Beer, Dirk de

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Beer, Dirk de

Official Name

Beer, Dirk de

Alternative Name

De Beer, Dirk

ORCID

0000-0001-5274-1781

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1261763831

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Microbial activity in energy-rich and redox-variable ecosystems
(2021-09-14)
van Erk, Marit Rianne
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Ferdelman, Timothy
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De Beer, Dirk
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De Beer, Dirk
Microbial mineralization in intertidal sandy sediments plays an essential role in coastal carbon cycling. Surface sediments in these dynamic systems frequently switch between oxic and anoxic conditions depending on factors such as tides and waves. Additionally, they are occasionally subjected to the sudden, high deposition of organic material. When the production rate of the reduced products of anaerobic degradation is higher than the transport rate of oxygen into the sediments, reduced intermediates can accumulate and eventually be exported from the sediments. The aim of this study was to improve the understanding of the response of microbial activity to dynamics in electron donor and acceptor availability, particularly of anaerobic microbial degradation of the organic material. In Chapter 2, a sandy beach on the island of Helgoland was explored, which regularly receives large depositions of kelp debris. A combination of in situ and laboratory microsensing, 35S radiotracer incubations, porewater and sediment analyses, and molecular analyses was used to address the impact of kelp deposition on microbial mineralization and community composition in underlying sandy sediments. The sedimentary biogeochemical conditions on the beach were distinct, with high concentrations of nutrients, dissolved organic and inorganic carbon, and a low pH. Kelp deposition shaped the microbial community, which is optimized for the use of kelp material. The community could immediately degrade kelp upon deposition, which fostered high production rates of reduced products. As these rates were higher than the transport rate of oxygen into the sediments, sulfide accumulated and was exported from the sediments. The export of sulfide to the sea led to the development of a diverse community of filamentous sulfide-oxidizing bacteria. As Chapter 2 highlighted that the microbial community in sediments associated with kelp deposits must be highly specialized to be able to deal with the complex organic material in kelp, Chapter 3 aimed to illuminate the adaptation of microbial communities in these sediments to the degradation of kelp-derived carbohydrate substrates. Oxygen microsensor and 35S radiotracer methods showed strong increases in aerobic respiration and sulfate reduction rates after the addition of specific carbohydrates. The community was indeed specialized to the degradation of kelp-derived carbohydrates. Remarkably, kelp-derived polysaccharides often led to higher aerobic respiration rates than monomers. Monosaccharide analysis and microarray analysis were used to determine the substrate pools in sediments. Respiration rates were up two orders of magnitude higher than in reference sediments, though substrate pools were approximately equal. Thus, substrate turnover rates are much higher on beaches with regular kelp deposition, where microbial communities are more active and are specialized in the carbohydrates they often encounter. Chapter 4 focused on illuminating the effect of transient oxygen exposure on the efficiency of microbial mineralization in an intertidal sandflat in the Wadden Sea. This included testing the hypothesis that reactive oxygen species (ROS) are present in high concentrations in intertidal permeable sediments and control microbial mineralization rates. We incubated sediment slurries that transitioned from oxic to anoxic conditions and slurries that were anoxic throughout the incubation period. Furthermore, we measured hydrogen peroxide concentrations in porewater. Sulfate-reducing bacteria in intertidal permeable sediments are frequently exposed to oxygen. Yet, this did not select for sulfate-reducing bacteria that perform sulfate reduction in the presence of oxygen. Whereas oxygen inhibited sulfate reduction, the sulfate-reducing bacteria were not eliminated by oxygen, but sulfate reduction instantly resumed after oxygen was depleted. The presence of oxygen even boosted subsequent sulfate reduction in the anoxic period. This could be related to oxygen-stimulated hydrolysis of macromolecules during the oxic period. High levels of ROS were found in the porewater of the intertidal flat. ROS are detrimental for microorganisms, as they are able to degrade cellular components and thus lead to cell death. Indeed, removal of ROS in slurry incubations led to strongly increased microbial mineralization rates. This study highlights the contradictory effects of redox shifts on mineralization efficiency, with the presence of oxygen increasing efficiency of subsequent anaerobic processes, even though ROS appeared to inhibit mineralization. In Chapter 5, a sulfide-oxidizing community forming egg-shaped sulfur structures on top of a hot smoker in the deep-sea was studied. Hydrodynamics around such structures are dominated by diffusion, contrary to the advection-dominated system of Chapter 2. Both studied systems are characterized by input of reduced material in an oxic ecosystem, and are therefore out of thermodynamic equilibrium. Comparison between the systems described in Chapter 2 and Chapter 5 aimed to further illuminate the oxidative side of the sulfur cycle in the two contrasting energy-rich redox-variable systems. Different environmental conditions, including hydrodynamics, select for specific sulfide-oxidizing communities and morphologies. The mixing of sulfide into turbulent oxygenated seawater led to the development of filamentous mats of sulfide-oxidizing bacteria growing on rocks at the low tide waterline of the beach (Chapter 2). This attachment prevents the sulfide-oxidizing bacteria from being washed away, and the filamentous structure allows them to make optimal use of the dynamic conditions of the turbulent seawater. On the other hand, the egg-shaped gelatinous sulfur structure produced by sulfide-oxidizing bacteria (Chapter 5) might result from the narrow overlap of oxygen and sulfide which are provided from the same direction. Overall, this study shows that changes in the availability of electron donors and acceptors, and thus redox dynamics, have a large effect on microbial activity. Large influxes of organic material result in a system that is out of thermodynamic equilibrium, and exports reduced compounds towards the sea. Microbial communities are optimized for these conditions, and can directly access the available organic material, while also being able to make use of the reduced compounds that result from microbial mineralization. Sulfide-oxidizing bacteria at the low tide waterline are adapted to the especially dynamic conditions of this environment. While the production of ROS reduces microbial mineralization, the presence of oxygen should not only be seen as an inhibitor of anaerobic microbial mineralization, but also as crucial to the production of electron donors available at the start of anoxia. This study therefore highlights the importance of spatio-temporal dynamics in electron donor and acceptor availability for microbial activity.
Dissertation
256 178
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How sediment damages corals
(2009-04-24)
Weber, Miriam
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Bischof, Kai
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Jørgensen, Bo Barker
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Beer, Dirk de
Worldwide about 80% of the warm-water coral reefs have been harmed, and about 25% irreversibly damaged from direct human pressures. The effects of sedimentation on reef-building corals are well documented, as previous studies focused mostly on the coral response. The processes of how sediment actually damages corals, and the role of contrasting sediment properties have remained poorly understood. In this study we therefore focused on the sediments and investigated the harming processes. Our central hypothesis was that bacteria play a crucial role in the damage that sediment causes to corals. This thesis presents the advancement of two existing methods, data from mesocosm experiments, as well as field data, obtained with the new submersible microsensor system DOMS. This work revealed that harmful effects of sediment exposure on reef-building warm-water corals are tightly linked to sediment properties, primarily the percentage of silt grains, the organic matter content and the microbial activity, demonstrating that the exposure to organic-rich fine sediment is particularly dangerous for coral reefs, and that the demise of sediment-covered corals is mediated by microbial activity.
Dissertation
338 207
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The far-reaching effect of the production, degradation, and trophic transfer of organic arsenic species in the cycle of arsenic
(2024-10-24)
Doherty, Daniel
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Harder, Tilmann
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Beer, Dirk de
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Klatt Judith M
Several organic compounds in aquatic environments contain arsenic, despite of its toxicity. Lipid-soluble arsenic-containing compounds, also known as arsenolipids, are the least studied. In fact, the metabolic origin, purpose and fate of arsenolipids remain shrouded in mystery. Particularly within the microbial realm their role in the arsenic cycle, and significance within trophic webs is still unknown. This thesis aims at improving our understanding about arsenolipids in terms of: 1) the factors that govern their production in microorganisms, 2) their lability, and 3) their trophic transfer from microbial primary producers to eukaryotic grazers. Considering these three approaches, this doctoral thesis follows the path of arsenic starting from cellular pathways to the aquatic environment, and ultimately through food webs, with the aim of assessing how the microbial production of arsenolipids influences arsenic cycling, and which are the factors that affect them. Arsenic methylation is a key process in the arsenic cycle, converting inorganic arsenic into methylated organic products that can evaporate, altering arsenic mobility. Evidence shows that the subsequent methylation of the highly toxic monomethylarsine (MMA) to a less toxic dimethylarsine (DMA) is regulated by thioredoxin (TRX), which in phototrophs TRX is tightly modulated by oxygenic photosynthesis and light. In Chapter I of this thesis, we investigated how light influences arsenic methylation in phototrophic microorganisms, and what effects could this have on arsenolipid production and arsenic mobility in the environment. We hypothesized that light would drive arsenic methylation and boost DMA production, while production of MMA will predominate in darkness. Using model cyanobacterial cultures and samples from natural arsenic-rich lakes, we found that light stimulates DMA production, while dark anoxic conditions promote toxic MMA production, possibly serving as an antibiotic. Dark oxic settings had no overall influence. This finding provides the first evidence of a physical factor such as light that can influence arsenic methylation, which can also impact arsenolipid production, as DMA is a crucial precursor for their synthesis. These results provide insights as to why arsenolipids are found to be synthesized by phototrophs, with the influence of light on arsenic methylation having an important role. This can also impact arsenic cycling, as the final methylated organic products that can evaporate out of the water column and remove arsenic from the system. Ultimately, this study found that light and oxygenic photosynthesis can be important regulators in the production of methylated arsenic species, which can influence the production of arsenolipids and arsenic cycling. So how can arsenolipids affect the arsenic cycle? And can light also have an effect on their abundance? In Chapter II, we delved deeper into these questions by characterizing how light affects the occurrence and concentration of arsenolipids within a naturally arsenic-rich microbial mat, as well as their degradation under laboratory conditions. We found arsenolipids in both the mat and water column, predominantly as novel phytyl 2-O-methyl arsenoribosides (arsenosugar phytols/AsPhy). The initial parent arsenosugar phytol (AsPhy 547) was rare in the mat, whereas its shorter chain degradation product (AsPhy 521) was abundant at the mat's surface but absent at greater depths. Given the absence of the initial parent AsPhy 547 on the light-exposed top of the mat and the high abundance of the shorter chain AsPhy 521, we hypothesized that light could degrade AsPhy 547 to AsPhy 521. Results showed light-driven degradation of AsPhy 547 within 24 hours, while AsPhy 521 was more resistant and increased in abundance, suggesting that it is a degradation product. In the dark, all AsPhy were preserved over 63 days. These results could explain the absence of the initial arsenosugar phytol in the illuminated surface layers of the mat, as well as the higher abundance of its degradation products there. AsPhy are so far only known to be made by microalgae, and since the studied mats were cyanobacteria-dominated, we suspect a microalgal-pelagic origin of these AsPhy, with their presence in sediment as detritus. The recalcitrant nature of degraded AsPhy that they can be a sink of arsenic, which eventually degrade over very long period of time with continued burial. These results show that the production of arsenolipids by microorganisms can impact arsenic cycling, as some of their degradation products can be highly refractile, and that light can be an important factor modulating their mobility. To better understand the role of arsenolipids in the arsenic cycle, studying their transport through the trophic web, from microbial producers to eucaryotes, is crucial. In the arsenic-rich hypersaline lakes of our studies, the aquatic grazer artemia are the main link between microalgae and larger eucaryotes. In Chapter III, we examined artemia's accumulation of arsenolipids during the diel cycle, considering reproductive sex. We conducted feeding experiments on both captured and commercial artemia with arsenic-enriched or non-enriched microalgal food, or under fasting conditions. Results showed that artemia primarily contained arsenosugar phytols (AsPhy) 547 and 521, similar to those in microorganisms from the same lakes, indicating uptake through feeding. In one site, female artemia contained higher amounts of arsenolipids than males, while arsenolipid content was similar between sexes in another site, hinting that environmental factors influence uptake. Long-term fasting and feed-washing incubations showed no significant decrease in arsenolipids, suggesting they are not stored in energy reserves affected during catabolism. Fecal pellets also contained arsenolipids, demonstrating artemia’s role actively in transportation arsenic from microalgae in the water column into the sediment. Thus, we show that the transfer of arsenolipids to eukaryotic grazers can influence arsenic cycling through transport of arsenolipids from the water column to the sediment, as well as their retention in tissue. Overall, the findings of this study show that microbial organisms, through the production of organic arsenic species, affect arsenic cycling across different scales and facets, starting from the molecular in their synthesis and degradation, to the interaction between organisms as antibiotics, and finally at ecosystem level throughout the food web.
Dissertation
90 70
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Little Things Become Big : Drivers and impacts of benthic cyanobacterial blooms on coral reefs
(2014-11-28)
Brocke, Hannah J
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Nugues, Maggy M.
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Bischof, Kai
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Beer, Dirk de
Over the past four decades, benthic cyanobacterial mat abundance has increased significantly on many coral reefs worldwide. It however remains unclear what actually drives their current success, and how they impact the reef ecosystem as a whole. This PhD thesis presents a missing link that explains - via a mechanistic approach - the recent proliferation of benthic cyanobacterial mats. Results indicate that benthic cyanobacterial mats have a large impact on the functioning of the reef, especially via their vast N2 fixation capacity and release of dissolved organic carbon into the water column. Additionally, in comparison to other reef organisms, benthic cyanobacterial mats have very high nutrient uptake kinetics and high primary productivity rates. These characteristics likely contribute to their recent successfulness on the reef. This thesis furthermore suggests that nutrient and organic matter reduction is essential to prevent benthic cyanobacterial blooms from occurring on the reef.
Dissertation
287 148
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The importance of microgradients for marine calcifiers
(2012-08-14)
Glas, Martin
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Rost, Björn
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Bischof, Kai
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de Beer, Dirk
This thesis describes the importance of microgradients around organic tissue of calcifiers in comparison to bulk seawater conditions. It is shown that microenvironmental acidification around calcifiers can result from various causes, such as calcification (Chapter 1), microbial mat or sediment exposure (Chapter 2), respiration (Chapter 2) or ocean acidification conditions (Chapter 3). Some calcifiers, like sediment dwelling foraminifera and bivalves, are naturally adapted to low pH and hypoxic conditions (Chapter 1, 2). Yet, microenvironmental low pH, hypoxia and high levels of sulphide resulted in tissue necrosis of corals, but only if those conditions were trapped close to the tissue of corals for extended periods of time (Chapter 2). The performance of some calcifiers under low pH and hypoxic conditions thus depends upon the duration of the exposure, as well as the diffusional resistance between the bulk seawater and their tissues. If diffusivity around their organic tissues is significantly reduced, some calcifiers may not be able to maintain pH homeostasis and thus severely suffer from extended exposure to low pH, hypoxia and high levels of sulphide (Chapter 2).
Dissertation
386 168
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Microbial activity and transport processes in near-shore, permeable sediments
(2005-10-14)
Werner, Ursula
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Jörgensen, Bo Barker
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Kirst, Gunther
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De Beer, Dirk
High organic carbon turnover in permeable sands is considered to be fueled by the efficient supply of solutes (e.g., oxygen) and organic matter from the overlying water by pore water advection. In situ quantifications of microbial activity in the presence of pore water advection are still rare. In this thesis, microbial activity and transport processes were investigated in near-shore, permeable sediments. A novel method for the measurement of volumetric oxygen consumption rate (OCR) profiles with high depth resolution in permeable sediments was evaluated in chapter 2. Three technical approaches were presented using either oxygen micro-sensors or planar optodes. For the calculation of areal OCR, the volumetric OCR can be integrated over the oxygen penetration depths measured in situ over extended time periods. These areal OCR reflect the influence of hydrodynamics on oxygen distribution. The method was consistent with established methods (interfacial gradients combined with Fick's first law of diffusion, benthic-chambers). The importance of pore water advection for sediment oxygenation and benthic mineralization was shown at the intertidal sand flat Hausstrand (Sylt/Germany) (chapter 3). Three stations were chosen on a transect from the low - to the high water line. Due to pore water advection, oxygen penetrated deeper and more dynamically during inundation than during exposure of the flat. The oxygen penetration depths were closely coupled to bottom water current velocities, proving the impact of pore water advection on sediment oxygenation. Driven by the advective oxygen supply, benthic OCR were high: 71 - 90% of oxygen consumption took place during inundation and aerobic mineralization was the dominant mineralization process at all stations. Mineralization rates were linked to the inundation time of the stations: Oxygen consumption rates were elevated at the lower flat, sulfate reduction rates decreased sharply from the low- to the high-waterline. At two stations (upper- and lower flat) at the intertidal sand flat Janssand near the island of Spiekeroog (German Wadden Sea), also a deeper oxygen penetration was found during inundation (chapter 4). Similar to the Hausstrand, OCR were high and highest during inundation, and sulfate reduction contributed only between 3 - 25% to total mineralization. However, at the two stations, similar surface mineralization rates were measured. In contrast to this, the concentrations of mineralization end products in the pore water at the low water flat were up to 15 times higher than at the upper flat, and the solute concentrations varied independent of season at this station. It was concluded that two filtration processes influence the distribution of metabolic products: (1) a rapid 'skin filtration' in the upper sediment layer during inundation driven by pore water advection and (2) a slow 'body filtration' through deeper sediment layers during exposure driven by drainage. In the coral reef sediments of Heron Reef (Australia), four sites exhibiting different hydrodynamic regimes were investigated (chapter 5). Oxygen penetration and dynamics as well as oxygen consumption, aerobic mineralization and sulfate reduction rates were highly variable between these sites. The supply of oxygen by pore water advection stimulated aerobic mineralization. A simple estimate of the organic matter supplied to the sediments by pore water advection only explained a fraction of the mineralization rates, indicating the importance of other organic carbon sources like benthic primary production. The microphytobenthos at Heron Reef was dominated by diatoms, dinoflagellates and cyanobacteria (chapter 6). Episammic colonies were highly diverse with respect to cyanobacterial 16S rDNA sequences. Photosynthesis was high per unit chlorophyll-a, indicating an active microphytobenthic community. Estimates on the microphytobenthic photosynthetic production in the entire reef were in the order of magnitude as the estimated production by corals. Photosynthesis stimulated calcification at the four investigated sites. The sediments of at least three stations were net calcifying. Sedimentary N2-fixation (acetylene reduction) was highest in the light, indicating the importance of heterocystous cyanobacteria. In coral fingers no N2-fixation was measurable, which stresses the importance of the sediment compartment for reef nitrogen cycling.
Dissertation
217 104
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The impact of electron acceptor variation and reactive oxygen species on microbial respiration rates
(2024-07-16)
Bourceau, Olivia
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Ferdelman, Tim
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Beer, Dirk de
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Beer, Dirk de
This thesis investigates how redox fluctuations in environments with chemical gradients, and the reactive oxygen species often produced by such fluctuations, affect microbial metabolism in permeable sediments in the German Wadden Sea and wastewater photogranules. Manuscript 1 finds that sulfate and nitrate reduction occur simultaneously, and that sulfate reduction rates are correlated with rates of dissimilatory nitrate reduction to ammonia in permeable sediments from the German Wadden Sea. Manuscript 2 finds that enzymatically removing reactive oxygen species from incubations of Wadden Sea sediments increases rates of sulfate and iron reduction and well as aerobic respiration. Furthermore, H2O2 was found in the upper sediments, controlling early diagenesis. Manuscript 2 also finds that while sulfate reduction does not occur simultaneously to oxygen consumption in permeable Wadden Sea sediments, it recovers instantly upon anoxia, meaning that the cells and their metabolic apparatus are not damaged by oxygen. Manuscript 3 finds that the removal of reactive oxygen species does not affect rates of denitrification or dissimilatory nitrate reduction to ammonia. It also finds that pretreatment of sediments with oxygen can increase sulfate reduction in the subsequent anoxic period. Furthermore, it finds that ROS can decrease sulfate reduction even in sediments that have not been recently exposed to oxygen. Manuscript 4 finds that wastewater photogranules are well adapted to extreme changes in nutrient and oxygen concentrations, performing carbon fixation over a large range of nutrient concentrations. It also finds evidence of aerobic denitrification. Overall, this thesis finds that resident microbes are well adapted to environments with frequent redox changes, and exhibit “braided” use of electron acceptors. It nonetheless finds that the reactive oxygen species produced over oxic-anoxic transitions can substantially decrease microbial activity.
Dissertation
47 57
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Chemical micro-environments, ventilation behaviour and microbial processes in sponges
(2008-09-19)
Schläppy, Marie-Lise
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Hagen, Wilhelm
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Jörgensen, Bo Barker
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Beer, Dirk de
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Hoffmann, Frederieke
The oxygen dynamics and ventilation behaviour in Dysidea avara and Chondrosia reniformis (Porifera) were investigated using oxygen micro-electrodes and hot-bead thermistors. Both field and laboratory experiments proved the common occurrences of anoxia in the sponge tissue that lasted up to approximately 1 h. Strong temporal and spatial heterogeneity of oxygen concentrations was observed with replicate oxygen profile series across the sponge surface, though tissue close to an osculum was generally better oxygenated. The microbial processes of sponge-associated microbes were investigated in D. avara and C. reniformis. Their presence and rates were established through microsensor measurements of product accumulation and isotope tracer experiments. Total net nitrification occurred at 8.8 and 14.7 nmol cm-3 sponge h-1 for C. reniformis and D. avara, respectively. Rates of denitrification, an anaerobic microbial process, were 10 nmol N consumed cm-3 wet weight sponge h-1 in C. reniformis and 14.9 nmol N cm-3 wet weight sponge h-1 in D. avara while anaerobic ammonium oxidation (anammox) and sulfate reduction were below detectable limits in both species.
Dissertation
208 86

Beer, Dirk de

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