The geochemical fingerprint of microbial long-distance electron transport in the seafloor

Recently, a novel “electrogenic” type of sulfur oxidation has been documented in marine sediments, whereby long filamentous cable bacteria are generating electrical currents over centimeter-scale distances. Here we propose a numerical model description that is capable of quantitatively simulating the solute depth profiles and biogeochemical transformations in such electro-active marine sediments. The model is based on a conventional reactive transport description of marine sediments, which is extended with a new model formulation for the long-distance electron transport induced by the cable bacteria. The mechanism of electron hopping is implemented to describe the electron transport along the longitudinal axis of the microbial filaments. We demonstrate that this model is capable of reproducing the observed geochemical fingerprint of electrogenic sulfur oxidation, which consists of a characteristic set of O2, pH and H2S depth profiles. Our simulation results suggest that the cable bacteria must have a high affinity for both oxygen and sulfide, and that intensive cryptic sulfur cycling takes place within the suboxic zone. A sensitivity analysis shows how electrogenic sulfur oxidation strongly impacts the biogeochemical cycling of sulfur, iron, carbon and calcium in marine sediments

Direct visualization of mucus production by the cold-water coral <i>Lophelia pertusa</i> with digital holographic microscopy

<i>Lophelia pertusa</i> is the dominant reef-building organism of cold-water coral reefs, and is known to produce significant amounts of mucus, which could involve an important metabolic cost. Mucus is involved in particle removal and feeding processes, yet the triggers and dynamics of mucus production are currently still poorly described because the existing tools to study these processes are not appropriate. Using a novel microscopic technique—digital holographic microscopy (DHM)–we studied the mucus release of <i>L</i>. <i>pertusa</i> under various experimental conditions. DHM technology permits µm-scale observations and allows the visualization of transparent mucoid substances in real time without staining. Fragments of <i>L</i>. <i>pertusa</i> were first maintained in flow-through chambers without stressors and imaged with DHM, then exposed to various stressors (suspended particles, particulate food and air exposure) and re-imaged. Under non-stressed conditions no release of mucus was observed, whilst mucus strings and sheaths were produced in response to suspended particles (activated charcoal and drill cuttings sediment) i.e. in a stressed condition. Mucus strings and so-called ‘string balls’ were also observed in response to exposure to particulate food (brine shrimp <i>Artemia salina</i>). Upon air-exposure, mucus production was clearly visible once the fragments were returned to the flow chamber. Distinct optical properties such as optical path length difference (OPD) were measured with DHM in response to the various stimuli suggesting that different mucus types are produced by <i>L</i>. <i>pertusa</i>. Mucus produced to reject particles is similar in refractive index to the surrounding seawater, suggesting that the energy content of this mucus is low. In contrast, mucus produced in response to either food particle addition or air exposure had a higher refractive index, suggesting a higher metabolic investment in the production of these mucoid substances. This paper shows for the first time the potential of DHM technology for the detection, characterization and quantification of mucus production through OPD measurements in <i>L</i>. <i>pertusa</i>

The influence of pore-water advection, benthic photosynthesis, and respiration on calcium carbonate dynamics in reef sands

To investigate diel calcium carbonate (CaCO₃) dynamics in permeable coral reef sands, we measured pore-water profiles and fluxes of oxygen (O₂), nutrients, pH, calcium (Ca²⁺), and alkalinity (TA) across the sediment-water interface in sands of different permeability at Heron Reef, Australia. Background flushing rates were high, most likely as a result of infaunal burrow irrigation, but flux chamber stirring enhanced pore-water exchange. Light and pore-water advection fueled high rates of benthic primary production and calcification in sunlit surface sediments. In the light, benthic photosynthesis and calcification induced surface minima in Ca²⁺ and TA and peaks in pH and O₂. Oxygen penetration depth in coarse sands decreased from ~ 1.2 cm during the day to ~ 0.6 cm at night. Total oxygen uptake (TOU) in dark chambers was three to fourteen times greater than diffusive uptake and showed a direct effect of pore-water advection. Greater sediment oxygen consumption rates were observed in higher permeability sands. In the dark, TA release was not stimulated by increasing TOU because of a damping effect of pore-water advection on metabolic CaCO₃ dissolution efficiency. On a daily basis, CaCO₃ undergoes net dissolution in Heron Reef sands. However, pore-water advection can reverse the CaCO₃ budget and promote CaCO₃ preservation under the most energetic conditions

Estimating primary production from oxygen time series: A novel approach in the frequency domain

Based on an analysis in the frequency domain of the governing equation of oxygen dynamics in aquatic systems, we derive a new method for estimating gross primary production (GPP) from oxygen time series. The central result of this article is a relation between time averaged GPP and the amplitude of the diel harmonic in an oxygen time series. We call this relation the Fourier method for estimating GPP. To assess the performance and accuracy of the method, we generate synthetic oxygen time series with a series of gradually more complex models, and compare the result with simulated GPP. We demonstrate that the method is applicable in systems with a range of rates of mixing, air–water exchange and primary production. We also apply the new method to oxygen time series from the Scheldt estuary (Belgium) and compare it with 14C-based GPP measurements. We demonstrate the Fourier method is particularly suited for estimating GPP in estuarine and coastal systems where tidal advection has a large imprint in observed oxygen concentrations. As such it enlarges the number of systems where GPP can be estimated from in situ oxygen concentrations. By shifting the focus to the frequency domain, we also gain some useful insights on the effect of observational error and of stochastic drivers of oxygen dynamics on metabolic estimates derived from oxygen time series

Imaging-in-flow: digital holographic microscopy as a novel tool to detect and classify nanoplanktonic organisms

Traditional taxonomic identification of planktonic organisms is based on light microscopy, which is both time-consuming and tedious. In response, novel ways of automated (machine) identification, such as flow cytometry, have been investigated over the last two decades. To improve the taxonomic resolution of particle analysis, recent developments have focused on "imaging-in-flow," i.e., the ability to acquire microscopic images of planktonic cells in a flow-through mode. Imaging-in-flow systems are traditionally based on classical brightfield microscopy and are faced with a number of issues that decrease the classification performance and accuracy (e. g., projection variance of cells, migration of cells out of the focus plane). Here, we demonstrate that a combination of digital holographic microscopy (DHM) with imaging-in-flow can improve the detection and classification of planktonic organisms. In addition to light intensity information, DHM provides quantitative phase information, which generates an additional and independent set of features that can be used in classification algorithms. Moreover, the capability of digitally refocusing greatly increases the depth of field, enables a more accurate focusing of cells, and reduces the effects of position variance. Nanoplanktonic organisms similar in shape were successfully classified from images captured with an off-axis DHM with partial coherence. Textural features based on DHM phase information proved more efficient in separating the three tested phytoplankton species compared with shape-based features or textural features based on light intensity. An overall classification score of 92.4% demonstrates the potential of holographic-based imaging-in-flow for similar looking organisms in the nanoplankton range

The impact of sedimentary alkalinity release on the water column CO₂ system in the North Sea

It has been previously proposed that alkalinity release from sediments can play an important role in the carbonate dynamics on continental shelves, lowering the <i>p</i>CO₂ of seawater and hence increasing the CO₂ uptake from the atmosphere. To test this hypothesis, sedimentary alkalinity generation was quantified within cohesive and permeable sediments across the North Sea during two cruises in September 2011 (basin-wide) and June 2012 (Dutch coastal zone). Benthic fluxes of oxygen (O₂), alkalinity (<i>A</i>_T) and dissolved inorganic carbon (DIC) were determined using shipboard closed sediment incubations. Our results show that sediments can form an important source of alkalinity for the overlying water, particularly in the shallow southern North Sea, where high <i>A</i>_T and DIC fluxes were recorded in near-shore sediments of the Belgian, Dutch and German coastal zone. In contrast, fluxes of <i>A</i>_T and DIC are substantially lower in the deeper, seasonally stratified, northern part of the North Sea. Based on the data collected, we performed a model analysis to constrain the main pathways of alkalinity generation in the sediment, and to quantify how sedimentary alkalinity drives atmospheric CO₂ uptake in the southern North Sea. Overall, our results show that sedimentary alkalinity generation should be regarded as a key component in the CO₂ dynamics of shallow coastal systems