In studies of plant-pollinator interactions, much attention has been paid to interspecific variation in foraging behaviors among pollinators and their consequences for plant reproduction and the stability of plant-pollinator communities. In contrast, there has been little consideration of intraspecific variation and its consequences. Specifically, male and female pollinators may forage differently due to differences in phenology, nutritional requirements, and behavior. Here, we compare male and female foraging patterns of the rare declining eastern regal fritillary butterfly, Speyeria idalia idalia. Using a 21-year dataset, which monitored the abundance, sex, and foraging of S. i.idalia across grasslands within Fort Indiantown Gap National Guard Training Center in Pennsylvania, USA, we asked whether males and females differed with respect to the diversity of nectar plants visited and the floral compositions which they visited. To better understand the behavior of individual butterflies and draw inferences about repercussions for plant fitness, in 2019 we collected pollen loads directly from male and female S. i.idalia in these same grasslands and compared the diversity, composition, and size of pollen loads between the sexes after identifying pollen grains to the lowest taxonomic unit. Both datasets point to the dominant use of three nectar species by both sexes, but also show evidence of sex specific foraging pattern. Males and females differ statistically, although slightly, in the composition of plant species visited and plant species per pollen load. Females visit a significantly greater diversity of plant species when accounting for both abundance and evenness of plants visited. In contrast, pollen loads found on males contained ~3 more species on average than female pollen loads, but this difference is not supported when accounting for evenness of pollen grains/species. Finally, we find individual male butterflies carry more pollen grains than females on average. Our results contribute to understanding pollinator resource use more broadly, with implications for pollination dynamics. For conservation of this rare species our results further emphasize the importance of nectar plants critically important for male and female members of S. i. idalia. / Biology

The mutualistic associations between Arbuscular mycorrhizal (AM) fungi and plant roots are ancient and ubiquitous across the plant kingdom, where AM fungi provide Phosphorus, Nitrogen, and water to the plant, and receive photosynthetically fixed Carbon in the form of fatty acids and sugars in return. Moreover, AM fungi are associated with increased plant resistance to both abiotic and biotic stressors such as drought and viral pathogens. Frequently used in agriculture, AM fungi are observed to increase crop yields and decrease chemical fertilizer needs for many economically important plant species. The potential to increase AM fungal effectiveness remains a driving force for current research. To determine their role in establishing and/or supporting AM symbiosis, we propose a reverse genetic study of two genes in the model legume Medicago truncatula. Based on RNA sequencing data indicating increased expression during AM symbiosis, we selected one gene that encodes for NAC TF-like protein, which belongs to a large family of plant transcription factors primarily involved in regulating the secretion of defence hormones. The second gene selected, PALM1, was recently discovered to play a role in the regulation of the trifoliate leaf structure of M. truncatula. We hypothesize that the genes under study play mechanistic roles in regulating AM fungal symbiosis and that we will observe a difference between the colonization rates of corresponding gene mutants and control groups. Firstly, we explored the involvement of the PALM1 and NAC TF genes by examining the root developmental phenotype of Medicago truncatula mutants. Secondly, we employed symbiosis assays to investigate the colonization rates of the genes in question. Results indicated that the NAC TF gene had no consistent role in the AM symbiosis, while the PALM1 gene revealed promising results, where significant increases in colonization rates were observed in PALM1 mutants throughout repeated experiments. Future research involves using this study to help pursue more effective ways to use AM fungi symbiosis in sustainable agro ecosystems.

<p>Plants and mycorrhizal fungi form a mutualism in which plants donate carbon to the fungus and, in return, receive benefits such as increased nutrient uptake and water. Mycorrhizal fungi colonize plant roots, forming nutrient exchange structures. The fungi also colonize the soil by growing long strands of hyphae that forage for nutrients and attach plants, forming a common mycorrhizal network (CMN). Plants attached to a well-supported CMN will receive greater benefits than those attached to a lesser CMN because the more carbon donations the fungal partner receives, the more it can grow and colonize the soil, accessing hard to reach soil nutrients. Kin selection theory predicts that relatives should donate more carbon to the fungal partner than non-relatives because benefits gained by neighbouring relatives through the CMN lead to inclusive fitness gains. Thus, social environment, i.e. relatedness of the group, could affect the mycorrhizal mutualism. Moreover, the presence of mycorrhizal fungi in the soil could affect plant responses to their social environment.</p> <p>For my PhD thesis I have investigated whether mycorrhizal fungi respond to plant social environment and whether the presence of mycorrhizal fungi affects plant responses to relatedness. I have addressed these topics in three greenhouse studies and two field studies, using herbaceous plants and trees. I have found strong evidence that siblings have an increased association with their mycorrhizal partner compared to strangers, resulting in greater benefits for siblings. Taken together, the results from this thesis demonstrate that the ability for plants to recognize kin has implications beyond intra-specific competitive interactions and that plant social environment has important effects on a widespread inter-specific mutualism. Additionally, the recently discovered phenomenon of plant kin recognition has been put into the context of mycorrhizae, and I have shown that mycorrhizal plants respond differently to their social environment than non-mycorrhizal plants.</p> / Doctor of Philosophy (PhD)

Urban designers are trained to think systematically, to simultaneously see the big picture for numerous human systems in the city—including multiple modes of transportation, barriers faced by the city's inhabitants, and food and waste systems—and synthesize them into a coherent design. However, many urban designers use architecture as their sole means of shaping our cities, rather than employing other design disciplines as well. One solution to this limited focus on the built environment is "landscape urbanism." First appearing in the 1990s, landscape urbanism is a theory that argues that the best way to organize a city is through the design of its landscape, rather than the design of its buildings. At its best, landscape urbanism encourages a new way to understand cities: through the horizontal domain that acts as every city's connective tissue. At its worst, landscape urbanism can emphasize a purely aesthetic view of nature in the city, rather than recognizing its full potential as an additional functional system within the urban landscape. This failing of landscape urbanism can be addressed by its next evolution: ecological urbanism. As MIT Professor and Landscape Architect Anne Whiston Spirn writes in The Granite Garden, we need to recognize nature as "an essential force that permeates the city." By embracing the presence of nature's processes within the city, we can create an ecological urbanism that combines human and natural systems for the betterment of both. "The realization that nature is ubiquitous, a whole that embraces the city, has powerful implications for how the city is built and maintained and for the health, safety, and welfare of every resident" (Spirn). Currently, the Anacostia River and the neighborhoods to the east are neglected parts of Washington D.C., and most of the river's tributaries are buried underground. This neglect is similar to cities' historic disregard for the productive processes of nature, settling instead for a superficial, idealized abstraction of nature in the city. What if the city decided that instead of viewing urban streams as a nuisance that needed to be hidden, the Anacostia River and its tributary system could provide a beautiful, functional, and memorable organizational structure for the East of the River neighborhoods? Highlighting the presence of this large natural system within the city could be an opportunity to develop an "urban ecology" and frame our future relationship with nature. Using Washington DC's Anacostia River, its tributaries, and the East of the River neighborhoods as its framework, this thesis explores a possible step past landscape urbanism by advocating for an ecological urbanism that demonstrates how human and natural systems can work together in an urban environment in a way that is ecologically productive, regionally connected, and mutually beneficial. / Master of Science / Urban designers are trained to think systematically. They must simultaneously see the big picture for numerous human systems in the city—including multiple modes of transportation, barriers faced by the city’s inhabitants, and food and waste systems—and synthesize them into a coherent design. However, many urban designers use architecture as their sole means of shaping our cities, rather than employing other design disciplines as well. One solution to this limited focus on the built environment is “landscape urbanism” which recognizes that cities (like landscapes) are constantly undergoing processes of change. First appearing in the 1990s, landscape urbanism is a theory that argues that the best way to organize a city is through the design of its landscape, rather than the design of its buildings. At its best, landscape urbanism encourages a new way to understand cities: through the horizontal domain that acts as every city’s connective tissue. At its worst, landscape urbanism can emphasize a purely aesthetic view of nature in the city, rather than recognizing nature’s full potential as an additional functional system within the urban landscape. This failing of landscape urbanism can be addressed by its next evolution: ecological urbanism. As MIT Professor and Landscape Architect Anne Whiston Spirn writes in The Granite Garden, we need to recognize nature as “an essential force that permeates the city.” By embracing the presence of nature’s processes within the city, we can create an ecological urbanism that combines human and natural systems for the betterment of both. “The realization that nature is ubiquitous, a whole that embraces the city, has powerful implications for how the city is built and maintained and for the health, safety, and welfare of every resident” (Spirn 5). Currently, the Anacostia River and the neighborhoods to the east are neglected parts of Washington DC, and most of the river’s tributaries are buried underground. This neglect is similar to cities’ historic disregard for the productive processes of nature, settling instead for a superficial, idealized abstraction of nature in the city. What if the city decided that instead of viewing urban streams as a nuisance that needed to be hidden, the Anacostia River and its tributary system could provide a beautiful, functional, and memorable organizational structure for the East of the River neighborhoods? Highlighting the presence of this large natural system within the city could be an opportunity to develop an “urban ecology” and frame our future relationship with nature. Using Washington DC’s Anacostia River, its tributaries, and the East of the River neighborhoods as its framework, this thesis explores a possible step past landscape urbanism by advocating for an ecological urbanism that demonstrates how human and natural systems can work together in an urban environment in a way that is ecologically productive, regionally connected, and mutually beneficial.

Doctor of Philosophy / Department of Biology / Ari M. Jumpponen / Dark septate endophytes (DSE) are darkly pigmented microfungal ascomycetes commonly observed in the healthy plant roots. Studying the functional roles of DSE is challenging as fundamental information about their identity, nutritional requirements, host range or host preference are lacking. Objective 1: root colonizing fungi were isolated from Konza plants roots and DSE fungi were identified by testing Koch’s postulates using leek plants. Periconia macrospinosa and Microdochium sp., were identified as DSE as they produced microsclerotia and chlamydospores in the root cortex. Select DSE were tested for their enzymatic capabilities and ability to utilize nitrogen sources: fungi tested positive for amylase, cellulase, polyphenol oxidases and gelatinase. Periconia isolates utilized organic and inorganic nitrogen suggesting facultative biotrophic and saprotrophic habits. Objective 2: a Microdochium isolate and three Periconia isolates were screened on 16 plant species (six native grasses and forbs, four crops) in a resynthesis system to test host range. DSE colonized all plant species, albeit to varying degrees. Host biomass and nutritional levels to DSE colonization varied within and among host species confirming the broad host range. Based on % responsiveness to DSE colonization, a metric similar to ‘mycorrhizal dependency’, grasses responded positively, while forbs and crops responded negatively. To test this observed ‘host preference’ under natural conditions, Konza roots from seven grass and nine forb species were surveyed for DSE colonization. Grasses hosted 50% greater DSE than forbs, supporting the broad host range and host preference of DSE fungi. Objective 3: three conspecific Arabidopsis ecotypes, Col-0, Cvi-0 and Kin-1 were inoculated with 25 P. macrospinosa isolates in resynthesis system. The three ecotypes responded differently to inoculation: Col-0 and Cvi-0 responded negatively, while Kin-1 response was neutral. Despite the negative or neutral response, each ecotype responded positively to one or two isolates. The outcomes were along the mutualism-parasitism continuum precluding an unambiguous assignment to any particular life-style. This study shows that the outcomes along this continuum are dictated by host and fungal genotypes. However, the more important question about their function remains. Additional studies with Arabidopsis microarrays are likely to provide unique insights into the potential roles of DSE.

No description available.

The principle of competitive exclusion holds that the strongest competitor for a single resource can exclude other species. Yet in many systems, more similar species appear to stably coexist than the small number of limiting resources. Understanding how and when similar species can stably coexist has taken on new urgency in managing biological invasions and their ecological impacts. Recent theoretical advances emphasize the importance of predators in determining coexistence. The effects of predators, however, can be mediated by behavioral changes induced in their prey as well as by their lethality. In this dissertation, I ask how considering multiple trophic levels changes our understanding of how a grass invasion (Pennisetum ciliare) affects species diversity and dynamics in southeastern Arizona. In considering interactions with plant consumers, and with the predators of those consumers, this research reveals more general ecological processes that determine species diversity across biological communities. I first present evidence from a grass removal experiment in the field that shows increased emergence and short-term survival of native perennial plants without grass. This is consistent with Pennisetum ciliare causing the observed concurrent decline in native plant abundance following invasion. I then present results from greenhouse and field studies consistent with that suppression of native plants being driven primarily through resource competition rather than increased rodent granivory. Granivorous rodents do not solely function as consumers, however, because they cache their harvested seeds in shallow scatter-hoards, from which seeds can germinate. Rodents thus act also as seed dispersers in a context-dependent mutualism. The primary granivores in areas invaded by Pennisetum ciliare are pocket mice (genus Chaetodipus), which have a well-studied tendency to concentrate their activity under plant cover to avoid predation by owls. Because the dense canopy of the grass may provide safer refuge, I hypothesized the pocket mice may be directly dispersing native seeds closer to the base of the invasive grass. Such a behavior could increase the competitive effect of the grass on native plant species, further driving the impacts of the invasion. By offering experimental seeds dusted in fluorescent powder and tracking where the seeds were cached, I show that rodents do preferentially cache experimental seeds under the grass. This dispersal interaction may be more general to plant interactions with seed-caching rodents across semi-arid regions that are experiencing plant invasions. Finally, I ask how the predator avoidance behavior exhibited by these rodents affects their ability to coexist with one another. Not only could their diversity affect that of the plant community, but the effects of plant invasions can cascade through other trophic levels. Theoretical understanding of how similar predator avoidance strategy alters coexistence had not yet been developed, however. Instead of a field study, therefore, I modified a general consumer-resource model with three trophic levels to ask whether avoidance behavior by the middle trophic level alters the ability of those species to coexist. I found that more effective avoidance behavior, or greater safety for less cost, increased the importance of resource partitioning in determining overall niche overlap. Lowering niche overlap between two species promotes their coexistence in the sense that their average fitness can be more different and still permit coexistence. These results provide novel understanding of behavioral modifications to population dynamics in multi-trophic coexistence theory applicable to this invasion and more broadly.

The interaction between figs (Ficus spp.) and their pollinating wasps (fig wasps; Chalcidoidea, Hymenoptera) is a classic example of an ancient and apparently stable mutualism. A striking property of this mutualism is that fig wasps consistently oviposit in the inner flowers of the fig syconium (gall flowers, which develop into galls that house developing larvae), but typically do not use the outer ring of flowers (seed flowers, which are pollinated and develop into seeds). This dissertation explores the potential differences between gall and seed flowers that might influence oviposition choices, and the unknown mechanisms underlying gall formation. To identify the microbial community that could influence oviposition choice, I identified fungi in both flower types across six species of Ficus. I found that whereas fungal communities differed significantly as a function of developmental stages of syconia and lineages of fig trees, communities did not differ significantly between receptive gall and seed flowers. Because secretions from the poison sac that are deposited at oviposition are thought to be important in gall formation by both pollinating fig wasps and non-pollinating, parasitic wasps, I examined poison sac morphology in diverse galling wasps from several species of Ficus in lowland Panama. I found that the size of the poison sac was positively associated with egg number across pollinating and non-pollinating fig wasps. Finally to determine difference in defense and metabolism between gall and seed flowers, and to identify genes involved in galling, I compared gene expression profiles of fig flowers at the time of oviposition choice and early gall development. I found a prominence of flavonoids and defensive genes in both pollinated and receptive gall flowers of Ficus obtusifolia, and revealed detectable differences between gall flowers and seed flowers before oviposition. Several highly expressed genes were also identified that have implications for the mechanism of gall initiation. This dissertation explores previously unstudied aspects of the fig and fig wasp mutualism and provides important molecular tools for future study of this iconic and ecologically important association.

Pour l'ensemble des organismes vivants, la communication (intra ou interspécifique) est le véhicule de l'information, un élément central dans l'interaction entre individus. Elle a ainsi des impacts primordiaux sur les traits d'histoire de vie des espèces, et est donc façonnée par la sélection naturelle. Au cours de cette thèse, nous nous sommes intéressés à l'évolution de la médiation chimique, c'est-à-dire à la transmission d'informations par voie chimique entredeux individus, dans les interactions plantes/animaux. Nous avons choisi le modèle figuier et ses partenaires mutualistes, de la guêpe pollinisatrice aux vertébrés disperseurs de graines. La médiation chimique (ici émission de bouquets volatils constitués de terpènes et de dérivés benzéniques et d'acides gras) permet aux figuiers d'assurer leur reproduction, par attraction des pollinisateurs et des disperseurs de graines. Il existe environ 800 espèces de figuiers à travers le monde, à distribution principalement tropicale. Les figuiers, fructifiant toute l'année,sont souvent qualifiés d'espèce clef de voute des écosystèmes tropicaux, car ils assurent ainsi le maintien des populations de frugivores dans les forêts tropicales dans les périodes où très peu d'espèces d'arbres fructifient. L'interaction figuier/disperseur est plutôt généraliste, alors que le mutualisme figuier/pollinisateur, un exemple de nursery pollination, est hautement spécifique et obligatoire. Au cours de cette thèse, nous avons mis en évidence que les contraintes phylogénétiques et géographiques exercées sur la médiation chimique étaient négligeables, alors que les pressions de sélection que représentent les mutualistes sont nettement plus importantes dans l'évolution de cette médiation. Ainsi, sexe et stade phénologique du figuier et identité du partenaire mutualiste sont des informations qui peuvent être portées par la médiation chimique. Notre approche, globale et multidisciplinaire, des interactions entre les figuiers et leurs partenaires mutualistes aux deux phases de dispersions des gènes de la plante, permet une meilleure compréhension de l'évolution de la communication, et montre que les pressions façonnant ce message façonnent l'interaction elle-même. / For all living organisms, communication (intra-or interspecific) is the vehicle of information, anelement central to interactions among individuals. It thus has fundamental impacts on lifehistory traits of species, and is shaped by natural selection. This thesis is concerned with thechemical mediation of communication, i.e., the transmission of information by chemical signals,in the context of animal-plant interactions. We chose as a model system the interactionsbetween figs and their mutualist partners, including both pollinating fig wasps and vertebrateseed dispersers. Chemical mediation (in this case the emission of bouquets of volatilecompounds comprising terpenes, benzenoids and fatty acid derivatives) enables figs to ensuretheir reproduction by attracting pollinators and seed dispersers. There exist about 800 species ofFicus worldwide, principally in tropical regions. Figs, which fruit throughout the year, are oftenconsidered keystone species of tropical ecosystems, because their year-round fruiting maintainspopulations of seed-dispersing frugivores during fruit-poor lean seasons'. Interactions betweenfig species and seed-dispersing animals are generalist' (i.e., broad food species ranges), whilefig/pollinator mutualisms, examples of nursery pollination' systems, are highly species-specificand obligatory. In this thesis, we showed that phylogenetic and geographic constraints actingon chemical mediation are negligible, whereas selection pressures grounded in pollination andseed-dispersal mutualisms play a strong role in shaping the evolution of chemical mediation.Thus, chemical mediation carries information such as the sex and developmental stage of thefig tree, as well as the identity of the mutualistic partner. Our comprehensive, multidisciplinaryapproach to interactions between figs and their mutualist partners in the two phases ofdispersal of the plant's genes leads to an improved understanding of the evolution ofcommunication, and showed that the selective pressures shaping the message are also thoseshaping the interaction itself.

A mesofauna edáfica compreende pequenos invertebrados que vivem nos primeiros centímetros do solo e na serapilheira. Sabe-se que o plantio de leguminosas com espécies arbóreas não fixadoras de nitrogênio melhora a fertilidade do solo, porém não se conhece o efeito desses plantios nos invertebrados edáficos. Diante disso, objetivou-se, com este estudo, avaliar o efeito de plantios puros e mistos de Eucalyptus grandis e Acacia mangium na mesofauna edáfica e estabelecer relações da mesofauna com os atributos químicos do solo e da serapilheira e os microbiológicos do solo, a fim de se construir um novo indicador de qualidade do solo. Para tanto, em outubro de 2015 (estação seca) e março de 2016 (estação chuvosa) foram avaliados os atributos físico-químicos da serapilheira (Ca, Mg, N, P, C, C/N, C/P, Mn, Cu, Fe, Zn, umidade), microbiológicos do solo (C mic, respiração do solo e atividade da desidrogenase), a umidade do solo e a mesofauna do solo e da serapilheira (riqueza, densidade e diversidade de mesofauna). Já os atributos químicos do solo (pH, Ca, Mg, C, N, P, Al, H+Al, Na, K) foram avaliados apenas em outubro. A média dos atributos foi comparada pelo teste de Tukey a 5%, enquanto que correlações, regressões e análises multivariadas foram feitas para estabelecer relações entre a mesofauna e os atributos do solo e da serapilheira e, posteriormente, construir um indicador geral de qualidade do solo. A fauna que habita a serapilheira, os atributos microbiológicos do solo e o indicador geral de qualidade do solo apresentaram maiores valores na estação chuvosa. A umidade foi muito correlacionada com os atributos biológicos do solo e da serapilheira. Foram também constatadas diferenças entre tratamentos, sendo que na estação seca há preferência da mesofauna pelo hábitat solo, possivelmente com a prevalência de relações mutualísticas entre microrganismos e mesofauna, enquanto há uma expressiva preferência da mesofauna pela serapilheira durante a estação úmida. / Soil mesofauna comprises small invertebrates that live in the first centimeters of the soil and in the litter. The consortium between leguminous trees and non-nitrogen-fixing tree species improves soil fertility, but the effect of these plantations on edaphic invertebrates is not known yet. Thus, we aimed at evaluating the effect of pure and mixed plantation of Eucalyptus grandis and Acacia mangium on the invertebrates that inhabit the soil and litter. We looked for correlations between those plantations, soil and litter chemical attributes and soil microbiological attributes to create a general indicator of soil quality in Acacia mangium (AC), Eucalyptus grandis (EU) and mixed plantations of Acacia and Eucalyptus (M). The chemical litter attributes evaluated were Ca, Mg, N, P, C, C/N, C/P, Mn, Cu, Fe, Zn, besides soil and litter moisture, soil microbiology (microbial carbon, soil respiration and dehydrogenase activity) and soil and litter mesofauna (richness, density and diversity) in two seasons: October 2015 (dry season) and March 2016 (rainy season). Soil chemical analyses (pH, Ca, Mg, C, N, P, Al, H+Al, Na, and K) were from samples collected in October. We made comparisons of the means between forest systems, and established a general indicator of soil quality based on regressions and multivariate analyses, to identify correlations between mesofaunaand chemical and microbiological attributes. Litter mesofauna, microbial activity and the general indicator of soil quality presented much higher values in the rainy season than in the dry season. Moisture correlated positively with most of the soil and litter biological attributes. There were few differences between the forest systems; although we observed a clear mesofauna preference for soil as habitat in the dry season, possibly linked to the prevailance of mutualistic interactions between soil mesofauna and microorganisms, while the mesofauna showed great preference for the litter as habitat during the moist season.