<p>Heterotrophic microorganisms are important for the flow of carbon and nutrients in the sea. Bacteria, nanoflagellates and ciliates are relevant components of the pelagic food web. In order to be able to predict the outcome of e.g. eutrophication or climate change we need to know how the different components of the pelagic food web are regulated. With the focus on the northern Baltic Sea food web, this thesis deals with limitation and control of heterotrophic protists, the effect of resource heterogeneity on food web efficiency and diversity of nanoflagellates.</p><p>In-situ microcosm experiments showed that the net growth of heterotrophic flagellates were resource limited throughout the year. Field data confirmed that the abundance of flagellates was bottom-up controlled. Furthermore, field data also showed that the annual average biomass of protists, flagellates and ciliates increased with primary productivity. On a smaller seasonal scale temperature and bacterial biomass were able to explain most of the variation in flagellate biovolume. The temporal variation in ciliate biovolume could not be explained by any bottom-up factors like bacterial biomass, flagellate biomass or chlorophyll a. This and an in-situ microcosm experiment implied that the seasonal dynamics of ciliates were more regulated by predators like mesozooplankton.</p><p>The food web efficiency i.e. how much of production at the resource level is converted to production at the top trophic level, may be affected by specific size or type of resource. Indoor mesocosms revealed that the food web efficiency was 11 times lower when heterotrophic bacteria dominated basal production instead of nano- and micro-sized phytoplankton. This was due to a lengthening of the food web when pico-sized bacteria constituted the main resource.</p><p>The PCR-DGGE molecular biological method was used to study the diversity of heterotrophic or mixotrophic chrysomonads. The focus was set on chrysomonads due to their relatively large contribution to the nanoflagellate community. Group-specific PCR primers were optimized for the target group. A field survey in the northern Baltic Sea showed that a handful of chrysomonad sequences were present throughout the year. Significantly more chrysomonads were recorded in the basin with higher primary productive and salinity. In total 15-16 different chrysomonad sequences were recorded. Most of them matched uncultured chrysomonad clones.</p>

Temporal and spatial variations of pelagic microorganisms in the northern Baltic Sea were studied, as well as factors influencing their abundance and growth rates. Three main questions were asked 1) How does increased productivity influence the structure of the microbial food web? 2) Does predation limitation vary between trophic levels? 3) What is the relative importance of resource and predation limitation at different trophic levels? A field study in the northern Baltic Sea showed that dominating protozoa, flagellates and ciliates, increased with increasing primary productivity from north to south. Furthermore, relatively small protozoan cells dominated in the low productive north, while larger cells became more dominant in the south. The relationship between plankton size structure and productivity was further studied in an experimental system. In agreement with present theories regarding nutrient status of pelagic food webs, increased productivity caused a lengthening of the food chain as well as a change in plankton size structure. While microplankton dominated in nutrient rich treatments pico- and nanoplankton dominated during nutrient poor treament. The flagellate community was dominated by a potentially mixotroph, Chrysochromulina sp., at low nutrient concentrations. To our knowledge this is the first experimental study showing that Chrysochromulina sp. in resemblance with other mixotrophs is favoured by nutrient poor conditions compared to strict autotrophs and heterotrophs. During a stratified summer period autotrophic microorganisms in the northern Baltic Sea did not respond to removal of potential predators, indicating that they were primarily limited by inorganic nutrients. An exception was small eucaryotic picoplankton that showed a large response to predator removal. Among the heterotrophic microorganisms direct effect of predation seemed to increase from ciliates, heterotrophic bacteria, small heterotrophic flagellates, medium flagellates to large flagellates. No quick indirect effect was observed, but after four days trophic cascades were detected. The relative importance of resource and predation limitation was studied among heterotrophic bacteria, flagellates and ciliates in the northern Baltic Sea. For all these groups, resource limitation seemed to prevail during the summer period. The results also indicated that the relative importance of predation increased with the productivity of the system. To our knowledge there are no earlier measurements on the relative importance of resource and predation limitation for micoorganisms in the pelagic environment.

Heterotrophic microorganisms are important for the flow of carbon and nutrients in the sea. Bacteria, nanoflagellates and ciliates are relevant components of the pelagic food web. In order to be able to predict the outcome of e.g. eutrophication or climate change we need to know how the different components of the pelagic food web are regulated. With the focus on the northern Baltic Sea food web, this thesis deals with limitation and control of heterotrophic protists, the effect of resource heterogeneity on food web efficiency and diversity of nanoflagellates. In-situ microcosm experiments showed that the net growth of heterotrophic flagellates were resource limited throughout the year. Field data confirmed that the abundance of flagellates was bottom-up controlled. Furthermore, field data also showed that the annual average biomass of protists, flagellates and ciliates increased with primary productivity. On a smaller seasonal scale temperature and bacterial biomass were able to explain most of the variation in flagellate biovolume. The temporal variation in ciliate biovolume could not be explained by any bottom-up factors like bacterial biomass, flagellate biomass or chlorophyll a. This and an in-situ microcosm experiment implied that the seasonal dynamics of ciliates were more regulated by predators like mesozooplankton. The food web efficiency i.e. how much of production at the resource level is converted to production at the top trophic level, may be affected by specific size or type of resource. Indoor mesocosms revealed that the food web efficiency was 11 times lower when heterotrophic bacteria dominated basal production instead of nano- and micro-sized phytoplankton. This was due to a lengthening of the food web when pico-sized bacteria constituted the main resource. The PCR-DGGE molecular biological method was used to study the diversity of heterotrophic or mixotrophic chrysomonads. The focus was set on chrysomonads due to their relatively large contribution to the nanoflagellate community. Group-specific PCR primers were optimized for the target group. A field survey in the northern Baltic Sea showed that a handful of chrysomonad sequences were present throughout the year. Significantly more chrysomonads were recorded in the basin with higher primary productive and salinity. In total 15-16 different chrysomonad sequences were recorded. Most of them matched uncultured chrysomonad clones.

Made available in DSpace on 2014-12-17T14:33:07Z (GMT). No. of bitstreams: 1 FabricioRC_DISSERT.pdf: 838962 bytes, checksum: 3096b614c5fa73cd030f8193624b3469 (MD5) Previous issue date: 2012-08-31 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / Protozoa may be an important alternative food source for Calanoida copepods in these environments. Aiming to quantify the feeding preferences of N. cearensis by ciliates in the presence of cyanobacteria, in vitro experiments were conducted, using mixed cultures in different concentrations of total food for copepod. Two ciliates species (Paramecium sp. and Cyclidium sp.) and a cyanobacteria toxic strain (Microcystis aeruginosa) were offered as food. Previous experiments were done to identify the copepod s maximum ingestion rate through the use of a type II functional response model when each prey is offered separately. High maximum ingestion rate were found when those protists were offered as prey. N. cearensis showed significant preference for protozoal prey over the cyanobacterium tested both in low (corresponding 95.15% of the diet) and in high food concentration treatments (about 91.56% of the diet), preferring the bigger ciliate in lower concentrations (67.52% of the diet). The meaningful involvement of heterotrophic organisms in the zooplankton diet emphasis the microbial loop participation in the energy transition from copepods to higher trophic levels. This data contributes to understand the stability of existing trophic interactions in reservoirs subjected to eutrophication and assists trophic cascade studies in these environments / Protozo?rios podem ser uma importante fonte alternativa de alimento para cop?podos Calanoida em ambientes dominados por cianobact?rias. Com o objetivo de quantificar a prefer?ncia alimentar de Notodiaptomus cearensis por ciliados em presen?a de cianobact?rias, experimentos in vitro foram conduzidos, utilizando-se culturas mistas em diferentes concentra??es totais de alimento para o cop?podo. Duas esp?cies de ciliados (Paramecium sp. e Cyclidium sp.) e uma cepa t?xica de cianobact?ria (Microcystis aeroginosa) foram ofertados como alimentos. Experimentos pr?vios visando identificar as taxas de ingest?o m?xima do cop?podo atrav?s do uso de um modelo de resposta funcional do tipo II quando cada uma das presas ? ofertada separadamente tamb?m foram realizados. O cop?podo apresentou maior taxa de ingest?o m?xima quando ciliados s?o ofertados como presa. N. cearensis mostrou prefer?ncia significativa por protozo?rios em detrimento da cianobact?ria testada tanto em tratamentos com menor (correspondendo a cerca de 95,15% da dieta) quanto com maior concentra??o de alimento (cerca de 91,56% da dieta), preferindo o ciliado de maior tamanho nas menores concentra??es (67,52% da dieta). A participa??o significativa de organismos heterotr?ficos na dieta do zoopl?ncton d? maior ?nfase ? participa??o da al?a microbiana na passagem de energia para n?veis tr?ficos superiores. Tal dado colabora para o entendimento da estabilidade das intera??es tr?ficas existentes em reservat?rios sujeitos a eutrofiza??o e auxilia estudos de cascata tr?fica nesses ambientes

Submitted by Renata Lopes (renatasil82@gmail.com) on 2016-12-13T12:21:07Z No. of bitstreams: 1 isabelmartinelecorrea.pdf: 473111 bytes, checksum: fef90be37cc2eb87e8dcbc88e8d3a4a5 (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2016-12-15T14:08:57Z (GMT) No. of bitstreams: 1 isabelmartinelecorrea.pdf: 473111 bytes, checksum: fef90be37cc2eb87e8dcbc88e8d3a4a5 (MD5) / Made available in DSpace on 2016-12-15T14:08:57Z (GMT). No. of bitstreams: 1 isabelmartinelecorrea.pdf: 473111 bytes, checksum: fef90be37cc2eb87e8dcbc88e8d3a4a5 (MD5) Previous issue date: 2007-02-23 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Os protozoários ciliados do rúmen integram a microbiota ruminal e junto das bactérias, fungos e protozoários flagelados participam da digestão fermentativa nos ruminantes. Entretanto, o papel desempenhado por estes microorganismos no metabolismo do hospedeiro apresenta pontos controversos os quais se devem em parte, à complexidade da dinâmica populacional e às relações estabelecidas com o hospedeiro e demais microorganismos ruminais. Objetivou-se caracterizar as populações de protozoários ciliados no rúmen de ovinos mestiços Santa Inês, verificando os efeitos da estacionalidade e aspectos relacionados às variações diurnas destas populações. Foram utilizados cinco ovinos mestiços Santa Inês, fistulados no rúmen, mantidos em pastagem natural de caatinga, no estado de Pernambuco, Brasil. As coletas foram realizadas em julho de 2005, período correspondente à estação chuvosa, e em janeiro de 2006, durante a estação seca. A composição botânica da dieta dos animais foi determinada através da análise da extrusa. Os horários de coleta das amostras de conteúdo ruminal seguiram o tempo de soltura dos animais, sendo a primeira coleta antes de se soltar os animais (zero hora) e às duas, quatro, seis, oito e dez horas após o animal estar em campo, sendo as amostras fixadas em formalina 18,5% (v/v). A dieta alimentar dos ovinos durante a estação chuvosa foi predominantemente composta por espécies vegetais herbáceas e na estação seca por espécies arbustivas o que retrata o efeito da xvi estacionalidade no hábito alimentar dos ovinos. Foram identificados e quantificados organismos dos gêneros Dasytricha, Diplodinium, Diploplastron, Entodinium, Eodinium, Elytroplastron, Enoploplastron, Epidinium, Eremoplastron, Eudiplodinium, Isotricha, Metadinium e Ophryoscolex, sendo os gêneros Enoploplastron e Eodinium observados apenas na estação chuvosa. Diplodinium, Elytroplastron, Metadinium e Ophryoscolex não apresentaram variações na concentração de suas populações em função da estação do ano. Observou-se a predominância de organismos do gênero Entodinium nas estações chuvosa e seca; entretanto, na estação seca houve significativo decréscimo na concentração deste gênero, e aumento de outros entodiniomorfos e de isotriquídeos. O número total de protozoários foi significativamente reduzido durante a estação seca. Diploplastron e Entodinium apresentaram variações na concentração de suas populações em função do horário de amostragem. O número de ciliados em divisão não apresentou correlação com o horário de amostragem, sendo que a estabilidade das taxas de divisão parece contribuir para a manutenção das concentrações dos ciliados no rúmen. O pH ruminal apresentou correlação negativa com o tempo de amostragem, não estando correlacionado com o número de protozoários, provavelmente porque as variações observadas compreenderam valores considerados ideais para o estabelecimento e manutenção das populações de protozoários no rúmen. Foi constatado o comportamento predatório de Elytroplastron sobre Enoploplastron, Epidinium e Entodinium; além de canibalismo entre organismos do gênero Elytroplastron. Evidências do comportamento alimentar foram obtidas através do registro da ingestão de fibras e formação de grânulos de amido no citoplasma, o que evidencia a atividade celulolítica e amilolítica atribuída a estes microorganismos no ambiente ruminal. / The ciliate protozoan of the rumen are part of the ruminal microbiota, and together with bacteria, fungus and flagellate protozoa, they participate of the fermentative digestion of the ruminants. However, there are controversial aspects about the hole of these microorganisms it the metabolism of the host, in part due to the complexity of the population dynamics, and also to the interrelations between protozoan, the host, and other ruminal microorganisms. The objective of this work was to characterize the ciliate protozoa populations in the rumen of Santa Inez crossbred sheep, verifying the effects of the seasonality and also aspects related to the diurnal changes of these populations. It was used five sheep fistulated in the rumen, maintained in natural pasturage of caatinga (scrubland) vegetation at the state of Pernambuco, Brazil. The samples were collected in july 2005 (rainy season) and january 2006 (dry season). The composition of animals diet was determined through the extrusa analysis. The samples were obtained at intervals of two hours, being the first sample took before the releasing of the animals, in a total of six samples. The samples were fixed in formalin at 18, 5% (v/v). The feed composition of the sheep during the rainy season was predominantly composed of herbaceous species, and at the dry season by species shrub, denoting the effect of the seasonality on the sheep feed habits. It was identified and quantified Dasytricha, Diplodinium, Diploplastron, Entodinium, Eodinium, xviii Elytroplastron, Enoploplastron, Epidinium, Eremoplastron, Eudiplodinium, Isotricha, Metadinium e Ophryoscolex. Eodinium and Enoploplastron genders were observed just at the rainy season. Diplodinium, Elytroplastron, Metadinium and Ophryoscolex didn’t show variations in the population concentration as a function of the season. It was observed the predominance of the gender Entodinium at both seasons; however, at the dry season it was noted significant decrease in the concentration of this gender, and increase in greater ophryoscolecidae and Isotrichidae. The total number of protozoa was significantly reduced during the dry season. Diploplastron and Entodinium showed variations in their populations concentrations, due to the time of sampling. The number ciliates undergoing division was not correlated with the sampling times. Stable division rate appears to contribute to maintenance of ciliates concentrations in the rumen. The ruminal pH was negatively correlated with sampling times, and was not correlated with the number of protozoa, probably because the variations observed included parameters considered ideal for establishment and maintenance protozoa populations of rumen. It was observed predatory behavior of Elytroplastron on Enoploplastron, Epidinium and Entodinium; besides cannibalism between organisms of the Elytroplastron gender. The registration of fiber ingestion and starch granules formation at the cytoplasm indicates cellulolytic and amilollytic activities, attributed to these microorganisms in the ruminal environment.

Il s’agit de l’étude des successions écologiques du phytoplancton dans la lagune de Ghar El Melh au niveau de 5 stations pendant (i) un suivi bimensuel allant du janvier 2011 à janvier 2012 et (ii) un suivi saisonnier à partir du novembre 2012 à mars 2013. L’étude écologique a été consacrée au microphytoplancton en relation avec les facteurs abiotiques (température, salinité et nutriments) et biotiques (microalgues épiphytes, kystes des dinoflagellés, ultraplancton et ciliés). L’analyse hydrologique du milieu a montré une variation principalement saisonnière de la plupart des paramètres avec des valeurs élevées de la température et de la salinité en été et des concentrations exceptionnelles des nutriments en automne et en hiver. Le phytoplancton de la lagune de Ghar El Melh a été principalement dominé par les dinoflagellés et les diatomées avec une manifestation alarmante des espèces nuisibles atteignant plus que 70 % du peuplement. Ces proliférations ont été remarquées durant toute l’année avec une manifestation plus marquante dans les régions internes de la lagune ce qui est principalement tributaire à la température de l’eau, l’azote total, le nitrogène et l’orthophosphate. Une importante contribution des espèces épiphytes au phytoplancton a été signalée notamment celle du dinoflagellé toxique Prorocentrum lima. L’inventaire spécifique du phytoplancton dominé par l’espèce Prorocentrum micans (> 28 %) et d’autres espèces ne produisant pas de kyste a été en concordance avec les faibles valeurs enregistrées pour les kystes de dinoflagellés dans le sédiment où le maximum enregistré a été de l’ordre de 229 kystes g-1. Une part importante de l’ultraplancton a été représentée par le nanophytoplancton et les hétérotrophes procaryotes, dépassant largement les concentrations microphytoplanctoniques, ce qui est un indice de l’eutrophisation du milieu. Des corrélations hautement significatives ont été trouvées entre le microphytoplancton et les organismes microzooplanctoniques évoquant un probable rôle de ces derniers dans le contrôle des proliférations microalguales nuisibles. / We explored the distribution of the microphytoplankton community in relation to both abiotic (temperature, salinity and nutrients) and biotic factors (epiphytes microalgae, dinoflagellate cysts, ultraplankton and ciliates) in Ghar al Melh Lagoon at 5 stations during (i) a biweekly sampling from January 2011 to January 2012 and (ii) a seasonal sampling from november 2012 to march 2013. The results pointed out a seasonal variation of all parameters with high water temperature and salinity in summer and exceptional concentrations of nutrients in autumn and winter. Microphytoplankton was mainly dominated by dinoflagellates and diatoms with sequences of harmful species proliferation attaining more than 70 % of total phytoplankton. These sporadic proliferations occurred throughout the year with exacerbation in the inner parts of the lagoon mainly related to temperature and total nitrogen, nitrogen and orthophosphate. An important contribution of epiphytic species to phytoplankton abundance was recorded with especially the presence of the toxic dinoflagellate Prorocentrum lima. Microphytoplankton was dominated by Prorocentrum micans (> 28 %) and other non-cyst former species consistent with the low dinoflagellate cysts found at sediment surface (maximum = 229 cysts g-1 DS). Urtraplankton was chiefly represented by nanophytoplankton and heterotrophic prokaryotes, with low microphytoplanktonic abundance. This indicates that the lagoon is undergoing eutrophication. Significant correlations were reported between phytoplankton and microzooplankton suggesting a potential role of the former in controlling harmful microalgae proliferations.

Among all nanomaterials, which are intentionally manufactured and applied, nanosilver (nAg) is one of the most frequently applied nanomaterials. It is introduced into wastewater treatment plants (WWTPs) due to its use as antimicrobial resource in household and medical care products and hence concern raised regarding its impact on activated sludge organisms and their purification efficiency. Within this thesis, the effects of nAg on single species, simple food chains and communities related to activated sludge were investigated. Among all tested species in this thesis, the gammaproteobacteria R. planticola was the most sensitive organism regarding the tested nAg material, NM-300K. The environmental risk assessment (ERA), based on an assumed predicted environmental concentration derived from modeled concentrations of other types of nAg, revealed no risk for the activated sludge. This result should be interpreted with care, considering the tolerantly chosen safety factor for calculation of the predicted no effect concentration and the assumptions which were made concerning environmental concentrations. Differences in acute toxic effects of nAg on the ciliate P. tetraurelia were observed depending on the type of medium and the exposure pathway (via medium or via bacterial food). More detailed investigations are required to analyze the distribution, availability and uptake of nAg into ciliates in the respective tests. In chronic experiments concentration response was very steep in the range between the effect concentration determined in acute toxicity testing (resulting in 100% mortality) and a tenfold lower concentration (no effect observed) for both exposure pathways. Community experiments with activated sludge exposed to realistic and high concentrations of nAg revealed acute effects on the protozoan community at high nAg concentration using multivariate statistics for data analysis. In contrast, the sludge biotic index was not meaningful for data interpretation, as no differences were observed between the samples of different treatments. For chronic testing, more preliminary work is required to develop a protocol for artificial wastewater which serves the needs of activated sludge organisms over longer time periods and which retains a typical composition of the activated sludge community.

Among all nanomaterials, which are intentionally manufactured and applied, nanosilver (nAg) is one of the most frequently applied nanomaterials. It is introduced into wastewater treatment plants (WWTPs) due to its use as antimicrobial resource in household and medical care products and hence concern raised regarding its impact on activated sludge organisms and their purification efficiency. Within this thesis, the effects of nAg on single species, simple food chains and communities related to activated sludge were investigated. Among all tested species in this thesis, the gammaproteobacteria R. planticola was the most sensitive organism regarding the tested nAg material, NM-300K. The environmental risk assessment (ERA), based on an assumed predicted environmental concentration derived from modeled concentrations of other types of nAg, revealed no risk for the activated sludge. This result should be interpreted with care, considering the tolerantly chosen safety factor for calculation of the predicted no effect concentration and the assumptions which were made concerning environmental concentrations. Differences in acute toxic effects of nAg on the ciliate P. tetraurelia were observed depending on the type of medium and the exposure pathway (via medium or via bacterial food). More detailed investigations are required to analyze the distribution, availability and uptake of nAg into ciliates in the respective tests. In chronic experiments concentration response was very steep in the range between the effect concentration determined in acute toxicity testing (resulting in 100% mortality) and a tenfold lower concentration (no effect observed) for both exposure pathways. Community experiments with activated sludge exposed to realistic and high concentrations of nAg revealed acute effects on the protozoan community at high nAg concentration using multivariate statistics for data analysis. In contrast, the sludge biotic index was not meaningful for data interpretation, as no differences were observed between the samples of different treatments. For chronic testing, more preliminary work is required to develop a protocol for artificial wastewater which serves the needs of activated sludge organisms over longer time periods and which retains a typical composition of the activated sludge community.

Alors que la Guadeloupe possède la plus grande bordure littorale de mangroves des Petites Antilles, la microfaune et la microflore bactérienne marine associées à cet écosystème sont très mal connues. Pourtant, ces diverses communautés de micro-organismes sont à la base du réseau trophique des sédiments marins de mangrove. En effet, grâce à leurs activités basées sur des processus hétérotrophes, ces micro-organismes vont permettre de dégrader la litière constituée de feuilles et branches de palétuviers tombées à la surface du sédiment. En condition anoxique, la dégradation des substrats végétaux par des bactéries sulfato-réductrices entraine la production de sulfures qui vont soutenir l’activité de bactéries chimiosynthétiques. Les protistes ciliés sont des micro-organismes eucaryotes unicellulaires caractérisés par la présence de cils sur la surface cellulaire et appartenant au micro-zooplancton. Leur mode de nutrition basé sur la phagocytose permet non seulement de favoriser la reminéralisation de la biomasse microbienne, ce qui augmente le transfert de nutriments à d'autres organismes du réseau trophique, mais facilite surtout l’émergence de nombreuses associations symbiotiques. Les résultats obtenus durant cette thèse ont permis de mettre en évidence la présence d’associations symbiotiques entre des bactéries sulfo-oxydantes ou hétérotrophes et des espèces de protistes ciliés faisant parties du périphyton de mangrove. / While Guadeloupe has the largest coastal edge of mangroves in the Lesser Antilles, the microfauna and marine bacterial microflora associated with this ecosystem are very poorly understood. However, these diverse communities of microorganisms are at the base of the marine mangrove sediment food web. Indeed, thanks to their activities based on heterotrophic processes, these micro-organisms will make it possible to degrade the litter composed of mangrove leaves and branches that have fallen to the surface of the sediment. In anoxic conditions, the degradation of plant substrates by sulfate-reducing bacteria leads to the production of sulfides that will support the activity of chemosynthetic bacteria. Ciliates protists are unicellular eukaryotic microorganisms characterized by the presence of cilia on the cell surface and belonging to micro-zooplankton. Their phagocytosis-based nutrition not only promotes the remineralization of microbial biomass, which increases the transfer of nutrients to other organisms in the food web, but also facilitates the emergence of many symbiotic associations. The results obtained during this thesis allowed to highlight the presence of symbiotic associations between sulfur-oxidizing or heterotrophic bacteria and ciliates protist species that are part of the mangrove periphyton.

[Truncated abstract] In Australia, there is pressure to reduce the amount of methane produced by ruminant livestock because they are the single largest source of methane emitted from anthropogenic sources, accounting for 70.7% of agricultural methane emissions. In addition, methane production represents a loss of gross energy intake to the animal. The organisms that are responsible for methane production in the animal gut are a distinct group of Archaea called methanogens. Methanogens occupy three different niches within the rumen. Some live freely in the rumen digesta (planktonic), others are attached to the outer surface of the rumen ciliates (ectosymbiotic), and some reside within the ciliates (endosymbiotic). The types and number of methanogens, as well as rumen ciliates and their symbiotic interactions, influence the amount of methane produced from the rumen. These factors in turn are affected by many factors, including diet and ruminal retention time. In this thesis, I tested the general hypothesis that increasing the amount of grain in the diet and reducing the retention time would affect the abundance and diversity of methanogens in their different niches, including their association with ruminal ciliates. Twenty-four fistulated sheep were used in a complete factorial design with the sheep randomly divided into four groups. ... The change in DGGE banding patterns and Shannon indices when sheep were fed grain indicated that the types of methanogens changed when sheep were fed low and high grain diets, but their diversity did not. In contrast, the diversity of rumen ciliates decreased when sheep were fed a high grain diet. A total of 18 bands from the DGGE analysis of the ciliates were sequenced. All except one, which was 98% similar to Cycloposthium sp. not found previously in the rumen, matched the sequences for previously identified rumen ciliates. Some of the rumen ciliates identified were not present in sheep fed the high grain diet. On a high grain diet, methanogens associate endosymbiotically with rumen ciliates to get better access to hydrogen. It appears that the association between methanogens and rumen ciliates is dictated by the availability of hydrogen in the rumen and not the generic composition of the ciliate population. Furthermore, endosymbiotic methanogens appear to produce less methane than methanogens in other niches. The pot scrubbers did not change ruminal retention time but they did reduce the acetate/propionate measurements observed in sheep on the high grain treatment. The reason why pot scrubbers had this effect remains unknown, but it is interesting to consider that some physical interaction has occurred between the pot scrubbers, the grain and the sheep that has improved the fermentation parameters in sheep fed a high grain diet. The results from this study have advanced our understanding of the interaction between methanogens and ruminal ciliates, and methanogenesis in the rumen in response to dietary changes and mechanical challenges. Extending this work to look more specifically at the species of methanogens that are most closely linked to high methane production and how they interact with the ruminal ciliates will be critical for manipulating enteric greenhouse gas emissions.