abstract: Water contamination with nitrate (NO3−) (from fertilizers) and perchlorate (ClO4−) (from rocket fuel and explosives) is a widespread environmental problem. I employed the Membrane Biofilm Reactor (MBfR), a novel bioremediation technology, to treat NO3− and ClO4− in the presence of naturally occurring sulfate (SO42−). In the MBfR, bacteria reduce oxidized pollutants that act as electron acceptors, and they grow as a biofilm on the outer surface of gas-transfer membranes that deliver the electron donor (hydrogen gas, (H2). The overarching objective of my research was to achieve a comprehensive understanding of ecological interactions among key microbial members in the MBfR when treating polluted water with NO3− and ClO4− in the presence of SO42−. First, I characterized competition and co-existence between denitrifying bacteria (DB) and sulfate-reducing bacteria (SRB) when the loading of either the electron donor or electron acceptor was varied. Then, I assessed the microbial community structure of biofilms mostly populated by DB and SRB, linking structure with function based on the electron-donor bioavailability and electron-acceptor loading. Next, I introduced ClO4− as a second oxidized contaminant and discovered that SRB harm the performance of perchlorate-reducing bacteria (PRB) when the aim is complete ClO4− destruction from a highly contaminated groundwater. SRB competed too successfully for H2 and space in the biofilm, forcing the PRB to unfavorable zones in the biofilm. To better control SRB, I tested a two-stage MBfR for total ClO4− removal from a groundwater highly contaminated with ClO4−. I document successful remediation of ClO4− after controlling SO4 2− reduction by restricting electron-donor availability and increasing the acceptor loading to the second stage reactor. Finally, I evaluated the performance of a two-stage pilot MBfR treating water polluted with NO3− and ClO4−, and I provided a holistic understanding of the microbial community structure and diversity. In summary, the microbial community structure in the MBfR contributes to and can be used to explain/predict successful or failed water bioremediation. Based on this understanding, I developed means to manage the microbial community to achieve desired water-decontamination results. This research shows the benefits of looking "inside the box" for "improving the box". / Dissertation/Thesis / Ph.D. Sustainability 2014

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Numerous studies have looked at biotic succession at the aboveground level; however, there are no studies describing fungal community change associated with long-term ecosystem development. To understand ecosystem development, the organisms responsible for shaping and driving these systems and their relationships with the vegetation and soil factors, it is critical to provide insight into aboveground and belowground linkages to ultimately include this new information into ecosystem theory. I hypothesized that fungal communities would change with pedogenesis, that these changes would correlate with vegetation community change, and that they should show change of composition and diversity as the seasons change. Chapter 1 discusses the main topics related to this dissertation. Chapter 2 includes a publication draft that describes a study of sand-dune soil samples from northern Michigan that were analyzed to pinpoint the structural change in the fungal community during the development of the ecosystem. The samples were analyzed by pyrosequencing the soil DNA, targeting the internal transcribed spacer region. Chapter 3 contains a coauthored published paper that describes plant invasion of fields in Virginia to determine how they impact soil bacterial and fungal communities. The bacterial and fungal communities that were invaded by 3 different plant species exhibited similar changes, regardless of plant species, suggesting that some functional traits of invasives may have similar impacts on belowground communities. Chapter 4 remarks the conclusions of this research. / Master of Science / Ecosystems, including the soils underneath, are the environments that surround us perform a large number of critical human-relevant functions (playing roles in production of food, filtration of water for drinking, sequestration of carbon and nitrogen to build soil organic matter, and buffer against flooding). Yet, how these systems naturally develop over time are still in need of detailed study. One particular area of interest and need is the study of belowground fungal communities. It is not commonly known, but plants and ecosystems are highly dependent on the underground web of fungal hyphae that transform nutrients and provide water to plants. A first step in gaining this understanding utilized a natural ecosystem development gradient known as a chronosequence. It was expected that fungal communities would change as soil and ecosystem development progressed and that they would mimic changes in soil and vegetative properties. Discerning if these linkages occur is the first step to assessing how they work together to create ecosystems and their valuable environmental services. Chapter 1 provides a discussion of the main topics in this dissertation. Chapter 2 is at the heart of the dissertation via a study of fungal communities in a developmental soil ecosystem in northern Michigan in addition, in Chapter 3, I include a coauthored published paper that describes plant invasion of fields in Virginia. Chapter 4 remarks on the major conclusions of this Master thesis, supporting the role that vegetation and fungal community change in soil are associated with one another.

Platinum mining activities contribute substantially to South Africa's economy since it exceeded gold as economical contributor in 2001. Mining activities contribute to large amounts of waste production in the form of tailings and rock waste, deposited in the surrounding environment of the mine premises. Mining companies are held responsible for damages caused to the surrounding environment. These companies are required to introduce the cost of ecological rehabilitation in their operation costs as well as compile an environmental management plan. Numerous attempts to rehabilitate mine waste have proven unsuccessful. New and improved rehabilitation techniques are required to facilitate in the rehabilitation of these mine spoils. Woodchip-vermicompost produced from platinum mining wastes (woodchips and sewage sludge) was used as an alternative amendment to inorganic fertilisers during the rehabilitation of platinum mine tailings. The effectiveness of the woodchip-vermicompost as an alternative amendment during the platinum mine tailings rehabilitation were monitored using different ecosystem components. A natural veldt in the vicinity of the mine area was randomly selected to serve as a reference site. These ecosystem components selected have previously been shown to be effective as indicators of ecosystem quality. The components selected for this study includes the use of microbial enzymatic activity, microbial community structure, nematode trophic structures, and other mesofaunal groups such as micro-arthropods. The physical and chemical properties of the platinum mine tailings and reference area as well as the vegetation cover of the platinum mine tailings were determined. Statistical and multivariate analyses were use to determine the correlation between the dependent microbial components and dominate independent chemical properties. Nematode trophic structure, Maturity Index, and Plant-Parasitic nematode Index were used to compare the two rehabilitation techniques in terms of nematodes as indicators. Microarthropods family structures were used to compare the two amendments in terms of diversity and abundance. Enzymatic activity was positively affected by the addition of woodchip-vermicompost, than in the sites treated with inorganic fertilisers. The microbial community structure showed no statistically significant (p < 0.05) differences between the two amendments. A higher abundance of nematodes especially plant-parasitic nematodes and bacterivorous nematodes were observed in the woodchip-vermicompost sites than in the inorganic fertilised sites. According to the Maturity Index, both amendments became more enriched during the study period, while the Plant-Parasitic nematode Index showed that the carrying capacity for plantparasitic nematodes on the woodchip-vermicompost sites increased while it decreased in the inorganic fertilised sites, which can be related to the decrease in vegetation cover on the inorganic fertilised sites. Both coloniser (Prostigmata) and persister (Cryptostigmata and Mesostigmata) groups of the micro-arthropods, as well as a higher diversity of micro-arthropods, were present on the woodchip-vermicompost sites whereas the inorganic fertilised sites showed only the presence of colonisers, with a decrease in diversity and abundance of micro-arthropods over the study. The colonisation of micro-arthropods may have been affected by the addition of woodchip-vermicompost and vegetation cover, which contribute to the establishment of suitable microhabitats for these soil biota. By intercorrelating the results, it may be concluded that the addition of woodchip-vermicompost may be an essential part of the rehabilitation process, by contributing to soil organic material to the ecosystem system, which may improve the recolonisation of soil biota and ecosystem processes. However further studies need to be conducted in order to determine the long-term sustainability of the woodchip-vermicompost in providing organic material and sustaining the ecosystem processes. The study also showed the necessity to integrate various ecosystem components when evaluating ecosystem development due to the unique role each component plays and the impact it may have on other components. / Thesis (M. Environmental Science)--North-West University, Potchefstroom Campus, 2006.

Agricultural intensification reliant on monocrops could change soil health in a way that does not support maximum crop productivity. Twenty-nine-year-old no-till field plots at the University of Kentucky Spindletop research farm showed a significant reduction in corn yields from continuous corn plots compared to those from plots in various types of rotation. The objective of this study was to determine what role soil microbes might play in yield reduction and how management and time effects microbial community structure. Samples were collected from the following treatments: continuous corn (CC), continuous soybean (SS), a 2-year corn/soybean rotation (CCSS), Corn in rotation with soybean with winter wheat cover (C/W/S), and sod controls (SOD). Soil health-related parameters were determined along with microbial community structure using phospholipid fatty acid analysis (PLFA). Results show that there is a strong seasonal dynamic in microbial communities with May, July and September showing the greatest differentiation between treatments. Nonparametric multidimensional analysis (NMDS) shows that microbial communities under SS, CC treatments were significantly different from the CS and CWS treatments across all four years of the study. My findings will prove useful for assessing the contribution of biological indicators to agroecosystem function and will aid in making recommendations of when and how to manage these parameters to improve soil health and maximize yield.

Thesis (M. Environmental Science)--North-West University, Potchefstroom Campus, 2006.

Recent work has demonstrated that vast amounts of soil organic carbon (SOC) are redistributed and buried within Canadian croplands; however, the effects of redistribution on SOC dynamics and biological properties of the soil environment remain unknown. Because soil microorganisms are drivers of carbon (C) turnover in soil, the effects of such processes on microbial community dynamics are important in assessing the overall effects of redistribution and the stability of displaced C. This is particularly important in the face of future climate change scenarios and potential disturbances. The objectives of this study were to examine microbial community dynamics with depth and among landscape positions in an eroded landscape, and to assess C mineralization response between surface and subsurface soil layers in a depositional position. Microbial abundance was highly influenced by SOC redistribution. This was most evident in the buried backslope position where substantial soil and SOC deposition had occurred, creating a very thick A horizon (ca. 80 cm). Phospholipid fatty acid (PLFA) analysis revealed substantial concentrations of microbial biomass located at depth (30-60 cm), which was greater than PLFA concentration at the soil surface and correlated with SOC concentration. Community structure analysis demonstrated the strong influence of landscape position and depth in structuring microbial communities near the soil surface (0-20 cm). Communities in positions that were predominantly erosional were the most different from those in the depositional position, accounting for the largest amount of variation (60%) in the overall analysis. The existence of distinct microbial communities found in depositional material (0-25 cm) and within the buried A horizon (30-80 cm) in the buried backslope position indicate a strong influence of depth and redistribution in structuring microbial communities. The existence of significant viable biomass in the buried A horizon of the depositional position leads to question the persistence of highly concentrated, buried SOC over many decades. When soils from surface (0-5 and 20-25 cm) and subsurface (40-45 and 65-70 cm) depths were incubated in surface-like conditions, greater mineralization response in surface relative to subsurface soils, despite relatively similar SOC concentration, suggests that redistribution protects buried C from decomposition. Distinct microbial communities found at the onset and completion of the mineralization study between surface and subsurface soil layers may indicate the influence of microbial community structure on mineralization response. Depth was the largest source of variation in microbial community structure, and although a shift occurred after exposure to incubation conditions, the effect of depth remained the strongest influence. This work indicates that SOC redistribution strongly influences microbial abundance and community structure development, primarily driven by altered substrate gradients occurring with depth, and suggests that C is less susceptible to decomposition once buried in depositional positions.

Platinum mining activities contribute substantially to South Africa's economy since it exceeded gold as economical contributor in 2001. Mining activities contribute to large amounts of waste production in the form of tailings and rock waste, deposited in the surrounding environment of the mine premises. Mining companies are held responsible for damages caused to the surrounding environment. These companies are required to introduce the cost of ecological rehabilitation in their operation costs as well as compile an environmental management plan. Numerous attempts to rehabilitate mine waste have proven unsuccessful. New and improved rehabilitation techniques are required to facilitate in the rehabilitation of these mine spoils. Woodchip-vermicompost produced from platinum mining wastes (woodchips and sewage sludge) was used as an alternative amendment to inorganic fertilisers during the rehabilitation of platinum mine tailings. The effectiveness of the woodchip-vermicompost as an alternative amendment during the platinum mine tailings rehabilitation were monitored using different ecosystem components. A natural veldt in the vicinity of the mine area was randomly selected to serve as a reference site. These ecosystem components selected have previously been shown to be effective as indicators of ecosystem quality. The components selected for this study includes the use of microbial enzymatic activity, microbial community structure, nematode trophic structures, and other mesofaunal groups such as micro-arthropods. The physical and chemical properties of the platinum mine tailings and reference area as well as the vegetation cover of the platinum mine tailings were determined. Statistical and multivariate analyses were use to determine the correlation between the dependent microbial components and dominate independent chemical properties. Nematode trophic structure, Maturity Index, and Plant-Parasitic nematode Index were used to compare the two rehabilitation techniques in terms of nematodes as indicators. Microarthropods family structures were used to compare the two amendments in terms of diversity and abundance. Enzymatic activity was positively affected by the addition of woodchip-vermicompost, than in the sites treated with inorganic fertilisers. The microbial community structure showed no statistically significant (p < 0.05) differences between the two amendments. A higher abundance of nematodes especially plant-parasitic nematodes and bacterivorous nematodes were observed in the woodchip-vermicompost sites than in the inorganic fertilised sites. According to the Maturity Index, both amendments became more enriched during the study period, while the Plant-Parasitic nematode Index showed that the carrying capacity for plantparasitic nematodes on the woodchip-vermicompost sites increased while it decreased in the inorganic fertilised sites, which can be related to the decrease in vegetation cover on the inorganic fertilised sites. Both coloniser (Prostigmata) and persister (Cryptostigmata and Mesostigmata) groups of the micro-arthropods, as well as a higher diversity of micro-arthropods, were present on the woodchip-vermicompost sites whereas the inorganic fertilised sites showed only the presence of colonisers, with a decrease in diversity and abundance of micro-arthropods over the study. The colonisation of micro-arthropods may have been affected by the addition of woodchip-vermicompost and vegetation cover, which contribute to the establishment of suitable microhabitats for these soil biota. By intercorrelating the results, it may be concluded that the addition of woodchip-vermicompost may be an essential part of the rehabilitation process, by contributing to soil organic material to the ecosystem system, which may improve the recolonisation of soil biota and ecosystem processes. However further studies need to be conducted in order to determine the long-term sustainability of the woodchip-vermicompost in providing organic material and sustaining the ecosystem processes. The study also showed the necessity to integrate various ecosystem components when evaluating ecosystem development due to the unique role each component plays and the impact it may have on other components. / Thesis (M. Environmental Science)--North-West University, Potchefstroom Campus, 2006.

To date, there has been little research into the role of microbial community structure in the functioning of the soil ecosystem and on the links between microbial biomass size, microbial activity and key soil processes that drive nutrient availability. The maintenance of structural and functional diversity of the soil microbial community is essential to ensure the sustainability of agricultural production systems. Soils of the same type with similar fertility that had been under long-term organic and conventional crop management in Canterbury, New Zealand, were selected to investigate relationships between microbial community composition, function and potential environmental impacts. The effects of different fertilisation strategies on soil biology and nitrogen (N) dynamics were investigated under field (farm site comparison), semi-controlled (lysimeter study) and controlled (incubation experiments) conditions by determining soil microbial biomass carbon (C) and N, enzyme activities (dehydrogenase, arginine deaminase, fluorescein diacetate hydrolysis), microbial community structure (denaturing gradient gel electrophoresis following PCR amplification of 16S and 18S rDNA fragments using selected primer sets) and N dynamics (mineralisation and leaching). The farm site comparison revealed distinct differences between the soils in microbial community structure, microbial biomass C (conventional > organic) and arginine deaminase activity (organic > conventional). In the lysimeter study, the soils were subjected to the same crop rotation (barley (Hordeum vulgare L.), maize (Zea mays L.), rape (Brassica napus L. ssp. oleifera (Moench)) plus a lupin green manure (Lupinus angustifolius L.) and two fertiliser regimes (following common organic and conventional practice). Soil biological properties, microbial community structure and mineral N leaching losses were determined over 2½ years. Differences in mineral leaching losses were not significant between treatments (total organic management: 24.2 kg N per ha; conventional management: 28.6 kg N per ha). Crop rotation and plant type had a larger influence on the microbial biomass, activity and community structure than fertilisation. Initial differences between soils decreased over time for most biological soil properties, while they persisted for the enzyme activities (e.g. dehydrogenase activity: 4.0 and 2.9 µg per g and h for organic and conventional management history, respectively). A lack of consistent positive links between enzyme activities and microbial biomass size indicated that similarly sized and structured microbial communities can express varying rates of activity. In two successive incubation experiments, the soils were amended with different rates of a lupin green manure (4 or 8t dry matter per ha), and different forms of N at 100 kg per ha (urea and lupin) and incubated for 3 months. Samples were taken periodically, and in addition to soil biological properties and community structure, gross N mineralisation was determined. The form of N had a strong effect on microbial soil properties. Organic amendment resulted in a 2 to 5-fold increase in microbial biomass and enzyme activities, while microbial community structure was influenced by the addition or lack of C or N substrate. Correlation analyses suggested treatment-related differences in nutrient availability, microbial structural diversity (species richness or evenness) and physiological properties of the microbial community. The findings of this thesis showed that using green manures and crop rotations improved soil biology in both production systems, that no relationships existed between microbial structure, enzyme activities and N mineralisation, and that enzyme activities and microbial community structure are more closely associated with inherent soil and environmental factors, which makes them less useful as early indicators of changes in soil quality.