Thèses sur le sujet « Sediment microbial communities »

Since the Industrial Revolution at the end of the 18th century, anthropogenic changes in the environment have shifted from the local to the global scale. Even remote environments such as the high Arctic are vulnerable to the effects of climate change. Similarly, anthropogenic mercury (Hg) has had a global reach because of atmospheric transport and deposition far from emission point sources. Whereas some effects of climate change are visible through melting permafrost, or toxic effects of Hg at higher trophic levels, the often-invisible changes in microbial community structures and functions have received much less attention. With recent and drastic warming-related changes in Arctic watersheds, previously uncharacterized phylogenetic and functional diversity in the sediment communities might be lost forever. The main objectives of my thesis were to uncover how microbial community structure, functional potential and the evolution of mercury specific functions in lake sediments in northern latitudes (>54ºN) are affected by increasing temperatures and Hg deposition. To address these questions, I examined environmental DNA from sediment core samples and high-throughput sequencing to reconstruct the community composition, functional potential, and evolutionary responses to historical Hg loading. In my thesis I show that the microbial community in Lake Hazen (NU, Canada) sediments is structured by redox gradients and pH. Furthermore, the microbes in this phylogenetically diverse community contain genomic features which might represent adaptations to the cold and oligotrophic conditions. Finally, historical Hg pollution from anthropogenic sources has likely affected the evolution of microbial Hg resistance and this deposition can be tracked using sediment DNA on the Northern Hemisphere. My thesis underscores the importance of using culture-independent methods to reconstruct the structure, functional potential and evolution of environmental microbial communities.

Microorganisms, particularly the Bacteria, are differentially impacted by metal toxicities, and will respond very quickly to changes in their environment, making them ideal bioindicators of environmental health. In this study, we evaluated the sediment-associated bacterial diversity of fifty-seven samples collected from twenty-four anthropogenically and endogenously metal impacted, geographically distinct sites in the Colorado Mineral Belt, and elucidated the factors that correlated with observed differences in the bacterial community structure. Overall, the geochemistry of all sites distinguished anthropogenic from endogenous sources of metal impact. Anthropogenic samples, on average, had higher concentrations of total recoverable and dissolved sodium and magnesium, and lower concentrations of aluminum and zinc, compared to the endogenous samples. Bacterial communities from both anthropogenically and endogenously metal impacted sites were characterized using Illumina high-throughput amplicon sequencing of the V4 region of the 16S rRNA gene. Overall, bacterial communities were remarkably diverse, with endogenously metal impacted sediments having higher diversity compared to anthropogenic sediments. The Actinobacteria and Betaproteobacteria dominated anthropogenic samples, and the Acidobacteria and Deltaproteobacteria dominated endogenous samples. Clustering of bacterial communities based on membership and structure (presence/absence and relative abundance of particular taxa, respectively) also distinguished samples based on their source of metal impact. Analysis of similarity (ANOSIM) tests indicated a significant difference between bacterial community structure based on source of metal impact (weighted UniFrac R_ANOSIM = 0.746, p = 0.001). Mantel tests indicated that total recoverable magnesium concentrations accounted for ∼54% of variance in community structure of all bacterial communities in the study. Dissolved aluminum concentrations accounted for ∼71% of the variation in all communities with an anthropogenic source of metal, and dissolved aluminum concentrations also accounted for ∼41% of the variation in bacterial communities with endogenous sources of metal impact.

This study provides one of the first direct comparisons between microbial community structures of sediments based on source of metal impact. This study is also one of the first comprehensive characterizations of bacterial communities from naturally occurring iron fen systems.

Terrestrial inputs of organic matter contribute greatly to the functioning of aquatic ecosystems, subsidizing between 30-70% of secondary production. This contribution of terrestrial resources is especially important in boreal lakes that are largely nutrient-poor and thus more responsive to these additions. Yet the mechanisms underlying initial processing of terrestrial resources by microbial communities at the base of lake food webs remain poorly understood. With this in mind, this thesis aims to advance our understanding of lake sediment microbial community assembly and functioning along abiotic gradients, primarily reflecting variation in terrestrial organic matter inputs that are predicted to increase with future environmental change. Chapter 1 reviews current knowledge on the terrestrial support of lake food webs and highlights gaps in understanding the factors influencing the microbial processing of terrestrial resources. It also provides an overview of metagenomics methods for microbial community analysis and their development over the course of the thesis. Chapter 2 tests how much of ecosystem functioning is explained by microbial community structure relative to other ecosystem properties such as the present-day and past environment. Theory predicts that ecosystem functioning, here measured as CO2 production, should increase with diversity, but the individual and interactive effects of other ecosystem properties on ecosystem functioning remain unresolved. Chapter 3 further questions the importance of microbial diversity for ecosystem functioning by asking whether more diverse microbial communities stabilize ubiquitous functions like CO2 production and microbial abundances through time. It also aims to identify the biotic and abiotic mechanisms underlying positive diversity-stability relationships. Chapter 4 then explores how microbial communities assemble and colonize sediments with varying types and amounts of terrestrial organic matter in three different lakes over a two-month period. Understanding how microbial communities change in relation to sediment and lake conditions can help predict downstream ecosystem functions. Finally, Chapter 5 discusses the main findings of the thesis and ends with proposed avenues for future research.

Les communautés microbiennes procèdent au recyclage des nutriments et à la degradation de la matière organique, et sont ainsi essentielles aux cycles biogéochimiques dans le sédiment et plus largement dans les océans. La contamination chronique aux hydrocarbures représente près de 80% des déversements totaux dans les océans. Toutefois, en comparaison des marées noires, son impact sur les communautés microbiennes est encore mal compris. Dans cette étude, nous avons d’abord utilisé une approche de type méta-analyse pour élucider l’effet global de la contamination aux hydrocarbures dans différents habitats. La réponse des communautés bactériennes à la contamination s’est révélée être dépendante du type d’habitat, les sols étant plus impactés que d’autres habitats, comme par exemple les sédiments marins. Nous nous sommes ensuite intéressés aux communautés microbiennes des trois domaines du vivant de sédiments côtiers provenant des côtes méditerranéennes et atlantiques. La contamination chronique n’influençait que marginallement les communautés benthiques, et la diversité alpha n’était pas réduite dans les sédiments contaminés. Cedendant, la comparaison des réseaux de co-occurrence des échantillons contaminés et non-contaminés a montré que le réseau des communautés contaminées présentait une topologie différente, indiquant une vulnérabilité plus importante à d’éventuelles perturbations environnementales. Des indicateurs potentiels de la contamination identifiés avec la méta-analyse ont été ciblés pour étudier l’impact de la contamination chronique aux hydrocarbures sur les services écologiques qu’ils assurent (i.e. la dégradation de la matière organique et des hydrocarbures) en utillisant la technique de Micro-FISH
Within the sediment, microbial communities play a pivotal role by driving essential processes such as nutrient cycling and organic matter degradation. Chronic hydrocarbons contamination represents almost 80% of the total input in the oceans. However, as compared to oil spills, its impact on microbial communities remains poorly understood. In this study, we first used a meta-analysis approach to decipher the global effect of hydrocarbons contamination in different habitats. Bacterial community response to the contamination was found to be dependant of the habitat studied, with soils being more impacted than other habitats, like marine sediments. Because bacteria are in interactions with other important members of microbial communities such as Archaea and Eukaryotes, we focused on microbial communities from the three domains of life in coastal marine sediments from the Mediterrranean and the French Atlantic coasts. Independently of the domains of life, chronic hydrocarbons contamination appeared to be a poor driver of communities structuration, and alpha diversity was not reduced in contaminated sediments. However, the comparison of co-occurences networks of contaminated and non-contaminated samples showed that the network from the contaminated samples exhibited a different topology, which suggests a higher vulnerability to eventual environmental perturbations. Potential indicators species identified using the meta-analysis approach were targeted to study the impact of chronic contamination on the ecological services they provide (i.e. organic matter and hydrocarbons degradation) using the Micro-FISH method

Doutoramento em Biologia
Os sedimentos marinhos são um reservatório de hidrocarbonetos petrogénicos libertados naturalmente ou acidentalmente para o ambiente marinho. Nos sedimentos marinhos, os hidrocarbonetos são usados como fonte de carbono e energia por comunidades bacterianas complexas. Contudo, a eficiência de biodegradação poderá ser limitada por fatores ambientais. Este trabalho aborda o previsível impacto das condições particulares do mar profundo, da acidificação dos oceanos e da adição de dispersantes químicos nos processos de biodegradação de hidrocarbonetos em ambientes marinhos. Numa primeira fase, a função de destoxificação primária das bactérias degradadoras de hidrocarbonetos aromáticos policíclicos (HAP) nos sedimentos do mar profundo foi avaliado através de uma compilação de informação disponível na literatura científica e também através de uma análise dependente do cultivo envolvendo culturas de enriquecimento de sedimentos de vulcões de lama do mar profundo. Posteriormente, o impacto interativo da acidificação do oceano e da contaminação por hidrocarbonetos petrogénicos em comunidades bacterianas bênticas foi avaliado, em experiências de simulação multifatorial em sistema de microcosmo previamente executadas, com sedimentos subsuperficiais estuarinos. Finalmente, foi executado uma experiência multifatorial em sistema de microcosmos para avaliar o impacto da aplicação de dispersantes químicos em situações simuladas de derrame de hidrocarbonetos em sedimentos estuarinos portuários. Os resultados obtidos, através da análise da fração cultivável, indicam que nos sedimentos do mar profundo a comunidade bacteriana degradadora de HAP é distinta da encontrada noutros sedimentos marinhos devido à predominância de bactérias relacionadas com o género Bacillus. Nos ensaios de microcosmos, apesar das diferenças entre os cenários testados, as comunidades bacterianas revelaram-se em geral, estáveis. Nos sedimentos subsuperficiais estuarinos, as alterações abióticas impostas foram provavelmente atenuadas pela barreira sedimentar sobrejacente e a comunidade bacteriana pareceu ser estável em termos de estrutura e atividade. Do mesmo modo, a dispersão química de hidrocarbonetos petrogénicos, apesar de aumentar a biodisponibilidade de PAH, não alterou significativamente a composição das comunidades bacteriana de sedimentos superficiais estuarinos. Possivelmente, a exposição prévia do sedimento portuário a poluição por hidrocarbonetos poderá ter condicionado a resposta da comunidade bêntica bacteriana à contaminação por petróleo. Em conclusão, a degradação bacteriana de hidrocarbonetos é um processo ubíquo em sedimentos marinhos e as comunidades bacterianas degradadoras revelam elevada estabilidade relativamente à variação de fatores ambientais.
The marine sediment compartment is a key sink for naturally and accidentally released oil hydrocarbons in the marine environment. Here, complex communities of interacting bacterial species will efficiently use oil hydrocarbons as sources of carbon and energy. However, the efficiency of the biodegradation process can be limited by some near-future scenarios. This work addresses different environmental scenarios regarding oil hydrocarbon biodegradation in marine sediments. First, the role of bacteria as primary detoxifiers of polycyclic aromatic hydrocarbons in deep-sea sediments was evaluated through the compilation of available data and through a culture-dependent analysis of enrichment cultures derived mud volcano sediments. Next, the impact of the interactive effects of ocean acidification and oil hydrocarbon contamination was further analyzed in subsurface estuarine sediments. Finally, the impact of chemically dispersed oil in estuarine port sediments is evaluated through a multi-factorial microcosm simulation. Results show that , in deep sea mud volcano sediments, the culturable fraction of the PAH-degrading bacterial community seems distinct from other environments, with a predominance of Bacillus-like bacteria. In the microcosmbased assays, despite the differences between them, the overall bacterial community exhibit a reliable stability. In subsurface sediments, abiotic changes tested were possibly attenuated by the superficial sediment barrier and bacterial seem stable to environmental changes. Also, the chemical dispersion of oil, despite enhancing PAH concentration, did not impose significant alterations to the bacterial community composition at the marine sediment surface. The potential pre-exposure of the port sediment to oil hydrocarbon pollution may have preconditioned the response of the benthic bacterial communities to oil contamination. In conclusion, oil-hydrocarbon biodegradation is ubiquitous and communities exhibit a structural stability to environmental changes.

L'éventail sous-marin profond du Congo, situé sur la marge continentale Congo-Angolaise (côte Ouest Africaine, Océan Atlantique Equatorial Sud) représente un écosystème sédimentaire marin profond unique.Celui-ci est caractérisé par de forts apports en matière organique provenant du fleuve Congo, qui se déversent le long du canyon et au travers de systèmes chenal Jevées actuels jusque dans les zones les plus profondes (5 000 m) où se développe le système des lobes.L'objectif de cette thèse est d'étudier la distribution spatiale et la diversité phylogénétique et fonctionnelle des communautés archéennes et bactériennes en relation avec les caractéristiques et les contraintes de I'environnement.Cette étude a permis de mettre en évidence une distribution géographique régionale et locale des communautés microbiennes contraintes par la distance des différents lobes par rapport à l'embouchure du chenal. La distribution des communautés microbiennes est liée à la disponibilité en accepteurs et donneurs d'électrons issus de la diagénèse précoce de la matière organique. La composition et l'identité taxonomique de ces communautés microbiennes sont comparables aux communautés rencontrées dans des sédiments marins et des zones d'émission de fluides froids riches en méthane.Cette étude révèle également des densités cellulaires relativement élevées de bactéries méthanotrophes aérobies associées à différents habitats sédimentaires particuliers, colonisés par des bivalves Vesicomyidae, des tapis microbiens et des sédiments réduits caractéristiques des environnements d'émissions de fluides froids riches en méthane et hydrogène sulfuré. Ces communautés sont non seulement apparentées à celles rencontrées dans des habitats d'émissions de fluides froids, mais également à celles des habitats terrestres, malgré la distance ~ 1000 km des côtes Africaines.Les travaux menés au cours de cette thèse montrent l'intérêt des études pluridisciplinaires pour comprendre la diversité et le fonctionnement des écosystèmes dans les lobes terminaux du système turbiditique du Congo et apportent de nouvelles informations sur la diversité des microorganismes peu explorée dans les éventails sous-marins profonds
The Congo deep sea fan, located in the Congo-Angola continental margin (West African coast, Equatorial South Atlantic Ocean) represents a unique deep-sea sedimentary ecosystem. It is characterized by high organic matter inputs from the Congo River, that flow along a canyon and through presently active channel system-lifted into the deeper areas (5 000 m) where the lobes system develops.The aim of this thesis is to study the spatial distribution as well as the phylogenetic and functional diversity of archaeal and bacterial communities in relation with environmental characteristics and constraints of the terminal lobes of the Congo deep see fan, one of the largest submarine fan systems in the world.This study highlights geographical distribution of microbial communities constrained by the distal and proximal distance of the different lobes from the Congo river's channel mouth as well as linked to the electron donor and acceptor availability from organic matter diagenesis. This study revealed quite high abundance of aerobic methane oxidizing bacteria cells at peculiar sedimentary habitats dominated by Vesicomyid bivalves, microbial mats and reduced sediments typical of cold-seep environments. These communities are not only related to the ones encountered in cold seeps, but also to the ones in terrestrial habitats despite an approximately distance of 1000 km offshore the African coast.This thesis underlines the interest of pluridisciplinary studies to understand the ecosystem diversity and functioning in the terminal lobes of the Congo turbiditic system and provides further insights into the underexplored microbial diversity from deep-sea fans

Nei sistemi di estuario, le interazioni tra microrganismi e la macrofauna sono probabilmente ampiamente diffuse e possono stabilirsi attraverso molteplici meccanismi. La macrofauna, oltre a pascolare, bioturbare i sedimenti e ventilare le tane, può ospitare o e fare da vettore di microrganismi nell'ambiente circostante. La macrofauna e i microrganismi ad essa associati formano olobionti, ovvero unità biologiche e funzionali in grado di eseguire più processi. Tuttavia, essi sono in gran parte poco studiati a causa di limitazioni metodologiche o di un'eccessiva semplificazione degli approcci sperimentali. Pertanto, gli effetti cumulativi degli olobionti sono raramente presi in considerazione negli studi biogeochimici e la loro effettiva entità può essere sottovalutata quando si valutano i processi a livello di ecosistema. In questa tesi, abbiamo studiato il contributo della macrofauna più rappresentata nei sedimenti bentonici di estuari poco profondi, con particolare enfasi sul ruolo delle interazioni ecologiche tra i microbi e i loro ospiti invertebrati sulla regolazione dei processi del ciclo dell'azoto (N). Abbiamo utilizzato una combinazione di approcci ecologici, biogeochimici e molecolari per suddividere il ruolo diretto e indiretto della macrofauna, comprese le attività di bioturbazione, fisiologiche e degli olobionti negli habitat bentonici. I risultati mostrano che tutti gli olobionti della macrofauna ospitavano microbiomi attivi e complessi, capaci di diverse trasformazioni di N come la denitrificazione, la riduzione dissimulativa dei nitrati ad ammonio e la fissazione dell’azoto. Il rilevamento di trasformazioni di N in comuni olobionti della macrofauna evidenzia effetti nascosti e interattivi tra microbi e animali. Nel sistema di estuari tropicali abbiamo evidenziato una intensa attività di azoto fissazione da parte degli olobionti del granchio violinista, tale da superare le perdite di N per denitrificazione e da costituire una sorgente significativa di ammonio e N organico per l'ambiente circostante. Al contrario, il ruolo degli olobionti nei sistemi estuariali temperati e boreali è risultata di minore importanza rispetto all'attività delle comunità microbiche associate ai sedimenti. In tali ambienti, vari gruppi della comunità macrobentonica hanno evidenziato una alterazione del metabolismo bentonico e del ciclo dell'N, direttamente influenzando i tassi di respirazione ed escrezione e indirettamente tramite l’alterazione fisica del sedimento. I risultati ottenuti supportano ulteriormente la tesi che i principali processi biogeochimici nei sedimenti sono prevalentemente il risultato degli effetti collettivi di diversi gruppi funzionali e delle loro mutue interazioni con i microbi associati. Sebbene il ruolo degli olobionti nei sistemi più freddi sia risultato relativamente basso rispetto a quello riscontrato negli ecosistemi tropicali, rimane da chiarire se ciò sia una costante o un quadro variabile da stagione a stagione. In futuro, ulteriori studi dovrebbero affrontare i fattori ambientali o biologici che regolano l'attività degli olobionti attraverso il condizionamento esercitato sui diversi taxa macrobentonici e nei diversi habitat.
In estuarine systems, interactions between microbes and macrofauna are likely widespread and may establish through multiple mechanisms. Macrofauna, besides grazing, bioturbating sediments and ventilating burrows, can host or inoculate microbes from ambient environment. Macrofauna hosts and their associated microbes form holobionts, which are biological and functional units capable of performing multiple processes. However, they are largely understudied due to methodological limitations or oversimplification of experimental approaches. Therefore, the cumulative effects of holobionts are rarely accounted for in biogeochemical studies and their actual magnitude may be underestimated when assessing ecosystem-wide processes. In this thesis, we investigated the contribution of common macrofauna in shallow estuarine benthic sediments with emphasis on the role of ecological interactions between microbes and their invertebrate hosts on regulation of nitrogen (N) cycling processes. We used a combination of ecological, biogeochemical, and molecular approaches to partitioning the direct and indirect role of macrofauna including bioturbation, physiological and holobionts activities in benthic habitats. The results show that all macrofauna holobionts hosted active and complex microbiomes, capable of different N transformations, such as denitrification, dissimulative nitrate reduction to ammonium, and dinitrogen fixation. The detection of N transformations in common macrofauna holobionts highlights hidden and interactive effects among microbes and animals. In tropical estuarine system, abundant fiddler crab holobionts are a net dinitrogen (N2) sink, with N2 fixation exceeding N losses, and as a significant source of ammonium and dissolved organic N to the surrounding environment. On the contrary, the role of the holobionts in the temperate and boreal estuarine systems were of minor importance as compared to the activity of sediment-associated microbial communities. There, distinct macrofauna taxa in community altered benthic metabolism and N cycling directly by impacting respiration and excretion rates and indirectly by reworking sediment. The findings in this thesis further support that main biogeochemical processes in sediment are predominantly the result of the collective effects of different functional groups and their mutual interactions with associated microbes. Although the role of holobionts in colder systems was relatively low to this found in tropics, however this might be different along seasons or habitats. In the future, more studies should address environmental or biological factors that regulate holobionts activity across different taxa of macrofauna and habitats.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2007.
Includes bibliographical references.
Basaltic ocean crust has the potential to host one of the largest endolithic communities on Earth. This portion of the biosphere, however, remains largely unexplored. In this study, we utilize molecular biological, microscopic, and geochemical tools to gain a better understanding of the geomicrobiology of the ocean crust. Specifically, we examine the phylogenetic diversity of microorganisms inhabiting basaltic lavas, the activities and abundances of these microorganisms, the spatial extent of the biosphere, and the potential effect that microbial activity has on the geochemistry of the ocean crust and overlying water column. Our study demonstrates that young, fresh volcanic lavas near mid-ocean ridges host an incredibly diverse and dense population of microorganisms dominated by Bacteria, quite distinct from the microbial communities found in surrounding deep seawater and hydrothermal vents. Furthermore, these communities may contribute to the elemental cycling of Fe, S, Mn, N, and C in this environment. The inability to definitively identify microorganisms in drill-cores of old (> 15 Ma) ocean crust, however, implies that these once prolific communities may become scarce as the crust ages and moves further away from the ridge axis. Finally, we provide evidence suggesting that these communities are fueled by oxidative alteration reactions occurring in the basaltic crust.
by Cara M. Santelli.
Ph.D.

L’écologie microbienne concerne l’étude des microorganismes et de leurs interactions biotiques et abiotiques dans un écosystème donné. Ces vingt dernières années, l’avancement des techniques moléculaires pour analyser la diversité microbienne et, notamment, les nouvelles technologies de séquençages (NGS) ont permis de surmonter les limitations associées aux approches traditionnelles basées sur la culture et la microscopie. Ces approches moléculaires ont conduit à une accumulation des données de diversité microbienne et de potentiel métabolique dans des communautés microbiennes des écosystèmes variés.Cependant, ces efforts ont été principalement appliqués sur des environnements facilement accessibles ou liés à l’humain, comme le plancton (marin principalement) et la flore intestinale. Néanmoins, ceci a conduit à une très forte augmentation de données environnementales et au développement de la bioinformatique par le biais de nombreux outils. Parmi les environnements délaissés des études, les environnements faibles en oxygène sont probablement également porteurs de nouveautés phylogénique ou métaboliques.Afin de palier à cela, nous avons choisi d’explorer deux environnements suboxiques relativement peu étudiés : la cave Movile (Roumanie) et les sédiments du lac Baikal (Sibérie, Russie). Notre but étant de montrer les diversités phylogénétiques et fonctionnelles des microbes de ces biotopes.Pour cela, j’ai d'abord développé un pipeline d’analyse de données métabarcoding (petite sous-unités ribosomique). Ensuite, j’ai appliqué cet outil sur des données de métabarcoding de protistes provenant d’échantillons d’eau et de tapis microbiens de la cave de Movile, un écosystème chemosynthétique pratiquement fermé. Nous avons montré que la diversité des protistes de la cave s’étendait à quasiment tous les grands groupes eucaryotes et provenait à la fois d’origine d’eaux douces et marines. De plus, la plupart ont été affiliées à des groupes d’organismes typiquement anaérobies, ce qui est concordant avec les paramètres abiotiques de la cave. Écologiquement, ces protistes sont des prédateurs mais aussi vraisemblablement des partenaires symbiotiques avec des espèces procaryotes de la cave.Dans une deuxième étude, j’ai eu l’opportunité d’appliquer ce pipeline de métabarcoding sur des données procaryotes et eucaryotes provenant des couches superficielles des sédiments du lac d’eau douce Baikal. Comme attendu, les communautés microbiennes dans ces sédiments sont particulièrement diverses et relativement enrichis en archées. Nous avons aussi pu mettre en évidence des lignées que l’on pensait exclusivement marines dans ces sédiments. Ces lignées sont probablement planctoniques mais s’accumulent au fond par sédimentation. Enfin, les échantillons ont été prélevés dans le but de tester les influences de la profondeur, du bassin et de la latitude sur les communautés. Aucune d’elles ne s’est révélée significative.Dans une troisième étude, j'ai utilisé une approche métagénomique afin de révéler les acteurs écologiquement majeurs dans les sédiments, leurs rôles et de reconstruire leurs génomes. Cela nous a permis notamment de mettre en évidence le rôle primordial des Thaumarchaeota dans le cycle de l’azote et la production primaire de molécules de carbone. Les chloroflexi et les protéobacteries ont aussi un rôle important dans la surface des sédiments du lac Baikal. Ce travail de thèse participe à la connaissance globale de la diversité microbienne sur la planète en mettant en lumière des environnements peu étudiés. De plus, l’étude de la surface des sédiments du lac Baikal apporte de nouvelles données sur le sujet de la transition eau douces/eau marines des microbes. Enfin, la métagénomique a permis de révéler le cycle des nutriments et les microorganismes y participant dans ces échantillons de sédiment. En résumé, ce travail vient mettre en lumière l’écologie microbienne d’écosystèmes suboxiques, notamment la surface des sédiments du lac Baikal
Microbial ecology is the science of micro-organisms and their biotic and abiotic interactions in a given ecosystem. As technology has advanced, molecular techniques have been widely used to overcome the limitations of classical approaches such as culturing and microscopy. Indeed, the development of Next Generation Sequencing (NGS) technologies in the past twenty years has largely helped to unravel the phylogenetic diversity and functional potential of microbial communities across ecosystems.Nonetheless, most of the environments studied through these techniques concentrated on relatively easily accessible, tractable and host-related ecosystems such as plankton (especially in marine ecosystems), soils and gut microbiomes. This has contributed to the rapid accumulation of a wealth of environmental diversity and metagenomic data along with advances in bioinformatics leading to the development of myriads of tools. Oxygen-depleted environments and especially their microbial eukaryote components are less studied and may lead to future phylogenetic and metabolic discoveries.In order to address this, we conducted analyses on two poorly studied suboxic ecosystems: Movile Cave (Romania) and lake Baikal sediments (Siberia, Russia). In this task, we aimed at unveiling the taxonomic and functional diversity of microorganims in these environments.To do so, I first evaluated the available bioinformatics tools and implemented a bioinformatics pipeline for 16S/18S rRNA gene-based metabarcoding analysis, making reasoned methodological choices. Then, as a case study, I carried out metabarcoding analyses of the water and floating microbial mats found in Movile Cave in order to investigate its protist diversity. Our study showed that Movile Cave, a sealed off chemosynthetic ecosystem, harbored a substantial protist diversity with species spanning most of the major eukaryotic super groups. The majority if these protists were related to species of freshwater and marine origins. Most of them were putatively anaerobic, in line with the cave environment, and suggesting that in addition to their predatory role, they might participate in prokaryote-protist symbioses.In a second study, I applied my metabarcoding pipeline to explore unique and relatively unexplored environment of Lake Baikal sediments. I first applied a metabarcoding approach using 16S and 18S rRNA genes to describe prokaryotic as well as protist diversity. Overall, the communities within these ecosystems were very diverse and enriched in ammonia-oxidizing Thaumarchaeota. We also identified several typical marine taxa which are likely planktonic but accumulate in sediments. Finally, our sampling plan allowed us to test whether differences across depth, basin or latitude affected microbial community structure. Our results showed that the composition of sediment microbial communities remained relatively stable across the samples regardless of depth or latitude.In a third study, we applied metagenomics to study the metabolic potential of communities associated to Baikal sediments and to reconstruct metagenome-assembled genomes (MAGs) of dominant organisms. This revealed the considerable ecological importance of Thaumarchaeota lineages in lake Baikal sediments, which were found to be the major autotrophic phyla and also very implicated in the nitrogen cycle. Chloroflexi and Proteobacteria-related species also appeared ecologically important.This PhD thesis reveals the taxonomic diversity of poorly studied suboxic ecosystems and therefore contributes to our knowledge of microbial diversity on Earth. Additionally, the analyses of surface sediment samples in lake Baikal adds new light on freshwater-marine transitions. The metagenomic analyses reported here allowed us to postulate a model of nutrient cycle carried out by microorganismsin these sediments. Overall, this work sheds light on the microbial ecology of oxygen-depleted environments, and most notably lake Baikal surface sediments

Au niveau des marges continentales, et plus particulièrement dans des zones dites d'émissions de fluides froids, des communautés microbiennes et animales complexes se développent localement à la surface des sédiments. Ces communautés utilisent pour leur croissance des composés chimiques réduits (H2S, Méthane, CO2 ...), contenus dans un fluide à basse température, percolant à travers les sédiments et issus de phénomènes géologiques et de divers processus microbiens. Afin d'étudier la diversité des communautés microbiennes associées à ces écosystèmes ainsi que leur rôle dans l'environnement, et d'appréhender les paramètres environnementaux influençant la distribution et l'écophysiologie de ces communautés, des sédiments de surface (0-20 cm) mais également plus profonds (<9 mbsf) ont été prélevés au niveau de la Marge de Sonora. Les communautés microbiennes présentes ont été étudiées par diverses approches de biologie moléculaire, de mise en culture et de microscopie. Ce travail de recherche a permis : i) de déterminer la structure et la diversité des communautés microbiennes métaboliquement actives dans ces sédiments, ii) de mettre en évidence des écophysiologies différentes entre les acteurs du cycle du méthane (méthanogènes, ANMEs, SRB), prépondérant dans cet écosystème et iii) de découvrir la présence de nouvelles lignées et fonctions microbiennes dans les sédiments de zones d'émission de fluides froids des marges continentales
At continental margins, and more particularly in cold seep areas, microbial and animal communities were locally detected at the surface of the sediments. These communities grow using reduced chemical compounds (H2S, Methane, COZ ...) contained in the percolated cold fluids and produced by both geological and microbial processes. ln order to study microbial community diversity in these ecosystems and their role in the environment as well as to understand the environmental factors influencing the distribution and ecophysiology of these communities, surface (0-20 cmbsf) but also deeper (<9 mbsf) sediments were collected at the Sonora Margin. Microbial communities have been studied using various molecular, cultural and microscopy approaches. This research allowed: i) to determine the structure and diversity of metabolically active microbial communities in sediments, ii) to highlight different ecophysiologies for methane cycling microorganisms (methanogens, ANME, SRB) and iii) to discover the presence of new microbial lineages and functions in the cold seeps sediments of the continental margins

Microbes are ubiquitous in the environment and are key component of Earth Biota, covering fundamental roles for the functioning of ecosystems. A comprehensive characterization of such astonishing diversity is of fundamental importance to better understand the functioning of ecosystems, and constitutes a starting point for new technological applications and for issues of natural conservation. Our understanding of the microbial world, however, has been heavily limited by the impossibility to apply classical microbiological techniques to natural populations, mostly due to our incapacity of growing them in laboratory media. In this regard, a great advance came from molecular biology and to its application to the study of molecular markers (primarily SSU rRNAs). Moreover, with the drop in costs of New Generation Sequencing (NGS) technologies, and with the consequent increase of their application to microbial ecology studies, a substantial boost in our understanding of natural microbial communities has been achieved. Molecular methods are actually the most comprehensive alternative for the study of natural microbial communities; and my PhD work has been primarily focused on the application of such methodologies to the study of microbial communities in natural environments affected by anthropogenic modifications. In this thesis, principles of the molecular analysis of microbial communities were covered, presenting the results of two case studies. Two molecular methodologies were applied: terminal restriction fragments length polymorphism (T- RFLP) and next generation sequencing (NGS) with MiSeq platform. In one case (chapter 4, 6, and 7), activities connected to the European project “DEMETRA” were presented. General aim of the project was to provide innovative instruments for the monitoring of the risk for biodiversity connected to the (hypothetical) introduction of genetically modified (GM) crops in the environment of the regional park of Migliarino San Rossore Massacciuccoli. For this reason, a primary step was the characterization of biodiversity at various levels, including those of soil microbial communities. Subject of the study were bacterial and fungal populations in soils from. Waiting for the whole botanical/forestry, entomological and microbiological data set will be processed to determine a risk index of GM crops, we have utilized the microbiological data to evaluate the long-lasting effects of a change within a single land-use category, by comparing microbial diversity in soils from two natural forests and a forest converted to poplar plantation about thirty years ago within the Park. Results from T-RFLP and NGS approach showed high concordance. Both identified the change in land-use as a major perturbative factor for bacterial 1communities (and also for fungal ones, considering T-RFLP results), individuating a decrease in richness in microbial communities from soils of the converted poplar plantation. Land-use was a stronger factor respect to vegetation cover in shaping microbial community. In fact, a higher similarity in community composition was found between the two natural forests (distant from each other in space, and characterized by a different vegetation cover), than between the converted and the natural poplar plantation (really close in space and characterized by the same vegetation cover) In the second case (chapter 5, 7, and 9), activities connected to the European project “MAPMED” were presented. General aim of the project was to improve the environmental sustainability of tourist coastal areas in the Countries of the Mediterranean Sea Basin and to optimize, validate, and transfer tools for the sustainable management of tourist ports with regard to monitoring and reduction of marine pollution. For this reason, the diversity and structure of bacterial and archaeal communities in sediments from three ports in the Mediterranean Sea (Cagliari, Italy; El Kantaoui, Tunisia; Heraklion Greece) were characterized. Results indicate that microbial communities in sediments from the three ports were different and that port of origin constituted the main grouping factor. The overall diversity levels however, regardless of the geographic position of port, where low, indicating that the port basin represent a peculiar habitat unconnected with well-established north-south and east- west gradients of diversity and environmental conditions at the level of Mediterranean basin. A peculiar community composition was observed in sediment from a shipyard in the port of Heraklion, highly different from the rest of samples. Activities linked to shipyards are characterized by pollutants and impacts strongly different from the rest of the touristic port environment, ultimately affecting microbial communities in sediments. The use of T-RFLP on three different molecular markers (16S rRNA on bacterial communities, 16S rRNA on archaeal communities, and dsrAB) as methodology of choice for monitoring plans was evaluated and compared to results from NGS analysis to provide a mean of validation. T-RFLP was able to recapture main results from NGS fairly well, and the marker that performed better was dsrAB. For those reasons, T-RFLP could be effectively be used as the routine technique in the monitoring of marine pollution in sediments of touristic ports from the Mediterranean Sea Basin, although its effectiveness should be exceptionally corroborated by NGS analysis.

This study examined temporal variation of pharmaceutical concentrations in two streams with differing land uses: 1) a suburban stream with combined sewer overflow point sources; and, 2) a rural stream influenced by septic systems and agricultural runoff. Sites were sampled monthly for pharmaceutical concentrations and stream physiochemical parameters. Pharmaceuticals were frequently detected in both the urban and agricultural stream with the highest concentrations measured during winter. Across sites, water column dissolved oxygen concentrations positively correlated with several pharmaceuticals suggesting microbial activity is important in pharmaceutical persistence. Potential for degradation of pharmaceuticals as a carbon or nitrogen source by stream sediment microbial communities was also estimated using pharmaceutical-amended basal salt media incubated under different temperature and ultraviolet (UV) light treatments. Under 4°C incubation, caffeine and acetaminophen were the most recalcitrant compounds whereas cotinine was the most labile. Under UV-B exposure, cotinine and sulfamethoxazole were the most recalcitrant compounds whereas ibuprofen was the most labile.
Temporal variation of pharmaceuticals in an urban and agriculturally influenced stream -- Degradation potential of six pharmaceuticals by sediment microbial communities.
Department of Biology

博士
國立海洋大學
海洋生物研究所
90
Abstract In this study, microorganisms in anoxic sediment slurries collected from the Tansui River and the Erjen River were used to test its ability to dechlorinate some polychlorinated biphenyl (PCB) congeners (3,3’,4,4’- tetrachlorobiphenyl (34-34 CB) , 3,4,4’,5-tetrachlrobiphenyl (345-4 CB) , 2,3’,4’,5-tetrachlrobiphenyl (25-34 CB) , 3,3’,4,4’,5- pentachlorobiphenyl (345-34 CB) , 3,3’,4,4’,5,5’-hexachlorobiphenyls (345-345 CB) ) and commercial PCBs (Aroclor 1221, 1248, 1260). Toluene-adapted sediment slurries or 3-chlorobenzoate-adapted sediment slurries, 4,4’-dibromo biphenyl (4-4 BB) , 2,6-dibromobiphenyl (26 BB) or Tween 20 was added to the sediment slurries in an attempt to stimulate the dechlorination of the PCB congeners. Dechlorination of commercial PCBs in sediment slurries from the Erjen River under sulfate reducing conditions and methanogenic conditions were compared. Enhancement of the dechlorinaiton of commercial PCBs was tested by amendment of 2,3’,4’,5-tetrachlorobiphenyl (25-34 CB)-adapted sediment slurries, 3,4,4’,5-tetrachlorobiphenyl (345-4 CB)-adapted sediment slurries, bromobiphneyls or chlorobiphenyls to sediment slurries from the Erjen River. The change of the microorganism communities during dechlorination in sediment slurries from the Tansui River and the Erjen River was observed by using the denaturing gradient gel electrophoresis (DGGE) method. Except 3,3’,4,4’,5,5’-hexachlorobiphenyls (345-345 CB) , all other congeners, e.g. 25-34 CB, 34-34 CB, 345-4 CB and 345-34 CB were dechlorinated by anaerobic microorganisms in sediment slurries from the Tansui River and the Erjen River. Chlorines at the para position of the biphenyl ring of PCB congeners were removed by microorganisms in sediment slurries from the Tansui River. However chlorines at both meta and para chlorines positions of the biphenyl ring of PCB congeners were removed by microorganisms in sediment slurries from the Erjen River. The dechloriantion rates of PCB congeners in sediment slurries from the Erjen River were greater than that from the Tansui River. Amendment of toluene-adapted sediment slurries or 3-chlorobenzoate-adapted sediment slurries, could enhance the dechloriantion of 34-34 CB and 345-4 CB in sediment slurries from the Tansui River. Amendment of 4-4 BB, 26 BB and Tween 20 colud not enhance the dechloriantion of 34-34 CB, 345-4 CB and 345-345 CB. Methanogen and sulfate reducing bacteria were involving in the dechlorination of PCB congeners in sediment slurries from the Tansui River, while sulfate reducing bacteria and eubacteria were involving in the dechlorination of PCB congeners in sediment slurries from the Erjen River. The rates and the extent of dechlorination of Aroclor 1221, 1248, 1260 in sediment slurries under sulfate reducing conditions were greater than that under methanogenic conditions. Amendment of 25-34 CB- or 345-4 CB-adapted sediment slurries to sediment slurries from the Erjen River with or without addition of 25-34 CB or 345-4 CB affected the dechlorination rates of Aroclor 1221, 1248, 1260. Dechlorination rates of Aroclor 1221 were greater in sediment slurries without addition than in sediment slurries with addition of 25-34 CB or 345-4 CB. While dechlorination rates of Aroclor 1248 were greater in sediment slurries with addition than in sediment slurries without addition of 25-34 CB or 345-4 CB. No significant differences were observed in the dechlorination rates of Aroclor 1260 in sediment slurries with or without addition of 25-34 CB or 345-4 CB. Amendment of 26 BB, 4-4 BB, 25-3 BB, 25-34 CB, 345-4 CB could not enhance dechlorination of Aroclor 1221, 1248, 1260 in sediment slurries from the Erjen River. Amendment of 4-4 BB could enhance removal of chlorines at the para positions of Aroclor 1221, 1248. 1260. Amendment of 25-34 CB and 345-4 CB could enhance removal of chlorines at the meta and para, and chlorines at para positions of Aroclor 1248 respectively. Amendment of 26 BB could enhance removal of chlorines at the meta positions of Aroclor 1260. DGGE method was used to analyze the change of the microorganism communities during the dechlorination of 345-34 CB in sediment slurries from the Tansui River and the Erjen River. The results indicated that microorganisms communities in the Tansui River and the Erjen River were different. P group were the major dechlorinating microorganisms in sediment slurries from the Tansui River, while L group were the major dechlorinating microorganisms in sediment slurries from Erjen River.

Thesis (Ph. D.)--Florida State University, 2005.
Advisor: Dr. Joel E. Kostka, Florida State University, College of Arts and Sciences, Dept. of Oceanography. Title and description from dissertation home page (viewed June 22, 2005). Document formatted into pages; contains xii, 94 pages. Includes bibliographical references.

Thesis (Ph. D.)--Florida State University, 2008.
Advisor: Joel E. Kostka, Florida State University, College of Arts and Sciences, Dept. of Oceanography. Title and description from dissertation home page (viewed February 10, 2009). Document formatted into pages; contains xiv, 116 pages. Includes bibliographical references.