O padrão de expansão física das ocupações urbanas nas principais regiões metropolitanas brasileiras tem deixado um legado de graves problemas urbanos e ambientais. Muitos desses problemas estão relacionados à ocupação de áreas naturais de importância ambiental tanto por moradias populares produzidas na ilegalidade, quanto por usos associados à atividade turística e de lazer, à indústria e ao comércio. Tal processo vem ocorrendo com maior intensidade desde a década de 1980. O objetivo deste estudo é evidenciar um aspecto desse processo de urbanização, que resulta em impactos ambientais. Busca-se relacionar expansão urbana, natureza das áreas impactadas e proteção legal existente, exemplificando diferentes contextos metropolitanos, usando como ferramenta de análise recursos de sensoriamento remoto e geoprocessamento. O processamento de imagens de satélite é um recurso auxiliar utilizado nos estudos urbanos e ambientais que possibilita longos períodos de análise e grandes escalas. A cartografia elaborada compreende a evolução das manchas urbanas, das áreas protegidas por lei e dos biomas e cobertura vegetal presentes nos diferentes contextos analisados e permite uma visão diversificada sobre a natureza e os serviços ambientais comprometidos pelo processo de urbanização em curso. / The pattern of the urban sprawl in the most important Brazilian metropolitan areas has left a legacy of grave urban and environmental problems. Several of these problems are related to the land use in natural areas of great environmental importance, such as illegally built low class dwellings, as well as use associated to tourism and leisure, industry and commerce. This process has been occurring more intensely since the 1980s. The aim of this study is to highlight an aspect of this urbanization process that results in environmental impact. It is intended to make connections among urban expansion, the nature of the areas under impact and existing legal protection, exemplifying different metropolitan contexts and using as analysis tool the resources of remote sensor and data geographic processing. The satellite image processing is an auxiliary resource used in urban and environmental studies enabling long periods of analysis and large scales. The cartography produced, which comprises the evolution of the urban sprawl, the areas protected by law, the ecosystems and the vegetation cover present in the different analyzed contexts, allows a diversified view of the nature and environmental services compromised by the process of urbanization in course.

Wetlands provide important ecosystem services (ES) by storing large amounts of organic carbon (OC) and being of high biological, cultural, and economical value. Uganda is covered by vast wetland areas but has with a booming population rapidly been decreasing due to pressure on lands. The aim of this report was to examine important socio-ecological dynamics of rural wetlands in relation to variations of land use in central and eastern Uganda. This by assessing above- (ABG) and belowground (BG) C stocks, soil pH, and capturing provisioning ES and related impacts on soil and vegetation. The methods involved initial spatial analysis followed by two field campaigns with collection of soil samples, biomass measurements and recordings of provisioning ES, following locally developed standardized methods. Laboratory soil analyses included bulk density, loss on ignition and pH. The results shows that the permanent wetland LUC classes store the most total ecosystem C (273.5 to 356.5 t C ha-1), with the BG pool being the largest. It further brings new insights to the much less studied seasonal wetlands that also proves to be an important C stock (331.1 t C ha-1) as well as providing essential ES. In line with previous research, the total ecosystem C and the provisioning ES of wetlands decreases with changing land use management (farmlands 185 to 209; grasslands 125; woodland 120 to 284 t C ha-1). Further knowledge of socio-ecological dynamics of wetlands is needed, especially in seasonal wetlands, to increase sustainable wetland management. This being urgently needed for many communities in Uganda that are dependent on agroecologically-based economies in close relation to wetland ES and vulnerable to climate variations.

Thesis (Ph.D. (Zoology)) -- University of the North, 1996 / Refer to document

This dissertation presents the development and application of a computational model called BioChemFOAM developed using the computation fluid dynamic software OpenFOAM (Open source Field Operation And Manipulation). BioChemFOAM is a three dimensional incompressible unsteady-flow model that is coupled with a water-quality model via the Reynolds Average Navier-Stokes (RANS) equations. BioChemFOAM was developed to model nutrient dynamics in inland riverine aquatic ecosystems. BioChemFOAM solves the RANS equations for the hydrodynamics with an available library in OpenFOAM and implements a new library to include coupled systems of species transport equations with reactions. Simulation of the flow and multicomponent reactive transport are studied in detail for fundamental numerical experiments as well as for a real application in a backwater area of the Mississippi River. BioChemFOAM is a robust model that enables the flexible parameterization of processes for the nitrogen cycle. The processes studied include the following main components: algae, organic carbon, phosphorus, nitrogen, and dissolved oxygen. In particular, the research presented has three phases. The first phase involves the identification of the common processes that influence the nitrogen removal. The second phase covers the development and validation of the model that uses common parameterization to simulate the main features of an aquatic ecosystem. The main processes considered in the model and implemented in BioChemFOAM are: fully resolved hydraulic parameters (velocity and pressure), temperature variation, light's influence on the ecosystem, nutrients dynamics, algae growth and death, advection and diffusion of species, and isotropic turbulence (using a two-equation k-epsilon model). The final phase covers the application and analysis of the model and is divided in two sub stages: 1) a qualitative comparison of the main processes involved in the model (validation with the exact solution of different components of the model under different degrees of complexity) and 2) the quantification of main processes affecting nitrate removal in a backwater floodplain lake (Round Lake) in Pool 8 of the Mississippi River near La Crosse, WI. The BioChemFOAM model was able to reproduce different levels of complexity in an aquatic ecosystem and expose several main features that may help understand nutrient dynamics. The validation process with fabricated numerical experiments, discussed in Chapter 4, not only presents a detailed evaluation of the equations and processes but also introduces a step-by-step method of validating the model, given a level of complexity and parameterization when modeling nutrient dynamics in aquatic ecosystems. The study cases maintain fixed coefficients and characteristic values of the concentration in order to compare the influences that increasing or decreasing complexity has on the model, BioChemFOAM. Chapter 4, which focuses on model validation with numerical experiments, demonstrates that, with characteristic concentration and coefficients, some processes do not greatly influence the nutrient dynamics for algae. Chapters 5 and 6 discuss how BioChemFOAM was subsequently applied to an actual field case in the Mississippi River to show the model's ability to reproduce real world conditions when nitrate samples are available and other concentrations are used from typical monitored values. The model was able to reproduce the main processes affecting nutrient dynamics in the proposed scenarios and for previous studies in the literature. First, the model was adapted to simulate one species, nitrate, and its concentration was comparable to measured data. Second, the model was tested under different initial conditions. The model shows independence on initial conditions when reaching a steady mass flow rate for nitrate. Finally, a sensitivity analysis was performed using all eleven species in the model. The sensitivity takes as its basis the influence of processes on nitrate fate and transport and it defines eight scenarios. It was found in the present parameterization that green algae as modeled does not have a significant influence on improving nitrate spatial distributions and percentage of nitrate removal (PNR). On the other hand, reaction rates for denitrification at the bed and nitrification in the water shows an important influence on the nitrate spatial distribution and the PNR. One physical solution, from the broad range of scenarios defined in the sensitivity analysis, was selected as most closely reproducing the backwater natural system. The selection was based on published values of the percentage of nitrate removal (PNR), nitrate spatial concentrations, total nitrogen spatial concentrations and mass loading rate balances. The scenario identified as a physically valid solution has a reaction rate of nitrification and denitrification at the bed of 2.37x10-5 s-1. The PNR was found to be 39% when reaching a steady solution for the species transport. The denitrification at the bed process was about 6.7% of the input nitrate mass loading rate and the nitrification was about 7.7% of the input nitrate mass loading rate. The present research and model development highlight the need for additional detailed field measurements to reduce the uncertainty of common processes included in advanced models (see Chapter 2 for a review of models and Chapter 3 for the proposed model). The application presented in Chapter 6 utilizes only spatial variations of nitrate and total nitrogen to validate the model, which limits the validation of the remaining species. Despite the fact that some species are not known a priori, numerical experiments serve as a guide that helps explain how the aquatic ecosystem responds under different initial and boundary conditions. In addition, the PNR curves presented in this research were useful when defining realistic removal rates in a backwater area. BioChemFOAM's ability to formulate scenarios under different driving forces makes the model invaluable in terms of understanding the potential connections between species concentration and flow variables. In general, the case study presents trends in spatial and temporal distributions of non-sampled species that were comparable to measured data.

The ecosystem services (ES) concept is meant to facilitate consideration of the value of nature in conservation and landscape management processes by translating ecosystem functions into human benefits. Incorporating the ES concept into policy and decision-making has proven difficult due to challenges in identifying, measuring, and locating services and in predicting the impacts of decisions upon them. ES mapping offers a key solution to increase our understanding of the spatial patterns of ES supply and demand and the spatial relationships between them, but may be challenging to implement given a lack of spatial data related to ES or existence of such data at coarse resolution that may not facilitate accurate ES quantification, mapping and modeling. This issue is particularly acute in urban settings where landscapes are highly heterogeneous and fragmented. This research seeks to improve our understanding of urban ES supply, demand and the relationships between them, as well as the impacts of spatial scale, input data quality and method choice on ES mapping in urban landscapes. The dissertation is composed of three studies. In the first study, I introduce a spatially-explicit framework for quantifying and mapping ES supply and demand using carbon storage and sequestration services as an example. This framework assesses supply based on biophysical conditions and demand based on socioeconomic characteristics, allowing for more integrative ES assessments in urban areas. In the second study, I evaluate the sensitivity of ES maps to input spatial data resolution and method choice (ecosystem component-based and land-cover proxy-based methods) in a heterogeneous urban landscape using biomass carbon storage as an example. I find that ES map accuracy is highly dependent on analytical scales and input data representativeness. ES estimates based on ecosystem-component data are more accurate than those based on land-cover proxies. The accuracy of land-cover proxy-based maps, however, can be increased by using high-resolution land-cover maps. The third study aims to increase understanding of ES supply, demand, and supply-demand balance in urban contexts. To this end, I create a high-thematic-resolution land-cover dataset and combine it with the InVEST pollination model to assess the capacity of urban ecosystems to supply pollination services to satisfy the demands of urban agriculture. I find using land-cover dataset at a higher thematic resolution enhances the accuracy of pollination estimates, highlighting the importance of considering scale and land-use dependencies in urban ES mapping. Combined, these studies advance our knowledge of ES supply, demand and the relationships between them, and provide new insight into the impacts of input data spatial and thematic resolution and method choice on the accuracy of urban ES maps.

Software systems increasingly interact with each other, forming ecosystems. Cloud is one such ecosystem that has evolved and enabled other technologies like IoT and containers. Such systems are very complex and heterogeneous because their components can have diverse origins, functions, security policies, and communication protocols, which makes it difficult to comprehend, utilize and consequently secure them. Abstract architectural models can be used to handle this complexity and heterogeneity but there is lack of work on precise, implementation/vendor neutral and holistic models which represent ecosystem components and their mutual interactions. We attempted to find similarities in systems and generalize to create abstract models for adding security. We represented the ecosystem as a Reference architecture (RA) and the ecosystem units as patterns. We started with a pattern diagram which showed all the components involved along with their mutual interactions and dependencies. We added components to the already existent Cloud security RA (SRA). Containers, being relatively new virtualization technology, did not have a precise and holistic reference architecture. We have built a partial RA for containers by identifying and modeling components of the ecosystem. Container security issues were identified from the literature as well as analysis of our patterns. We added corresponding security countermeasures to container RA as security patterns to build a container SRA. Finally, using container SRA as an example, we demonstrated an approach for RA validation. We have also built a composite pattern for fog computing that is an intermediate platform between Cloud and IoT devices. We represented an attack, Distributed Denial of Service (DDoS) using IoT devices, in the form of a misuse pattern which explains it from the attacker’s perspective. We found this modelbased approach useful to build RAs in a flexible and incremental way as components can be identified and added as the ecosystems expand. This provided us better insight to analyze security issues across boundaries of individual ecosystems. A unified, precise and holistic view of the system is not just useful for adding or evaluating security, this approach can also be used to ensure compliance, privacy, safety, reliability and/or governance for cloud and related ecosystems. This is the first work we know of where patterns and RAs are used to represent ecosystems and analyze their security. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2019. / FAU Electronic Theses and Dissertations Collection

Microorganisms are of great importance for the large scale elemental cycles and overallfunctioning of most natural ecosystems, and this also includes the ecology and maintenance offreshwater resources. Anthropogenic actions as well as climate change has greatly affectedfreshwaters and it is therefore important to understand how microorganisms react to suchenvironmental changes. I investigated how one such pressure, increased nutrient levels,influenced freshwater microbial communities and their potential to degrade the globallyabundant biopolymer chitin. To assess the effects of changed nutrient levels on functionalsubcommunities within the natural microbiota, I established a collection of mixed culturesoriginating from Lake Erken and two mesocosms from the same lake subjected to either highor low nutrient amendments. I observed that higher nutrient addition greatly increasedbacterial cell numbers in the source community. However, for the emerging mixed culturesgrowing on chitin as a substrate, those originating from the “Low” nutrient amendmentmesocosm treatment featured higher cell growth potential compared to cultures originatingfrom the “High” ones or inoculated with the natural lake water. Moreover, mixed culturesfrom the mesocosms presented higher chitinase extracellular enzymatic activity compared tothe lake cultures. Interestingly, “High” and “Low” mesocosm cultures were quite constrainedin bacterial growth response (low variance for the respective treatment) while the growthpotential in cultures from the lake were much more diverse, indicating a higher degree ofpatchiness and subcommunities with variable ability to profit from chitin as a substrate.Ongoing work will assess how individual microbial lineages react to variable nutrient levelsand how the composition of less diverse but fully functional subcommunities profiting fromchitin will change under such conditions.

Research into the polyculture of finfish and crayfish has been conducted in Western Australia for over a decade now. This research was instigated out of a need to increase revenues from freshwater crayfish farmers wishing to diversify their income base with a view to increasing profitability and reducing risk. It has become clear that several key variables dictate how the polyculture system (i.e. polysystem) will perform. These include biological factors like: size of participating species, relative densities, gender, planktonic turbidity, natural feeds; and abiotic factors like: light intensity, clay turbidity, floating cages for segregation, water quality, and habitat/shelter complexity. Many of these factors can be controlled / adjusted by the manager of the polysystem to maximise performance, production and profitability.While much of the research to date has focussed on the marron (Cherax tenuimanus) industry, it is also important to realise that an understanding of these factors can also assist other crayfish polysystems, like integrated agri-aquaculture systems containing yabbies (Cherax albidus). Some of the factors that influence how the system will perform may become more prevalent, like suspended clay turbidity and the associated role of light intensity in species interactions, or shelter complexity and the resulting choice of shelter material. But overall, they are the same basic variables and we must understand how they affect the particular multi-species system that we are dealing with. There is a lot to be learned from the literature on how these variables affect multi-species aquatic environments in the wild. Perhaps aquaculturists have not considered this enough in the past. Some farmers seem to believe that these variables are different JUST because it is a culture system. This is not true. / The variables will take on different levels in a culture system (i.e. a manager will stimulate turbidity, provide artificial feeds, stock different sizes, and supply particular types of shelter) BUT the actual variables themselves (e.g. food, density, light, shelter) are basic to ALL aquatic ecosystems. Other researchers have looked at important factors like density, gender, and light intensity / turbidity in crayfish polysystems - but the issue of habitat complexity and the role of shelter has not been adequately addressed. This thesis will investigate some basic questions about shelter and endeavour to apply them to crayfish polysystems, with the emphasis on marron (C. tenuimanus) and yabbies (C. albidus) because these are the two most commercially important species of crayfish in Western Australia. Importantly, it should be noted that due to the invasive nature of yabbies, and their apparent ability to displace native marron in the wild, findings will be related to yabby-marron competition / displacement where relevant. We need to know many things about shelter: what type is best in a multi-species system? Should the shelter size match the crayfish size? Do marron have different requirements for shelter than yabbies? Does it matter who gets first use of a shelter (i.e. prior residence effect)? Can we learn about crayfish shelter requirements by examining the behaviour / plasticity of crayfish species? If crayfish are stocked with finfish and they retreat into shelter as a predator-avoidance measure, is the complexity important given that their densities will be higher? If densities of crayfish inside shelters are higher in polysystems, will cannibalism be a concern, particularly when conditions are right for moulting? Does visual recognition and / or chemo-detection of a predator affect the shelter usage by marron or yabbies? / Does temperature affect shelter usage behaviour for a burrowing species like yabbies? Shelter is an important factor in the life history of a freshwater crayfish and an understanding of its influence on different species is important for maximising system performance. Crayfish are categorised depending on their ability to construct shelters (i.e. burrows). Yabbies have evolved in systems with fluctuating water quality and many predators and, as such, have learned to burrow (to escape drought and also to escape predators). Marron, on the other hand, are a non-burrowing native crayfish species that have existed with relatively few predators in the South-West. As a result, marron are less capable of modifying their behaviour when confronted with a predator (i.e. low behavioural plasticity). Species with high plasticity, like yabbies, are more capable of adapting to new environments, because they can change their behaviour to increase their chance of survival. Therefore we can expect yabbies and marron to utilize habitats differently and we should compare these behaviours as a basis to developing management strategies. This type of knowledge may also assist with managing the translocation and spread of yabbies in the wild and their displacement of native marron.Within multi-species systems, the physical structure of shelter plays an important role inprotecting crayfish and the perfect shelter would not only provide safety from co-stocked finfish, but also from conspecific cannibalism. Given the different life histories and behaviours, it is probable that both species of crayfish will have different refuge requirements.Over the course of this four-year investigation, trials were conducted in four culture systems (72L aquariums, 300L circular tanks, 80t mesocosm tank, and 720m2 earthen ponds) using marron and yabbies as the species of interest. / Silver perch and Murray cod were chosen as the finfish species of interest as they appear to have the highest aquaculture potential for native freshwater finfish in Australia at the present time. Further, both of these fish have been documented as potential predators of crayfish, resulting in a challenge to understand the role of shelter in minimising the negative effects of fish-crayfish interactions within a polysystem. This study has confirmed that shelter plays a critical role in multi-species system dynamics. In the case of polysystems, it will affect both interspecific and intra-specific interactions, ultimately governing production and profitability, along with the other, previously defined factors. This means that the manager of a polysystem can influenceproductivity by understanding: a) the behavioural characteristics and biology of the crayfish; b) the feeding biology of the finfish; and c) the system variables (both biotic and abiotic) that will affect the overall well being of the fish and crayfish. In the case ofshelter, the manager should understand the available shelter types, the appropriatedensities, the importance of matching complexity to the crayfish size, and the prior residence effect when choosing a timing strategy for stocking and harvesting. Prior residence increased resource holding potential for both marron and yabbies in the short term. In fact, prior residence was a stronger determinant of successful sheltering than crayfish gender or species. However, in longer-term trials the physical size of the crayfish (larger animals evicted smaller animals) and reproductive status (berried females were successful at evicting all other crayfish) were more important factors in determining successful shelter acquisition, although the temporal variations (i.e. growth and release of young) complicate the issue. / When stocking crayfish of different sizes, and in polysystems, the correct size of shelter becomes critical, as smaller individuals will be forced to leave over-sized shelter and locate a shelter commensurate with their own body size to avoid predators. This is relevant to crayfish nurseries where complex habitat is paramount for juvenile cohorts that display variation in sizes and gender. The expansion of crayfish polyculture holds considerable promise; however, furtherinvestigations are required into shelter complexity within floating fish cages, shelter types and arrangement of shelters within ponds (for increased production and ease-of-harvesting), potential of yabbies in polyculture (comparison of monosex and hybrid strains), and the impact of shelter on escape behaviour of marron in a polysystem.

Soil microorganisms play important roles in maintaining soil quality and ecosystem health. Development of effective methods for studying the composition, diversity, and behavior of microorganisms in soil habitats is essential for a broader understanding of soil quality. Forest management strategies and practices are of vital significance for sustainable forest production. How the different forest management measures will influence soil microbial communities is a widespread concern of forest industry and scientific communities. Only a small proportion (~0.1%) of the bacteria from natural habitats can be cultured on laboratory growth media. Direct extraction of whole-community DNA from soil, followed by polymerase chain reaction (PCR) and other analysis circumvents the problems of the culture-dependent methods and may shed light on a broader range of microbial communities in the soil. DNA-based molecular methods rely on high quality soil microbial DNA as template, and thus extraction of good quality DNA from soil samples has been a challenge because of the complex and heterogeneous nature of the soil matrix. The objectives of this research were to establish a set of DNA-based molecular methods and to apply them to investigate forest soil microbial composition and diversity. Soil samples were collected from different forest ecosystems, i.e., the natural forest (YNF) and the first rotation (~ 50 years) (Y1R) and the second rotation (~ 1 year) (Y2R) of hoop pine plantations at Yarraman, and from different forest residue management practices (the experiments had established 6.4 years before the samples were collected) at Gympie, two long-term experimental sites of the Queensland Department of Primary Industry-Forestry in subtropical Queensland, Australia. Some DNA-based molecular techniques, including DNA extraction and purification, PCR amplification, DNA screening, cloning, sequencing and phylogenetic analyses, were explored using Yarraman soil samples, which were high in organic matter, clay and iron oxide contents. A set of methods was assembled based on the recommendations of the method development experiments and applied to the investigations of the microbial composition and diversity of the Yarraman and Gympie soil samples. Four soil DNA extraction methods, including the Zhou method (Zhou et al., 1996), the Holben method (Holben, 1994), the UltraClean (Mo Bio) and FastDNA (Bio 101) soil DNA extraction kits, were explored. It was necessary to modify these methods for Yarraman soil. I designed and introduced a pre-lysis buffer washing step, to partially remove soil humic substances and promote soil dispersion. This modification greatly improved the quality of the extracted DNA, decreasing co-extracted humic substances by 31% and increasing DNA yield by 24%. The improved Holben method was recommended for fungal community studies, and the improved Zhou method for bacterial community studies. The extracted DNA was good in quality, with a consistent size of ~20 kb and a yield of 48-87 g g-1 soil, and could be successfully used for 16S (Zhou method) and 18S (Holben method) rDNA amplifications. For less difficult environmental samples, UltraClean kits could be a good option, because they are simple and fast and the extracted DNA are also of good quality. Screening of the DNA PCR products using TGGE, Heteroduplex-TGGE and SSCP was also explored. These methods were not so effective for the screening of the soil DNA PCR products, owing to the difficulty in interpretation of the results. Cloning was a necessary step to obtain a single sequence at species level in soil microbial community studies. The screening of the clone library by TGGE, Heteroduplex-TGGE and SSCP could only separate the clones into several major bands, although SSCP gave better separation. Sequencing of selected clones directly from the clone library obtained ultimate results of microbial taxonomic composition and diversity through well-established sequence analysis software packages and the databases. It was recommended that, in this project with the target of microbial community composition and diversity, soil DNA PCR products were directly cloned to construct clone libraries and a sample of clones were sequenced to achieve an estimate of the taxonomic composition of the soil. Fungal communities of the Yarraman soil samples under the natural forest (YNF) and the hoop pine plantations (YHP) were investigated using 18S rDNA based cloning and sequencing approaches. Twenty-eight clone sequences were obtained and analysed. Three fungal orders, i.e., Zygomycota, Ascomycota and Basidiomycota were detected from the YNF and YHP samples. By contrast, culture-based analyses of fungi in the literature were mostly Ascomycetes. YNF appeared to have more Ascomycota but less Zygomycota than YHP, and within the Zygomycota order, YHP had more unidentified species than YNF. Bacterial communities of Yarraman soil samples of YNF, Y1R and Y2R were investigated using 16S rDNA-based cloning and sequencing approaches. 305 16S rDNA clone sequences were analysed and showed an overall bacterial community composition of Unclassified bacteria (34.4%), Proteobacteria (22.0%), Verrucomicrobia (15.7%), Acidobacteria (10.2%), Chloroflexi (6.9%), Gemmatimonadetes (5.6%), and Actinobacteria (5.2%). There was a significant difference among YNF, Y1R and Y2R in the taxonomic group composition. YNF had a greater proportion of Acidobacteria (18.0%), Verrucomicrobia (23.0%) and Chloroflexi (9.0%) than Y1R and Y2R (corresponding to 6.3%, 12.1% and 5.9%, respectively), while Y1R and Y2R had a higher percentage of the Unclassified group (38.5% for Y1R and 46.5% for Y2R) than YNF (18.0%). For the Proteobacteria group, YNF had more Alpha-subdivision but Y1R and Y2R had more Delta-subdivision. From YNF to Y1R to Y2R, the clone sequence variable site ratios, 5% and 10% OTU numbers and Shannon's diversity index H' values tended to decrease, indicating the soil bacterial diversity decreased from the natural forest to the first and the second rotation hoop pine plantations. The large amount of unclassified clone sequences could imply a novel group of bacteria in the soil, particularly in the hoop pine soil samples. Alternatively they may result from artefacts during the PCR process. Bacterial communities of the Gympie soil under different residue management practices, i.e., residue (litter plus logging residue) removed (G0R), residue retained (G1R), and residue doubled (G2R), were also investigated using the 16S rDNA-based cloning and sequencing approaches. Acidobacteria (37.6%) and Proteobacteria (35.6%, including Alpha-subdivision of 29.9% and Gamma-subdivision of 5.7%) were dominant components of the communities, followed by Actinobacteria (14.7%), Verrucomicrobia (7.3%) and Unclassified bacteria. There was no significant difference among G0R, G1R and G2R in the bacterial community compositions and diversity. These findings provided an in-depth vision of the soil microbial communities under different forest management practices. Their combination with other soil analysis results, such as physical and chemical properties, and forest production data, could provide an improved understanding of sustainable forest management strategies.

Healthy riparian vegetation has a positive impact on the adjacent river. Unfortunately, riparian vegetation is often threatened by human impacts such as dam construction and clearing. To gain the knowledge underlying the effects of such impacts and to aid riparian rehabilitation, the objective of this thesis was: to determine riparian vegetation association with, and response to, variation in fluvial geomorphology over several scales and consequently to fluvial disturbance. Only woody riparian plant species were considered. Flood disturbance was the unifying theme of this thesis. Linked to this theme and arising from the main objective was the supposition that plant interactions with the abiotic environment, but not biotic interactions between species, control riparian species distribution because of frequent fluvial disturbances. Woody riparian vegetation and riverine environmental variables were recorded along the upper Murrumbidgee River at three spatial scales based on a geomorphic hierarchy for Chapter 2. Multivariate analysis was used to group species and to associate environmental variables with vegetation at the three spatial scales. Observations at the two larger scales, of river segment (site) and riparian reach (transect), identified a river-longitudinal speciescomposition gradient associated with geology, river width and stream channel slope. Observations at the smallest scale of geomorphic units (plot) identified a lateral riparian gradient and also the longitudinal gradient; these gradients were associated with geomorphic variation, land use, plot elevation and also river longitudinal variables. Using the same data set, but varying the spatial scale of analysis caused the species composition pattern to change between scales. Increase in scale of observation, that is from geomorphic unit to reach and segment scales, resulted in disproportionate importance of rarer species and decreased importance of some key riparian species at the larger scales. It would appear that in this instance the geomorphic unit scale best described patches of different species composition because this scale had high spatial resolution and was also able to identify multiple gradients of environmental variation. It was recommended that riparian sampling take place at scales that represent dominant gradients in the riparian zone. These gradients are represented by geomorphic scales, indicating the appropriateness of using geomorphic based scales for observation of riparian vegetation. Chapter 3 considered whether there is a geomorphic template upon which riparian vegetation is patterned and whether it is associated with process variables, such as flooding and soil type. This question was investigated at different spatial scales in three ways: i) by an experiment to determine whether soil nutrient condition affects plant growth; ii) by graphical analysis of trends between geomorphic units, species and process variables; and iii) by analysis of vegetation distribution data. The smallest scale (meso) found experimental differences in plant growth because of soil type. Plants growing in sand had the lowest performance, with an average plant Relative Growth Rate (RGR) of 0.01, compared to plants growing in soils with small amounts of silt or clay particles, with an average plant RGR of 0.04. This pattern was attributed to differences in nutrients. Clear relationships were demonstrated at the larger geomorphic unit scale between species distribution and process variables. For example, hydrology and substratum type were found to be associated with geomorphic units and species. The largest scale considered in Chapter 3 was the riparian reach scale. At this scale species were clearly grouped around reach type. Therefore, geomorphology was considered to be a template for riparian species distribution. Findings in this chapter suggested that geomorphic variables should be good predictors of riparian species distribution. This hypothesis was tested and supported in Chapter 6. The experiments reported in Chapter 4 aimed to determine whether inundation depth and duration affected plant performance and survival for five common riparian zone species. Riparian seedling patterns in the field were also compared with experimental results to test whether species performance was reflected by field distribution. The experiments that were conducted included an inundation period and depth experiment, and a survival period test whilst under complete inundation. Biomass and height relative growth rates were determined, and the results were analysed using factorial Analysis of Variance. Obligate riparian species (Callistemon sieberi, Casuarina Cunninghamiana, Leptospermum obovatum) were found to be tolerant of inundation duration and depth, to the point where inundation provided a growth subsidy. On the other hand, non-obligate riparian species (Acacia dealbata, Kunzea ericoides) were either just tolerant of inundation or showed a negative growth response. For instance, C. sieberi demonstrated an average height RGR of 0.04 after complete inundation and 0.007 when not inundated, while A. dealbata had an average height RGR of 0.001 after complete inundation and 0.01 when not inundated. These experimental findings were found to closely reflect both seedling and adult plant distribution in the field such that inundation tolerant species were found close to the river and intolerant species further away. Thus, the conclusion was drawn that riparian species establishment and distribution is affected by inundation and that change to the flood regime could have serious impacts on riparian zone plant composition. The other aim of this chapter was to determine whether optimum germination temperatures were associated with flood or rainfall. Growth chamber germination trials were conducted at air temperatures of 15�C, 20�C and 25�C to determine the 'best' germination temperature. These germination patterns at different temperatures were then related to annual variation in field temperature, flooding period and rainfall. No evidence was found to suggest a relationship between ideal germination temperature and flood season, rather it was suggested that germination was patchy through time and may simply reflect recent rainfall. Investigations that were reported in Chapter 5 aimed to elucidate relationships between species and flow velocity variables. Two experiments were conducted: i) a flume experiment to determine the effect of flow velocity on plant growth; and ii) an experiment to observe the response of plants to damage (imitating flood damage) and inundation. Field observations of species distribution and flow velocity related variables were also conducted to put the flume results into a real-world context. Treatments for the flume experiment were fast flow velocity (0.74 m s-1), slow velocity (0.22 m s-1) and no velocity (control) but still inundated. All treatments were flooded completely for four days. Subsequent biomass and height relative growth rates were determined, and the results were analysed using factorial Analysis of Variance. Results were unexpected, given that obligate species exposed to the fastest velocity had the highest growth rate with an average height RGR of 0.046, compared to plants in still water, which grew the least with an average height RGR of 0.013. It was hypothesised that this response was because relatively greater carbon dioxide and oxygen levels were available in the moving water compared to the still water. With regard to shoot damage, the species that were nonobligate riparian species lost more leaves from velocity treatment than the obligate riparian species. The cut and flood experiment found growth of the obligate species (Casuarina cunninghamiana) to be greater after cutting than the non-obligate species. Flooding was not found to have an effect in the cut and flood experiment, probably because the period to sampling after flood treatment was longer (4 weeks) than other flooding experiments (3 weeks). Field observations were found to support the experimental findings, with a gradient of species across the riparian zone that reflected potential flood velocities. Therefore, velocity is one of a suite of riparian hydrological factors that are partially responsible for the gradient of species across the riparian zone. Potentially the absence of flooding could result in a homogeneous mix of species, rather than a gradient, except on the very edge of the river. The study that was reported in Chapter 6 investigated a technique for predicting riparian vegetation distribution. One of the aims of this investigation was to address a current riparian rehabilitation shortfall, which was how to objectively select species to plant for rehabilitation. Field data were collected from three confined river valleys in south-eastern New South Wales. Using data on plant species occurrence and site and plot measures of soils, hydrology and climate, an AUSRIVAS-style statistical model, based on cluster and discriminant analysis, was developed to predict the probability of species occurrence. The prediction accuracy was 85 % when tested with a separate set of plots not used in model construction. Problems were encountered with the prediction of rarer species, but if the probability of selection was varied according to the frequency of species occurrence then rarer species would be predicted more often. Various models were tested for accuracy including three rivers combined at the geomorphic unit (plot) scale and riparian reach (transect) scale in addition to a Murrumbidgee River plot scale model. Surprisingly, the predictive accuracy of the all rivers and single river models were approximately the same. However, the difference between the large scale and small scale models pointed to the importance of including small scale flood-related parameters to predict riparian vegetation. When these riparian predictions were compared to predictive outcomes from a hill slope model, which was assumed to be affected by fewer disturbances (i.e. flooding), predictive accuracies were not very different. Overall though, predictive accuracy for riparian vegetation was high, but not good enough to support the supposition that riparian vegetation is abiotically controlled because of frequent flood disturbance. Nevertheless, geomorphology and consequently flood effects are still important for the determination of the riparian community composition. Overall, riparian vegetation was found to be closely linked to its environment (evidenced in Chapters 2, 3, 4, 5) in a predictable manner (Chapter 6). Species pattern relied on flood disturbance affecting species distribution. Some riparian species were found to be highly tolerant of flooding and gained a growth advantage after flooding (Chapters 4 and 5). Therefore, flood tolerance was important for the formation of a species gradient across the riparian zone. These species tolerances and growth requirements reflect riparian geomorphic pattern (Chapter 3), which was suggested to form a template on which riparian vegetation is structured.