The cell envelope structure of cable bacteria

Cable bacteria are long, multicellular micro-organisms that are capable of transporting electrons from cell to cell along the longitudinal axis of their centimeter-long filaments. The conductive structures that mediate this long-distance electron transport are thought to be located in the cell envelope. Therefore, this study examines in detail the architecture of the cell envelope of cable bacterium filaments by combining different sample preparation methods (chemical fixation, resin-embedding, and cryo-fixation) with a portfolio of imaging techniques (scanning electron microscopy, transmission electron microscopy and tomography, focused ion beam scanning electron microscopy, and atomic force microscopy). We systematically imaged intact filaments with varying diameters. In addition, we investigated the periplasmic fiber sheath that remains after the cytoplasm and membranes were removed by chemical extraction. Based on these investigations, we present a quantitative structural model of a cable bacterium. Cable bacteria build their cell envelope by a parallel concatenation of ridge compartments that have a standard size. Larger diameter filaments simply incorporate more parallel ridge compartments. Each ridge compartment contains a similar to 50 nm diameter fiber in the periplasmic space. These fibers are continuous across cell-to-cell junctions, which display a conspicuous cartwheel structure that is likely made by invaginations of the outer cell membrane around the periplasmic fibers. The continuity of the periplasmic fibers across cells makes them a prime candidate for the sought-after electron conducting structure in cable bacteria

The Cell Envelope Structure of Cable Bacteria

Cable bacteria are long, multicellular micro-organisms that are capable of transporting electrons from cell to cell along the longitudinal axis of their centimeter-long filaments. The conductive structures that mediate this long-distance electron transport are thought to be located in the cell envelope. Therefore, this study examines in detail the architecture of the cell envelope of cable bacterium filaments by combining different sample preparation methods (chemical fixation, resin-embedding, and cryo-fixation) with a portfolio of imaging techniques (scanning electron microscopy, transmission electron microscopy and tomography, focused ion beam scanning electron microscopy, and atomic force microscopy). We systematically imaged intact filaments with varying diameters. In addition, we investigated the periplasmic fiber sheath that remains after the cytoplasm and membranes were removed by chemical extraction. Based on these investigations, we present a quantitative structural model of a cable bacterium. Cable bacteria build their cell envelope by a parallel concatenation of ridge compartments that have a standard size. Larger diameter filaments simply incorporate more parallel ridge compartments. Each ridge compartment contains a ~50 nm diameter fiber in the periplasmic space. These fibers are continuous across cell-to-cell junctions, which display a conspicuous cartwheel structure that is likely made by invaginations of the outer cell membrane around the periplasmic fibers. The continuity of the periplasmic fibers across cells makes them a prime candidate for the sought-after electron conducting structure in cable bacteria

Metabolic activity in intertidal sands : the role of permeability and carbon sources

This thesis set out to improve our current understanding specifically of the role of permeability and carbon sources for the metabolic functioning of permeable sands.  Sampling of an intertidal sandy sediment in a shallow estuary over a 1-yr period revealed that permeability, being influenced by natural seasonal changes in biology and environmental conditions, varied temporally.  More specifically, the extracellular polymeric substances in the sediment were proven to substantially contribute to this temporal variability.  Sediment oxygen consumption also demonstrated seasonal variation and could be related to changes in temperature and total organic carbon, but, more importantly, also to permeability. Different carbon (C) sources were shown to influence the time series station but were also identified for other parts of the estuary.  A better understanding of the sedimentary Corg pool and the Corg undergoing mineralization was furthermore obtained with the novel application of methods developed in the soil sciences comparing the δ13C of respired CO2 to that of available source material and sedimentary Corg.  Overall, the results presented here demonstrate the crucial importance of permeability and carbon sources to metabolic processes and their mediation by biological factors. This thesis highlights the importance of continued research into the complexities of these permeable sands.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Flow and diffusion around and within diatom aggregates: effects of aggregate composition and shape

Diatom aggregates constitute a significant fraction of the particle flux from the euphotic zone into the mesopelagic ocean as part of the ocean's biological carbon pump. Modeling studies of their exchange processes with the surrounding water usually assume spherical shape and that aggregates are impermeable to flow. Using particle image velocimetry, we examined flow distributions around individual aggregates of various irregular shapes formed from two different diatom species: (1) Skeletonema marinoi, known for its cell–cell stickiness, and (2) Chaetoceros affinis, exhibiting cell-TEP (transparent exopolymeric particles) stickiness. Chaetoceros aggregates formed porous, highly irregularly shaped aggregates as compared to the more compact and near-spherical Skeletonema aggregates, yet flow distributions around both types of aggregates were relatively similar at a millimeter scale. At a micrometer scale, the irregular shape of diatom aggregates caused velocity gradients and vorticity close to the surface to locally vary more than for spherical model aggregates (agar-yeast spheres). Water was deflected from the surface of all aggregate types and we found no direct evidence that flow occurred within aggregates. Digital holographic imaging and Alcian blue staining revealed a substantial presence of TEP likely clogging the interstitial pore spaces in Chaetoceros aggregates. Radial oxygen concentration distributions measured by O2 microsensors within the aggregates were similar to those modeled for aggregates and spheres impermeable to flow. Thus, transport of gases, nutrients, and solutes likely occurs by diffusion, even within large, irregularly shaped diatom aggregates during sinking

Digital holographic microscopy: A novel tool to study the morphology, physiology and ecology of diatoms

Recent advances in optical components, computational hardware and image analysis algorithms have led to the development of a powerful new imaging tool, digital holographic microscopy (DHM). So far, DHM has been predominantly applied in the life sciences and medical research, and here, we evaluate the potential of DHM within a marine context, i.e. for studying the morphology, physiology and ecology of diatoms. Like classical light microscopy, DHM captures light-intensity information from objects, but in addition, it also records the so-called phase information. Because this phase information is recorded in a fully quantitative way, it gives access to a whole new type of image properties, which suitably extend the range of microscopy applications in diatom research. Here, we demonstrate the ability of DHM to provide structural information on internal cell organelles as well as the silica frustules of diatoms. By combining the light intensity and phase information, one also obtains the optical fingerprint of a cell, which can be used to discriminate between cells of separate diatom species or to differentiate between living and dead cells (as demonstrated here for two diatom species Navicula sp. and Nitzschia cf. pellucida). Finally, we use chains of Melosira sp. to demonstrate the capacity of DHM to refocus post-acquisition, and combine holograms with fluorescent images, and the ability of DHM to image transparent substances, such as extracellular polymeric substances. Overall, DHM is a promising versatile microscopic technique, allowing diatoms to be investigated in vivo, over time, without the need for staining, and quantitatively in terms of their phase information. Thus, DHM can provide new insights into the structure, as well as the physiology and ecology of diatoms.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

IMAGERIE EN FLUX PAR MICROSCOPIE HOLOGRAPHIQUE DIGITALE POUR L'IDENTIFICATION D'ORGANISMES DU NANOPLANCTON

International audienceL'identification et classification taxonomique des organismes planctoniques s'effectuent habituellement avec des techniques de microscopie classique, ce qui demande beaucoup de travail, d'effort et de temps. Pour remédier à cela, de nouvelles techniques d'identification automatisée, comme la cytométrie en flux, ont été investiguées ces dernières années. Pour améliorer l'analyse et l'identification des organismes planctoniques, de récents développements se sont focalisés sur l'imagerie en flux, c'est-à-dire la capacité d'acquérir des images de cellules planctoniques dans un flux d'eau. Les systèmes d'imagerie en flux traditionnelles sont basés sur la microscopie en champ clair, et sont soumis à plusieurs problèmes, comme par exemple la migration des cellules hors du plan de netteté, qui décroit la performance de la classification. Nous démontrons ici que la combinaison de la microscopie holographique digitale (MHD) et de l'imagerie en flux [1] améliore la détection et la classification d'organismes planctoniques. En effet, en plus de l'information d'intensité classique, la MHD fournit une information de phase quantitative, qui permet de générer un ensemble d'attributs discriminants pour la classification. De plus, la possibilité de pouvoir remettre au net numériquement des organismes enregistrés flous augmente considérablement la profondeur d’investigation et permet le calcul précis des attributs de classification. En effet,pour qu’un attribut soit bien représentatif, il doit être calculé dans le plan de netteté de l’organisme. Des organismes planctoniques ayant des formes similaires ont été identifiés et classifiés avec succès à partir d’hologrammes enregistrés à l’aide d’un MHD fonctionnant avec une sourcelumineuse partiellement cohérente. Les attributs basés sur l’information de phase quantitative se sont révélés très efficaces et ont permis d’atteindre un taux de classification correcte de 92.4%

Mineral formation induced by cable bacteria performing long-distance electron transport in marine sediments

Cable bacteria are multicellular, filamentous microorganisms that are capable of transporting electrons over centimeter-scale distances. Although recently discovered, these bacteria appear to be widely present in the seafloor, and when active they exert a strong imprint on the local geochemistry. In particular, their electrogenic metabolism induces unusually strong pH excursions in aquatic sediments, which induces considerable mineral dissolution, and subsequent mineral reprecipitation. However, at present, it is unknown whether and how cable bacteria play an active or direct role in the mineral reprecipitation process. To this end we present an explorative study of the formation of sedimentary minerals in and near filamentous cable bacteria using a combined approach of electron microscopy and spectroscopic techniques. Our observations reveal the formation of polyphosphate granules within the cells and two different types of biomineral formation directly associated with multicellular filaments of these cable bacteria: (i) the attachment and incorporation of clay particles in a coating surrounding the bacteria and (ii) encrustation of the cell envelope by iron minerals. These findings suggest a complex interaction between cable bacteria and the surrounding sediment matrix, and a substantial imprint of the electrogenic metabolism on mineral diagenesis and sedimentary biogeochemical cycling. In particular, the encrustation process leaves many open questions for further research. For example, we hypothesize that the complete encrustation of filaments might create a diffusion barrier and negatively impact the metabolism of the cable bacteria

Mineral formation induced by cable bacteria performing long-distance electron transport in marine sediments

Cable bacteria are multicellular, filamentous microorganisms that are capable of transporting electrons over centimeter-scale distances. Although recently discovered, these bacteria appear to be widely present in the seafloor, and when active they exert a strong imprint on the local geochemistry. In particular, their electrogenic metabolism induces unusually strong pH excursions in aquatic sediments, which induces considerable mineral dissolution, and subsequent mineral reprecipitation. However, at present, it is unknown whether and how cable bacteria play an active or direct role in the mineral reprecipitation process. To this end we present an explorative study of the formation of sedimentary minerals in and near filamentous cable bacteria using a combined approach of electron microscopy and spectroscopic techniques. Our observations reveal the formation of polyphosphate granules within the cells and two different types of biomineral formation directly associated with multicellular filaments of these cable bacteria: (i) the attachment and incorporation of clay particles in a coating surrounding the bacteria and (ii) encrustation of the cell envelope by iron minerals. These findings suggest a complex interaction between cable bacteria and the surrounding sediment matrix, and a substantial imprint of the electrogenic metabolism on mineral diagenesis and sedimentary biogeochemical cycling. In particular, the encrustation process leaves many open questions for further research. For example, we hypothesize that the complete encrustation of filaments might create a diffusion barrier and negatively impact the metabolism of the cable bacteria

Particle sources and transport in stratified Nordic coastal seas in the Anthropocene

Particles of all origins (biogenic, lithogenic, as well as anthropogenic) are fundamental components of the coastal ocean and are re-distributed by a wide variety of transport processes at both horizontal and vertical scales. Suspended particles can act as vehicles, as well as carbon and nutrient sources, for microorganisms and zooplankton before eventually settling onto the seafloor where they also provide food to benthic organisms. Different particle aggregation processes, driven by turbulence and particle stickiness, composition, abundance and size, impact the transport and sinking behavior of particles from the surface to the seafloor. In deep coastal waters, the deposition, resuspension, and accumulation of particles are driven by particle stickiness, composition and aggregate structure. In contrast, wave-driven and bottom current-driven processes in the nepheloid benthic boundary layer of shallow waters are of greater importance to the settling behavior of particles, while the retention capacity of benthic vegetation (e.g., seagrasses) further influences particle behavior. In this review, we consider the various processes by which particles are transported, as well as their sources and characteristics, in stratified coastal waters with a focus on Nordic seas. The role of particles in diminishing the quality of coastal waters is increasing in the Anthropocene, as particle loading by rivers and surface run-off includes not only natural particles, but also urban and agricultural particles with sorbed pollutants and contaminants of organic, inorganic and microplastic composition. Human activities such as trawling and dredging increase turbidity and further impact the transport of particles by resuspending particles and influencing their vertical and horizontal distribution patterns. An interdisciplinary approach combining physical, chemical and biological processes will allow us to better understand particle transport and its impact on coastal waters and estuaries at an ecosystem level. There is a need for development of novel analytical and characterization techniques, as well as new in situ sensors to improve our capacity to follow particle dynamics from nanometer to millimeter size scales

High single-cell diversity in carbon and nitrogen assimilations by a chain-forming diatom across a century

Summary Almost a century ago Redfield discovered a relatively constant ratio between carbon, nitrogen and phosphorus in particulate organic matter and nitrogen and phosphorus of dissolved nutrients in seawater. Since then, the riverine export of nitrogen to the ocean has increased 20 fold. High abundance of resting stages in sediment layers dated more than a century back indicate that the common planktonic diatom Skeletonema marinoi has endured this eutrophication. We germinated unique genotypes from resting stages originating from isotope-dated sediment layers (15 and 80 years old) in a eutrophied fjord. Using secondary ion mass spectrometry (SIMS) combined with stable isotopic tracers, we show that the cell-specific carbon and nitrogen assimilation rates vary by an order of magnitude on a single-cell level but are significantly correlated during the exponential growth phase, resulting in constant assimilation quota in cells with identical genotypes. The assimilation quota varies largely between different clones independent of age. We hypothesize that the success of S. marinoi in coastal waters may be explained by its high diversity of nutrient demand not only at a clone-specific level but also at the single-cell level, whereby the population can sustain and adapt to dynamic nutrient conditions in the environment