L'objectiu d'aquest estudi és el d'investigar sobre l'ús de matèria orgànica per part dels fongs i bacteris que colonitzen diferents substrats bentònics en rius Mediterranis i analitzar l'efecte dels factors ambientals i antròpics sobre l'estabilitat estructural i funcional de les comunitats del biofilm. La metodologia emprada en aquest estudi consisteix en: i) anàlisi de la biomassa bacteriana i fúngica, ii) anàlisi de la composició de les comunitats bentòniques (identificació d'hifomicets aquàtics i anàlisi del 16S rDNA bacterià), i iii) anàlisi de l'activitat enzimàtica extracel·lular relacionada amb el reciclatge de matèria orgànica en rius. / This study aimed to investigate on the use of organic matter by fungi and bacteria inhabiting different benthic substrata and to analyze the effect of environmental and anthropogenic perturbations on the structural and functional stability of biofilms. The following methodologies has been used in this study: i) analysis of fungal and bacterial biomass, ii) analysis of benthic community composition (identification of hyphomycete taxa, analysis of the bacterial 16S rDNA), and iii) analysis of extracellular enzyme activities involved in organic matter recycling in rivers.

Doctor of Philosophy / Department of Agronomy / Charles W. Rice / Gretchen F. Sassenrath / Soil microorganisms are a critical component of ecosystem services provided by soil. Soil management drives soil physical, chemical, and biological properties. Pedogenesis and management interact to change microbial structure and function in the soil profile. Soil microbial properties may vary temporally with crop development and crop species. The objective of this study was to explore the pedogenetic and anthropogenic controls on key soil microbial properties by (i) assessing the profile of a claypan soil under conventional tillage (CT), no-till (NT), and hay meadow (HM); (ii) assessing seasonal changes of soil microbial properties in a corn/winter wheat/soybean rotation under CT and NT; and (iii) assessing vertical changes of soil microbial properties in response to long-term (28 yrs) tillage and mineral and organic fertilization. Selected microbial properties included extracellular enzyme activity, microbial structure as measured by phospholipid fatty acid (PLFA), as well as soil chemical properties. Soil C, enzyme activities, and microbial biomass were greatest in HM soils, followed by NT and then CT in the claypan soil. Wheat in the rotation increased hydrolase activity and bacterial biomass more than corn, while microbial activities were stable during soybean growth. Increased enzyme activities in the claypan layer resulted from the combination of clay-enzyme interaction and impacts from management practices. In a Mollisol soil, an increase in C-acquiring enzyme activity and microbial PLFAs in a buried A horizon was a result of root growth under no-till practice and mineral fertilization. Surprisingly, long-term mineral fertilizer applications had little effect on enzyme activities and microbial biomass. Long-term organic fertilization increased soil C, enzyme activities, and PLFAs but decreased arbuscular mycorrhizal fungi (AMF) throughout the soil profile to a depth of 90 cm. Microbial properties are controlled by crop and soil management at the soil surface and by the interaction of management and pedogenetic properties deeper in the soil profile. Incorporating grasses in the crop rotation may allow nutrients to be extracted from deeper within the soil profile, enhancing the utilization of the entire soil profile and providing additional nutrient resources to cash crops. Incorporating wheat in the crop rotation supports greater microbial activity and biomass after corn harvest, especially in no-till management. Additional research is required to delineate further causative factors impacting enzyme activity in the claypan layer, a finer resolution in soil microbial community at the species level to explore the linkage between ecological function and microbiome structure, and a network analysis for the soil-plant-microbe interactions.

Membrane-based filtration technologies have seen rapid inclusion in a variety of industrial processes, especially production of drinking water by desalination. Biological fouling of membranes is a challenge that leads to increased costs from efficiency reductions, membrane damage, and ultimately, membrane replacement over time. Such costs can be mitigated by monitoring and optimizing cleaning processes for better prognosis. A fluorescence-based sensor for early biofouling detection capable of measuring extracellular enzyme activity was developed. The selected fluorogen and fluorogen-substrate were characterized and down selected by in vitro screening for compatibility in seawater and profiled over relevant Red Sea desalination parameters (pH and temperature). ATP measurements are currently regarded as start-of-the-art when assessing biomass accumulation in membrane-based filtration systems Therefore, the fluorescence sensor response was measured for a range of bacterial concentrations and validated using an ATP assay. We demonstrate the efficacy of the proposed approach for the quantitative assessment of bacteria activity in seawater rapidly and sensitively. Following in vitro testing, the method was employed in a lab-scale seawater reverse osmosis (SWRO) system for suitability in monitoring biofouling formation. The sensor successfully measured bacterial biomass accumulation rapidly and non-invasively using exogenously applied fluorogen-substrates. The sensor response was corroborated with real-time in situ non-destructive imaging of the membrane surface. This approach demonstrates the practicality of prototyping an early-detection biofouling sensor in membrane based processes using extracellular enzyme activity as a measure of bacterial abundance.

Recent work in microbial ecology has focused on elucidating controls over biogeographic patterns and connecting microbial community composition to ecosystem function. My objective was to investigate the relative influences of landscape legacies and contemporary environmental factors on the distribution of soil microbial communities and their contribution to ecosystem processes across a glacial till sequence in Taylor Valley, Antarctica. Within each till unit, I sampled from dry areas and areas with visible evidence of recent surface water movement generated by seasonal melting of ephemeral snow packs and hillslope ground ice. Using T-RFLP 16S rRNA gene profiles of microbial communities, I analyzed the contribution of till and environmental factors to community similarity, and assessed the functional potential of the microbial community using extracellular enzyme activity assays. Microbial communities were influenced by geochemical differences among both tills and local environments, but especially organized by variables associated with water availability as the first axis of an NMDS ordination was strongly related to shifts in soil moisture content. CCA revealed that tills explained only 3.4% of the variability in community similarity among sites, while geochemical variables explained 18.5%. Extracellular enzyme activity was correlated with relevant geochemical variables reflecting the influence of nutrient limitation on microbial activity. In addition, enzyme activity was related to changes in community similarity, particularly in wet environments with a partial Mantel correlation of 0.32. These results demonstrate how landscape history and environmental conditions can shape the functional potential of a microbial community mediated through shifts in microbial community composition. / Master of Science

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The relationship between biodiversity and ecosystem functioning is important in maintaining agroecosystem sustainability. Plant-microbe symbioses, such as exists between the grass tall fescue (Schedonorus arundinaceum) and the asexual fungal endophyte Epichloë coenophiala, can be utilized to enhance agroecosystem functions, such as herbivore resistance. “Novel” E. coenophiala strains that vary in the production of mammal- and insect-toxic compounds have been identified, inserted into tall fescue cultivars, and are planted in pastures globally. Novel fungal endophyte-tall fescue associations may have divergent ecosystem function effects. This study assessed effects of different fescue-endophyte symbiotic combinations on pasture ecosystem function, including aboveground (fescue biomass, plant species richness, alkaloid synthesis, arthropod abundance) and belowground (soil microbial biomass, soil enzyme activity, trace gas fluxes) parameters. Results showed no significant effects of increasing symbiotic diversity within a fescue stand on aboveground measurements, bar arthropod abundance and alkaloid synthesis. Most soil parameters quantified had significant symbiotic diversity effects. For example, soil microbial biomass decreased whereas soil enzyme activity increased with increasing symbiotic diversity. Overall, our results suggested that increasing symbiotic diversity had weak to moderate effects on aboveground processes and stronger effects on certain belowground processes, indicating that symbiotic diversity can impact ecosystem functions and warrants further research.

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