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Iron is an essential nutrient for the proper functioning of many bacterial physiological processes. A deficiency of iron in bacteria can cause inhibition of cell growth and changes in morphology. Under iron restricted environments, microorganisms seek out different methods of acquiring iron. Our lab reported that RhizobiumLeguminosarum ATCC 14479, a gram-negative soil bacterium, is capable of utilizing heme as the sole source of iron. This work focuses on identifying and sequencing the hmuPSTUVoperon to assess its’ possible role in heme utilization in R. leguminosarum biovar trifoliiATCC 14479. We have confirmed the presence of this operon and have completed the sequencing of each gene involved in the operon. We have used in-silico analysis to assess the possible function of each gene. In the future, gene knockout will be performed to confirm the function of the hmuPSTUVoperon.

For millions of years, the nutrient exchange symbiosis between corals and their endosymbiotic algae has formed the foundation of the ecological success of coral reefs. Yet, in recent decades anthropogenic climate change is increasingly destabilizing this symbiosis, and thus the reefs that rely on it. High-temperature anomalies have caused mass mortality of corals due to repeated coral bleaching, the expulsion or digestion of symbionts by the host during stress. Hence, in-depth knowledge of the cellular processes of bleaching is required to conceive strategies to maintain the ecological functioning of coral reefs. In this thesis, we investigated the role of symbiotic nutrient cycling in the bleaching response of corals. For this, we examined the mechanisms that underlie the functioning of the symbiosis in a stable state and how heat stress affects these metabolic interactions during coral bleaching. Our findings reveal that the functioning of the coral – algae symbiosis depends on the resource competition between host and symbionts. In a stable state, symbiotic competition for ammonium limits nitrogen availability for the algal symbiont, thereby ensuring symbiotic carbon translocation and recycling. During heat stress, however, increased metabolic energy demand shifts host metabolism from amino acid synthesis to degradation. The resulting net release of ammonium by the host, coupled with the stimulated activity of associated nitrogen-fixing microbes, substantially increases nitrogen availability for algal symbionts. Subsequently, stimulated algal growth causes selfish retention of carbon, thereby further reducing energy availability for the host. This positive feedback loop disturbs symbiotic nutrient recycling, eventually causing the collapse of carbon translocation by the symbiont. Hence, heat stress causes shifts in metabolic interactions, which directly and indirectly destabilizes the symbiosis, and ultimately undermines the ecological benefits of hosting algal symbionts for corals. In summary, this thesis shows that integrating symbiotic nutrient cycling into our conceptual understanding of coral bleaching is likely to improve our ability to predict coral bleaching in light of environmental conditions and may ultimately help to conceive new strategies to preserve coral reef functioning.

This thesis consists of three published articles and one submitted article, and is focused on the evaluation of the effects of vegetation on soil microbial communities and processes on brown coal post-mining sites. The research sites served as deposits of infertile waste material, by which the indigenous vegetation has been buried and thus the whole ecosystem was destroyed. The restoration of the ecosystem structure and functions at these areas was based on the improvement of biotic and abiotic properties of excavated soil substrate either using assisted afforestation or using spontaneous plant succession. In this work, biochemical and molecular techniques were employed in order to testify the effect of the vegetation on soil microbial processes, structure of soil microbial communities and to follow the chemical changes in the litter composition during its decomposition. Litter chemistry, enzymatic activities and microbial biomass were followed by standard biochemical procedures including spectrometry and HPLC. Bacterial microarray was used for assessing the composition of bacterial communities in the soil of successional plots. 454-pyrosequencing was employed for detailed identification of fungal and bacterial community composition in the litter layer and the bulk soil under different tree...

In the United States, symptoms caused by pathogenic strains of Escherichia coli are on the rise. A major source of these pathogenic strains is the E. coli in the digestive tract of cattle. The purpose of this project was to determine if E. coli are transferred between individuals of the same species and if interspecies transmission is possible. Proximity of cattle was also studied as a contributing factor to the transfer of E. coli. To accomplish this goal, E. coli isolates from cattle and cohabitating ground squirrels were compared through a new method of bacterial strain typing called pyroprinting. Bulls from the Cal Poly Bull Test were sampled every summer from May to September when around 200 bulls from ranches across California are housed together to be tested and eventually auctioned off. The impact of cattle origin (ranch, city) and habitation (pen) on E.coli isolate strain type were evaluated via pyroprinting . The cattle were studied to see if transfer was related to proximity of cohabitation. Since the complete population of intestinal E. coli could not be sampled, transfer could not be directly seen. The probability of sharing E. coli in each time point was used to infer transfer. There was an increase in the probability of sharing E. coli from the May sample date to the September date, indicating that some form of transfer was occurring. There was an even greater increase in the probability of sharing E. coli when the bulls were housed in close proximity. Lastly, ground squirrels cohabitating in the area were found to house some of the same strains as the cattle. This makes transfer between squirrels and cattle a possibility. Overall, this paper shows that the intestinal E. coli composition of bulls may be readily altered by the introduction of new bulls into a population.

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...

archives@tulane.edu / During the Deepwater Horizon (DWH) oil spill in 2010, approximately 0.5 billion liters (3.1 million barrels) of oil were released into the northern Gulf of Mexico during the largest marine oil spill in history . A significant portion of the released oil was weathered into residues by physical, photochemical, and biological processes prior to landing on 1773 km of coastline, including 754 km of marsh shoreline in Louisiana. Researchers endeavored to describe effects of oil residues in the soil on salt marsh organisms and communities. Many studies focused on two pillars of salt marsh ecology: the microbial communities through which a large portion of the salt marsh food web is connected and Spartina alterniflora, a foundational species of Gulf Coast salt marshes. In this dissertation I describe how cryptic, or difficult to observe, elements of salt marsh ecology, like microbial communities and plant genetics, respond to oil residues in the environment. Using a suite of field, growth chamber, and greenhouse experiments I show that these microbial communities are difficult to characterize and may respond to other factors more strongly than they do to oil residues. I present evidence that the plant is resilient to oil in the environment, and changes in its microbiome, but exerts a measurable influence on the biodegradation of oil residues and the microbiome in the soil. This dissertation provides a greater understanding of the complexity of the salt marsh response to an oil spill. / 1 / Stephen K. Formel