilisation rates for Clinorg in the three soil horizons correspond to the amount of organic material detected in the different soil horizons indicating a strong connection between the occurrence of organic matter in soil and the immobilisation of Clinorg.</p>

Inorganic chlorine (Clinorg) is generally considered to be inert and has been used as a tracer for groundwater movements. This assumption is thereby fundamental for current knowledge about soil biogeochemistry. However, recent work showed that Clinorg can be retained, i.e. immobilised, in soil, which contradicts the previous assumptions. The aim of this laboratory study was to investigate if the processes that immobilise Clinorg in soil are affected by molecular oxygen (O2), and if the immobilisation occurs in the top soil layer only or also further down were the soil structure is different from the upper soil layer. Two experimental set-ups have been established. In the first experiment regarding the O2 regime (OXANIS), the immobilisation of Clinorg was studied in soil under oxic and anoxic conditions, respectively. In a second incubation study (SOLIS) the immobilisation was studied under oxic conditions in different layers of a coniferous forest soil. To investigate the immobilisation of Clinorg, a method using radiolabelled chloride 36 (36Clinorg) was applied. The use of radiolabelled chloride is an excellent and reliable method for studying transformation processes in soil systems. The results of the laboratory study showed that Clinorg retention rates under oxic conditions were much higher than retention rates under anoxic conditions, indicating an important role of O2. Furthermore, the immobilisation of Clinorg occurred in all soil layers were oxygen is provided, but rates were highest in the top soil layer (organic layer, O-horizon). Clearly, O2 influenced the net Clinorg retention, but additional studies are required to identify the processes behind this result. The calculated immobilisation rates for Clinorg in the three soil horizons correspond to the amount of organic material detected in the different soil horizons indicating a strong connection between the occurrence of organic matter in soil and the immobilisation of Clinorg.

Research has shown that formation of chlorinated organic matter occurs naturally and that organic chlorine is as abundant as the chloride ion in organic soils. A large number of organisms are known to convert inorganic chloride (Clin) to organic chlorine (Clorg) (e.g. bacteria, lichen, fungi and algae) and some enzymes associated to these organisms are capable of chlorinating soil organic matter. The aim with the study was to compare organic matter chlorination rates in soils from several different locations dominated by either coniferous forest or pasture. Soil from eight samples sites in the southern of Sweden were incubated at 20°C with addition of 36Clin in a 138 days long radiotracer experiment. The results show that transformation of 36Clin to 36Clorg occurred and that the amounts of 36Clorg increased over time. The chlorination rate was higher in the samples from coniferous forest than in samples containing pasture soil, where the specific chlorination rate was 3-4 times smaller. This study contributes new information about chlorination in various soil types and soil from different locations in southern central Sweden. The similarity between the chlorination rates measured in coniferous forest soils so far indicate that up scaling to regional estimates may be less problematic than expected.

During oil-sands mining all vegetation cover, soil, overburden and oil-sand is removed, leaving pits several kilometres wide and hundreds of metres deep. These pits are reclaimed by a variety of treatments using mineral soil or a mixed peat and mineral soil as the capping layer and planted with trees with natural colonisation from adjacent sites. A number of reclamation treatments covering different age classes were compared with a range of natural forest ecotypes to identify the age at which the treatments become similar to a natural site with respect to vegetation composition and key soil attributes relevant to nutrient cycling. Ecosystem function was estimated from plant community composition, litter decomposition, development of an organic layer and bio-available nutrients. Key response variables including moisture, pH, C:N ratios, bio-available nutrients and ground-cover were analysed by non-metric multidimensional scaling and cluster analysis to discover which reclamation treatments were moving towards or merging with natural forest ecotypes and at what age this occurs. On reclaimed sites, bio-available nutrients including nitrate generally were above the natural range of variability but ammonium, phosphorus, potassium, sodium and manganese were generally very low and limiting to ecosystem development. Plant diversity was similar to natural sites from 5 years to 30 years after reclamation, but declined as reclaimed sites approached canopy closure. Grass and forb leaf litters decomposed faster than aspen or pine in the first year, but decomposition on one reclamation treatment fell below the natural range of variability. Development of an organic layer appeared to be facilitated by the presence of shrubs, while forbs correlated negatively with first-year decomposition of aspen litter. The better restoration amendments for tailings sands involved repeated fertilisation of peat: mineral mixtures in the early years of plant establishment, these became similar to a target ecotype at about 25 years. Good results were also shown by subsoil laid over non-saline overburden and fertilised once, these became similar to a target ecotype at about 15 years. Other treatments receiving a single application of fertiliser remain entrenched in the early reclamation phase for up to 25 years.

During oil-sands mining all vegetation cover, soil, overburden and oil-sand is removed, leaving pits several kilometres wide and hundreds of metres deep. These pits are reclaimed by a variety of treatments using mineral soil or a mixed peat and mineral soil as the capping layer and planted with trees with natural colonisation from adjacent sites. A number of reclamation treatments covering different age classes were compared with a range of natural forest ecotypes to identify the age at which the treatments become similar to a natural site with respect to vegetation composition and key soil attributes relevant to nutrient cycling. Ecosystem function was estimated from plant community composition, litter decomposition, development of an organic layer and bio-available nutrients. Key response variables including moisture, pH, C:N ratios, bio-available nutrients and ground-cover were analysed by non-metric multidimensional scaling and cluster analysis to discover which reclamation treatments were moving towards or merging with natural forest ecotypes and at what age this occurs. On reclaimed sites, bio-available nutrients including nitrate generally were above the natural range of variability but ammonium, phosphorus, potassium, sodium and manganese were generally very low and limiting to ecosystem development. Plant diversity was similar to natural sites from 5 years to 30 years after reclamation, but declined as reclaimed sites approached canopy closure. Grass and forb leaf litters decomposed faster than aspen or pine in the first year, but decomposition on one reclamation treatment fell below the natural range of variability. Development of an organic layer appeared to be facilitated by the presence of shrubs, while forbs correlated negatively with first-year decomposition of aspen litter. The better restoration amendments for tailings sands involved repeated fertilisation of peat: mineral mixtures in the early years of plant establishment, these became similar to a target ecotype at about 25 years. Good results were also shown by subsoil laid over non-saline overburden and fertilised once, these became similar to a target ecotype at about 15 years. Other treatments receiving a single application of fertiliser remain entrenched in the early reclamation phase for up to 25 years.

Phytophthora cinnamomi is an important pathogen of many plant species in natural ecosystems and horticulture industries around the world. In Western Australia, a high proportion of native plant species are susceptible to P. cinnamomi attack. Acacia pulchella, a resistant legume species native to Western Australia has been considered as a potential biological control tool against P. cinnamomi. To develop effective control methods, it is important to understand the interactions between the control agent and the different life forms of the pathogen. In this thesis the interactions are investigated between P. cinnamomi and varieties of A. pulchella which occur in jarrah (Eucalyptus marginata) forest and sand plain ecosystems. The soil inoculum of P. cinnamomi was compared under the potted plants of the three common varieties of A. pulchella, var. pulchella, var. glaberrima and var. goadbyi. These were grown in infected jarrah forest soil in the glasshouse and in vitro in a sterilised soil-less mix aseptically. Acacia urophylla (a species non suppressive towards P. cinnamomi) was also included as a control. An isolate of the most commonly found clonal lineage of P. cinnamomi in the jarrah forest, A2 type 1 was selected for use in experiments after testing showed it reliably produced zoospores and chlamydospores both axenically and in non-sterile conditions, in comparison to several other isolates. The lowest survival of P. cinnamomi inoculum was found under A. pulchella var. goadbyi plants grown both in non sterile soil and in aseptic soil-less mix. All the life forms of P. cinnamomi were affected by A. pulchella (Chapters 2, 3, 4 and 5). The soil leachates from potted plants of A. pulchella var. goadbyi reduced sporangial production (Chapter 2) and caused cytoplasm collapse of chlamydospores (Chapter 3). The confirmation was obtained that soil under A. pulchella was inhibitory to sporangial stage of P. cinnamomi and new evidence was obtained on chlamydospore inactivation. Cytoplasm collapse in the chlamydospores was observed both for chlamydospores on mycelial discs on Mira cloth exposed to the soil leachate and within infected roots buried in soils under the three varieties of A. pulchella plants. The effect was strongest under the plants of A. pulchella var. goadbyi and indicated that the chlamydospores of P. cinnamomi are unlikely to act as persistent structures under A. pulchella var. goadbyi plants. In Chapter 4, bioassays were conducted with axenically produced mycelia, chlamydospores and zoospores to test the inhibitory effect of the root exudates collected from aseptically grown A. pulchella var. goadbyi plants. The zoospores of the same isolate used in the soil leachate tests were immobilised (became sluggish and encysted) within one to two minutes. When incubated for 24 h, zoospores predominantly clumped and germ tubes were observed only from the clumped ones. Chlamydospores produced by four isolates of the common A2 type 1 strain and the only one A2 type 2 strain available at the time were tested. A higher percentage of chlamydospores collapsed and a very low percentage germinated after 24 h. Chlamydospores of all the A2 type 1 isolates were inhibited by the root exudates whilst the A2 type 2 isolate remained viable. The findings showed that the suppressive effect must be due at least in part to substances exuded by the A. pulchella plants. However, it appeared that the A2 type 1 isolates were more vulnerable to this effect than the single A2 type 2 isolate. In Chapter 5, the effect of season on sporangial suppression of P. cinnamomi was shown using field soils collected from three jarrah forest soil vegetation types and a Banksia woodland on Bassendean sand, collected in winter and summer. The effect of age of A. pulchella plants was demonstrated using the soils collected from rehabilitated bauxite mine pits. In all the locations soils were collected under A. pulchella plants and 5 m away from the nearest A. pulchella. An effect of soil type was evident as whilst the soil leachates made from the three lateritic jarrah forest soil types where A. pulchella is common in the understorey were suppressive to the sporangial stage of P. cinnamomi, this effect was not evident in the Bassendean sand under A. pulchella. A. pulchella soils collected in winter were less suppressive towards sporangial production than soils collected in summer. An effect of plant age was demonstrated as soil leachates from four year-old A. pulchella stands in rehabilitated bauxite mine sites were more suppressive for sporangia than leachates from one year-old stands. Further information on the behaviour of the pathogen in soil and in potting mix with and without A. pulchella was obtained by infecting lupin radicles with an isolate of each A2 type, 1 and 2 strains of P. cinnamomi and burying them in the soil under the three varieties of A. pulchella plants. After a week, the chlamydospores were mostly collapsed and hyphae deteriorated. Oospores were observed and in significant numbers under the potted plants of A. pulchella var. glaberrima. Isolates of all three clonal lineages of P. cinnamomi found in Australian soil were tested for the ability to produce oospores. Two isolates of the A1 and A2 type 2 and three isolates of the common A2 type 1 were screened. The two isozyme types of the A2 clonal lineage isolated in Australia varied in ability to self and produce oospores in planta in several soils from the jarrah forest. The isozyme type 2 of the A2 clonal lineage of P. cinnamomi produced oospores under these experimental conditions. This stimulation was not effective for most of the tested isolates of the A2 type 1 and the A1 clonal lineage. The in planta oospores were viable but dormant and the oogonial-antheridial associations were amphigynous both in vitro and in vivo. For the first time it was established that, the stimulus for selfing and oospore formation in the A2 type 2 of P. cinnamomi is available in some jarrah forest soils, with and without A. pulchella and also in the potting mix used. This raises important questions for the management of the pathogen. Several factors were identified as potential stimuli for selfing. Among them, soil nutrient levels and essentially enhanced sulphur presence were found important. Temperature also played a key role. Oospores were produced abundantly at 21 – 25 ºC but not over 28 ºC. The biology of P. cinnamomi has been studied for several decades but some important aspects remain un-researched. This thesis pioneers research into the in planta selfing aspect of the pathogen in soil. It also improved the understanding of the interactions between P. cinnamomi and A. pulchella which to some extent supports use of A. pulchella as a biological control tool against P. cinnamomi. However, attention is drawn to the natural mechanisms of this complex pathogen to survive in planta by producing oospores, the most persistent form of its life cycle.

Des études ont démontré que du chlore organique est retenu dans les sols et serait formé par un processus de chloruration issu de l’activité microbienne des sols. Le but de cette étude est d’estimer les formes organiques de chlore dans des sols contrastés et de mettre en évidence l’évolution de ces formes de chlore selon certains paramètres environnementaux ou modalités d’incubations en fonction de l’activité des microorganismes. Les horizons organo-minéraux de sols contrastés ont été étudiés (i) in situ : Les quantités de chlore et les paramètres physico-chimiques et microbiologiques de sols ont été mesuré ; (ii) dans deux dispositifs d’incubations sous différentes modalités. Les mesures des teneurs en chlore entre le début et la fin de la première expérience ont été mesurées par analyseur d’AOX. Pour la deuxième expérience, les sols ont été enrichis en Na37Cl et les teneurs en 37Cl ont été mesurées par ICP MS HR. Des mesures par spectrométrie Xanes ont été réalisées pour préciser la spéciation du chlore des sols. Les teneurs en chlore organique non extractibles représentent presque la totalité du chlore. Les paramètres qui influencent la répartition des teneurs en chlore correspondent au couvert végétal, au pH, à la teneur en carbone organique et aux quantités de microorganismes. Les teneurs en chlore mesurées par analyseur d’AOX et par ICP MS HR ont permis de mettre en évidence une formation de chlore organique en relation avec les paramètres microbiologiques. Les mesures par ICP MS HR ont montré une formation de chlore organique en conditions abiotiques. Les analyses par spectrométrie XANES n’ont pas permis de mettre en évidence une formation de chlore organique / Recent studies have shown that organic chlorine is retained in the soil and is formed by a chlorination process mainly from the microbial activity of the soi still poorly documented. The aim of this study is to estimate the organic and inorganic forms of chlorine in contrasting soil and highlight the evolution of these forms according to certain environmental parameters or terms of incubations and to the activity of microorganisms. For this, the organo-mineral horizons of contrasting soil were studied (i) in situ: The amounts of chlorine and physico-chemical and microbiological parameters of soil were measured; (ii) in two experimental devices incubations under different conditions. Measurements of chlorine levels between the beginning and the end of the first experiment were measured by AOX analyzer. For the second experiment, the soil was previously enriched with Na37Cl and 37Cl levels were measured by HR ICP MS. Soil samples from these incubations were analyzed by Xanes spectrometry to identify the speciation of chlorine forms in soils. Soil non-extractable organic chlorine contents represent almost all of the chlorine. The parameters that influence the distribution of chlorine contents in soils correspond to vegetation cover, pH, organic carbon content and quantities of microorganisms. The chlorine contents measured by AOX analyzer and by HR ICP MS highlight an organic chlorine formation over time in relation to the microorganims in the soil. The measures carried out by HR ICP MS show also an organic chlorine formation in abiotic conditions. Conversely, XANES spectrometry measurements have show any organic chlorine formation