Academic literature on the topic 'Aquatic 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.

In order to assess and to compare the abundances of prokaryotes in coral sands from three different areas in the Indo-Pacific, a technique was developed and evaluated for enumeration of prokaryotes living on and within calcareous grains. Propidium iodide labelling of prokaryotes and consecutive confocal laser scanning microscopy showed microbial colonisation within pores and small fissures of the coral sands. This embedded microbial colonisation required at least four extractions with weak acetic acid to dissolve the grain surface layer in order to detach 97% of the prokaryotic cells. Microbial enumeration based on this technique revealed that the abundance of prokaryotes in the carbonate sands were not significantly different among the three sites, but were about one order of magnitude higher than reported for silicate sands of a similar grain size spectrum. A possible reason for this high abundance of prokaryotes is the complex surface structure of the biogenic calcareous grains, their correspondingly highly porous matrix and the associated ability of prokaryotes to penetrate into carbonate grains. Our results highlight the role of calcareous reef sands as a substratum with a large specific surface area for prokaryotic colonisation and emphasise the contribution of calcium carbonate reef sands for element cycles in subtropical and tropical ecosystems.

Due to the chemico-physical differences between air and water, the transition from aquatic life to the land poses several challenges for animal evolution, necessitating morphological, physiological and behavioural adaptations. Microbial symbiosis is known to have played an important role in eukaryote evolution, favouring host adaptation under changing environmental conditions. We selected mangrove brachyuran crabs as a model group to investigate the prokaryotes associated with the gill of crabs dwelling at different tidal levels (subtidal, intertidal and supratidal). In these animals, the gill undergoes a high selective pressure, finely regulating multiple physiological functions during both animal submersion under and emersion from the periodical tidal events. We hypothesize that similarly to other marine animals, the gills of tidal crabs are consistently colonized by prokaryotes that may quantitatively change along the environmental gradient driven by the tides. Using electron microscopy techniques, we found a thick layer of prokaryotes over the gill surfaces of all of 12 crab species from the mangrove forests of Saudi Arabia, Kenya and South Africa. We consistently observed two distinct morphotypes (rod- and spherical-shaped), positioned horizontally and/or perpendicularly to the gill surface. The presence of replicating cells indicated that the prokaryote layer is actively growing on the gill surface. Quantitative analysis of scanning electron microscopy images and the quantification of the bacterial 16S rRNA gene by qPCR revealed a higher specific abundance of prokaryote cells per gill surface area in the subtidal species than those living in the supratidal zone. Our results revealed a correlation between prokaryote colonization of the gill surfaces and the host lifestyle. This finding indicates a possible role of prokaryote partnership within the crab gills, with potential effects on animal adaptation to different levels of the intertidal gradient present in the mangrove ecosystem.

Viral burst size (BS), i.e. the number of viruses released during cell lysis, is a critical parameter for assessing the ecological and biogeochemical role of viruses in aquatic systems. Burst size is typically estimated by enumerating the viral particles in bacteria using transmission electron microscopy. Here, we review the average BS reported for different aquatic systems, present several hypotheses on the control of the BS and evaluate whether there are relationships between BS and bacterial activity parameters across systems. Based on reports from a variety of different aquatic environments, we calculated a mean BS of 24 and 34 for marine and freshwater environments, respectively. Generally, the BS increased with the trophic status of the environment and with the percentage of infected cells in marine populations. When diel dynamics were investigated or averages from large-scale environments were used, BS was positively related to bacterial production but no trend was detectable across systems. The across systems' finding that BS was significantly related to the frequency of infected cells (FIC) could be due to co-infection or superinfection. At any given site, BS seems to be influenced by a number of factors such as the size of the host cell and the viruses, the metabolic activity of the host and phage and host diversity. Thus, based on the available data collected over the past two decades on a variety of aquatic systems, some relations between BS and bacterial variables were detectable.

Viral abundance was assessed in different water masses of the NW Atlantic, and the development of viral abundance, lytic viral infection and lysogeny was followed for the first ca. 5000 km (corresponding to ca. 50 yr in the oceanic conveyor belt) of the western branch of the North Atlantic Deep Water (NADW). Viral abundance was significantly higher in the 100 m layer than in the NADW (2400-2700 m depth) and the Denmark Strait Overflow Water (2400-3600 m depth). The virus-to-prokaryote ratio (VPR) increased with depth, ranging from 32-43 for different water masses of the bathypelagic ocean, thus corroborating the enigma of high viral abundance in the dark ocean. The O2-minimum layer (250-600 m) also showed high viral abundance and VPRs. Viral abundance, a viral subgroup and VPRs decreased in a non-linear form with distance from the NADW origin. Viral production (range: 0.2-2.4 × 107 viruses l-1) and the fraction of lytically infected cells (range: 1-22%) decreased with increasing distance from the formation site of the NADW. Conservative estimations of virus-mediated mortality of prokaryotes in the NADW averaged 20 ± 12%. The fraction of the prokaryotic community with lysogens (i.e. harboring a functional viral DNA) in the NADW averaged 21 ± 14%. Hence, we conclude that (1) viral abundance and subgroups differ between water masses, (2) virus-mediated mortality of prokaryotes as well as lysogeny are significant in the dark ocean and (3) the lysogenic life strategy became more important than the lytic life style during the early formation of the NADW.

ABSTRACT It is generally assumed that hypersaline environments with sodium chloride concentrations close to saturation are dominated by halophilic members of the domain Archaea, while Bacteriaare not considered to be relevant in this kind of environment. Here, we report the high abundance and growth of a new group of hitherto-uncultured Bacteria in crystallizer ponds (salinity, from 30 to 37%) from multipond solar salterns. In the present study, these Bacteria constituted from 5 to 25% of the total prokaryotic community and were affiliated with theCytophaga-Flavobacterium-Bacteroides phylum. Growth was demonstrated in saturated NaCl. A provisional classification of this new bacterial group as “Candidatus Salinibacter gen. nov.” is proposed. The perception that Archaea are the only ecologically relevant prokaryotes in hypersaline aquatic environments should be revised.

The bivalves Thyasiraflexuosa and T. sarsi have enlarged gills which contain numerous prokaryotes. Gills from freshly collected animals contain high concentrations of elemental sulphur. Homogenates of gill tissue show activity for ribulosebisphosphate carboxylase, adenylylsulphate reductase, sulphate adenylyltransferase and sulphate adenylyltransferase (ADP), indicating that the prokaryotes are sulphur-oxidizing autotrophs. Both species can burrow to depths of 8 cm below the sediment surface and use their vermiform feet to construct channels penetrating deeper into the sediment. T.flexuosa and T. sarsi are scarce in sediments with high hydrogen sulphide concentrations and are not found in sediments where the sulphide zone is below their burrowing depth.

The distribution of abundance and biomass of prokaryotes, flagellates, ciliates and phytoplankton, were studied in five ponds of increasing salinity in the Sfax solar saltern (Tunisia) coupled with environmental factors. The results showed that abundance of eukaryotic microorganisms decreased with increasing salinity of the ponds whereas prokaryotes (heterotrophic bacteria and Archaea) were abundant in the hyper-saline ponds. Phototrophic picoplankton was found in a large range of salinity values (70 and 200‰). Phototrophic non-flagellated nanoplankton which dominated in the first sampled pond was substituted by phototrophic flagellated nanoplankton in the other ponds. Heterotrophic nanoplankton dominated in the crystallizer pond but its quantitative importance declined in the less saline ponds. Diatoms and dinoflagellates were the major contributors to phytoplankton abundance in the first ponds (>90% of total abundance). Ciliated protozoa were found in all the ponds except in the crystallizer in which prokaryotes proliferated. Oligotrichida and Heterotrichida were the most abundant ciliate groups. Overall, species richness decreased with salinity gradient. We propose a simplified diagram of the Sfax saltern's food web showing the dominant role of the microbial loop along the salinity gradient.

In coastal aquatic ecosystems, prokaryotic communities play an important role in regulating the cycling of nutrients and greenhouse gases. In the coastal zone, estuaries are complex and delicately balanced systems containing a multitude of specific ecological niches for resident microbes. Anthropogenic influences (i.e. urban, industrial and agricultural land uses) along the estuarine continuum can invoke physical and biochemical changes that impact these niches. In this study, we investigate the relative abundance of methanogenic archaea and other prokaryotic communities, distributed along a land use gradient in the subtropical Burnett River Estuary, situated within the Great Barrier Reef catchment, Australia. Microbiological assemblages were compared to physicochemical, nutrient and greenhouse gas distributions in both pore and surface water. Pore water samples from within the most urbanised site showed a high relative abundance of methanogenic Euryarchaeota (7.8% of all detected prokaryotes), which coincided with elevated methane concentrations in the water column, ranging from 0.51 to 0.68 μM at the urban and sewage treatment plant (STP) sites, respectively. These sites also featured elevated dissolved organic carbon (DOC) concentrations (0.66 to 1.16 mM), potentially fuelling methanogenesis. At the upstream freshwater site, both methane and DOC concentrations were considerably higher (2.68 μM and 1.8 mM respectively) than at the estuarine sites (0.02 to 0.66 μM and 0.39 to 1.16 mM respectively) and corresponded to the highest relative abundance of methanotrophic bacteria. The proportion of sulfate reducing bacteria in the prokaryotic community was elevated within the urban and STP sites (relative abundances of 8.0%– 10.5%), consistent with electron acceptors with higher redox potentials (e.g. O2, NO3-) being scarce. Overall, this study showed that ecological niches in anthropogenically altered environments appear to give an advantage to specialized prokaryotes invoking a potential change in the thermodynamic landscape of the ecosystem and in turn facilitating the generation of methane–a potent greenhouse gas.

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

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

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

Protists are involved in many ecological roles in natural environments, including primary production, herbivory and carnivory, and parasitism. Microbial ecologists have been interested in these single-cell eukaryotes since Antonie van Leeuwenhoek saw them in his stool and scum from his teeth. This chapter focuses on the role of protozoa (purely heterotrophic protists) and other protists in grazing on other microbes. Heterotrophic nanoflagellates, 3–5 microns long, are the most important grazers of bacteria and small phytoplankton in aquatic environments. In soils, flagellates are also important, followed by naked amoebae, testate amoebae, and ciliates. Many of these protists feed on their prey by phagocytosis, in which the prey particle is engulfed into a food vacuole into which digestive enzymes are released. This mechanism of grazing explains many factors affecting grazing rates, such as prey numbers, size, and composition. Ingestion rates increase with prey numbers before reaching a maximum, similar to the Michaelis–Menten equation describing uptake as a function of substrate concentration. Protists generally eat prey that are about ten-fold smaller than they are. In addition to flagellates, ciliates and dinoflagellates are often important predators in the microbial world and are critical links between microbial food chains and larger organisms Many protists are capable of photosynthesis. In some cases, the predator benefits from photosynthesis carried out by engulfed, but undigested photosynthetic prey or its chloroplasts. Although much can be learnt from the morphology of large protists, small protists (<10 μ‎m) often cannot be distinguished by morphology, and as seen several times in this book, many of the most abundant and presumably important protists are difficult to cultivate, necessitating the use of cultivation-independent methods analogous to those developed for prokaryotes. Instead of the 16S rRNA gene used for bacteria and archaea, the 18S rRNA gene is key for protists. Studies of this gene have uncovered high diversity in natural protist communities and, along with sequences of other genes, have upended models of eukaryote evolution. These studies indicate that the eukaryotic Tree of Life consists almost entirely of protists, with higher plants, fungi, and animals as mere branches.

As viruses are known to be the most distinct source of biodiversity, it is not surprising that they are the most abundant biological group in hypersaline environments such as aquatic systems which have saturated salt concentrations. However, of more than 6000 known prokaryote viruses less than 100 are considered to be extremely halophilic (salt loving) and have the ability to infect bacteria. Combination of information obtained from culture dependent and culture independent methods allow better understanding of these viruses. This review will update the advances in halophilic viruses and its impact on the bacteriophage studies.

Abstract Heterotrophic flagellates are an integral and important component of the plankton communities of aquatic ecosystems. Abundances of heterotrophic flagellates in most natural plankton assemblages range from 10 to 10 cells per ml. Recent advances in the methods of counting flagellates and of examining their trophic activities have established that they are significant consumers of bacterial, cyanobacterial, and micro-algal biomass in these environments. Their grazing activities arc the primary factor controlling bacterial densities. Flagellate herbivory can significantly affect the abundances of photosynthetic prokaryotes and eukaryotes. Collectively, the trophic behaviour of these protozoa dictates the fate of a substantial portion of primary and secondary productivity in plank tonic ecosystems.

Leishmaniasis, an infectious disease that affects humans, domestic dogs, and wild animals, is caused by 20 of the 53 Leishmania genus species and is transmitted by sandflies. Despite its significant impact, the disease is often neglected. Leishmania genus, belong to Trypanosomatide Family and Kinetoplastida Order, are grouped in five subgroups according to biogeographic and evolution history of parasites and hosts. The GH18 Leishmania chitinase is encoded by a specie-specific single copy gene, conserved in basal groups of trypanosomatids, and is absent in the genus Trypanosoma. Preservation of the chitinase genomic locus in the aquatic free-living protozoan Bodo saltans, discloses a primitive common origin. Trypanosomatid chitinase amino acid sequence comparative analysis revealed high similarity with chitinase from sea living prokaryotes and protozoan microorganisms, indicating a probable marine origin. Amino acid sequence comparative analysis revealed that perhaps the trypanosomatid chitinase derived from a water living Kinetoplastida ancestor and its phylogenetic reconstruction corroborates the Supercontinent Origins theory for Leishmania. The chitinase-encoding gene was effective for differential molecular diagnosis among Leishmania clinical important species worldwide.

Marine cyanobacteria are oxygenic, gram-negative nitrogen-fixing photosynthetic prokaryotes in different environments. It is a universal organism present in aquatic and terrestrial and also extensively scattered in extreme habitats such as hot springs, deserts and glacial environments. Growing concerns over disease outbreaks and other environmental concerns require alternative ways that are economically viable, sustainable, as well as feasible. Recently, cyanobacteria have achieved much consideration because of their potential relevance in various fields, including aquaculture, wastewater treatment, food, fodder, and the production of secondary metabolites, including polysaccharides, vitamins, toxins, enzymes and pharmaceuticals; they also secrete important novel bioactive antimicrobials including antibacterial, antifungal and anti-viral compounds. The emergence of antimicrobial resistance among pathogenic microbes against common antibiotics imposed the search for new antimicrobial agents from natural sources. Various features of cyanobacteria, including their ability to produce novel antimicrobials, make them suitable candidates for their exploitation as a natural source. Hence, this chapter presents an overview of marine cyanobacterial features, antimicrobials isolated from marine cyanobacteria, as well as the mode of action. Among the known cyanobacterial bioactive compounds, many are pharmacologically important and hold immense potential for drug development at the clinical level<br>

Abstract Purified DNA polymerases are one of the primary tools for molecular biology. Yet choosing the most appropriate DNA polymerase for any particular application requires an understanding of the substantial biochemical differences between the available enzymes. One aspect of interest for PCR is the fidelity of DNA polymerization, i.e. the number of errors produced per nucleotide synthesized. We begin this chapter by discussing the enzymology of error discrimination by DNA polymerases during DNA synthesis in vitro. We then describe the fidelity of several prokaryotic DNA polymerases using a simple assay for scoring DNA polymerase errors. Next we examine the parameters that affect the fidelity of the polymerase most often used for PCR, the Taq DNA polymerase isolated from Thermus aquaticus.