Academic literature on the topic 'Marine prokaryotes'

Though a large number of techniques are available for the study of aquatic bacteria, the aim of this study was to establish a technique for analysing free-living and biofilm prokaryotic cells through laboratory assays. In particular, we wished to analyse the efficiency of ultrasound to detach and disrupt biofilm, to obtain an efficient stain treatment for quantifying free-living and biofilm prokaryotes in flow cytometry (FC), and to compare epifluorescence microscopy (EFM), scanning electron microscopy (SEM) and FC for quantifying free-living and biofilm prokaryotes#. Marine-grade plywood substrates were immersed in natural marine water that was conditioned for 12 days. At 6 and 12 days, water aliquots and substrates were removed to estimate free-living and biofilm prokaryote density. Ultrasound efficiently removed marine biofilm from substrates (up to 94%) without cell damage. FC analysis (unstained) reliably quantified marine plankton and young or mature biofilm prokaryotes compared with other staining (acridine orange, 4′,6-diamidino-2-phenylindole, propidium iodide and green fluorescent nucleic acid), EFM or SEM techniques. FC and SEM achieved similar results, while a high variability was observed in the EFM technique. FC was faster and more precise than SEM because the count is not dependent on the observer.

Abstract. We experimentally evaluated the temporal (interday and interseason) and spatial variability in microbial plankton responses to vitamin B12 and/or B1 supply (solely or in combination with inorganic nutrients) in coastal and oceanic waters of the northeast Atlantic Ocean. Phytoplankton and, to a lesser extent, prokaryotes were strongly limited by inorganic nutrients. Interday variability in microbial plankton responses to B vitamins was limited compared to interseason variability, suggesting that B-vitamin availability might be partially controlled by factors operating at seasonal scale. Chlorophyll a (Chl a) concentration and prokaryote biomass (PB) significantly increased after B-vitamin amendments in 13 % and 21 %, respectively, of the 216 cases (36 experiments × 6 treatments). Most of these positive responses were produced by treatments containing either B12 solely or B12 combined with B1 in oceanic waters, which was consistent with the significantly lower average vitamin-B12 ambient concentrations compared to that in the coastal station. Negative responses, implying a decrease in Chl a or PB, represented 21 % for phytoplankton and 26 % for prokaryotes. Growth stimulation by B1 addition was more frequent on prokaryotes than in phytoplankton, suggesting that B1 auxotrophy in the sampling area could be more widespread in prokaryotes than in phytoplankton. Negative responses to B vitamins were generalized in coastal surface waters in summer and were associated with a high contribution of Flavobacteriales to the prokaryote community. This observation suggests that the external supply of B12 and/or B1 may promote negative interactions between microbial components when B-vitamin auxotrophs are abundant. The microbial response patterns to B12 and/or B1 amendments were significantly correlated with changes in the prokaryotic community composition, highlighting the pivotal role of prokaryotes in B-vitamin cycling in marine ecosystems.

In benthic ecosystems, organic matter (OM), prokaryotes, and meiofauna represent a functional bottleneck in the energy transfer towards higher trophic levels and all respond to a variety of natural and anthropogenic disturbances. The relationships between OM and the different components of benthic communities are influenced by multiple environmental variables, which can vary across different habitats. However, analyses of these relationships have mostly been conducted by considering the different habitats separately, even though freshwater, transitional, and marine ecosystems, physically linked to each other, are not worlds apart. Here, we investigated the quantity and nutritional quality of sedimentary OM, along with the prokaryotic and meiofauna abundance, biomass, and biodiversity, in two sampling periods, corresponding to high vs. low freshwater inputs to the sea, along a river-to-sea transect. The highest values of sedimentary organic loads and their nutritional quality, prokaryotic and meiofaunal abundance, and biomass were consistently observed in lagoon systems. Differences in the prokaryotic Operational Taxonomic Units (OTUs) and meiofaunal taxonomic composition, rather than changes in the richness of taxa, were observed among the three habitats and, in each habitat, between sampling periods. Such differences were driven by either physical or trophic variables, though with differences between seasons. Overall, our results indicate that the apparent positive relationship between sedimentary OM, prokaryote and meiofaunal abundance, and biomass across the river-lagoon-sea transect under scrutiny is more the result of a pattern of specifically adapted prokaryotic and meiofaunal communities to different habitats, rather than an actually positive ‘response’ to OM enrichment. We conclude that the synoptic analysis of prokaryotes and meiofauna can provide useful information on the relative effect of organic enrichment and environmental settings across gradients of environmental continuums, including rivers, lagoons, and marine coastal ecosystems.

Abstract. High-latitude oceans have been identified as particularly vulnerable to ocean acidification if anthropogenic CO2 emissions continue. Marine microbes are an essential part of the marine food web and are a critical link in biogeochemical processes in the ocean, such as the cycling of nutrients and carbon. Despite this, the response of Antarctic marine microbial communities to ocean acidification is poorly understood. We investigated the effect of increasing fCO2 on the growth of heterotrophic nanoflagellates (HNFs), nano- and picophytoplankton, and prokaryotes (heterotrophic Bacteria and Archaea) in a natural coastal Antarctic marine microbial community from Prydz Bay, East Antarctica. At CO2 levels ≥634 µatm, HNF abundance was reduced, coinciding with increased abundance of picophytoplankton and prokaryotes. This increase in picophytoplankton and prokaryote abundance was likely due to a reduction in top-down control of grazing HNFs. Nanophytoplankton abundance was elevated in the 634 µatm treatment, suggesting that moderate increases in CO2 may stimulate growth. The taxonomic and morphological differences in CO2 tolerance we observed are likely to favour dominance of microbial communities by prokaryotes, nanophytoplankton, and picophytoplankton. Such changes in predator–prey interactions with ocean acidification could have a significant effect on the food web and biogeochemistry in the Southern Ocean, intensifying organic-matter recycling in surface waters; reducing vertical carbon flux; and reducing the quality, quantity, and availability of food for higher trophic levels.

Understanding the mechanisms that generate and maintain diversity in marine prokaryotic communities is one of the main challenges for contemporary marine microbiology. We here review how observational, experimental, and theoretical evidence converge on the conclusion that the marine pelagic community of heterotrophic prokaryotes consists of organisms with two main types of life strategies. We illustrate this dichotomy by SAR11 and Vibrio spp. as typical representatives of the two strategies. A theory for life strategy dichotomy exists in classical r/K-selection. We here discuss an additional dichotomy introduced by what we term S/L-selection (for Small and Large, respectively). While r/K-selection focuses on the role of environmental disturbances, steady-state models suggest that high abundance at species level should be closely related to a low trade-off between competition and defense. We summarize literature indicating that the high availability of organic C is an essential environmental factor favoring Vibrio spp. and suggest that the essence of the generalized L-strategy is to reduce the competition-predator defense trade-off by using non-limiting organic C to increase size. The “streamlining” theory that has been suggested for the S-strategist SAR11 proposes the opposite: that low trade-off is achieved by a reduction in size. We show how this apparent contradiction disappears when the basic assumptions of diffusion-limited uptake are considered. We propose a classification scheme that combines S/L and r/K-selection using the two dimensions of organic C availability and environmental disturbance. As organic C in terrestrial runoff and size of the oligotrophic oceanic gyres are both changing, habitat size for both S- and L-strategists are affected by global change. A theory capturing the main aspects of prokaryote life strategies is therefore crucial for predicting responses of the marine microbial food web to climate change and other anthropogenic influences.

Perhaps two of the most important groups of fossils are the prokaryotes and protists, both single-celled organisms. They are not spectacular fossils and so may be less interesting to students than the more complicated metazoans and metaphytes, yet these two groups not only dominate life on Earth today, but they contribute enormously to our understanding of Earth and life history. Prokaryotes dominated the fossil record of Earth from 3.5 to nearly .5 billion years ago (Knoll, 1985). For the last 1.5 billion years, protists have been an important element in marine and probably other ecosystems.

Abstract DNA chemical modifications, including methylation, are widespread and play important roles in prokaryotes and viruses. However, current knowledge of these modification systems is severely biased towards a limited number of culturable prokaryotes, despite the fact that a vast majority of microorganisms have not yet been cultured. Here, using single-molecule real-time sequencing, we conducted culture-independent ‘metaepigenomic’ analyses (an integrated analysis of metagenomics and epigenomics) of marine microbial communities. A total of 233 and 163 metagenomic-assembled genomes (MAGs) were constructed from diverse prokaryotes and viruses, respectively, and 220 modified motifs and 276 DNA methyltransferases (MTases) were identified. Most of the MTase genes were not genetically linked with the endonuclease genes predicted to be involved in defense mechanisms against extracellular DNA. The MTase-motif correspondence found in the MAGs revealed 10 novel pairs, 5 of which showed novel specificities and experimentally confirmed the catalytic specificities of the MTases. We revealed novel alternative specificities in MTases that are highly conserved in Alphaproteobacteria, which may enhance our understanding of the co-evolutionary history of the methylation systems and the genomes. Our findings highlight diverse unexplored DNA modifications that potentially affect the ecology and evolution of prokaryotes and viruses in nature.

Durant les últimes dècades s’han aplicat noves tècniques d’estudi dels microorganismes marins per investigar aquells que no creixen en cultiu. La combinació de metodologies independents de cultiu, seqüenciació massiva i mostrejos oceanogràfics a gran escala ens han permès explorar una diversitat taxonòmica i funcional de microorganismes marins fins ara desconeguda. Els microorganismes marins juguen un paper fonamental en els cicles dels nutrients i la regulació del clima. Per això, és vital que definim la seva taxonomia, distribució, hàbitats i propietats funcionals a l’oceà. Relacionar taxonomia i funció sempre ha estat un repte en aquesta disciplina, però en els últims anys s’han desenvolupat dues alternatives que persegueixen aquest objectiu. La genòmica de cèl·lules individuals permet seqüenciar genomes ambientals i la reconstrucció de genomes a partir de metagenomes aprofita el contingut total d’ADN de la comunitat. En aquesta tesi, he generat genomes mitjançant aquestes dues estratègies en mostres d’aigua de zones relativament menys explorades com l’Índic Nord i l’Oceà Àrtic. L’Índic Nord és subjecte d’afloraments estacionals d’aigua profunda rica en nutrients, que a superfície afavoreixen el creixement de fitoplàncton. La producció primària a la superfície és tal que el metabolisme heterotròfic que es nodreix dels productes derivats del fitoplàncton consumeix la majoria d’oxigen, generant zones mínimes d’oxigen (OMZ) que es mantenen gràcies a processos físics que eviten que es mesclin amb altres masses d’aigües. Aquestes OMZ s’ha predit que augmentaran per l’escalfament global i han atret l’atenció d’ecòlegs microbians perquè són riques en microorganismes relacionats amb el cicle del nitrogen i diversos metabolismes micro-aerobis i anaerobis. Tot i que l’Índic Nord presenti una de les OMZ més extenses, la diversitat microbiana d’aquest ambient s’ha estudiat poc. Mitjançant genòmica de cèl·lules individuals vaig obtenir 98 genomes ambientals del gènere Kordia, dels que se’n van seqüenciar deu, després d’analitzar-ne microdiversitat. El seu co-assemblatge es va revisar manualment per generar un genoma de referència gairebé complet. Vaig descriure la nova espècie amb múltiples filogènies i anàlisis de genòmica comparada amb altres espècies del mateix gènere. També vaig definir el seu potencial metabòlic i nínxol de preferència combinant la seva anotació funcional amb la distribució a varis metagenomes de la columna d’aigua d’origen, incloent-hi diferents fondàries i mides de plàncton. L’Oceà Àrtic té un gran impacte a la regulació climàtica del nostre planeta i està severament afectat per l’escalfament global. La diversitat procariòtica de les seves aigües s’ha estudiat en mostrejos esporàdics, majoritàriament centrats en estacions de l’any concretes o certes regions geogràfiques. En aquesta tesi he construït 3550 genomes a partir de metagenomes de diferents regions àrtiques i durant diverses estacions de l’any, en una circumnavegació de les aigües l’Oceà Àrtic. Representen gairebé la meitat del contingut genètic de les comunitats i d’aquests, 530 es poden classificar com a genomes de qualitat mitjana i alta. Inclouen una elevada novetat taxonòmica, sobretot a nivell d’espècie però fins i tot a nivell de Classe, pel que fa als Bacteris. He estudiat les seves implicacions al cicle del carboni a l`Àrtic, així com la seva distribució i preferències d’hàbitat, definint generalistes i especialistes que poden servir com a espès sentinella en futurs estudis de canvi climàtic a l’Àrtic. En resum, aquesta tesi aporta una nova visió en la diversitat funcional i taxonòmica de procariotes no cultivats i proposa noves metodologies per millorar l’assemblatge de genomes i controls de qualitat en els mapejos meta-òmics.
En las últimas décadas se han aplicado nuevas metodologías al estudio de los microorganismos marinos para recuperar taxones que no crecen en cultivo. La combinación de técnicas independientes de cultivo, secuenciación masiva y muestreos oceanográficos a gran escala han permitido explorar la diversidad taxonómica y funcional microbiana a un nivel de resolución previamente desconocido. Los microorganismos marinos juegan un papel fundamental en los ciclos biogeoquímicos y regulación del clima a escala planetaria. Por eso es importante que definamos su taxonomía, distribución, hábitats y propiedades funcionales en el océano. Relacionar la taxonomía con la función a nivel genómico ha sido un reto en la ecología microbiana, pero en los últimos años se han desarrollado dos alternativas con este objetivo. La genómica de células individuales permite secuenciar genomas ambientales y la reconstrucción de genomas a través de metagenomas usa el contenido de ADN de la comunidad como material de partida. En esta tesis, he estudiado genomas usando estas dos estrategias en muestras de agua de zonas relativamente poco exploradas como el Océano Índico Norte y el Océano Ártico. El Océano Índico Norte está sujeto a afloramientos estacionales de agua profunda rica en nutrientes que favorecen el crecimiento masivo de fitoplancton en superfície. La producción primaria es tal que el metabolismo heterotrófico que se nutre de productos derivados de fitoplancton consume la mayoría la oxigeno disponible, generando zonas mínimas de oxigeno (OMZ). Éstas se mantienen por procesos físicos que impiden su mezcla con otras masas de agua. Se prevé que estas zonas aumentarán debido al calentamiento global. Además han captado el interés de los ecólogos microbianos porque son aguas ricas en microorganismos involucrados en el ciclo del nitrógeno, y en metabolismos micro-aerobios y anaeróbicos. A pesar de que en el Índico Norte exista una de las OMZ más extensas del planeta, su diversidad microbiana ha sido poco estudiada. Mediante genómica de células individuales obtuve 98 genomas ambientales del género Kordia de los cuales, tras su análisis de microdiversidad, se seleccionaron diez para su secuenciación y co-ensamblado. El genoma co-ensamblado fue revisado manualmente para generar un genoma de referencia casi completo. Describí la novedad taxonómica de la especie con filogenias y análisis de genómica comparada con otras especies del mismo género. También definí su potencial metabólico y nicho de preferencia combinando la anotación funcional con su distribución en distintos metagenomas de la columna de agua de origen, de distintas profundidades y tamaños de plancton. El Océano Árctico tiene un gran impacto en la regulación climática de nuestro planeta, siendo actualmente severamente afectado por el calentamiento global. La diversidad procariótica de sus aguas se ha estudiado en muestreos esporádicos, mayormente centrados en estaciones del año específicas o en ciertas regiones geográficas. En esta tesis he construido 3550 genomas a partir de metagenomes Árticos, de diferentes regiones y durante distintas estaciones del año, los cuales representan casi la mitad del contenido genético de la comunidad. De estos, 530 se pueden clasificar como genomas de calidad media y alta, e incluyen una mayoría de taxones no descritos hasta ahora, cuya novedad taxonómica es incluso a nivel de Clase en el caso de las Bacterias. He estudiado sus implicaciones en el ciclo del carbono en el Ártico, sus patrones de distribución y sus preferencias de hábitat, definiendo generalistas y especialistas que pueden servir como especies centinela en futuros estudios de cambio climático en el Ártico. En resumen, esta tesis aporta una nueva visión en la diversidad funcional y taxonómica de procariotas marinos no cultivados, y propone nuevas metodologías para mejorar el ensamblaje de genomas y controles de calidad en los mapeos meta-ómicos.
In the last few decades, novel approaches have been applied to the study of marine microorganism aiming to retrieve taxa that escape isolation in culture. Culture independent methodologies, together with high-throughput sequencing and oceanographic samplings, have provided insight into a previously unknown taxonomic and functional diversity of marine microorganisms. Marine microorganisms play a fundamental role in nutrient cycling and climate regulation at a planetary scale. Thus, it is of paramount importance to define their taxonomic classification, distribution, habitat preferences and functional properties in the ocean. Linking taxonomy with function has been a challenge in Microbial Ecology, and in the recent years two alternatives have been developed towards this end. Single Cell Genomics allows the sequencing of individual genomes from environmental samples (Single Amplified Genomes, SAGs) and genome reconstruction from metagenomes allows building genomes from the community’s DNA content (Metagenomic Assembled Genomes, MAGs). In the present dissertation, I have retrieved SAGs and MAGs from underexplored areas like the North Indian Ocean and the Arctic Ocean. The North Indian Ocean is subject to seasonal upwellings that provide surface waters with fresh nutrients, resulting in phytoplankton blooms. Such high primary productivity in the surface waters results in heterotrophic metabolism in the subsurface, by prokaryotes that feed on the products released by primary producers. Such high heterotrophic activity consumes the available oxygen, and together with physical processes than prevent water mixing, generates an oxygen-depleted layer in the water column: the Oxygen Minimum Zone. These water layers are predicted to increase due to global warming and have caught the attention of microbial ecologists as they are rich in microbes involved in the cycling of nitrogen and several microaerophilic and anaerobic metabolisms. Even though the North Indian Ocean has one of the most intense and large OMZs, little is known about the prokaryotic diversity of this environment. With Single Cell Genomics I was able to retrieve 98 SAGs of a novel species in the genus Kordia and after genetically screening them for microdiversity patterns, ten were selected for complete sequencing. The ten genomes were co-assembled together and manually curated for the generation of a reference, almost complete, draft genome. I described the novelty of this species based on multiple phylogenies and comparative genomics with the other described species of the genus Kordia. I also defined the functional potential and niche preference of the novel species combining its functional annotation with its distribution in the different metagenomes of the water column of origin, that included multiple depths and size fractions. The Arctic Ocean has a huge impact in climate regulation of our Planet and is currently being affected severely by global warming. The prokaryotic diversity of its waters has been assessed in sporadic sampling events, mostly focused on a specific season or geographic extension. In the present work I have built 3550 bins from Arctic metagenomes from different regions and seasons that are representative of almost half of the genetic content of the community. Of these, 530 can be classified as MAGs due to their medium and high-quality features and include a majority of novel taxa, especially at the species level but also at higher taxonomic ranks like Class in the case of Bacteria. I have studied their implications for the Arctic’s carbon cycle, their distribution patterns and habitat preferences, and have defined habitat generalists and specialists that can serve as future sentinels of climate change in the Arctic. Overall, this dissertation provides new insights into the taxonomic and functional diversity of uncultured taxa, and proposes new methodologies to improve genome assembly and quality controls in meta-omic mappings

2012/2013
Heterotrophic nanoflagellate (HNF) grazing is one of the major source of prokaryotic mortality in marine ecosystems, acting as a strong selection pressure on communities. Protozoans may thus affect prokaryotic abundance and alter the diversity and the taxonomic composition of the prey community, as individual prokaryotes can develop distinct grazing-resistant mechanisms. Moreover, the microbial loop is well known to regulate carbon fluxes in surface marine environments but few studies have quantified the impact of HNF predation on prokaryotes in the dark ocean. The present work was aimed to: (1) quantify the impact of HNF predation on the deep prokaryotes biomass; (2) investigate if and how prey diversity varies in response to different predation pressure; (3) define taxonomic community composition in studied areas and identify most affected prokaryotic phylotypes by HNF grazing (4) evaluate the effects of small HNF (<3 µm), which are known to dominate nano-sized compartment and represent the main bacterivores in aquatic ecosystems, being an important link between bacteria and larger protists; (5) evidence differences in community sensitivity to grazing between surface and mesopelagic ecosystems (6) identify the main environmental drivers shaping microbial community diversity. Predation experiments were performed with surface and mesopelagic water samples collected from the Southern Adriatic and Northern Ionian basins. An additional predation experiment was set up in the North-eastern Adriatic Sea. We coupled the traditional ‘dilution method’ with high-throughput molecular analysis (ARISA and Ion Torrent/454 sequencing) to provide a quantitatively and qualitatively evaluation of the grazing process occurring in marine microbial communities. The present work is structured by four manuscripts in preparation and one manuscript already submitted. 1. Heterotrophic nanoflagellate grazing on picoplankton in deep waters (manuscript in preparation) 2. Effects of heterotrophic flagellate predation on bacterial community diversity (manuscript in preparation) 3. HNF grazing impact on taxonomic composition of marine prokaryotic community (manuscript in preparation) 4. Environmental drivers structuring surface and deep bacterial communities in Adriatic and Ionian Seas (manuscript in preparation) 5. Biodiversity changes of bacterial community under predation pressure analyzed by 16S rRNA pyrosequencing (manuscript submitted) My PhD research led to important progresses in the comprehension of microbial dynamics regulating carbon cycles and bacterial diversity in the Adriatic and Ionian basins. Prokaryotic abundance and biomass were one order of magnitude higher in the photic than in the aphotic layers of Southern Adriatic and Ionian Seas (surface biomass 1.68 ± 1.76 µC L-1, deep biomass 9.00 ± 2.11 µC L-1). The Northern Adriatic community presented the highest biomass value (57.46 µC L-1), according to its richer trophic status. All in situ communities displayed the same evenness, being dominated by rare phylotypes. Rare taxa were confirmed to represent the major contributors of microbial communities, with only a few phylotypes dominant. Mesopelagic bacterial communities were as rich and variable as surface assemblages, despite the significant biomass decrease along the water column. Natural archaeal assemblages were characterized by very low richness as we recovered only two genera (Cenarchaeum and Nitrosopumilus), while in situ bacterial communities were composed by the six major marine phyla (Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria, Firmicutes and Deinococcus-Thermus), whose contribution varied according to sampling depth. Flagellates were demonstrated to efficiently control their preys (ingestion rates: 7.86-22.26 µg C L-1 in surface experiments, 0.53-10.61 µg C L-1 in deep experiments), causing important losses in the potentially produced prokaryotic biomass. Despite picoplankton and HNF abundance reduction with depth contrasts with the hypothesis that at least 108 picoplanktonic cells L-1 are necessary to sustain HNF community, our data confirm that also in mesopelagic waters prey and predator concentrations are sufficient to sustain efficient microbial food webs. HNF grazing modified bacterial community diversity in both surface and deep marine systems but with different strength. Mesopelagic communities were more sensitive to grazing impact, evidencing a bell-shaped response to the increasing ingestion rates. Moderate-high top-down control preserved or enhanced bacterial diversity, that fell at low predation. In upper communities grazing did not induce wide variations of bacterial richness and evenness, revealing to be more stable. Small HNF (<3 µm) were the dominant size fraction within flagellate communities and likely constituted the main bacterivores. After the removal of large HNF, a higher fraction of prokaryotic phylotypes was affected. Larger protists partially reduced small flagellate impact on their preys. Larger HNF had a more important role in photic systems compared to mesopelagic waters. The fraction of bacterial taxa favored or affected by predation when small HNF were the only predators more markedly varied in surface experiments, while few phylotypes changes their behavior between the two size treatments in deep experiments. Some taxa were consumed mainly by larger HNF (3-10 µm), while others were grazed by smaller ones (<3 µm). Over 50% of the predated phylotypes belonged to the rare biosphere, mainly in the surface experiments. Rare bacteria are thus not only a dormant ‘seed bank’ but constitute a fundamental component of microbial food webs and actively vector the carbon transfer toward higher trophic levels, being as important as dominant organisms. Although general patterns applicable to all communities were not found, trends of selectivity over different phylotypes were highlighted within sampling layer along the water column and between different systems. While the majority of predator-prey interactions were characteristic to specific environments, some can be considered common to different systems (e.g. Burkholderiaceae and Pseudomonadaceae were exclusively selected in all mesopelagic sites, Bacterivoracaceae were subjected to small HNF predation independently from sampling site or depth). The Southern Adriatic and Ionian basins were significantly distinguished by both the physicochemical water characteristics and the prokaryotes and protists abundance distributions. Cluster analysis based on Jaccard and Bray-Curtis metrics evidenced that depth and geographical location of sampling sites influenced bacterial community similarity. The Southern Adriatic Sea was clearly distinguished from the Ionian Sea. The Northern Adriatic samples were always separated from the others, coherently with different biotic and abiotic characteristics of the sub-basin. Additionally, temperature, chl a and O2 concentration represented important environmental drivers shaping biodiversity of bacterial communities that inhabit Adriatic and Ionian basins. In conclusion, we evidenced that heterotrophic flagellates control bacterial biomass and select certain taxa among all possible preys, grazing also on the rare ones. HNF predation thus shapes bacterial community structures, which in turn influence the ecosystem functioning. Despite the cell abundance decrease of both predators and preys reduces encounter probabilities, the dark ocean hosts complex microbial food webs, structured around three trophic levels (i.e. prokaryotes, small and large heterotrophic flagellates).
I nanoflagellati eterotrofi (HNF) costituiscono una delle principali cause di mortalità dei procarioti in ambiente marino, esercitando una forte selezione sulle comunità predate. Possono modificarne l’abbondanza cellulare e alterarne la diversità e la composizione tassonomica, in quanto le diverse specie procariotiche possono sviluppare distintivi meccanismi di resistenza alla predazione. Mentre l’impatto degli HNF sui procarioti degli acque marine superficiali è ben noto, pochi studi si sono focalizzati sullo studio degli ambienti profondi. Il presenta lavoro di dottorato è stato finalizzato a: (1) quantificare l’impatto della predazione da parte degli HNF sulla biomassa procariotica profonda; (2) capire se e come la biodiversità della comunità predata vari in risposta alla diversa pressione di predazione; (3) definire la composizione tassonomica delle comunità presenti nell’area di studio e identificare i filotipi maggiormente colpiti dalla predazione da parte degli HNF; (4) valutare il contributo dei piccolo flagellati (<3 µm), i quali costituiscono la più abbondante frazione nanoplanctonica e rappresentano i principali organismi batterivori negli ambienti acquatici; (5) evidenziare possibili differenze nella risposta alla predazione tra comunità procariotiche che vivono in acque superficiali e profonde; (6) identificare i principali fattori ambientali che modulano la diversità delle comunità microbiche. Esperimenti di predazione sono stati condotti su campioni di acqua superficiale e mesopelagica raccolti nel Mar Adriatico meridionale e nel Mar Ionio settentrionale. Un ulteriore esperimento è stato condotto nel Mar Adriatico nord-orientale. Il tradizionale metodo delle diluizioni è stato abbinato ad analisi molecolari quali elettroforesi capillare (ARISA) e sequenziamento (Ion Torrent e 454) per consentire una valutazione quali-quantitativa degli effetti della predazione sulle comunità microbiche marine. La presente tesi è costituita da quattro articoli in preparazione e un articolo già sottomesso: 1. Heterotrophic nanoflagellate grazing on picoplankton in deep waters (articolo in preparazione) 2. Effects of heterotrophic flagellate predation on bacterial community diversity (articolo in preparazione) 3. HNF grazing impact on taxonomic composition of marine prokaryotic community (articolo in preparazione) 4. Environmental drivers structuring surface and deep bacterial communities in Adriatic and Ionian Seas (articolo in preparazione) 5. Biodiversity changes of bacterial community under predation pressure analyzed by 16S rRNA pyrosequencing (articolo sottomesso) La ricerca condotta durante il mio dottorato ha portato a interessanti progressi nella comprensione delle dinamiche microbiche che regolano i cicli del carbonio e la diversità batterica nei bacini adriatico e ionico. L’abbondanza e la biomassa delle comunità procariotiche superficiali è risultata un ordine di grandezza superiore rispetto alle comunità profonde in Mar Adriatico meridionale e Mar Ionio (biomassa superficiale 9.00 ± 2.11 µC L-1, biomassa profonda 1.68 ± 1.76 µC L-1). La comunità descritta nel Mar Adriatico settentrionale è caratterizzata dai valori più elevati di biomassa (57.46 µC L-1), coerentemente con l’eutrofia del bacino. I flagellati eterotrofi hanno causando perdite significative nella biomassa procariotica in tutti gli esperimenti condotti, con tassi di ingestione pari a 7.86-22.26 µgC L-1 negli esperimenti superficiali e 0.53-10.61 µgC L-1 negli esperimenti profondi. Un’abbondanza picoplanctonica di 108 cellule L-1 è stata ipotizzata come necessaria per sostenere la comunità degli flagellati. Nonostante l’aumento della profondità comporti una riduzione dell’abbondanza del picoplancton tale da non raggiungere questa soglia, i nostri dati confermano che anche negli ambienti profondi si instaurano interazione preda-predatore sufficienti a sostenere le reti trofiche microbiche. Tutte le comunità in situ hanno mostrato la medesima distribuzione, con prevalenza di filotipi rari e pochi gruppi dominanti. Le comunità mesopelagiche presentano diversità e variabilità analoghe a quelle superficiali, nonostante il decremento in biomassa lungo la colonna d’acqua. Una bassa diversità è stata osservata nelle comunità naturali di Archea, dove sono stati rilevati due soli generi (Cenarchaeum e Nitrosopumilus), mentre le comunità batteriche sono composte dai sei principali phyla marini (Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria, Firmicutes e Deinococcus-Thermus), la cui frequenza varia in base alla profondità di campionamento. La predazione esercitata dagli HNF ha modificato la diversità delle comunità sia superficiali che profonde ma con diversi effetti. Le comunità profonde si sono dimostrate più suscettibili alla diversa intensità della predazione. Un controllo top-down medio-alto ha preservato o incrementato la diversità batterica, che invece è risultata fortemente ridotta con bassa pressione di predazione. Al contrario, le comunità superficiali hanno subito solo leggere variazioni nella biodiversità batterica in risposta ai diversi tassi di ingestione, dimostrandosi più stabili. I piccoli flagellati (<3 µm) costituiscono la frazione dominante delle comunità nanoplanctoniche. In seguito alla rimozione dei predatori >3 µm, variazione significative dell’abbondanza sono state riscontrate in una maggiore percentuale di filotipi procariotici. Flagellati di maggiori dimensioni possono quindi mitigare l’impatto dei piccoli predatori sulle prede, con una maggior influenza nei sistemi fotici. Alcuni taxa batterici sono stati consumati prevalentemente dal grandi HNF (3-10 µm), mentre altri sono stati selezionati dai piccoli flagellati (<3 µm). Oltre il 50% dei filotipi predati apparteneva alla biosfera rara, soprattutto negli esperimenti condotti in superficie. I batteri rari (0.1-1% dell’abbondanza totale) non rappresentano quindi una frazione ‘dormiente’ il cui contributo varia in seguito a cambiamenti delle condizioni ambientali, come inizialmente ipotizzato. Costituiscono invece una componente fondamentale delle reti trofiche microbiche e contribuiscono attivamente al trasferimento di carbonio verso i livelli trofici superiori, così come gli organismi dominanti. Nonostante ciascuna comunità risponda in maniera distintiva alla predazione, in funzione della composizione tassonomica delle comunità stesse e dello stato trofico del sistema, alcuni indizi di selettività sono stati individuati. Alcune interazioni preda-predatore si sono rivelate tipiche delle comunità profonde o superficiali, mentre altre erano comuni ad entrambi i sistemi (es. Burkholderiaceae e Pseudomonadaceae sono stati selezionati sono in ambiente pelagico, Bacterivoracaceae sono stati sottoposti a predazione da parte di piccolo flagellati in tutti gli esperimenti, indipendentemente dalla profondità e dal sito di campionamento). I bacini Adriatico meridionale e Ionio settentrionale sono significativamente distinti sia per le caratteristiche chimico-fisiche della colonna d’acqua, sia per l’abbondanza di pico- e nanoplancton. La cluster analisi basata sugli indici di Jaccard e Bray-Curtis ha evidenziato che profondità di campionamento e localizzazione geografica sono i principali fattori che determinano la similarità tra le comunità batteriche. Il Mar Adriatico settentrionale è risultato sempre separato dagli altri campioni, coerentemente con le diverse caratteristiche biotiche e abiotiche del bacino. Oltre a profondità e sito geografico, temperatura, concentrazione di chl a e ossigeno contribuiscono a determinare la biodiversità batterica adriatica e ionica. In conclusione, il presente lavoro ha evidenziato come i flagellati eterotrofi controllino la biomassa procariotica e mostrino preferenza per determinati taxa, selezionando anche quelli rari. La predazione influenza la struttura delle comunità e di conseguenza il funzionamento degli ecosistemi. Anche gli ambienti marini profondi ospitano complesse reti trofiche, strutturate attorno a tre livelli principali (procarioti, piccoli e grandi flagellati eterotrofi) così come le acque superficiali.
XXVI Ciclo
1986

La contaminazione da metalli nei sedimenti di origine acquatica e` un problema ambientale di scala globale. Il sedimento marino agisce come trappola dei contaminanti presenti nella colonna d’acqua, così che i sedimenti delle zone ad elevato livello di antropizzazione possono raggiungere levate concentrazioni di contaminanti metallici. Le strategie biologiche per il recupero di matrici ambientali contaminate accrescono la loro importanza e sono considerate molto promettenti nel caso di un futuro trattamento dei sedimenti contaminati. A differenza degli inquinanti organici , i metalli (e i semimetalli) non possono essere degradati, né i processi naturali di decomposizione possono rimuoverli. Di conseguenza, qualsiasi azione di biorimedio può essere solo finalizzata alla loro trasformazione in composti più solubili/insolubili e/o in specie meno tossiche. Questa tesi riguarda il potenziale di procarioti nella mobilizzazione/immobilizzazione di (semi-)metalli in sedimenti marini contaminati, con un focus particolare sulle interazioni biogeochimiche tra sedimento, batteri e (semi-)metalli. Le attività di ricerca hanno affrontato le seguenti questioni specifiche: 1. Può la bioaugmentazione con batteri acidofili Fe/S ossidanti (biolisciviazione) essere applicata sui sedimenti marini per mobilitare i contaminanti metallici? Quali fattori influenzano l'efficienza di mobilitazione e la reale applicabilità su sedimenti marini contaminati? 2. Le proprietà geochimiche del sedimento influenzano la bio-mobilitazione di metalli? Come le interazioni fra processi abiotici e biotici influenzano la bio-mobilitazione di metalli dai sedimenti marini contaminati? 3. Può la bio-stimolazione delle associazioni microbiche autoctone influenzare il destino dei metalli nei sedimenti marini contaminati? Quali sono i vincoli biotici e abiotici che influenzano la mobilità dei metalli durante bio-stimolazione azioni? 4. Che tipo di interazioni tra fattori abiotici e biotici effetto mobilitazione metallo/immobilizzazione in sedimenti marini? Possono i principali risultati di questa ricerca di essere generalizzati al fine di descrivere la mobilitazione / immobilizzazione di metalli nel sedimento marino? Per rispondere a queste domande, le attività di ricerca sono stati organizzati in quattro pacchetti di lavoro. La prima fase sperimentale e` stata mirata a testare il potenziale dei batteri acidofili nel trattamento di sedimenti marini contaminati con metalli e semimetalli. Esperimenti di bioaugmentazione sono stati effettuati con una concentrazione maggiore di sedimenti generalmente indagato in letteratura scientifica. La capacità di batteri Fe-riducenti nel favorire i batteri acidofili Fe/S ossidanti è stato investigato. Ulteriori fattori indagati sono stati la presenza/assenza di diversi substrati di crescita (ferro ferroso, zolfo elementare, glucosio). I risultati hanno rivelato che l'alta concentrazione di sedimenti ha avuto un effetto negativo sull'efficienza di solubilizzazione metallo. Al contrario, il fattore principale che ha favorito la mobilitazione dei metalli era la presenza di ferro come substrato di crescita. Il ruolo dei batteri Fe/S ossidanti sembrava limitato alla produzione e rigenerazione di specie chimiche chiave, responsabili lisciviazione dei metalli (come H+ e Fe3+). Sulla base dei risultati ottenuti durante la prima sperimentazione, una seconda fase sperimentale è stato progettata per valutare l'effetto delle proprietà geochimiche del sedimento. Per raggiungere questo obiettivo, abbiamo effettuato nuovi esperimenti bioaugmentazione su tre diversi campioni di sedimento, provenienti da diversi porti. Le condizioni sperimentali erano simili a quelli della prima serie di esperimenti. I risultati di questa fase hanno confermato il ruolo indiretto dei batteri ossidanti Fe/S e il ruolo chiave del ferro. Tuttavia, i risultati hanno evidenziato che le efficienze di mobilitazione erano metallo-specifiche e sito-specifiche. Infatti, proprieta` geochimica del sedimento (ad esempio, la capacità tampone) influenzavano l'attività biologica di batteri Fe/S ossidanti, e la capacità di mantenere stabili i metalli in fase solubile. Abbiamo anche trovato, che il tipo di contaminanti metallici coinvolti e la ripartizione tra le frazioni geochimica dei sedimenti svolgono un ruolo aggiuntivo nel determinare le efficienza finali di biomobilizzazione. Di conseguenza, il mantenimento di condizioni acide e ossidative, il comportamento chimico in ambiente acquoso di ciascuna specie metallica e le caratteristiche geochimiche del sedimento interagiscono intimamente per determinare l'efficienza di soliubilizzazione. Considerando la necessità di strategie efficaci ed economicamente fattibile bioaugmentazione , tutte queste prove devono essere prese in considerazione per la definizione dei trattamenti ex-situ sostenibili. L' ultima serie di esperimenti ha riguardato il potenziale della comunità microbica autoctona nell'influenzare il destino dei metalli nei sedimenti marini contaminati, in Dissertation outline connessione con eventuali strategie di biorisanamento in situ. Esperimenti di biostimolazione sono stati eseguiti in condizioni anossiche, con differenti ammendanti. Contrariamente a quanto normalmente previsto, i nostri risultati hanno evidenziato che la biostimolazione in condizioni anossiche può portare ad un aumento della mobilità dei (semi-)metalli e che questa non è necessariamente associata ad eventi di solubilizzazione. Infatti, la comunità microbica puo` influenzare il destino dei metalli e semimetalli, ma fattori biotici, come la composizione delle associazioni microbiche e il tipo di biostimolazione, producono effetti che interagisce con i processi geochimici guidati dalle proprietà del sedimento, il tipo di contaminazione e dalle condizioni ambientali. Di conseguenza, le interazioni tra tutti questi fattori rappresentano il reale vettore che determina il destino dei metalli e dei semimetalli in sedimenti marini contaminati. I principali risultati ottenuti da tutta la ricerca sono stati utilizzati per delineare due modelli concettuali che riassumono e descrivono le principali interazioni biogeochimiche che riguardano il destino dei (semi-)metalli durante i trattamenti di bioaugmentazione con batteri Fe/S ossidanti e durante azioni di biostimolazione. Anche se essi sono rappresentazioni semplicistiche di un insieme molto complesso di processi che si verificano nella realtà, la definizione di modelli concettuali può migliorare la nostra comprensione dei fattori coinvolti in questo campo. Infatti, un modello concettuale che descrive le interazioni biogeochimici che avvengono durante la biolisciviazione era completamente assente, mentre il modello concettuale ottenuto dagli esperimenti di biostimolazione riempie le lacune conoscitive di modelli esistenti e rappresenta un miglioramento nella comprensione dei processi che si verificano.
The contamination of aquatic sediments with metals is a widespread environmental problem. The marine sediment is a sink for contaminants in the water column, so that in areas with high level of anthropization the sediment can reach very high concentrations of metal contaminants. The biological strategies for remediation of contaminates environmental matrices is gaining increasing prominence and they are often considered as a very promising approach for the potential treatment of contaminated sediments. Unlike organic pollutants, metal contaminants cannot be degraded, neither the natural processes of decomposition can remove them. As a consequence, any bioremediation strategy can be just aimed at transforming metals and semi-metals in more soluble/insoluble compounds and/or in less toxic species. This dissertation deals with the potential of prokaryotes in the mobilization/ immobilization of (semi-)metals in marine contaminated sediments, with a particular focus on the biogeochemical interactions between sediment, bacteria and (semi-) metals. The research activities have addressed the following specific questions: 1. Can the bioaugmentation with acidophilic Fe/S oxidizing bacteria (Bioleaching) be applied on marine sediments to mobilize the metal contaminants? Which factors do influence the mobilization efficiency and the real applicability on contaminated marine sediments? 2. Do the geochemical properties of the sediment affect the bio-mobilization of metals? How do the interactions among abiotic and biotic processes affect the bio-mobilization of metals from contaminated marine sediments? 3. Can the biostimulation of autochthonous microbial assemblages affect the fate of metals in marine contaminated sediments? Which are the abiotic and abiotic constrains influencing the mobility of metals during biostimulation actions? 4. Which kind of interactions among abiotic and biotic factors affect metal mobilization/immobilization in marine sediments? Can the key findings from this research be generalized in order to describe the mobilization/immobilization of metals in the marine sediment? To answer these questions, the research activities were organized in four work-packages. The first experimental campaign was aimed at testing the potential of acidophilic bacteria as bioremediation strategy for the treatment of marine sediments contaminated with metals and semi-metals. Bioaugmentation experiments were carried out with a sediment concentration higher than usually investigated in the scientific literature. The potential of Fe-reducing bacteria in favoring the acidophilic Fe/S oxidizing bacteria was investigated. Additional factors investigated were the presence/absence of different growth substrates (ferrous iron, elemental sulfur, glucose). Our results revealed that the high concentration of sediment had a negative effect on the efficiency of metal solubilization. On the contrary, the main factor that favored the mobilization of metals was the presence of iron as growth substrate. The role of Fe/S oxidizing bacteria appeared to be limited at the production and regeneration of key chemical species, responsible for metal leaching (like H+ and Fe3+). On the basis of the results obtained during the first experimentation, a second experimental campaign was designed to investigate the effect of the geochemical properties of the sediment. In order to goal this objective, we performed new bioaugmentation experiments with the same acidophilic strains on three different sediment samples, coming from different seaports. The experimental conditions were similar to those in the first set of experiments. The results of this set of experiment confirmed the indirect role of the Fe/S oxidizing bacteria and the key role of iron. Nevertheless, the results pointed out also that the mobilization efficiencies were metal specific and site-specific. Indeed, geochemical properties of the sediment (e.g., the buffering capacity) influence the biological activity of Fe/S oxidizing bacteria and the ability of metals to be stable in the solution phase. However, the kind of metal contaminants involved and the partitioning among the geochemical fractions of the sediment, were found to play an additional role in determining the final bio-mobilization efficiencies. Thus, the maintenance of acid and oxidative conditions, the chemical behavior of each metal species in aqueous environment and the geochemical characteristics of sediment interact intimately to determine the metal mobilization efficiencies. Considering the need for effective and cost-feasible bioremediation strategies, all these evidences need to be taken into account for the definition of sustainable ex-situ treatments. Dissertation outline The last set of experiments addressed the potential of the autochthonous microbial community in influencing the fate of metals in marine contaminated sediments, in connection with eventual in-situ bioremediation strategies. Biostimulation experiments were performed in anoxic conditions, with different amendants. Contrary to what is usually expected, our results pointed out that the biostimulation in anoxic conditions can lead to an increase in metal mobility and that the latter is not necessary associated to solubilization events. Indeed, the microbial community does drive the fate of metals and semi-metals, but biotic factors, like the composition of the microbial assemblages and the kind of biostimulation, produce effects that interacts with geochemical processes driven by the properties of the sediment, the kind of metal contamination and the environmental conditions. As a consequence, the interactions among all these factors are the true vector to determine the fate of metals and semi-metals in contaminated marine sediments. The main results obtained from the whole research were used to outline two conceptual models that summarize and describe the main biogeochemical interactions affecting the fate of (semi-)metals during treatments of bioaugmentation with Fe/S oxidizing bacteria and during biostimulation actions. Although they are simplistic representations of a highly complex set of processes that occur in the reality, the definition of conceptual models can improve our understanding of factors involved in this field. Indeed, a conceptual model that describes the biogeochemical interactions occurring during bioleaching was completely lacking, while the conceptual model obtained by the biostimulation experiments fills the gaps of the existing models and represents an improvement in the understanding of the processes occurring.

L’interaction entre les micro-organismes a de profondes répercussions sur les cycles biogéochimiques de l’océan. Cependant, la question de savoir comment les microbes s’associent les uns aux autres aux échelles spatiale et temporelle et si les associations de diatom-procaryote et de DOM-procaryote affectent la distribution de ces trois composants est ouverte. Au chapitre 1, nous observons des compositions distinctes de diatomées et de communautés procaryotes parmi les principales zones océaniques. Des relations significatives entre les changements de composition des diatomées et des procaryotes ont été trouvées. Au chapitre 2, nous avons observé deux proliférations consécutives de phytoplancton, chacune composée d’assemblages de diatomées distincts. À l’aide d’une analyse de réseau, nous avons identifié deux groupes de diatomées ayant eu des modèles de corrélation avec des taxa procaryotes. Au chapitre 3, nous avons trouvé la composition distincte de la MOM et celle des procaryotes totaux et actifs sur et hors du plateau. Les corrélations DOM-procaryotes étaient plus fortes sur le plateau que sur le plateau. Les principaux groupes de procaryotes actifs fortement corrélés à la MOM étaient qualitativement similaires dans les deux écosystèmes et quantitativement plus élevés sur le plateau. Pris ensemble, nos résultats démontrent les associations significatives entre les diatomées et les procaryotes, et entre les procaryotes et les DOM. Les compositions des communautés procaryotes sont influencées à la fois par les diatomées et les DOM
The interplay among microorganisms profoundly impacts biogeochemical cycles in the ocean. However, the questions of how microbes associated with each other on the spatial and temporal scale, and whether the associations of diatom-prokaryote and of DOM-prokaryote affect the distributions of these three components are open. In chapter 1, we observed distinct compositions of diatom and prokaryotic communities among the major ocean zones. Significant relationships between compositional changes of diatoms and of prokaryotes were found. In chapter 2, we observed two consecutive phytoplankton blooms, each composed of distinct diatom assemblages. Using network analysis, we identified two groups of diatoms representative of the spring and summer bloom, respectively, that had opposite correlation patterns with prokaryotic taxa. In chapter 3, we found the distinct composition of DOM and that of total and active prokaryotes on and off the plateau. The DOM-prokaryote correlations were overall stronger on the plateau than that off the plateau. The key active prokaryotic groups that strongly correlated with DOM were qualitatively similar in both ecosystems and quantitatively higher on the plateau. Taken together, our results demonstrate the significant associations between diatoms and prokaryotes, and between prokaryotes and DOM. The compositions of prokaryotic communities are influenced by both diatoms and DOM

Studies were undertaken to examine the roles of iron and carbon in modulating prokaryotic growth in the ocean. The context of the first study was an open-open iron fertilization experiment in the high nutrient, low chlorophyll (HNLC) regime in the Southern Ocean. The context of the second study was the oligotrophic, iron-replete, and organic carbon-limited northwest Sargasso Sea. Experimental sea water cultures were amended with an iron chelator, desferrioxamine B (DFOB), and other nutrients to examine the effects of iron and carbon limitation on growth. In the first study prokaryotic abundance, carbon production, and growth rate increased in response to iron in two experimental locations north and south of the Antarctic Polar Front Zone (North Patch and South Patch, respectively). However, prokaryotes responded indirectly to iron-induced phytoplankton production. Prokaryotic production was highly correlated to particulate primary production (r2 = 0.80). Prokaryotes comprised a larger percentage of particulate organic carbon (POC) in the North versus the South Patch relative to non-fertilized waters. Analysis of prokaryotic community structure was also examined. Results showed unique prokaryotic communities existed in the North and South Patch for both iron-fertilized and non-fertilized waters. Additionally, community composition shifted over time in the South Patch and was distinct from non-fertilized waters. Measures of community diversity indicated an increase in taxonomic richness and diversity in iron-fertilized waters over time. Specific taxonomic groups monitored over time in the South Patch exhibited a differential response to the iron-induced phytoplankton bloom. at the domain level, the biomass response was greater for Eubacteria compared to Archaea. at the clade level, Cytophaga-Flavobacteria net biomass yields outpaced SAR11, although both exhibited significant increases (p < 0.05) in net growth rate over time in the South Patch. In the second study DFOB did not limit utilization of organic carbon (glucose). Conversely, DFOB stimulated prokaryotic growth in a dose-dependent manner. The trend of the response to DFOB was similar to glucose; however, the magnitude of the response (i.e. growth rate and biomass yield) at higher equivalent carbon doses was greater than that of glucose. Additionally, DFOB and glucose elicited a differential taxonomic response.

L’objectif de cette thèse a été d’identifier des micro-organismes encore inconnus présents dans divers environnements et de caractériser certains de leurs métabolismes. Cette diversité non identifiée, à la fois taxonomique et fonctionnelle, est communément appelée matière noire microbienne. J’ai utilisé et développé de nouvelles méthodes de réseaux, et notamment des réseaux de similarité de séquences, afin d’exploiter de très grands jeux de données de séquences, issus de projets de métagénomique. En particulier, mon travail a mis en évidence le rôle écologique de micro-organismes ultra-petits dans certaines voies métaboliques autotrophes des océans. Il montre également que les CPR et DPANN, bactéries et archées ultra-petites récemment découvertes, participent à la dynamique des communautés microbiennes via des systèmes de quorum sensing homologues à ceux d’organismes mieux caractérisés. Une application des réseaux de similarité de séquences à des données de métabarcoding a également révélé une diversité jusque là inconnue d’Holozoa, qui pourrait nous permettre de mieux comprendre la transition vers la multicellularité des Metazoa. Enfin, j’ai développé une méthode et un logiciel destiné à la recherche d’homologues distants de protéines d’intérêt dans de très grands jeux de données, tels que ceux issus de la métagénomique. Cette méthode, maintenant validée, devrait permettre de rechercher des séquences appartenant à des organismes encore inconnus et très divergents, dans l’espoir de découvrir de nouveaux phylums profonds, voire même de nouveaux domaines du vivant
The objective of this thesis was to identify as yet unknown microorganisms present in various environments and to characterize some of their metabolisms. This unidentified diversity, both taxonomic and functional, is commonly referred to as microbial dark matter. I have used and developed new network methods, including sequence similarity networks, to exploit very large sequence datasets from metagenomic projects. In particular, my work has highlighted the ecological role of ultra-small micro-organisms in some autotrophic metabolic pathways in the oceans. It also shows that CPR and DPANN, recently discovered ultra-small bacteria and archaea, participate in the dynamics of microbial communities through quorum sensing systems similar to those of better characterized organisms. An application of sequence similarity networks to meta-barcoding data also revealed a previously unknown diversity of Holozoans, which could allow us to better understand the transition to multicellularity of Metazoans. Finally, I have developed a method and software for searching for remote homologs of proteins of interest in very large datasets, such as those from metagenomics. This method, now validated, should make it possible to search for sequences belonging to still unknown and very divergent organisms, in the hope of discovering new deep branching phyla, or even new domains of life

Thesis (M.S.)--Florida State University, 2009.
Advisor: Joel E. Kostka, Florida State University, College of Arts and Sciences, Dept. of Oceanography. Title and description from dissertation home page (viewed Oct. 22, 2009). Document formatted into pages; contains viii, 49 pages. Includes bibliographical references.