311 research outputs found
Characterization of long-range conduction in cable bacteria down to cryogenic temperatures
No full text<p>Dataset accompanying the manuscript "Characterization of long-range conduction in cable bacteria down to cryogenic temperatures reveals a multi-step hopping mechanism" by<br>Jasper R. van der Veen, Silvia Hidalgo Martinez, Albert Wieland, Matteo De Pellegrin, Rick Verweij,<br>Yaroslav M. Blanter, Herre S.J. van der Zant and Filip J.R. Meysman</p>
<p>The dataset is described in the accompanying file:</p>
<p>ReadMe_DatasetDescription.txt</p>
<p> </p>
Combining citizen science and deep learning for large-scale estimation of outdoor nitrogen dioxide concentrations
No full textReliable estimates of outdoor air pollution concentrations are needed to support global actions to improve public health. We developed a new approach to estimating annual average outdoor nitrogen dioxide (NO2) concentrations using approximately 20,000 ground-level measurements in Flanders, Belgium combined with aerial images and deep neural networks. Our final model explained 79% of the spatial variability in NO2 (root mean square error of 10-fold cross-validation = 3.58 μg/m3) using only images as model inputs. This novel approach offers an alternative means of estimating large-scale spatial variations in ambient air quality and may be particularly useful for regions of the world without detailed emissions data or land use information typically used to estimate outdoor air pollution concentrations.This work was supported by an NSERC Discovery Grant and a CIHR Foundation Grant (Weichenthal PI) and a postdoctoral scholarship from FWO Research Foundation Flanders (Dons)
An Ordered and Fail-Safe Electrical Network in Cable Bacteria
No full textCable bacteria are an emerging class of electroactive organisms that sustain unprecedented long-range electron transport across centimeter-scale distances. The local pathways of the electrical currents in these filamentous microorganisms remain unresolved. Here, the electrical circuitry in a single cable bacterium is visualized with nanoscopic resolution using conductive atomic force microscopy. Combined with perturbation experiments, it is demonstrated that electrical currents are conveyed through a parallel network of conductive fibers embedded in the cell envelope, which are electrically interconnected between adjacent cells. This structural organization provides a fail-safe electrical network for long-distance electron transport in these filamentous microorganisms. The observed electrical circuit architecture is unique in biology and can inspire future technological applications in bioelectronics.BT/Environmental Biotechnolog
Diffusion in a lattice-automaton model of bioturbation by small deposit feeders
No full textThe mixing of 210Pb and tagged particles is examined in a lattice-automaton model for bioturbation containing small deposit feeders. The values of the biodiffusion coefficient, DB, calculated using typical biological parameter values, i.e., size, abundance, feeding and locomotion rates, are similar to those expected from marine sediments of a given sedimentation rate. Most biological parameters appear to exert primarily linear effects on DB values, while most nonlinearities seem to be model artifacts or failures of the assumptions in the basic DB model. The model highlights the importance of ingestion-egestion, over simple particle displacement, as an agent of bioturbation. The tagged particles are used to calculate root-mean-squared displacement plots, which are linear over long time spans, indicating diffusive behavior. However, initial trends on such plots are not usually linear, indicating that the calculated DB is time dependent for surprisingly long periods after the beginning of such experiments. The latter constitutes a warning to the interpretation of short-term tracer experiments where tagged-particles are salted onto the sediment-water interface and mixing is dominated by small deposit feeders
Enhanced Laterally Resolved ToF-SIMS and AFM Imaging of the Electrically Conductive Structures in Cable Bacteria
No full textCable bacteria are electroactive bacteria that form a long, linear chain of ridged cylindrical cells. These filamentous bacteria conduct centimeter-scale long-range electron transport through parallel, interconnected conductive pathways of which the detailed chemical and electrical properties are still unclear. Here, we combine time-of-flight secondary-ion mass spectrometry (ToF-SIMS) and atomic force microscopy (AFM) to investigate the structure and composition of this naturally occurring electrical network. The enhanced lateral resolution achieved allows differentiation between the cell body and the cell-cell junctions that contain a conspicuous cartwheel structure. Three ToF-SIMS modes were compared in the study of so-called fiber sheaths (i.e., the cell material that remains after the removal of cytoplasm and membranes, and which embeds the electrical network). Among these, fast imaging delayed extraction (FI-DE) was found to balance lateral and mass resolution, thus yielding the following multiple benefits in the study of structure-composition relations in cable bacteria: (i) it enables the separate study of the cell body and cell-cell junctions; (ii) by combining FI-DE with in situ AFM, the depth of Ni-containing protein - key in the electrical transport - is determined with greater precision; and (iii) this combination prevents contamination, which is possible when using an ex situ AFM. Our results imply that the interconnects in extracted fiber sheaths are either damaged during extraction, or that their composition is different from fibers, or both. From a more general analytical perspective, the proposed methodology of ToF-SIMS in the FI-DE mode combined with in situ AFM holds great promise for studying the chemical structure of other biological systems.BT/Environmental Biotechnolog
Genomic characterization of cable bacteria and their capacity for long-range electron transport
No full textAbstract: Cable bacteria are filamentous, multicellular microbes that conduct electrical currents across centimetre-scale distances\u2014extending previously known limits of biological electron transport by several orders of magnitude. By transferring electrons from cell to cell, these bacteria can connect spatially separated electron donors and acceptors, establishing a unique redox metabolism with distinct anodic (electron-donating) and cathodic (electron-accepting) zones along the filament. This spatially organized metabolism is unprecedented in biology. To uncover the genetic basis of these processes, obtaining complete cable bacteria genomes is crucial. However, since their discovery in 2012, genomic data have been limited to incomplete and fragmented assemblies consisting of multiple segments, despite bacterial genomes generally consisting of a single circular chromosome. This challenge stems from cable bacteria being complex environmental organisms that cannot be cultured in isolation, complicating genome sequencing. To address this, we developed a novel approach called "targeted metagenomics\u201d, which allows for genome closure of complex unculturable microorganisms like cable bacteria. Using this method, we successfully generated complete genomes for several cable bacteria species. Having complete genomes allowed us to probe deeper into cable bacteria\u2019s unique metabolism. First, we identified unique genetic adaptations enabling efficient nickel cycling within cells, specifically by transporting large quantities of nickel to the periplasm. This finding aligns with prior studies showing that cable bacteria have a unique nickel cofactor located in electricity-conducting fibers within the periplasm. We also used the genomes to examine the sulphur metabolism genes essential for the anodic half of the redox process, which is crucial to the bacteria\u2019s spatially-separated metabolism. Finally, we identified a \u201cunique core genome\u201d\u2014a set of genes shared across all cable bacteria species yet not found in related organisms. This core set likely holds the key to understanding the mechanisms behind long-distance electron transport, and provides a foundation for future biochemical studies to further unravel how cable bacteria achieve this remarkable capability. Ultimately, this research deepens our understanding of the molecular adaptations enabling cable bacteria to conduct electricity, revealing insights into biological electron transport that could one day lead to biotechnological applications, such as sustainably produced electric wires made of biological material
Biogeochemical cycling in a subarctic fjord adjacent to the Greenland Ice Sheet
No full textTemperatures in the Arctic have increased rapidly in recent years resulting in the melting of sea ice and glaciers at unprecedented rates. In 2012, sea ice extent across the Arctic reached a record minimum and the melt extent of Greenland Ice Sheet reached a record maximum. The accelerated mass loss of the Greenland Ice Sheet has resulted in increased meltwater input to Greenland’s fjords and coastal waters. While the impact of changes in sea ice cover on the marine ecosystem has been well documented, the effect of meltwater runoff on Greenland’s ecosystems remained largely unstudied. By linking the complex physical oceanography to biogeochemistry in Greenland fjords, this thesis aimed to increase our understanding of the annual carbon dynamics in high latitude fjord systems and specifically identify the impact of melting of the Ice Sheet on Greenland’s fjord ecosystems. In Chapter 2, the environmental factors that control the timing and intensity of the spring bloom in Godthåbsfjord are described. In high-latitude fjord ecosystems, the spring bloom generates a major part of the annual primary production and thus provides a crucial energy supply to the marine food web. A combination of out-fjord winds and dense coastal inflows drive an upwelling in the inner part of Godthåbsfjord during spring (April-May), which supplies nutrient-rich water to the surface layer that is subsequently transported downstream. The upwelling results in strong biogeochemical gradient in fjord with absence of blooming close to the tidewater glaciers where the upwelling occurs but the development of an intense and prolonged spring bloom in the central region of the fjord from mid-March to May. Weakening of the upwelling and changes in the dominant wind direction in late May, reversed the surface water transport, so that warmer water was transported towards the inner outlet glacier terminus, and a bloom was now observed close to the glacier. Our results suggest that the timing, intensity and location of the spring bloom in Godthåbsfjord are controlled by a combination of upwelling strength and wind forcing. These physical processes hence play together with sea ice cover a crucial role in structuring food web dynamics of the fjord ecosystem. During summer, the Greenland Ice Sheet releases large amounts of freshwater, which strongly influences the physical and chemical properties of the adjacent fjord systems and continental shelves (Chapter 3 and 4). Freshwater runoff itself influences circulation patterns and stratification in Greenland fjords. Observations from different meltwater rivers around Greenland show that the meltwater is not an important source of inorganic nitrate and phosphate, and the direct surface input of meltwater will consequently not stimulate primary production within the fjords (Chapter 3). However the input of glacial meltwater does strongly impact the fjord circulation and consequently the marine ecosystem productivity although this is very differently regulated in fjords with either land-terminating or marine-terminating glaciers (Chapter 4). Rising subsurface meltwater plumes originating from marine-terminating glaciers entrain large volumes of deep water, and the resulting nutrient upwelling sustains high phytoplankton productivity in the inner fjord throughout summer. In contrast, fjords with land-terminating glaciers lack this upwelling mechanism, and hence, are characterized by substantially lower productivity. Data on commercial halibut landings confirms that coastal regions under the influence of large marineterminating glaciers are hotspots of marine productivity. As the shrinking of the Greenland Ice Sheet will induce a switch from marine-terminating to land-terminating glaciers, our results suggest that ongoing climate change can drastically alter the productivity in the coastal zone around Greenland with large socio-economic implications. Furthermore Chapter 3 shows that glacial meltwater leads to high input of dissolved silica as glacial activity stimulates rock weathering. Up-scaled to the entire Greenland Ice Sheet, the export of dissolved silica to adjacent coastal areas equals 22 ± 10 Gmol Si yr-1, and this value could increase 160% by the year 2100 following projections of accelerated mass loss from the Greenland Ice Sheet. This increased silica export may substantially affect phytoplankton communities as silica is an essential element for diatoms. When this silica-rich meltwater mixes with upwelled deep water, we also observed that growth of diatoms is stimulated relative to other phytoplankton groups, thus providing a high quality food source for higher trophic levels. In Chapter 5, the impact of meltwater on the carbonate dynamics of these productive coastal systems is quantified. Our data reveal that the surface layer of the entire fjord and adjacent continental shelf are undersaturated in CO2 throughout the year. This results in an average annual CO2 uptake of 65 g C m-2 yr-1, indicating that the fjord system is a strong sink for CO2 compared to other coastal areas. The largest CO2 uptake occurs in the inner fjord near to the Greenland Ice Sheet and high glacial meltwater input correlates strongly with low pCO2 values. Model simulation of the impact of meltwater on the carbonate system revealed that around a quarter of the CO2 uptake can be attributed to the non-conservative behavior of pCO2 during the mixing of fresh water and saline fjord water. This result in a CO2 uptake of 1.8 mg C per kg of glacial ice melted implying that glacial meltwater is a driver for CO2 uptake in Greenland fjords. The largest part of the high CO2 sink is however due to the strong biological activity both during spring and summer. The fate of this organic matter determines the carbon sink in the fjord system in the end. The POC export from the photic zone followed the seasonality of the primary production both in Kobbefjord and Godthåbsfjord (Chapter 6 and 7). But the strong seasonality in pelagic productivity was not reflected in the sediment biogeochemistry, showing only moderate variation. The largest fraction of the sedimented organic material is buried in the sediment while ~ 38 % is mineralized in the sediment, mainly through sulfate reduction (69% of the benthic mineralization). Both studies highlight a discrepancy between POC flux and primary production, with higher export of carbon compared to local production. My findings demonstrate that glaciers have a fundamental impact on hydrographic circulation and consequently on biogeochemical cycling in Greenland’s fjords
The life cycle of cable bacteria
No full textAbstract: Cable bacteria are multicellular filamentous microorganisms that perform electrogenic sulphur oxidation, coupling the oxidation of sulphide in deeper sediments to oxygen reduction at the sediment-water interface via long-distance electron transport. Despite reshaping our understanding of sedimentary microbial processes, key aspects of cable bacteria biology remain unresolved, particularly regarding their life cycle, dispersal mechanisms, and ecological interactions. This thesis aims to address these gaps by investigating the growth, dispersal, and decline of cable bacteria populations in natural sediment environments. We demonstrate that cable bacteria can disperse via small filament fragments transported through the oxygenated water column, despite oxygen previously being shown to inhibit their electron transport capabilities. This dispersal is facilitated by sediment particles that offer partial protection, enabling colonisation of new sediment patches. Following colonisation, cable bacteria populations exhibit characteristic boom-and-bust dynamics, with a rapid expansion of filaments and high rates of electron transport, followed by stagnation and gradual decline. Interestingly, multiple cable bacteria strains can coexist through desynchronised growth cycles, although these dynamics exert limited influence on the broader microbial community, except in the oxic zone where cable bacteria suppress single-cell sulphur oxidisers. Manipulative experiments revealed that severing filaments disrupts connectivity to oxygen, leading to increased activity and possible upward migration of disconnected cable bacteria. This highlights the importance of uninterrupted electron pathways for maintaining population integrity. Additionally, the study explored the occurrence of \u201cghost cells\u201d and found that their presence does not impair filament motility or electron transport. Microscopy further revealed signs of predatory interactions, including viral attachments, bacterial invasions, and ciliates feeding on cable bacteria, suggesting previously underappreciated ecological pressures. Finally, we isolated and characterised a novel cable bacterium strain, YB6, expanding the known diversity of the genus Ca. Electrothrix and underscoring the ecological and evolutionary complexity of this group. Overall, this research provides critical insights into the life cycle of cable bacteria, from dispersal and colonisation to population collapse. It reveals how these organisms, despite their ecological dominance, remain subject to environmental constraints and microbial interactions, particularly in the oxic zone where cells serve as sacrificial electron sinks. These findings contribute to a deeper understanding of the ecological strategies and resilience of cable bacteria in sedimentary environments
Cadmium transport in sediments by tubificid bioturbation: An assessment of model complexity
No full textBiogeochemistry of metals in aquatic sediments is strongly influenced by bioturbation. To determine the effects of biological transport on cadmium distribution in freshwater sediments, a bioturbation model is explored that describes the conveyor-belt feeding of tubificid oligochaetes. A stepwise modelling strategy was adopted to constrain the many parameters of the model: (i) the tubificid transport model was first calibrated on four sets of microspheres (inert solid tracer) profiles to constrain tubificid transport; (ii) the resulting transport coefficients were subsequently applied to simulate the distribution of both particulate and dissolved cadmium. Firstly, these simulations provide quantitative insight into the mechanism of tubificid bioturbation. Values of transport coefficients compare very well with the literature, and based on this, a generic model of tubificid bioturbation is proposed. Secondly, the application of the model to cadmium dataset sheds a light on the behaviour of cadmium under tubificid bioturbation. Cadmium enters the sediment in two ways. In one pathway, cadmium enters the sediment in the dissolved phase, is rapidly absorbed onto solid particles, which are then rapidly transported to depth by the tubificids. In the other pathway, cadmium is adsorbed to particles in suspension in the overlying water, which then settle on the sediment surface, and are transported downwards by bioturbation. In a final step, we assessed the optimal model complexity for the present dataset. To this end, the two-phase conveyor-belt model was compared to two simplified versions. A solid phase-only conveyorbelt model also provides good results: the dissolved phase should not be explicitly incorporated because cadmium adsorption is fast and bioirrigation is weak. Yet, a solid phase-only biodiffusive model does not perform adequately, as it does not mechanistically capture the conveyor-belt transport at short time-scales
Shining light on the electrical network of cable bacteria
No full textAbstract: Long before humans, microbes harnessed the power of electricity by evolving specialized cell structures and electrogenic metabolisms. In the last two decades, several types of electroactive bacteria have been discovered, and so-called \u201ccable bacteria\u201d present a recent and remarkable addition to this list. These long, filamentous bacteria are members of the Desulfobulbaceae family and thrive in marine and freshwater sediments worldwide. Cable bacteria transport electrical currents across centimetre-scale distances to couple the oxidation of free sulphide deep in the sediment column to oxygen reduction within the upper sediment layer. In doing so, cable bacteria substantially impact the local geochemistry to their benefit. An important outstanding question is how electrical currents are conducted through the cable bacterium filaments. Previously, it has been shown that electrical currents run through a network of parallel, highly conductive protein fibres in the cell envelope. These fibres are connected to one another in the cell junctions by an intriguing cartwheel structure, which is also conductive. This way, the cartwheel adds redundancy to the electric network, making it failsafe. Together, the fibres and cartwheels form the most elaborate electron transport network known in biology. The central objective of this PhD project is to elucidate the molecular structure of this electron transport network
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