Academic literature on the topic 'Aquatic prokaryotes'

Les microbes sont affectés par les perturbations environnementales qui affectent la stabilité fonctionnelle des communautés microbiennes. Cependant, leurs réponses sont complexes, difficiles à élucider et les mécanismes de la stabilité fonctionnelle sont encore mal compris. Dans cette thèse, j'ai étudié les réponses microbiennes aux perturbations environnementales, des populations uniques aux communautés complexes. Dans le cas d'une population unique, nous avons étudié la réponse transcriptionnelle de populations bactériennes uniques dont la niche varie le long d'un gradient environnemental. Pour aborder les conséquences des perturbations au niveau de la communauté, nous avons établi et testé un protocole de cryoconservation de communautés microbiennes complexes afin d'améliorer la reproductibilité des études expérimentales avec des assemblages de communautés microbiennes aquatiques naturelles comme sources d'inoculum. En outre, nous avons exposé expérimentalement des communautés microbiennes aquatiques complexes à des perturbations pulsées afin d'étudier les conséquences de ces perturbations sur les changements structurels de la communauté et les paramètres fonctionnels généraux, tels que l'efficacité de la croissance bactérienne. Enfin, nous avons inspecté plus en détail les conséquences des perturbations pulsées sur les processus impliqués dans le cycle de l'azote. Au cours de cette thèse, je me suis particulièrement intéressé aux isolats et aux communautés provenant d'habitats aquatiques côtiers qui fournissent d'importants services écosystémiques<br>Microbes are impacted by environmental disturbances affecting the functional stability of microbial communities. However, their responses are complex, difficult to elucidate and the mechanics of functional stability are still poorly understood. In this thesis, I investigated microbial responses to environmental disturbances from single populations to complex communities. For the single population approach, we addressed the transcriptional response of single bacterial populations with varying niche breadths along an environmental gradient. To address the consequences of disturbances at the community level, we have established and tested a protocol for cryopreserving complex microbial communities to improve the replicability of experimental studies with natural microbial aquatic community assemblies as inoculum sources. Furthermore, we have experimentally exposed complex aquatic microbial communities to pulsed disturbances to study the consequences of such disturbances on community structural changes and broad functional parameters, such as bacterial growth efficiency. Finally, we have inspected in more detail the consequences of pulsed disturbances on processes involved in nitrogen cycling. During this thesis, I particularly focused on isolates and communities that originated from coastal aquatic habitats that provide important ecosystem services

The present work proposes to show the most recent information regarding the microorganisms present in mineral and thermal springs, talking about the influence that different environmental variables, with a focus on radioactivity, have on the prokaryote and virus communities. The dissertation consists of Part 1, which is a literature review that addresses prokaryotes and viruses in water sources. The review addresses the impact of variables such as temperature, pH and radioactivity on both groups, both in the freshwater context in general and specifically in water sources. Then, in Part 2, what was done in the practical work is discussed, which consists of the treatment of flow cytometry data from various water sources in the Auverge region, France. The practical work consisted of a three-month Erasmus+ internship at the LMGE, Université Clermont-Auvergne, France. An analysis of biotic and abiotic parameters was then carried out in various water sources in the volcanic area of the Massif Central, Auvergne region. Statistical analysis of flow cytometry data was performed using Excel and XLSTAT and with the aim of analyzing the interaction between the various variables in the studied sources. For this, a PCA was performed for all variables and all sources, along with a dendrogram for analysis of similarity/dissimilarity between sources. The PCA results allowed us to make some observations: a strong positive correlation between the concentration of prokaryotes and gamma radiation and conductivity, but a negative correlation between these variables and the concentration of radon; virus concentration had a weak correlation with both prokaryote concentration and gamma radiation, and a negative correlation with radon activity. The negative correlation between radon and gamma radiation, together with the strong correlation between gamma radiation and prokaryotes, were the observations that drew the most attention and the current understanding of the interactions between these variables is still poor. No literature was found that explained these two observations. For the negative correlation between radon and gamma radiation, it is known that radon activity is characterized by the release of alpha radiation, while gamma radiation is released by radon daughters such as 214Pb. Therefore, in my hypothesis, the amount of gamma radiation would be directly correlated with the quantity of these daughters that form from radon decay. The results of the dendrogram allowed to observe three separations of sources in terms of dissimilarity. There was a font with greater dissimilarity, Par, and two other font groups. The isolation of the Par source is due to the fact that it is by a good margin the hottest source, with 78ºC. Another group of sources is separated mainly by the action of the radon concentration variable, while the other is separated by the action of other variables such as gamma radiation and conductivity. Research about the influence of radioactivity in microorganisms in freshwater and springwater is still a subject of limited interest, and research is lacking. Also, the results mentioned are still preliminary and limited by the action of COVID. Still, this offers a start in terms of future research, namely on the impacts of radioactivity on different groups of microorganisms in water sources. Still, this offers a starting point in terms of future research, namely on the impacts of radioactivity on different groups of microorganisms in water sources. Future studies are needed that include analysis of prokaryotic and viral communities (species and strains), which will allow to obtain a full perspective of the influence of radioactivity on these microorganisms.<br>O presente trabalho propõe-se a mostrar as informações mais recentes a respeito dos microrganismos presentes em fontes minerais e termais, falando sobre a influência que diferentes variáveis ambientais, com foco na radioatividade, têm nas comunidades procariotas e virais. A dissertação consiste na Parte 1, que é uma revisão da literatura que aborda procariotas e vírus em fontes de água. A revisão aborda o impacto de variáveis como temperatura, pH e radioatividade em ambos os grupos, tanto no contexto de água doce em geral quanto especificamente nas fontes de água. Em seguida, na Parte 2, é discutido o que foi feito no trabalho prático, que consiste no tratamento de dados de citometria de fluxo de várias fontes de água na região de Auverge, França. O trabalho prático consistiu em um estágio Erasmus + de três meses na LMGE, Université Clermont-Auvergne, França. Uma análise dos parâmetros bióticos e abióticos foi então realizada em várias fontes de água na área vulcânica do Maciço Central, região de Auvergne. A análise estatística dos dados da citometria de fluxo foi realizada no Excel e XLSTAT e com o objetivo de analisar a interação entre as diversas variáveis nas fontes estudadas. Para isso, foi realizada uma PCA para todas as variáveis e todas as fontes, juntamente com um dendrograma para análise de similaridade / dissimilaridade entre as fontes. Os resultados da PCA permitiram fazer algumas observações: uma forte correlação positiva entre a concentração de procariotas e a radiação gama e condutividade, mas uma correlação negativa entre essas variáveis e a concentração de radon; a concentração do vírus teve uma correlação fraca com a concentração de procariotas e radiação gama, e uma correlação negativa com a atividade do radon. A correlação negativa entre radão e radiação gama, juntamente com a forte correlação entre radiação gama e procariotas, foram as observações que mais chamaram a atenção, e o entendimento atual das interações entre essas variáveis ainda é pobre. Não foi encontrada literatura que explicasse essas duas observações. Para a correlação negativa entre radão e radiação gama, sabe-se que a atividade do radon é caracterizada pela libertação de radiação alfa, que é libertada pelas filhas do radão, como o 214Pb. Portanto, pela minha hipótese, a quantidade de radiação gama seria diretamente correlacionada com a quantidade dessas filhas que se formam a partir do decaimento do radão. Os resultados do dendrograma permitiram observar três separações de fontes em termos de dissimilaridade. Havia uma fonte com maior dissimilaridade, Par, e dois outros grupos de fontes. O isolamento da fonte Par deve-se ao fato de ser por uma boa margem a fonte mais quente, com 78ºC. Outro grupo de fontes é separado principalmente pela ação da variável concentração de radon, enquanto o outro é separado pela ação de outras variáveis como radiação gama e condutividade. A pesquisa sobre a influência da radioatividade em microrganismos em água doce e nascente ainda é um assunto de interesse limitado, e há carência de pesquisa. Além disso, os resultados mencionados ainda são preliminares e limitados pela ação do COVID. Ainda assim, isto oferece um ponto de partida em termos de pesquisas futuras, nomeadamente sobre os impactos da radioatividade em diferentes grupos de microrganismos nas fontes de água. Futuros estudos são necessários e que incluam análise das comunidades procarióticas e virais (espécies e estirpes), o que permitirá obter uma perspectiva total da influência da radioatividade nestes microorganismos.<br>Mestrado em Microbiologia

Dans les océans, les procaryotes sont des acteurs clés dans le cycle du carbone puisqu’ils consomment une fraction importante de la matière organique dissoute (MOD) relâchée par les producteurs primaires. Puisque cette matière organique est très complexe et de biodisponibilité variable, les communautés de procaryotes qui la consomme sont très diversifiées et spécialisées pour certains types de composés organiques. En utilisant cette matière organique, les procaryotes contribuent à réintroduire ce carbone dans le réseau trophique, une source d’énergie essentielle dans les gyres oligotrophes de l’océan. Toutefois, puisque cette consommation n’est pas parfaite, une quantité importante de carbone est relâchée sous forme de CO2 lors de la respiration, mais aussi sous forme de MOD récalcitrante, contribuant à séquestrer du carbone dans les océans. Le but de cette thèse est d’une part, de dresser un portrait global de la biodisponibilité de la MOD et d’autre part, de déterminer l’influence de la biodisponibilité de cette dernière sur la composition et le métabolisme des procaryotes dans la mer du Labrador, une mer dont le rôle est critique dans la régulation du climat. Plus spécifiquement, nous identifions pour la première fois comment la distribution spatiale des procaryotes influencent leur métabolisme et est influencée par leur préférence alimentaire dans les eaux de surface de la mer du Labrador. Finalement, nous regardons comment la matière organique produite en surface est transformée et séquestrée en profondeur suite à la convection hivernale dans la mer du Labrador. Le budget de carbone dans les océans n’est toujours pas balancé. Afin de mieux connaître les sources et la biodisponibilité du carbone dans les différents milieux aquatiques, nous avons évalué la biodisponibilité de la MOD à travers le continuum aquatique, des lacs jusqu’à l’océan. En menant une méta-analyse sur le sujet, nos résultats montrent que la proportion de matière organique labile, c’est-à-dire facilement utilisable par les procaryotes, est d’environ 6% dans tous les environnements aquatiques. Toutefois, la proportion de matière organique semi-labile, celle qui nécessite plus de transformation par les procaryotes, est grandement liée à la proximité au milieu terrestre. Les seuls écosystèmes aquatiques déviant de ces deux constats sont ceux en période d’efflorescence algale: ils contiennent beaucoup plus de carbone labile et semi-labile que ceux à l’équilibre. Nous avons estimé que le carbone semi-labile peut soutenir 62% de la biomasse de procaryotes dans les lacs et les milieux côtiers. Dans un deuxième temps, nous évaluons l’influence de la MOD sur le métabolisme et les communautés de procaryotes. Nous avons fait trois missions océanographiques sur la mer du Labrador à bord du navire Hudson pour déterminer la composition de la MOD et la communauté des procaryotes ainsi que leur métabolisme. En utilisant une approche novatrice, la modélisation de la distribution spatiale de l’abondance des procaryotes, nous avons montré à quel point celle-ci est importante pour déterminer leur préférence alimentaire ainsi que leur métabolisme. Nous avons également proposé un nouveau cadre conceptuel qui vise à faciliter la recherche à l’interface de la biogéochimie, de l’écologie microbienne et du métabolisme microbien. Dans un dernier temps, nous avons comparé la capacité des procaryotes venant de différentes profondeurs océaniques à séquestrer le carbone. Lors de la consommation de la MOD, les procaryotes en relâche une petite fraction sous forme plus récalcitrante. En répétant ce processus, le carbone résiduel devient très récalcitrant et peut résister à la consommation par les procaryotes durant des centaines d’années. Nous avons montré que les procaryotes de l’océan profond sont plus efficaces pour séquestrer le carbone de cette façon. Nos résultats montrent que ce sont les taxons rares des procaryotes qui sont les éléments clés dans cette suite de transformation qui mène à la séquestration du carbone appelée pompe microbienne. Cette thèse contribue à la compréhension du cycle du carbone dans la mer du Labrador et dans les écosystèmes aquatiques en général. Nous avons proposé une approche novatrice permettant de lier la qualité de la MOD à la composition des communautés de procaryotes qui la dégrade, un défi qui perdure depuis des dizaines d’années. De plus, nous montrons pour la première fois la que la pompe microbienne de carbone est un processus itératif fortement relié à la succession de la communauté de procaryotes. Nous montrons également que la pompe microbienne est active dans chaque strate océanique, mais que les procaryotes rares issus de l’océan profond sont plus efficaces à séquestrer le carbone. Mieux comprendre comment la composition de la MOD influence les procaryotes est primordial puisqu’ils sont centraux au cycle du carbone océanique.<br>Oceanic prokaryotes are key players in the carbon cycle by consuming dissolved organic mat-ter (DOM) produced by primary producers. As this organic matter is highly complex with varying degree of bioavailability, prokaryotic communities are highly diverse and different taxa target certain types of organic compounds. By consuming this organic matter, prokary-otes reintroduce this carbon into the food web, a critical energy flow in oligotrophic gyres. However, this consumption is not perfect and they release a lot of carbon as CO2 through respiration, but also as recalcitrant DOM. Thus, they contribute to carbon sequestration in aquatic ecosystems. The objective of this thesis is to characterize DOM bioavailability and its influence on the composition and metabolism of prokaryotic communities in the Labrador Sea, described as one of the Earth’s climate system tipping elements. More precisely, we quantify for the first time how the spatial abundance distribution of prokaryotes influences ecosystem metabolism and organic matter association in the surface waters of the Labrador Sea. Lastly, we look at how DOM produced at the surface is transformed and sequestered following the Labrador Sea winter convective mixing. The oceanic carbon budget is still unbalanced. In order to better understand its carbon sources and bioavailability, we characterize DOM bioavailability across the aquatic contin-uum, from lakes to the open ocean. Using a meta-analysis, our results show that the propor-tion of labile organic matter, i.e. readily available for prokaryotes, is similar at around 6% in all aquatic ecosystems. However, the proportion of semi-labile organic matter, i.e requiring transformations to be consumed by prokaryotes, is highly related to terrestrial connectivity. The only ecosystems that did not follow these patterns were in a phytoplankton bloom pe-riod and had a high proportion of labile and semi-labile organic matter as their counterparts at equilibrium. Finally, we estimated that semi-labile organic matter could sustain 62% of prokaryotic biomass in lakes and coastal zones. Second, we evaluated the influence of DOM on prokaryotic metabolism and community composition. In order to determine organic matter composition, prokaryotic community composition and metabolic rates, we did three oceanic cruises in the Labrador Sea onboard the Hudson ship. By using spatial abundance distribution modelling of prokaryotes, we identified strong associations between groups of this novel approach and organic matter composition. We also proposed a framework to bridge the gap between prokaryotic diversity, microbial ecology, and biogeochemistry among methods and across scales. Lastly, we compared how prokaryotic communities from different oceanic strata could se-quester carbon. When they consume organic matter, prokaryotes release a small amount in recalcitrant forms. Through this iterative process, called the microbial carbon pump, prokaryotes contribute to carbon sequestration by creating highly recalcitrant compounds that resist further degradation for hundreds of years. We have shown that all prokaryotes enable the microbial carbon pump, but that prokaryotes from deeper strata are more effi-cient. Our results also conclusively show that the rare prokaryotic taxa are key players in the microbial carbon pump. This thesis contributes to better understand the carbon cycle in the Labrador Sea and in all aquatic ecosystems. We proposed a novel framework to relate biogeochemistry, prokaryotic diversity and microbial ecology which has been a challenge for decades. Moreover, we con-clusively showed for the first time that the iterative process of the microbial carbon pump is related to prokaryotic succession. We also show that it happens in all oceanic strata, but that rare prokaryotes from the deep ocean are more efficient to sequester carbon. Better understanding how DOM composition influences prokaryotes is of prime importance as they are the main drivers of the oceanic carbon cycle.