Manure nitrogen in dairy cattle represents a substantial economic and environmental loss to the industry. Current strategies used to improve N efficiency (Neff) have shown limited progress and thus, warrant more effective approaches. Considering that the gastrointestinal bacterial community has been associated with various phenotypes of economic importance, the objective of this project was to evaluate the associations between the rumen and fecal bacteriomes and Neff phenotypes in dairy cows. Results showed similarities in the overall bacterial community composition and structure of cows differing in Neff. However, the relative abundance of specific bacterial ASV differed between low and high Neff cows. Furthermore, bacterial ASV strongly correlated with Neff could be involved in processes such as nutrient supply, performance, and feed efficiency. These suggest that the gastrointestinal bacterial community is a factor influencing Neff in dairy cows and specific bacterial members can potentially serve as markers of Neff phenotypes.

Diaphorina citri depende dos endossimbiontes presentes em seu bacterioma, as bactérias Carsonella e Profftella, para o fornecimento de nutrientes essenciais ao seu desenvolvimento. D. citri também está associada à bactéria Wolbachia, que infecta inúmeros tecidos desse inseto, incluindo seu bacterioma. Esses simbiontes são transmitidos verticalmente, sendo incorporados ao bacterioma. Neste estudo, são abordados os eventos relacionados à formação do bacterioma, à dinâmica da densidade dos simbiontes durante o ciclo biológico do hospedeiro e à sensibilidade dos simbiontes ao estresse térmico. A morfogênese do bacterioma durante a embriogênese de D. citri foi descrita por meio de histologia e marcação com sondas oligonucleotídicas fluorescentes (FISH) específicas para os simbiontes do bacterioma. No início da embriogênese, as bactérias permanecem agrupadas em uma massa no polo posterior do ovo. Vitelófagos se aderem à massa de simbiontes no início da blastulação, precedendo à formação dos bacteriócitos. O bacterioma transitório resultante possui bacteriócitos que contém o simbionte do sincício (Profftella), localizado externamente aos que contém o simbionte do bacteriócito (Carsonella). Na sequência do desenvolvimento, ocorre a reorganização dos bacteriócitos, evento seguido pela formação da região sincicial. O bacterioma é movido para a região abdominal do embrião durante a catatrepsis, passando ao formato trilobado típico ao final da embriogênese. A densidade dos simbiontes associados ao psílideo dos citros durante o seu desenvolvimento foi determinada por PCR quantitativo em tempo real (qPCR). A densidade dos diferentes simbiontes, dada pela análise do número de cópias dos genes 16S rRNA (Carsonella e Profftella) e ftsZ (Wolbachia), revelaram o crescimento contínuo dos simbiontes ao longo do desenvolvimento do hospedeiro. As curvas e taxas de crescimento dos simbiontes, estimadas por meio da equação de Gompertz, indicaram relação inversamente proporcional à especificidade das relações simbiontehospedeiro e o tempo para atingir a taxa máxima de crescimento. A densidade de Carsonella foi significativamente menor daquela de Profftella em todos os estágios analisados, apesar da tendência de aumento paralelo. As taxas de crescimento de Wolbachia foram similares às de Carsonella, mas a densidade foi inferior. Nos adultos, a densidade dos três simbiontes foi maior nos machos. Entretanto, esses simbiontes continuaram a apresentar crescimento em fêmeas em atividade de oviposição, mesmo com a sua incorporação aos oócitos, o que diverge da diminuição normalmente observada em outros sistemas. Os simbiontes de D. citri responderam de forma variável ao estresse térmico. Os diferentes simbiontes apresentaram resposta própria aos diversos períodos de exposição às diferentes condições térmicas de estresse. Ainda, foi detectada a influência de um simbionte na capacidade de resposta do outro, demonstrando a existência de mecanismos de comunicação e regulação entre os simbiontes de D. citri. O estudo demonstra a influência do estresse térmico sobre a densidade dos simbiontes e a necessidade de se compreender melhor a biologia das interações insetosimbiontes e a dinâmica das relações com o ambiente. / Diaphorina citri feeds on phloem-sap and depends on bacterial symbionts harbored in the bacteriome as a supplementary source of nutrients lacking in the diet. These bacteria are vertically transmitted, being incorporated into the developing bacteriome. Here, we focus on the events related to bacteriome morphogenesis, symbiont density during host development and the effects of exposure to high temperatures on the establishment of endosymbionts during immature development. The bacteriome morphogenesis during D. citri embryogenesis was investigated by means of histology and fluorescence in situ hybridization analysis (FISH) using symbiont-specific oligonucleotide probes. During early embryogenesis, the bacteria remain aggregated in a symbiont-ball at the posterior pole of the egg. Vitellophages adhere to the symbiont mass during early blastulation, preceding bacteriocyte formation. As a result, the transient bacteriome has the bacteriocytes that harbors the syncytium symbiont (Profftella) arranged externally to those harboring Carsonella. The bacteriome is moved to the embryo abdominal region as a result of katatrepsis, becoming trilobated during the later embryonic development. The infection density of the endosymbionts associated to the Asian citrus psyllid was determined using real-time quantitative PCR (qPCR), throughout the host life cycle. Copy number of genes 16S rRNA (Carsonella and Profftella) and ftsZ (Wolbachia), revealed the continuous growth of symbionts during host development. Growth curves and rates of symbionts estimated using the Gompertz equation indicated an inversely proportional correlation between the degree of symbiont cospeciation with the host and the time to achieve the maximum growth rate. Carsonella density was significantly lower than that of Profftella at all stages analyzed, despite their joint growth trend. The growth rates of Wolbachia were similar to those of Carsonella, but Wolbachia had a lower density. In adults, the density of the three symbionts was higher in males. However, density in reproductive females remained high, despite the incorporation of symbionts in the oocytes. The increased density of symbionts in postreproductive adults contrasts with the decrease observed in other symbiotic systems. The infection density is mutually related to biological effects, but the symbiont may vary the response to heat stress. Density of Profftella and Carsonella was higher than that of Wolbachia, although there were different response patterns related to temperatures and treatment times. Symbionts associated with D. citri have their growth affected by the symbionts. This study demonstrates the effects of the heat shock on symbiont density during nymphal development and illustrates the need of further work the biology of insect-symbiont interactions and the dynamics of its relationships with the environment for a better understading of such associations.

Diaphorina citri depende dos endossimbiontes presentes em seu bacterioma, as bactérias Carsonella e Profftella, para o fornecimento de nutrientes essenciais ao seu desenvolvimento. D. citri também está associada à bactéria Wolbachia, que infecta inúmeros tecidos desse inseto, incluindo seu bacterioma. Esses simbiontes são transmitidos verticalmente, sendo incorporados ao bacterioma. Neste estudo, são abordados os eventos relacionados à formação do bacterioma, à dinâmica da densidade dos simbiontes durante o ciclo biológico do hospedeiro e à sensibilidade dos simbiontes ao estresse térmico. A morfogênese do bacterioma durante a embriogênese de D. citri foi descrita por meio de histologia e marcação com sondas oligonucleotídicas fluorescentes (FISH) específicas para os simbiontes do bacterioma. No início da embriogênese, as bactérias permanecem agrupadas em uma massa no polo posterior do ovo. Vitelófagos se aderem à massa de simbiontes no início da blastulação, precedendo à formação dos bacteriócitos. O bacterioma transitório resultante possui bacteriócitos que contém o simbionte do sincício (Profftella), localizado externamente aos que contém o simbionte do bacteriócito (Carsonella). Na sequência do desenvolvimento, ocorre a reorganização dos bacteriócitos, evento seguido pela formação da região sincicial. O bacterioma é movido para a região abdominal do embrião durante a catatrepsis, passando ao formato trilobado típico ao final da embriogênese. A densidade dos simbiontes associados ao psílideo dos citros durante o seu desenvolvimento foi determinada por PCR quantitativo em tempo real (qPCR). A densidade dos diferentes simbiontes, dada pela análise do número de cópias dos genes 16S rRNA (Carsonella e Profftella) e ftsZ (Wolbachia), revelaram o crescimento contínuo dos simbiontes ao longo do desenvolvimento do hospedeiro. As curvas e taxas de crescimento dos simbiontes, estimadas por meio da equação de Gompertz, indicaram relação inversamente proporcional à especificidade das relações simbiontehospedeiro e o tempo para atingir a taxa máxima de crescimento. A densidade de Carsonella foi significativamente menor daquela de Profftella em todos os estágios analisados, apesar da tendência de aumento paralelo. As taxas de crescimento de Wolbachia foram similares às de Carsonella, mas a densidade foi inferior. Nos adultos, a densidade dos três simbiontes foi maior nos machos. Entretanto, esses simbiontes continuaram a apresentar crescimento em fêmeas em atividade de oviposição, mesmo com a sua incorporação aos oócitos, o que diverge da diminuição normalmente observada em outros sistemas. Os simbiontes de D. citri responderam de forma variável ao estresse térmico. Os diferentes simbiontes apresentaram resposta própria aos diversos períodos de exposição às diferentes condições térmicas de estresse. Ainda, foi detectada a influência de um simbionte na capacidade de resposta do outro, demonstrando a existência de mecanismos de comunicação e regulação entre os simbiontes de D. citri. O estudo demonstra a influência do estresse térmico sobre a densidade dos simbiontes e a necessidade de se compreender melhor a biologia das interações insetosimbiontes e a dinâmica das relações com o ambiente. / Diaphorina citri feeds on phloem-sap and depends on bacterial symbionts harbored in the bacteriome as a supplementary source of nutrients lacking in the diet. These bacteria are vertically transmitted, being incorporated into the developing bacteriome. Here, we focus on the events related to bacteriome morphogenesis, symbiont density during host development and the effects of exposure to high temperatures on the establishment of endosymbionts during immature development. The bacteriome morphogenesis during D. citri embryogenesis was investigated by means of histology and fluorescence in situ hybridization analysis (FISH) using symbiont-specific oligonucleotide probes. During early embryogenesis, the bacteria remain aggregated in a symbiont-ball at the posterior pole of the egg. Vitellophages adhere to the symbiont mass during early blastulation, preceding bacteriocyte formation. As a result, the transient bacteriome has the bacteriocytes that harbors the syncytium symbiont (Profftella) arranged externally to those harboring Carsonella. The bacteriome is moved to the embryo abdominal region as a result of katatrepsis, becoming trilobated during the later embryonic development. The infection density of the endosymbionts associated to the Asian citrus psyllid was determined using real-time quantitative PCR (qPCR), throughout the host life cycle. Copy number of genes 16S rRNA (Carsonella and Profftella) and ftsZ (Wolbachia), revealed the continuous growth of symbionts during host development. Growth curves and rates of symbionts estimated using the Gompertz equation indicated an inversely proportional correlation between the degree of symbiont cospeciation with the host and the time to achieve the maximum growth rate. Carsonella density was significantly lower than that of Profftella at all stages analyzed, despite their joint growth trend. The growth rates of Wolbachia were similar to those of Carsonella, but Wolbachia had a lower density. In adults, the density of the three symbionts was higher in males. However, density in reproductive females remained high, despite the incorporation of symbionts in the oocytes. The increased density of symbionts in postreproductive adults contrasts with the decrease observed in other symbiotic systems. The infection density is mutually related to biological effects, but the symbiont may vary the response to heat stress. Density of Profftella and Carsonella was higher than that of Wolbachia, although there were different response patterns related to temperatures and treatment times. Symbionts associated with D. citri have their growth affected by the symbionts. This study demonstrates the effects of the heat shock on symbiont density during nymphal development and illustrates the need of further work the biology of insect-symbiont interactions and the dynamics of its relationships with the environment for a better understading of such associations.

Diazotrophs supply legumes such as soybean (Glycine max L. Merr) with nitrogen (N) needed for protein synthesis through biological nitrogen fixation (BNF). Through BNF, these bacteria such as Bradyrhizobium that reside in soybean root nodules, convert atmospheric nitrogen (N2) into ammonia (NH3/ NH4), a form that is biologically available for use by the plants, in return for photosynthate carbon from the plant. Abiotic stresses such as drought disrupt BNF and subsequently affects soybean yield. In addition, increasing demand for soybean is leading to supplementing its growth with synthetic N fertilizer. However, fertilizer application is known for its detrimental effects on the environment causing waterways eutrophication contributing to global warming. On the other hand, diazotrophs can supply soybean with up to 90% of N need. As such, improving the understanding and exploiting the relationship between soybean and diazotrophs is key to promoting the sustainable growing of soybean. This dissertation here investigates three main questions. First, how the soybean-diazotrophs respond to changes in water such as rainfall and irrigation. Second, how changes in these bacterial diazotrophs are related to levels of BNF, and N-related soybean molecular markers. Finally, as my colleagues and I found non-diazotrophs in the nodules of some soybean plants, I was curious about the role they are playing inside the nodules in concert with the diazotrophs. The main hypotheses tested in this dissertation are that root nodule bacterial community (bacteriome) would (1) vary by plant type, (2) respond to changes in water, and (3) be related to BNF. To answer the research questions, I devised the dissertation as follows. In Chapter 2, my colleagues and I used nine commercial cultivars of soybean that vary in drought tolerance and agronomic traits. We show that soybean sometimes, but not always, harbor a consortium of non-nitrogen fixing bacteria belonging to Pseudomonadaceae and Enterobacteriaceae families. However, as expected, nodules diazotrophs rather than non-diazotrophs responded most to changes in soil water status. In chapter 3, I used a collection of 24 genotypes of soybean that vary in their ability to fix nitrogen. The results revealed that the bacteriome diazotroph alpha diversity metrics, phylogenetic richness and evenness, was correlated with changes in BNF. Moreover, few N-related molecular markers were associated with some of the bacteria. However, we have also observed a strong effect of the environment on the diazotroph driven process of BNF (i.e. 39%-75%). For chapter 4, we sequenced three of the Pseudomonas spp. strains that were subsequently recovered again from a diversity of soybean nodules in field trials. I found that one of the strains has the ability to adapt to the nodule's unique hypoxic conditions, supporting Bradyrhizobium nodulation and possibly nodule iron. The results include the draft assembly of the proposed Pseudomonas nodulensis sp. nov. as a novel species of nodule adapted bacteria belonging to the P. fluorescens complex. The results of this dissertation contribute to the basic knowledge needed to advance sustainable breeding and management of soybean. Nodule diazotrophs are sensitive to water status e.g. drought, and other experiments have shown that the nodule bacteriome is the driver of BNF. Thus, improving the understanding and exploiting the nodule bacteriome will support developing more resilient cultivars of soybean that are efficient in BNF, and tolerant of stress. Identifying and testing diazotrophs and atypical nodule bacteria will provide a platform for developing new inoculants and biofertilizers. / Doctor of Philosophy / Soybean, the top harvested crop in the USA and 4th worldwide, is an important protein input of the livestock industry and an affordable alternative protein source for human consumption. Soybean depends on Nitrogen (N), provided by bacteria helpers, diazotrophs, that reside in nodules on soybean roots, to synthesize protein. While N makes up 80% of air, it is not suitable in its breathable form for use by most living organisms. Diazotrophs, converts this N to ammonium, a form more useful by soybean, through a process called biological nitrogen fixation (BNF). Root nodules provide a special habitat to support BNF, where soybean provides the diazotrophs with carbon as an energy source in return for the fixed ammonium. BNF is sensitive to environmental stress such as drought, which in turn affects soybean yield. While synthetic fertilizer supplementation may help reduce yield loss, it contributes to global warming and water systems pollution. Understanding the associations between soybean and diazotrophs has the potential to improve the sustainable growing of soybean. In this dissertation, we first determine the changes in the soybean root nodule bacteria in response to different water treatments. We then study how the bacterial community inside the nodules change based on different rates of BNF. After that, we look for the connections between soybean-based nitrogen molecular markers and these bacteria. Finally, we take a deeper look at how some different types of bacteria can help support N fixation. Our results have revealed that soybean hosts non-nitrogen fixing bacteria, and in high abundances. These bacteria seem to be supporting soybean growth. However, the soybean-diazotroph relationship is more sensitive to changes in water. We also found variation in nodule bacterial diversity that is related to N fixation. As well, we found that these, previously undescribed, non-nitrogen fixing bacteria are capable of living inside the nodules and they could help support the diazotrophs, under certain conditions. We provide some possible explanations to how these, previously undescribed and novel, bacteria may have adapted to the nodules. These results are very useful in the development of new inoculation products that would serve as biofertilizers for soybean, thus improving the sustainability of the agriculture industry.

The intestinal microbiota is composed of up to 100 trillion microorganisms of which bacteria are overwhelming majority. The microbiota affects the development of the immune system, defence against pathogens, host nutrition, vitamin synthesis or fat storage and its composition is changing throughout life. Some studies point to an association between microbiota composition and the development of inflammatory bowel disease. One of the treatment options is anti-TNFα antibodies therapy, which uptake or antagonize the TNFα cytokine that otherwise mediates inflammation in the intestinal mucosa. The aim of the thesis was to examine how this treatment affects the composition of the intestinal bacteriome in paediatric patients with Crohn's disease, and to find specific bacterial taxa, whose abundance changes during the treatment. By inclusion of patients with juvenile idiopathic arthritis, also treated with anti-TNFα, the study aims to discern specific effects of therapeutically induced intestinal restitution (observable in patients with Crohn's disease) from general effects of anti-TNFα therapy. Stool samples from healthy children were used to determine "healthy" bacteriome. The composition of the bacteriome was studied by profiling the variable region of the V4 gene of 16S rDNA from patients stool samples...