Sessile communities provide an ideal opportunity to understand how population interactions are structured in space, and in turn, how this structure influences population dynamics. The yellow tube sponge, Aplysina fistularis is common on Caribbean coral reefs and is involved in four main types of ecological interactions: symbiosis, predation, disease, and competition. We used spatial and multivariate analysis to describe the population structure of A. fistularis on the Belizean barrier reef, and consequently, how the observed spatial structure influenced sponge morphology and the frequency of population interactions. We found that sponges were non-randomly distributed across the reef, with both local density and tendency towards a clustered spatial distribution increasing with depth. Sponge morphology also varied with depth; deeper sponges were larger and had fewer tubes then their shallower conspecifics. Local density and spatial autocorrelational patterns were not significant predictors of population interactions. The frequency of symbiosis, characterized by the presence of the fish Elacatinus lori, increased with depth, sponge size, and number of sponge tubes. The incidence of predation increased with depth, number of tubes, and the interaction between these two variables. The chance of disease decreased with increasing sponge size. Lastly, the frequency of spatial competition decreased with depth. These results highlight the unexpected finding that in this system, symbiosis, predation, disease, and competition, are density independent, specifically they are not predicted by local density or spatial autocorrelational patterns. Overall, this study provides an essential framework that will greatly enhance our knowledge of sponge ecology on coral reefs.

A mutualistic symbiosis exists between the alga Sargassum spp. and two shrimp species, L. tenuicornis and L. fucorum. But little is known about how the shrimp locate their host alga. Both visual and chemical cues are potentially available. Visual cues would be presumably restricted at night but chemical cues are potentially available continuously. Additionally, a previous study has looked at both cue variables with results that are mixed. This current research elaborates on the previous study in an attempt to fully understand Sargassum shrimp chemoreception. A y-maze and four-chambered apparatus were used to test if the shrimp were able to detect Sargassum cues, conspecific cues, and Dimethylsulfoniopropionate (DMSP) cues. Neither shrimp species showed a strong directional response to any of the chemical cues, but the Sargassum and DMSP cues did cause more shrimp to exhibit searching behavior. Additionally, several differences in response between male and female shrimp were found for each cue. A weaker dilution of DMSP was tested in an attempt to determine sensitivity of L. fucorum shrimp to the chemical cue. This weaker dilution also caused L. fucorum to exhibit searching behavior, but the sensitivity to the cue was not found and further research is needed to fully answer this question. These results show the shrimp are able to detect chemical cues in their environment and help determine more accurately the role of chemoreception in initiating and maintaining this shrimp/algal association. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2019. / FAU Electronic Theses and Dissertations Collection

The research field of industrial ecology studies energy and material flows within and between different systems in our society while the concept of industrial ecology strives toward mimicking similar flows in natural eco-systems. Industrial ecology can be a means of achieving decoupling between economic growth and environmental impact within the industry sector. A sub-field of industrial ecology is industrial symbiosis which focuses on material, energy and water exchanges between traditionally separate actors in order to achieve economic and environmental benefits. Energy provider E.ON is a part of the industrial symbiosis network on Händelö outside of Norrköping. E.ON also has operations in the Northern Harbour industrial area in Malmö, and sees an opportunity for the development of industrial symbiosis in that area which has unexploited land. The aim of this thesis is to explore how a private actor can influence the industrial development of an area to facilitate the formation of industrial symbiosis connections. This is done by studying the emergence and development of industrial symbiosis in Händelö and how different actors have influenced that development, as well as the conditions for such development in the Northern Harbour. Industrial symbiosis in Händelö has evolved spontaneously because of profitability in each connection. This study shows that the establishment of Agroetanol’s ethanol pilot plant next to Händelöverket was an enabling event in the development of the industrial symbiosis network. The diversity of fuels used in Händelöverket, and the number of energy products that it provides suggest that it served as a so called anchor tenant in this development, attracting Agroetanol with its availability of steam produced from renewable fuels. This was one important aspect for the establishment of Agroetanol. Political instruments such as a tax exemption on Agroetanol’s plant and CO2 and energy taxes on fossil fuels have also contributed to this development. Conditions for industrial symbiosis in the Northern Harbour in Malmö are quite different from those in Norrköping. An important difference is that industrial symbiosis has been recognized as a tool for sustainability and might be considered when planning the unexploited land. There are however many interest in this land, especially by the port company CMP and the City of Malmö’s Real Estate Office who have invested large sums in expanding the port business. They prefer goods intensive businesses that utilize the infrastructure provided by the port and railway in the area. Malmö has also set some ambitious environmental targets to be fulfilled 2030. They create a need to transition from the partly natural gas powered energy system today to one based on renewable fuels. There are also opportunities in a gasification plant which is planned by E.ON, and an EU-funded project seeking to make use of the biofuels potentials of port sites by using industrial symbiosis. The conclusions of the study are that there are ways for a private actor to influence industrial symbiosis development. Some that have been identified in this work are: As an anchor tenant with multiple large input and output streams, by attracting businesses to the area. As an enabler of a biorefinery network with multiple end-products and by-products. As a part of a coordinating entity that aims to facilitate industrial symbiosis.

Fungal endophytes live inside plants without causing apparent symptoms of infection. All plant species surveyed thus far, including liverworts, mosses, seedless vascular plants, conifers, and angiosperms, harbor one or more endophytic fungi. Fungal endophytes can be divided into four groups including class 1, class 2, class 3 and class 4 endophytic fungi according to host range, colonization pattern, transmission, and ecological function. Class 2 fungal endophytes benefit their host by increasing environmental stress tolerance (i.e. water, temperature, salt) in a habitat-specific manner. In my study, class 2 fungal endophytes were studied from weedy plants growing in an environmentally stressed area: mine tailings from the Athabasca oil sands. This area is a vast hydrocarbon reserve in western Canada that supplies 10% of Canadian oil needs. Hydrocarbons are extracted from tar sands with hot water, alkali, and solvents. The tailing sands can later be remediated (by adding organic material and fertilizer) to establish new plant communities. Prior to remediation, tailing sands have extremely low content of organic carbon and available minerals, and are hydrophobic compared to unimpacted and remediated soils. Nevertheless, <i>Taraxacum</i> (dandelion) and <i>Sonchus</i> (sow-thistle) can colonize extracted tailing sands even prior to remediation. Preliminary results show that pioneer plants have similar fungal abundance as plants of unextracted treatments. Fungal endophytes were isolated from surface sterilized <i>Taraxacum</i> and <i>Sonchus</i> that had been growing upon unimpacted, remediated and extracted soil. Fungi isolated in this way included <i>Alternaria, Tricoderma, Fusarium</i> and an unidentified <i>Perithecial Ascomycote</i>. These endophytic fungi were used to inoculate tomato plants in a greenhouse trial to determine whether they confer stress tolerance to host plants, especially for drought and low mineral nutrition. Before exposing the tomato plants to environmental stresses, the specific endophytic fungal strains applied were successfully recovered from tomato plants originally inoculated with the same endophytic fungi. Although the other endophytic fungi turned out to be harmful to the tomato plants in the test, a <i>Trichoderma spp.</i> strain isolated from samples of extracted treatment appears to confer tolerance of tailing sands to the tomato plants. This <i>Trichoderma spp.</i> strain which we can call <i>TSTh20-1</i> was molecularly identified as <i>Trichoderma harzianum</i>. Despite an identification to species, all strains of <i>T. harzianum</i> are not necessarily identical regarding strain-specific attributes. Using similar techniques described here, it is possible to isolate and potentially use beneficial class 2 endophytic fungal strains for the remediation process in the Athabasca oil sands or to assist plant growth in other high stress environments.

The concept of integration of industries in urban setup is the current trend among researchers and engineers in the field of industrial ecology and environmental engineering. Trend of urbanization forces an increasing human demand for energy, materials, water and other resources. Urban symbiosis nowadays is closely related to the controlling of urban metabolism. Closing material loops works as an effective way for a circular economy where theoretically no waste is generated. In this thesis work, an investigation has been made for studying current symbiotic activities in the city of Linköping and look for any potential energy or by-product synergies from industrial activities and the urban waste streams. Some of the companies have been found to be already engaged in such type of activities, directly or indirectly. Hence, uncovering symbiotic activity is also an important task to consider while assessing the feasibility of a network of industries and urban settlement. Finally, it is concluded that the symbiotic activity in the city of Linköping is developing with discovering of new opportunities from waste and by-products from industries and the city area.  The municipal utility company Tekniska Verken and its subsidiary Svensk Biogas could play the role as anchor tenants and the aeronautics company SAAB, for its huge production line, has good potential to participate in exchange of physical materials.

Fungal endophytes live inside plants without causing apparent symptoms of infection. All plant species surveyed thus far, including liverworts, mosses, seedless vascular plants, conifers, and angiosperms, harbor one or more endophytic fungi. Fungal endophytes can be divided into four groups including class 1, class 2, class 3 and class 4 endophytic fungi according to host range, colonization pattern, transmission, and ecological function. Class 2 fungal endophytes benefit their host by increasing environmental stress tolerance (i.e. water, temperature, salt) in a habitat-specific manner. In my study, class 2 fungal endophytes were studied from weedy plants growing in an environmentally stressed area: mine tailings from the Athabasca oil sands. This area is a vast hydrocarbon reserve in western Canada that supplies 10% of Canadian oil needs. Hydrocarbons are extracted from tar sands with hot water, alkali, and solvents. The tailing sands can later be remediated (by adding organic material and fertilizer) to establish new plant communities. Prior to remediation, tailing sands have extremely low content of organic carbon and available minerals, and are hydrophobic compared to unimpacted and remediated soils. Nevertheless, <i>Taraxacum</i> (dandelion) and <i>Sonchus</i> (sow-thistle) can colonize extracted tailing sands even prior to remediation. Preliminary results show that pioneer plants have similar fungal abundance as plants of unextracted treatments. Fungal endophytes were isolated from surface sterilized <i>Taraxacum</i> and <i>Sonchus</i> that had been growing upon unimpacted, remediated and extracted soil. Fungi isolated in this way included <i>Alternaria, Tricoderma, Fusarium</i> and an unidentified <i>Perithecial Ascomycote</i>. These endophytic fungi were used to inoculate tomato plants in a greenhouse trial to determine whether they confer stress tolerance to host plants, especially for drought and low mineral nutrition. Before exposing the tomato plants to environmental stresses, the specific endophytic fungal strains applied were successfully recovered from tomato plants originally inoculated with the same endophytic fungi. Although the other endophytic fungi turned out to be harmful to the tomato plants in the test, a <i>Trichoderma spp.</i> strain isolated from samples of extracted treatment appears to confer tolerance of tailing sands to the tomato plants. This <i>Trichoderma spp.</i> strain which we can call <i>TSTh20-1</i> was molecularly identified as <i>Trichoderma harzianum</i>. Despite an identification to species, all strains of <i>T. harzianum</i> are not necessarily identical regarding strain-specific attributes. Using similar techniques described here, it is possible to isolate and potentially use beneficial class 2 endophytic fungal strains for the remediation process in the Athabasca oil sands or to assist plant growth in other high stress environments.

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Leiognathid fish (Perciformes: Leiognathidae) contain 17 species in Taiwan in three genera: Gaza, Leiognathus, and Secutor. Leiognathid fish form mutualistic bio- luminescent symbiosis with the luminous bacteria Photobacterium leiognathi and have developed a specialized light organ to harbor bacteria and other structures to control light emission. The ecological dependence of leiognathid fish to its symbiont for light production and the specialized adaptations suggest that there co-evolution might have taken place. A single symbiont species were thought to be harbored in the light organ of leiognathid fishes. However, different oxygen rates, light production, and cell morphology have been observed in bacteria culturing during previous studies. To investigate the co-evolutionary interaction between P. leiognathi and leiognathid species, I examined the 2-DE patterns of the outer membrane protein (OMP) of symbiotic bacteria from specimens of five leiognathid species; OMPs have been proposed to be essential in symbiotic interaction. The 2-DE results of the P. leiognathi OMP pattern from five leiognathid species displayed intra-specific similarity, when inter-specific differences also exist. Intra-specific consistence revealed five proteins that are essential in the symbiotic interaction. Spot differences between various leiognathid species have shown that closely related species have significant protein spots which may have effect on speciation. In Secutor ruconius absence of the protein responsible for motility might result the difficulty on bacteria culturing. Intra-specific similarity excludes the possible of individual differentiation, and the inter-specific differences of bacterial OMP suggested that P. leiognathi in various leiognathid species might have developed various OMPs to adapt to different host species.

Symbioses between prokaryotes and eukaryotes are ubiquitous in our biosphere, nevertheless, the effects of such associations on the partners' ecology and evolution are poorly understood. At hydrothermal vents, dominant invertebrate species typically host bacterial symbionts, which use chemical energy to fix carbon to nourish their hosts and themselves. In this dissertation, I present evidence that symbiont metabolism plays a substantive, if not major, role in habitat use by vent symbioses. A study of nearly 300 individuals of the symbiotic snail Alviniconcha sp. showed specificity between three host species and three specific symbiont phylotypes, as well as a novel lineage of Oceanospirillales. Additionally, this study revealed a structured distribution of each Alviniconcha-symbiont combination across ~300 km of hydrothermal vents that exhibited a gradient in geochemical composition, which is consistent with the physiological tendencies of the specific symbiont phylotypes. I also present a comparison of the in situ gene expression of the symbionts of Alviniconcha across that same geochemical gradient, which further implicates symbiont energy and nitrogen metabolism in governing the habitat partitioning of Alviniconcha. Finally, I present data that allies productivity and sulfur metabolism in three coexisting vent symbioses, demonstrating specific interaction with the environment. Three symbioses, namely the snails Alviniconcha and Ifremeria, and the mussel Bathymodiolus, are found around vents with differing concentrations of sulfide, thiosulfate and polysulfide. Using high-pressure, flow-through incubations and stable isotopic tracers, I quantified symbiont productivity via sulfide and thiosulfate oxidation, and provided the first demonstration of thiosulfate-dependent autotrophy in intact hydrothermal vent symbioses. I further demonstrated that vent symbioses can excrete thiosulfate and/or polysulfides, implicating them in substantively influencing the sulfur chemistry of their habitats. In summary, this dissertation demonstrates the importance of symbiont physiology to the ecology of prokaryote-eukaryote symbioses by revealing that symbiont activity may be critically important to the distribution of symbioses among specific niches, as well as can alter the geochemical environment through uptake and excretion of chemicals.

Much of biology, especially evolutionary theory, makes assumptions about the individuality of living things. A population, for example, is made up of individuals. Those individuals sometimes reproduce, creating new individuals. The very use of these concepts requires that living individuals can be distinguished both synchronically and diachronically. There are many examples in nature, however, in which a living system is present, but it is not clear how to understand that system's individuality. Plants, fungi, colonial marine invertebrates, insect colonies, and symbiosis are all classic cases that have puzzled biologists interested in understanding their population structure and evolution. Scientific exploration of these issues has connections with traditional philosophical terrain, particularly the ontology of persistence and the nature of individuality broadly construed. A biologically informed philosophical literature has arisen in recent years, aimed at understanding the nature of biological individuality and its role in biological theorizing. My dissertation makes two kinds of contributions to this current literature. One contribution is theoretical, reframing our thinking about biological individuality. I distinguish between two categories of individuality and argue that they play different roles in theorizing about nature. One important kind of individual is that of the organism, understood as an entity that persists through space and time, takes in and processes resources from the environment, and maintains physiological autonomy. Another important kind of individual is that of the evolutionary individual, understood as an entity that has the capacity to participate in processes of natural selection. Distinguishing between these two types of individuality has theoretical utility, keeping clear the distinctive kinds of biological processes that individuals engage in. The other contribution of my dissertation involves detailed natural historical analysis of three kinds of problem cases. Using the framework articulated earlier in the dissertation, I assess the individuality of symbioses between larger organisms and their microbial associates, mushroom-producing fungi, and the classic case of ant colonies. The combined result of the assessments is a hierarchical pluralism about biological individuality. / Philosophy