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Hypersaline microbial mats are dense microbial ecosystems capable of performing complete element cycling and are considered analogs of early Earth and hypothetical extraterrestrial ecosystems. We studied the functionality and limits of key biogeochemical processes, such as photosynthesis, aerobic respiration, and sulfur cycling, in salt crust-covered microbial mats from a tidal flat at the coast of Oman. We measured light, oxygen, and sulfide microprofiles as well as sulfate reduction rates at salt saturation and in flood conditions and determined fine-scale stratification of pigments, biomass, and microbial taxa in the resident microbial community. The salt crust did not protect the mats against irradiation or evaporation. Although some oxygen production was measurable at salinities of ≤30% (wt/vol) in situ, at saturation-level salinity (40%), oxygenic photosynthesis was completely inhibited and only resumed 2 days after reducing the porewater salinity to 12%. Aerobic respiration and active sulfur cycling occurred at low rates under salt saturation and increased strongly upon salinity reduction. Apart from high relative abundances of Chloroflexi, photoheterotrophic Alphaproteobacteria, Bacteroidetes, and Archaea, the mat contained a distinct layer harboring filamentous Cyanobacteria, which is unusual for such high salinities. Our results show that the diverse microbial community inhabiting this salt flat mat ultimately depends on periodic salt dilution to be self-sustaining and is rather adapted to merely survive salt saturation than to thrive under the salt crust. IMPORTANCE Due to their abilities to survive intense radiation and low water availability, hypersaline microbial mats are often suggested to be analogs of potential extraterrestrial life. However, even the limitations imposed on microbial processes by saturation-level salinity found on Earth have rarely been studied in situ. While abundance and diversity of microbial life in salt-saturated environments are well documented, most of our knowledge on process limitations stems from culture-based studies, few in situ studies, and theoretical calculations. In particular, oxygenic photosynthesis has barely been explored beyond 5 M NaCl (28% wt/vol). By applying a variety of biogeochemical and molecular methods, we show that despite abundance of photoautotrophic microorganisms, oxygenic photosynthesis is inhibited in salt-crust-covered microbial mats at saturation salinities, while rates of other energy generation processes are decreased several-fold. Hence, the complete element cycling required for self-sustaining microbial communities only occurs at lower salt concentrations, Applied and Environmental Microbiology, 87 (17), ISSN:0099-2240, ISSN:1098-5336

Summary To understand the role of micrometer‐scale oxygen (O2) gradients in facilitating dinitrogen (N2) fixation, we characterized O2 dynamics in the microenvironment around free‐floating trichomes and colonies of Trichodesmium erythraeum IMS101. Diurnal and spatial variability in O2 concentrations in the bulk medium, within colonies, along trichomes and within single cells were determined using O2 optodes, microsensors and model calculations. Carbon (C) and N2 fixation as well as O2 evolution and uptake under different O2 concentrations were analyzed by stable isotope incubations and membrane inlet mass spectrometry. We observed a pronounced diel rhythm in O2 fluxes, with net O2 evolution restricted to short periods in the morning and evening, and net O2 uptake driven by dark respiration and light‐dependent O2 uptake during the major part of the light period. Remarkably, colonies showed lower N2 fixation and C fixation rates than free‐floating trichomes despite the long period of O2 undersaturation in the colony microenvironment. Model calculations demonstrate that low permeability of the cell wall in combination with metabolic heterogeneity between single cells allows for anoxic intracellular conditions in colonies but also free‐floating trichomes of Trichodesmium. Therefore, whereas colony formation must have benefits for Trichodesmium, it does not favor N2 fixation.

Rhodolith beds built by free-living coralline algae are important ecosystems for marine biodiversity and carbonate production. Yet, our mechanistic understanding regarding rhodolith physiology and its drivers is still limited. Using three rhodolith species with different branching morphologies, we investigated the role of morphology in species' physiology and the implications for their susceptibility to ocean acidification (OA). For this, we determined the effects of thallus topography on diffusive boundary layer (DBL) thickness, the associated microscale oxygen and pH dynamics and their relationship with species' metabolic and light and dark calcification rates, as well as species' responses to short-term OA exposure. Our results show that rhodolith branching creates low-flow microenvironments that exhibit increasing DBL thickness with increasing branch length. This, together with species' metabolic rates, determined the light-dependent pH dynamics at the algal surface, which in turn dictated species' calcification rates. While these differences did not translate in species-specific responses to short-term OA exposure, the differences in the magnitude of diurnal pH fluctuations (~ 0.1-1.2 pH units) between species suggest potential differences in phenotypic plasticity to OA that may result in different susceptibilities to long-term OA exposure, supporting the general view that species' ecomechanical characteristics must be considered for predicting OA responses. UID/Multi/04326/2019, 426215/2016-8, 1521610, HO 5439/2-1 info:eu-repo/semantics/publishedVersion

Carbon capture and storage (CCS) is a key technology to reduce carbon dioxide (CO2) emissions from industrial processes in a feasible, substantial, and timely manner. For geological CO2 storage to be safe, reliable, and accepted by society, robust strategies for CO2 leakage detection, quantification and management are crucial. The STEMM-CCS (Strategies for Environmental Monitoring of Marine Carbon Capture and Storage) project aimed to provide techniques and understanding to enable and inform cost-effective monitoring of CCS sites in the marine environment. A controlled CO2 release experiment was carried out in the central North Sea, designed to mimic an unintended emission of CO2 from a subsurface CO2 storage site to the seafloor. A total of 675 kg of CO2 were released into the shallow sediments (∼3 m below seafloor), at flow rates between 6 and 143 kg/d. A combination of novel techniques, adapted versions of existing techniques, and well-proven standard techniques were used to detect, characterise and quantify gaseous and dissolved CO2 in the sediments and the overlying seawater. This paper provides an overview of this ambitious field experiment. We describe the preparatory work prior to the release experiment, the experimental layout and procedures, the methods tested, and summarise the main results and the lessons learnt. publishedVersion

Thermal stress reduces pocilloporid coral resilience to ocean acidification by impairing control over calcifying fluid chemistry., The combination of thermal stress and ocean acidification (OA) can more negatively affect coral calcification than an individual stressors, but the mechanism behind this interaction is unknown. We used two independent methods (microelectrode and boron geochemistry) to measure calcifying fluid pH (pHcf) and carbonate chemistry of the corals Pocillopora damicornis and Stylophora pistillata grown under various temperature and pCO2 conditions. Although these approaches demonstrate that they record pHcf over different time scales, they reveal that both species can cope with OA under optimal temperatures (28°C) by elevating pHcf and aragonite saturation state (Ωcf) in support of calcification. At 31°C, neither species elevated these parameters as they did at 28°C and, likewise, could not maintain substantially positive calcification rates under any pH treatment. These results reveal a previously uncharacterized influence of temperature on coral pHcf regulation—the apparent mechanism behind the negative interaction between thermal stress and OA on coral calcification.

Highlights • A mechanistic explanation is provided for the observed CO2 loss in the sediments. • Reactions of CO2 with the sediment lead to significant heating. • The observations were modeled including reactions and losses due to lateral transport. • CO2 leakage will lead to very local effects. Abstract We investigated the effect of an artificial CO2 vent (0.0015−0.037 mol s−1), simulating a leak from a reservoir for carbon capture and storage (CCS), on the sediment geochemistry. CO2 was injected 3 m deep into the seafloor at 120 m depth. With increasing mass flow an increasing number of vents were observed, distributed over an area of approximately 3 m. In situ profiling with microsensors for pH, T, O2 and ORP showed the geochemical effects are localized in a small area around the vents and highly variable. In measurements remote from the vent, the pH reached a value of 7.6 at a depth of 0.06 m. In a CO2 venting channel, pH reduced to below 5. Steep temperature profiles were indicative of a heat source inside the sediment. Elevated total alkalinity and Ca2+ levels showed calcite dissolution. Venting decreased sulfate reduction rates, but not aerobic respiration. A transport-reaction model confirmed that a large fraction of the injected CO2 is transported laterally into the sediment and that the reactions between CO2 and sediment generate enough heat to elevate the temperature significantly. A CO2 leak will have only local consequences for sediment biogeochemistry, and only a small fraction of the escaped CO2 will reach the sediment surface.

Diatoms are among the few eukaryotes known to store nitrate (NO3- ) and to use it as an electron acceptor for respiration in the absence of light and O2 . Using microscopy and 15 N stable isotope incubations, we studied the relationship between dissimilatory nitrate/nitrite reduction to ammonium (DNRA) and diel vertical migration of diatoms in phototrophic microbial mats and the underlying sediment of a sinkhole in Lake Huron (USA). We found that the diatoms rapidly accumulated NO3- at the mat-water interface in the afternoon and 40% of the population migrated deep into the sediment, where they were exposed to dark and anoxic conditions for ~75% of the day. The vertical distribution of DNRA rates and diatom abundance maxima coincided, suggesting that DNRA was the main energy generating metabolism of the diatom population. We conclude that the illuminated redox-dynamic ecosystem selects for migratory diatoms that can store nitrate for respiration in the absence of light. A major implication of this study is that the dominance of DNRA over denitrification is not explained by kinetics or thermodynamics. Rather, the dynamic conditions select for migratory diatoms that perform DNRA and can outcompete sessile denitrifiers.

Background Dental plaque biofilms are the causative agents of caries, gingivitis and periodontitis. Both mechanical and chemical strategies are used in routine oral hygiene strategies to reduce plaque build-up. If allowed to mature biofilms can create anoxic microenvironments leading to communities which harbor pathogenic Gram-negative anaerobes. When subjected to high velocity fluid jets and sprays biofilms can be fluidized which disrupts the biofilm structure and allows the more efficient delivery of antimicrobial agents. Methods To investigate how such jets may disrupt anoxic niches in the biofilm, we used planar optodes to measure the dissolved oxygen (DO) concentration at the base of in-vitro biofilms grown from human saliva and dental plaque. These biofilms were subject to “shooting” treatments with a commercial high velocity microspray (HVM) device. Results HVM treatment resulted in removal of much of the biofilm and a concurrent rapid shift from anoxic to oxic conditions at the base of the surrounding biofilm. We also assessed the impact of HVM treatment on the microbial community by tracking 7 target species by qPCR. There was a general reduction in copy numbers of the universal 16S RNA by approximately 95%, and changes of individual species in the target region ranged from approximately 1 to 4 log reductions. Conclusion We concluded that high velocity microsprays removed a sufficient amount of biofilm to disrupt the anoxic region at the biofilm-surface interface.

We studied the growth of giant filamentous sulfur oxidizing bacteria of the family Beggiatoaceae collected from a hydrothermal seep area in the Guaymas Basin. We measured the incorporation of 14C-bicarbonate tracer into individual filaments using a microimager that allows quantitative determination of the distribution of radioisotopes with 20 µm resolution. Filaments incorporated label along their entire length; thus growth occurred uniformly throughout these whole filaments and not only at their tips. Uptake of 14C-bicarbonate was strongly stimulated by reducing the pH from 8.2, the value near the sediment surface, to 7.05, as found within 1–2 mm below the surface; the presence of oxygen or sulfide had no effect. Thus, Beggiatoaceae strongly prefer assimilation of CO2 over other DIC species. In consequence, migration of these motile filaments into deeper sediments, where sharply decreasing pH increases the availability of CO2, will favor cell growth. Genomic evidence was found for periplasmic carbonic anhydrases, indicative of the carbon concentration mechanism.

The Arabian Gulf is exposed to intensive dust storms during summer until early winter. We investigated the nutritive effect of the dust on microbial biodiversity of the water column and the productivity of the Gulf. We collected samples from three sites in a transect perpendicular to the shore in March (before the strong dust storms) and in October (after the dust season) in 2013. At the three sites, we sampled the water column at three depths, and see-floor sediments using a HAPS corer. We also sampled the sand dunes that are the source of the dust. We analyzed the samples for pigments, microbial community composition using a 16S rRNA analysis, and nutrients. Our results showed that species richness and biodiversity were higher in October than in March. The relative abundances of key-player microorganisms were strongly pronounced in October. We assume that the dust rapidly sinks to the seafloor where the nutrients Fe and P are liberated through iron reduction. Assuming that all phosphate diffusing from the seafloor originates from the dust particles after deposition, we estimated a contribution of minimum 30,000 tons of fish produced every year in the Gulf. We found no close temporal coupling between dust storms and productivity. This is because nutrient liberation from the seafloor is slow and its transport from the seafloor to the photic zone by circulation processes is irregular. This study highlights the importance of dust as a source of nutrients in the Gulf ecosystem.

Large areas of the oceanic shelf are composed of sandy sediments through which reactive solutes are transported via porewater advection fueling active microbial communities. The advective oxygen transport in permeable sands of the North Sea was investigated under in situ conditions using a new benthic observatory to assess the dynamic interaction of hydrodynamics, sediment morphodynamics, and oxygen penetration depth. During 16 deployments, concurrent measurement of current velocity, sediment topography, and porewater oxygen concentration were carried out. In all cases the oxyclines were found at depths of 1–6 cm, correlating with the topography of stationary and migrating bedforms (ripples). Different conditions in terms of bottom water currents and bedform migration led to fluctuating oxygen penetration depths and, hence, highly variable redox conditions in up to 2.5 cm thick layers beneath the surface. Volumetric oxygen consumption rates of surface sediments were measured on board in flow-through reactors. Bedform migration was found to reduce consumption rates by up to 50%, presumably caused by the washout of organic carbon that is otherwise trapped in the pore space of the sediment. Based on the observations we found oxygen penetration depths to be largely controlled by oxygen consumption rates, grain size, and current velocity. These controlling variables are summarized by an adapted Damkohler number which allows for prediction of oxygen penetretion depths based on a simple scaling law. By integrating the oxygen consumption rates over the oxygen penetration depth, oxygen fluxes of 8–34 mmol m−2 d−1 were estimated

Oxygenic and anoxygenic photosynthesis were studied with microsensors in microbial mats found at 9-10 m depth in anoxic and sulfidic water in Little Salt Spring (Florida, USA). The lake sediments were covered with a 1-2 mm thick red mat dominated by filamentous Cyanobacteria, below which Green Sulfur Bacteria (GSB, Chlorobiaceae) were highly abundant. Within 4 mm inside the mats, the incident radiation was attenuated to undetectable levels. In situ microsensor data showed both oxygenic photosynthesis in the red surface layer and light-induced sulfide dynamics up to 1 cm depth. Anoxygenic photosynthesis occurred during all daylight hours, with complete sulfide depletion around midday. Oxygenic photosynthesis was limited to 4 h per day, due to sulfide inhibition in the early morning and late afternoon. Laboratory measurements on retrieved samples showed that oxygenic photosynthesis was fully but reversibly inhibited by sulfide. In patches Fe(III) alleviated the inhibition of oxygenic photosynthesis by sulfide. GSB were resistant to oxygen and showed a low affinity to sulfide. Their light response showed saturation at very low intensities.

Background Dental plaque biofilms are the causative agents of caries, gingivitis and periodontitis. Both mechanical and chemical strategies are used in routine oral hygiene strategies to reduce plaque build-up. If allowed to mature biofilms can create anoxic microenvironments leading to communities which harbor pathogenic Gram-negative anaerobes. When subjected to high velocity fluid jets and sprays biofilms can be fluidized which disrupts the biofilm structure and allows the more efficient delivery of antimicrobial agents. Methods To investigate how such jets may disrupt anoxic niches in the biofilm, we used planar optodes to measure the dissolved oxygen (DO) concentration at the base of in-vitro biofilms grown from human dental saliva and plaque. These biofilms were subject to “shooting” treatments with a commercial high velocity microspray (HVM) device. Results HVM treatment resulted in removal of much of the biofilm and a concurrent rapid shift from anoxic to oxic conditions at the base of the surrounding biofilm. We also assessed the impact of HVM treatment on the microbial community by tracking 7 target species by qRT-PCR. There was a general reduction in copy numbers of the universal 16S RNA by approximately 95%, and changes of individual species in the target region ranged from approximately 1 to 4 log reductions. Conclusion We concluded that high velocity microsprays removed a sufficient amount of biofilm to disrupt the anoxic region at the biofilm-surface interface.

Iron (Fe) bioavailability limits phytoplankton growth in vast ocean regions. Iron-rich dust uplifted from deserts is transported in the atmosphere and deposited on the ocean surface. However, this dust is a poor source of iron for most phytoplankton since dust-bound Fe is poorly soluble in seawater and dust rapidly sinks out of the photic zone. An exception is Trichodesmium, a globally important, N2 fixing, colony forming, cyanobacterium, which efficiently captures and shuffles dust to its colony core. Trichodesmium and bacteria that reside within its colonies carry out diverse metabolic interactions. Here we show evidence for mutualistic interactions between Trichodesmium and associated bacteria for utilization of iron from dust, where bacteria promote dust dissolution by producing Fe-complexing molecules (siderophores) and Trichodesmium provides dust and optimal physical settings for dissolution and uptake. Our results demonstrate how intricate relationships between producers and consumers can influence productivity in the nutrient starved open ocean. Subhajit Basu et al. provide evidence for mutualistic interactions between the nitrogen-fixing marine cyanobacteria Trichodesmium and associated bacteria in using iron from dust. Adding siderophores increases iron oxide dissolution and iron uptake, benefiting both Trichodesmium and the associated bacteria.

In vivo measurements of [Ca2+] and [CO32−] indicate biological control of carbonate chemistry at site of calcification in corals., Reef-building corals form their calcium carbonate skeletons within an extracellular calcifying medium (ECM). Despite the critical role of the ECM in coral calcification, ECM carbonate chemistry is poorly constrained in vivo, and full ECM carbonate chemistry has never been characterized based solely on direct in vivo measurements. Here, we measure pHECM in the growing edge of Stylophora pistillata by simultaneously using microsensors and the fluorescent dye SNARF-1, showing that, when measured at the same time and place, the results agree. We then conduct microscope-guided microsensor measurements of pH, [Ca2+], and [CO32−] in the ECM and, from this, determine [DIC]ECM and aragonite saturation state (Ωarag), showing that all parameters are elevated with respect to the surrounding seawater. Our study provides the most complete in vivo characterization of ECM carbonate chemistry parameters in a coral species to date, pointing to the key role of calcium- and carbon-concentrating mechanisms in coral calcification.

While intertidal flats only make up less than 10% of the world's coastlines, they are among the most productive continental shelf ecosystems. They are important sites of recycling for both terrestrially and marine-derived organic matter and nutrients and also support high rates of primary productivity. These tidal flats are located between the spring high- and low-tide marks, lack rooted vegetation, and span a range of composition from mudbanks to coarse sand flats. They are found in sheltered bays, estuaries, and coasts that are protected by barrier islands. Biogeochemical processes in tidal flat sediments are regulated by the dynamic interaction of microbial reactions and water and sediment transport processes. Temporal and spatial heterogeneity and strong forcing by tidal and wind dynamics generate extreme biogeochemical variability in intertidal flats and distinguish these habitats from subtidal coastal sediments. Here, we synthesize the last several decades of research on biogeochemical patterns and processes in tidal flat sediments and place them within their geological and hydrodynamic contexts. We first define and describe the processes that control water and solute exchange between different types of intertidal flats and the overlying or adjacent seawater. We go on to discuss how organic matter is broken down or altered in tidal flat sediments. Finally, we discuss microbial nitrogen, phosphorus, and silica cycling within tidal flat sediments and the influence of these processes on water column nutrient availability.

Iron (Fe) bioavailability limits phytoplankton growth in vast ocean regions. Iron-rich dust uplifted from deserts is transported in the atmosphere and deposited on the ocean surface. However, this dust is a poor source of iron for most phytoplankton since dust-bound Fe is poorly soluble in seawater and dust rapidly sinks out of the photic zone. An exception is Trichodesmium, a globally important, N2 fixing, colony forming, cyanobacterium, which efficiently captures and shuffles dust to its colony core. Trichodesmium and bacteria that reside within its colonies carry out diverse metabolic interactions. Here we show evidence for mutualistic interactions between Trichodesmium and associated bacteria for utilization of iron from dust, where bacteria promote dust dissolution by producing Fe-complexing molecules (siderophores) and Trichodesmium provides dust and optimal physical settings for dissolution and uptake. Our results demonstrate how intricate relationships between producers and consumers can influence productivity in the nutrient starved open ocean., Subhajit Basu et al. provide evidence for mutualistic interactions between the nitrogen-fixing marine cyanobacteria Trichodesmium and associated bacteria in using iron from dust. Adding siderophores increases iron oxide dissolution and iron uptake, benefiting both Trichodesmium and the associated bacteria.

Telemetry devices are generating and transferring increasingly more data, with notable potential for decision makers. In this paper we consider the accelerometer and speed data produced by in-vehicle data recorders as a proxy for driver behaviour. Instead of extracting harsh events to cope with the large volumes of data, we discretise the data into a tractable and finite risk space. This novel methodology allows us to track both acceptable and non-acceptable driving behaviour, and calculate a more comprehensive risk model using the envelope of the data, and nota priorithresholds. We show how thresholds suggested in literature can characterise some driving behaviour as good, even though our empirical evidence has not even registered such extreme driving behaviour. We demonstrate the model using accelerometer data from 124 vehicles over a one month period. Three rules, each a combination of accelerometer and/or speed data, are applied to the risk space to derive person-specific scores that are comparable among the individuals. The results show that the scoring is useful to identify specific risk groups. The proposed model is also dynamic in that it dynamically adjusts to the observed records, instead of data having to abide by a limited model specification.

The Pacific white shrimp ( Litopenaeus vannamei ) is widely used in aquaculture, where it is reared at high stocking densities, temperatures, and nutrient concentrations. Here we report that adult L. vannamei shrimp emit the greenhouse gas nitrous oxide (N 2 O) at an average rate of 4.3 nmol N 2 O/individual × h, which is 1 to 2 orders of magnitude higher than previously measured N 2 O emission rates for free-living aquatic invertebrates. Dissection, incubation, and inhibitor experiments with specimens from a shrimp farm in Germany indicated that N 2 O is mainly produced in the animal's gut by microbial denitrification. Microsensor measurements demonstrated that the gut interior is anoxic and nearly neutral and thus is favorable for denitrification by ingested bacteria. Dinitrogen (N 2 ) and N 2 O accounted for 64% and 36%, respectively, of the nitrogen gas flux from the gut, suggesting that the gut passage is too fast for complete denitrification to be fully established. Indeed, shifting the rearing water bacterial community, a diet component of shrimp, from oxic to anoxic conditions induced N 2 O accumulation that outlasted the gut passage time. Shrimp-associated N 2 O production was estimated to account for 6.5% of total N 2 O production in the shrimp farm studied here and to contribute to the very high N 2 O supersaturation measured in the rearing tanks (2,099%). Microbial N 2 O production directly associated with aquacultured animals should be implemented into life cycle assessments of seafood production. IMPORTANCE The most widely used shrimp species in global aquaculture, Litopenaeus vannamei , is shown to emit the potent greenhouse gas nitrous oxide (N 2 O) at a particularly high rate. Detailed experiments reveal that N 2 O is produced in the oxygen-depleted gut of the animal by bacteria that are part of the shrimp diet. Upon ingestion, these bacteria experience a shift from oxic to anoxic conditions and therefore switch their metabolism to the anaerobic denitrification process, which produces N 2 O as an intermediate and dinitrogen (N 2 ) gas as an end product. The N 2 O/N 2 production ratio is unusually high in the shrimp gut, because denitrification cannot be fully established during the short gut passage time of food-associated bacteria. Nitrous oxide emission directly mediated by L. vannamei contributes significantly to the overall N 2 O emission from aquaculture facilities.

Biofilm activities and their interactions with physical, chemical and biological processes are of great importance for a variety of ecosystem functions, impacting hydrogeomorphology, water quality and aquatic ecosystem health. Effective management of water bodies requires advancing our understanding of how flow influences biofilm-bound sediment and ecosystem processes and vice-versa. However, research on this triangle of flow-biofilm-sediment is still at its infancy. In this Review, we summarize the current state of the art and methodological approaches in the flow-biofilm-sediment research with an emphasis on biostabilization and fine sediment dynamics mainly in the benthic zone of lotic and lentic environments. Example studies of this three-way interaction across a range of spatial scales from cell (nm - µm) to patch scale (mm - dm) are highlighted in view of the urgent need for interdisciplinary approaches. As a contribution to the review, we combine a literature survey with results of a pilot experiment that was conducted in the framework of a joint workshop to explore the feasibility of asking interdisciplinary questions. Further, within this workshop various observation and measuring approaches were tested and the quality of the achieved results was evaluated individually and in combination. Accordingly, the paper concludes by highlighting the following research challenges to be considered within the forthcoming years in the triangle of flow-biofilm-sediment: i) Establish a collaborative work among hydraulic and sedimentation engineers as well as ecologists to study mutual goals with appropriate methods. Perform realistic experimental studies to test hypotheses on flow-biofilm-sediment interactions as well as structural and mechanical characteristics of the bed. ii) Consider spatially varying characteristics of flow at the sediment-water interface. Utilize combinations of microsensors and non-intrusive optical methods, such as particle image velocimetry and laser scanner to elucidate the mechanism behind biofilm growth as well as mass and momentum flux exchanges between biofilm and water. Use molecular approaches (DNA, pigments, staining, microscopy) for sophisticated community analyses. Link varying flow regimes to microbial communities (and processes) and fine sediment properties to explore the role of key microbial players and functions in enhancing sediment stability (biostabilization). iii) Link laboratory-scale observations to larger scales relevant for management of water bodies. Conduct field experiments to better understand the complex effects of variable flow and sediment regimes on biostabilization. Employ scalable and informative observation techniques (e.g., hyperspectral imaging, particle tracking) that can support predictions on the functional aspects, such as metabolic activity, bed stability, nutrient fluxes under variable regimes of flow-biofilm-sediment.

Red coralline algae are projected to be sensitive to ocean acidification, particularly in polar oceans. As important ecosystem engineers, their potential sensitivity has broad implications, and understanding their carbon acquisition mechanisms is necessary for making reliable predictions. Therefore, we investigated the localized carbonate chemistry at the surface of Arctic coralline algae using microsensors. We report for the first time carbonate ion concentration and pH measurements ([CO3 2-]) at and above the algal surface in the microenvironment. We show that surface pH and [CO3 2-] are higher than the bulk seawater in the light, and even after hours of darkness. We further show that three species of Arctic coralline algae have efficient carbon concentrating mechanisms including direct bicarbonate uptake and indirect bicarbonate use via a carbonic anhydrase enzyme. Our results suggest that Arctic corallines have strong biological control over their surface chemistry, where active calcification occurs, and that net dissolution in the dark does not occur. We suggest that the elevated pH and [CO3 2-] in the dark could be explained by a high rate of light independent carbon fixation that reduces respiratory CO2 release. This mechanism could provide a potential adaptation to ocean acidification in Arctic coralline algae, which has important implications for future Arctic marine ecosystems.

We report extremely low-light-adapted anoxygenic photosynthesis in a thick microbial mat in Magical Blue Hole, Abaco Island, The Bahamas. Sulfur cycling was reduced by iron oxides and organic carbon limitation. The mat grows below the halocline/oxycline at 30 m depth on the walls of the flooded sinkhole. In situ irradiance at the mat surface on a sunny December day was between 0.021 and 0.084 mu mol photons m(-2) s(-1), and UV light (97% sequence identity) of clones affiliated with Prosthecochloris, a genus within the green sulfur bacteria (GSB), which are obligate anoxygenic phototrophs. Typical photopigments of brown-colored GSB, bacteriochlorophyll e and (beta-)isorenieratene, were abundant in mat samples and their absorption properties are well-adapted to harvest light in the available green and possibly even UV-A spectra. Sulfide from the water column (3-6 mu mol L-1) was the main source of sulfide to the mat as sulfate reduction rates in the mats were very low (undetectable-99.2 nmol cm(-3) d(-1)). The anoxic water column was oligotrophic and low in dissolved organic carbon (175-228 mu mol L-1). High concentrations of pyrite (FeS2; 1-47 mu mol cm(-3)) together with low microbial process rates (sulfate reduction, CO2 fixation) indicate that the mats function as net sulfide sinks mainly by abiotic processes. We suggest that abundant Fe(III) (4.3-22.21 mu mol cm(-3)) is the major source of oxidizing power in the mat, and that abiotic Fe-S-reactions play the main role in pyrite formation. Limitation of sulfate reduction by low organic carbon availability along with the presence of abundant sulfide-scavenging iron oxides considerably slowed down sulfur cycling in these mats.

We investigated light, water velocity, and CO2 as drivers of primary production in Mediterranean seagrass (Posidonia oceanica) meadows and neighboring bare sands using the aquatic eddy covariance technique. Study locations included an open-water meadow and a nearshore meadow, the nearshore meadow being exposed to greater hydrodynamic exchange. A third meadow was located at a CO2 vent. We found that, despite the oligotrophic environment, the meadows had a remarkably high metabolic activity, up to 20 times higher than the surrounding sands. They were strongly autotrophic, with net production half of gross primary production. Thus, P. oceanica meadows are oases of productivity in an unproductive environment. Secondly, we found that turbulent oxygen fluxes above the meadow can be significantly higher in the afternoon than in the morning at the same light levels. This hysteresis can be explained by the replenishment of nighttime-depleted oxygen within the meadow during the morning. Oxygen depletion and replenishment within the meadow do not contribute to turbulent O2 flux. The hysteresis disappeared when fluxes were corrected for the O2 storage within the meadow and, consequently, accurate metabolic rate measurements require measurements of meadow oxygen content. We further argue that oxygen-depleted waters in the meadow provide a source of CO2 and inorganic nutrients for fixation, especially in the morning. Contrary to expectation, meadow metabolic activity at the CO2 vent was lower than at the other sites, with negligible net primary production.

Este artículo contiene 16 páginas, 5 figuras, 3 tablas., Subseabed CO2 storage is considered a future climate change mitigation technology. We investigated the ecological consequences of CO2 leakage for a marine benthic ecosystem. For the first time with a multidisciplinary integrated study, we tested hypotheses derived from a meta-analysis of previous experimental and in situ high-CO2 impact studies. For this, we compared ecological functions of naturally CO2-vented seafloor off the Mediterranean island Panarea (Tyrrhenian Sea, Italy) to those of nonvented sands, with a focus on biogeochemical processes and microbial and faunal community composition. High CO2 fluxes (up to 4 to 7 mol CO2 m−2 hour−1) dissolved all sedimentary carbonate, and comigration of silicate and iron led to local increases of microphytobenthos productivity (+450%) and standing stocks (+300%). Despite the higher food availability, faunal biomass (−80%) and trophic diversity were substantially lower compared to those at the reference site. Bacterial communities were also structurally and functionally affected, most notably in the composition of heterotrophs and microbial sulfate reduction rates (−90%). The observed ecological effects of CO2 leakage on submarine sands were reproduced with medium-term transplant experiments. This study assesses indicators of environmental impact by CO2 leakage and finds that community compositions and important ecological functions are permanently altered under high CO2., This work was funded by the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement number 265847 [Sub-seabed CO2 storage: Impact on Marine Ecosystems (ECO2)] and supported by the Max Planck Society and by the Flemish Fund for Scientific Research (grant number 1242114N). This study is also a contribution of D.M. to the research project MarSymBiomics (reference number CTM2013-43287-P), funded by the Spanish “Agencia Estatal de Investigación” (AEI), and PopCOmics (CTM2017-88080), funded by the AEI and the European Funds for Regional Development (FEDER) and to the Consolidated Research Group on Marine Benthic Ecology (2014SGR120) of the Generalitat de Catalunya.

Benthic cyanobacterial mats (BCMs) have increased in abundance on coral reefs worldwide. However, their species diversity and role in nitrogen fixation are poorly understood. We assessed the cyanobacterial diversity of BCMs at four coral reef sites in Curacao, Southern Caribbean. In addition, nitrogen fixation rates of six common mats were measured. Microscopic examinations showed 22 cyanobacterial species, all from the order Oscillatoriales. Species diversity was similar among sites despite differences in overall BCM abundance. Dominant mats were primarily composed of Hydrocoletan glutinosum, Oscillatoria bonnemaisonii or Lyngbya majuscula. However, some mats exhibited highly variable species composition despite consistent macroscopic appearance. 16S rRNA-based phylogeny revealed similar species as those identified by microscopy, with additional sequences of unicellular (Xenococcus and Chroococcidiopsis) and heterocystous (Rivularia and Calothrix) cyanobacteria. Vice versa, morphotypes of Tychonema, Schizothrix and Dichothrix were found by microscopy only. The detection of similar species at the same sites in a study conducted 40 years ago indicates that changes in environmental conditions over these years may have favored indigenous species to bloom, rather than facilitated the introduction and proliferation of invasive species. Nitrogen fixation rates of mats were 3-10 times higher in the light than in the dark. The highest areal nitrogen fixation rate (169.1 mg N m(-2) d(-1)) was recorded in the cyanobacterial patch dominated by O. bonnemaisonii. A scale-up of nitrogen fixation at a site with 26% BCM cover at 7 m depth yielded an aerial rate of 13 mg N m(-2) reef d(-1), which exceeds rates reported in open ocean blooms of Trichodesmiun in the Caribbean. Our results suggest that the Caribbean basin is not only a hotspot for planktonic nitrogen fixation, but also for benthic nitrogen fixation. Because BCMs fix vast amounts of nitrogen, their proliferation will strongly alter the nitrogen budget of coral reefs.

International audience; Aerobic heterotrophic microorganisms (AH) play a significant role in carbon cycling in cyanobacterial mats; however, little is known about their abundance, diversity and interaction with cyanobacteria. Using catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH), bacterial counts in the mat's oxic layer reached a mean of 2.23 +/- 0.4 x 10(10) cells g(-1). Cultivation of AH yielded strains belonging to Actinobacteria, Bacteroidetes, Firmicutes, Gammaproteobacteria and Haloarchaea. 16S rRNA bacterial sequences retrieved from the mat's oxic layer were related to Bacteroidetes, Chloroflexi and Proteobacteria, whereas archaeal sequences belonged to Crenarchaeota and Haloarchaea. Monocultures of cyanobacteria from the same mat were associated with different AH, although Bacteroidetes were found in most cultures. CARD-FISH showed that Bacteroidetes- and Chloroflexi-related bacteria were closely associated with filaments of Microcoleus chthonoplastes. The growth of an axenic culture of M. chthonoplastes PCC7420 was stimulated on the addition of a filtrate obtained from a non-axenic Microcoleus culture and containing only AH and released substances. In contrast, a similar filtrate from a non-axenic Cyanothece-related culture killed Cyanothece PCC 7418. We conclude that a diverse community of AH exist in close association with cyanobacteria in microbial mats and the interactions between AH and cyanobacteria are species-specific and involve the release of substances.

Whether large sulfur bacteria of the family Beggiatoaceae reduce NO3− to N2 via denitrification or to NH4+ via DNRA has been debated in the literature for more than 25 years. We resolve this debate by showing that certain members of the Beggiatoaceae use both metabolic pathways. This is important for the ecological role of these bacteria, as N2 production removes bioavailable nitrogen from the ecosystem, whereas NH4+ production retains it. For this reason, the topic of environmental controls on the competition for NO3− between N2-producing and NH4+-producing bacteria is of great scientific interest. Recent experiments on the competition between these two types of microorganisms have demonstrated that the balance between electron donor and electron acceptor availability strongly influences the end product of NO3− reduction. Our results suggest that this is also the case at the even more fundamental level of enzyme system regulation within a single organism., Filamentous large sulfur-oxidizing bacteria (FLSB) of the family Beggiatoaceae are globally distributed aquatic bacteria that can control geochemical fluxes from the sediment to the water column through their metabolic activity. FLSB mats from hydrothermal sediments of Guaymas Basin, Mexico, typically have a “fried-egg” appearance, with orange filaments dominating near the center and wider white filaments at the periphery, likely reflecting areas of higher and lower sulfide fluxes, respectively. These FLSB store large quantities of intracellular nitrate that they use to oxidize sulfide. By applying a combination of 15N-labeling techniques and genome sequence analysis, we demonstrate that the white FLSB filaments were capable of reducing their intracellular nitrate stores to both nitrogen gas and ammonium by denitrification and dissimilatory nitrate reduction to ammonium (DNRA), respectively. On the other hand, our combined results show that the orange filaments were primarily capable of DNRA. Microsensor profiles through a laboratory-incubated white FLSB mat revealed a 2- to 3-mm vertical separation between the oxic and sulfidic zones. Denitrification was most intense just below the oxic zone, as shown by the production of nitrous oxide following exposure to acetylene, which blocks nitrous oxide reduction to nitrogen gas. Below this zone, a local pH maximum coincided with sulfide oxidation, consistent with nitrate reduction by DNRA. The balance between internally and externally available electron acceptors (nitrate) and electron donors (reduced sulfur) likely controlled the end product of nitrate reduction both between orange and white FLSB mats and between different spatial and geochemical niches within the white FLSB mat. IMPORTANCE Whether large sulfur bacteria of the family Beggiatoaceae reduce NO3− to N2 via denitrification or to NH4+ via DNRA has been debated in the literature for more than 25 years. We resolve this debate by showing that certain members of the Beggiatoaceae use both metabolic pathways. This is important for the ecological role of these bacteria, as N2 production removes bioavailable nitrogen from the ecosystem, whereas NH4+ production retains it. For this reason, the topic of environmental controls on the competition for NO3− between N2-producing and NH4+-producing bacteria is of great scientific interest. Recent experiments on the competition between these two types of microorganisms have demonstrated that the balance between electron donor and electron acceptor availability strongly influences the end product of NO3− reduction. Our results suggest that this is also the case at the even more fundamental level of enzyme system regulation within a single organism.

In the present study depth profiles of light, oxygen, pH and photosynthetic performance in an artificial biofilm of the green alga Halochlorella rubescens in a porous substrate photobioreactor (PSBR) were recorded with microsensors. Biofilms were exposed to different light intensities (50-1,000 μmol photons m(-2) s(-1) ) and CO2 levels (0.04-5% v/v in air). The distribution of photosynthetically active radiation showed almost identical trends for different surface irradiances, namely: a relatively fast drop to a depth of about 250 µm, (to 5% of the incident), followed by a slower decrease. Light penetrated into the biofilm deeper than the Lambert-Beer Law predicted, which may be attributed to forward scattering of light, thus improving the overall light availability. Oxygen concentration profiles showed maxima at a depth between 50 and 150 μm, depending on the incident light intensity. A very fast gas exchange was observed at the biofilm surface. The highest oxygen concentration of 3.2 mM was measured with 1,000 μmol photons m(-2) s(-1) and 5% supplementary CO2. Photosynthetic productivity increased with light intensity and/or CO2 concentration and was always highest at the biofilm surface; the stimulating effect of elevated CO2 concentration in the gas phase on photosynthesis was enhanced by higher light intensities. The dissolved inorganic carbon concentration profiles suggest that the availability of the dissolved free CO2 has the strongest impact on photosynthetic productivity. The results suggest that dark respiration could explain previously observed decrease in growth rate over cultivation time in this type of PSBR. Our results represent a basis for understanding the complex dynamics of environmental variables and metabolic processes in artificial phototrophic biofilms exposed to a gas phase and can be used to improve the design and operational parameters of PSBRs.

Intertidal sand flats in the Wadden Sea (North Sea, Germany) act as large (2–3 km wide) permeable filters that very actively mineralize particulate organics from the water column. Most of the degradation occurs aerobically, but the sand flats contain a source of biogenic methane that is released directly to the water column and to the atmosphere during low tide (tidal range 2–3 m) via vents near the low water line. These seeps emit sulfide and methane independent of seasons. We investigated where in the flats this methane is formed. During low tide in the summer months, we sampled sediments and pore water at different depths, in the central tidal flat and near the low-water line. The sulfate-methane transition zone (SMTZ) was found at 2–4 m depth below the central flat and approximately at the level of the low-water line, thus intersecting with the sediment surface of the low-water line at the edge of the flat. We followed the consumption of sulfate and formation of methane during anoxic incubations of the sampled sediments. The anaerobic process rates were highest in the surface sediments of the central tidal flats, probably due to input of fresh organic matter from the water column. Yet, this zone is not likely to be the largest source of methane: low rates of methanogenesis were detected in the presence of sulfate; the rates increased by more than an order of magnitude only after sulfate depletion. Below the SMTZ of the central flat, sulfate is depleted and high levels of methane were present. These deeper sulfate-free layers are more likely the source of the methane that seeps out at the low water line. The methane found in the low water line seeps is not formed from fresh organic material, which is mostly degraded aerobically and by sulfate reduction in the sulfate-rich surface sediments. Methane is rather produced slowly in the sulfate-depleted areas deeper in the central flat sediments from older refractory organic matter. Methane originating from this zone, with pore water residence time of decades, is transported by slow pore water flow to the seepage areas at the low water line.

Phototrophic biofilms are widely distributed in nature and their ecological importance is well recognized. More recently, there has been a growing interest in using artificial phototrophic biofilms in innovative photobioreactors for production of microalgal biomass in biotechnological applications. To study physiological processes within these biofilms, microsensors have been applied in several studies. Here, the 'light-dark shift method' relies on measurement of photosynthetic activity in terms of light-induced oxygen production. However, when applied to non-submerged biofilms that can be found in numerous locations in nature, as well as in some types of photobioreactors, limitations of this approach are obvious due to rapid removal of gaseous species at the biofilm surface. Here, we introduce a mathematical correction to recover the distribution of the actual photosynthetic activity along the depth gradient in the biofilm, based on a numerical solution of the inversed diffusion equation of oxygen. This method considers changes in mass transport during the measurement period as can found on biofilms possessing a thin flow/mass transfer boundary layer (e. g., non-submerged biofilms). Using both simulated and real microsensor data, the proposed method was shown to be much more accurate than the classical method, which leads to underestimations of rates near the biofilm surface. All test profiles could be recovered with a high fit. According to our simulated microsensor measurements, a depth resolution of ≤20 μm is recommended near the surface. We conclude that our method strongly improves the quality of data acquired from light-dark measurements of photosynthetic activity in biofilms.

We studied the interaction between phototrophic and chemolithoautotrophic sulphide-oxidizing microorganisms in natural microbial mats forming in sulphidic streams. The structure of these mats varied between two end-members: one characterized by a layer dominated by large sulphur-oxidizing bacteria (SOB; mostly Beggiatoa-like) on top of a cyanobacterial layer (B/C mats) and the other with an inverted structure (C/B mats). C/B mats formed where the availability of oxygen from the water column was limited (

Two different cyanobacterial biofilms from German karstwater creeks were investigated with respect to their photosynthetic effect on Ca2+ removal and potential CaCO3 precipitation in artificial creek waters of different CO2 partial pressures at a given, constant calcite supersaturation. CO2 partial pressures were adjusted to 350 ppmV, 2200 ppmV and 8700 ppmV respectively, covering the range of Phanerozoic atmospheric CO2 partial pressures inferred from palaeosoils, stomatal indices and model calculations. Microsensor measurements of calcium, pH and oxygen revealed differences in the potential to precipitate CaCO3 between the two model organisms Tychonema-relative strain SAG 2388 and Synechococcus sp. strain SAG 2387. Whereas a strong removal of Ca2+ from the solution was measured at Tychonema-relative biofilm, the Synechococcus sp. biofilm exercised a much lower Ca2+ removal during photosynthesis. Photosynthesis was enhanced in both organisms with increasing CO2 and HCO3−, as indicated by enhanced O2 prod...

Before the Earth's complete oxygenation (0.58 to 0.55 billion years [Ga] ago), the photic zone of the Proterozoic oceans was probably redox stratified, with a slightly aerobic, nutrient-limited upper layer above a light-limited layer that tended toward euxinia. In such oceans, cyanobacteria capable of both oxygenic and sulfide-driven anoxygenic photosynthesis played a fundamental role in the global carbon, oxygen, and sulfur cycle. We have isolated a cyanobacterium, Pseudanabaena strain FS39, in which this versatility is still conserved, and we show that the transition between the two photosynthetic modes follows a surprisingly simple kinetic regulation controlled by this organism's affinity for H 2 S. Specifically, oxygenic photosynthesis is performed in addition to anoxygenic photosynthesis only when H 2 S becomes limiting and its concentration decreases below a threshold that increases predictably with the available ambient light. The carbon-based growth rates during oxygenic and anoxygenic photosynthesis were similar. However, Pseudanabaena FS39 additionally assimilated NO 3 − during anoxygenic photosynthesis. Thus, the transition between anoxygenic and oxygenic photosynthesis was accompanied by a shift of the C/N ratio of the total bulk biomass. These mechanisms offer new insights into the way in which, despite nutrient limitation in the oxic photic zone in the mid-Proterozoic oceans, versatile cyanobacteria might have promoted oxygenic photosynthesis and total primary productivity, a key step that enabled the complete oxygenation of our planet and the subsequent diversification of life.

We used microsensors to investigate the combinatory effect of hydrogen sulfide (H2 S) and light on oxygenic photosynthesis in biofilms formed by a cyanobacterium from sulfidic springs. We found that photosynthesis was both positively and negatively affected by H2 S: (i) H2 S accelerated the recovery of photosynthesis after prolonged exposure to darkness and anoxia. We suggest that this is possibly due to regulatory effects of H2 S on photosystem I components and/or on the Calvin cycle. (ii) H2 S concentrations of up to 210 μM temporarily enhanced the photosynthetic rates at low irradiance. Modelling showed that this enhancement is plausibly based on changes in the light-harvesting efficiency. (iii) Above a certain light-dependent concentration threshold H2 S also acted as an inhibitor. Intriguingly, this inhibition was not instant but occurred only after a specific time interval that decreased with increasing light intensity. That photosynthesis is most sensitive to inhibition at high light intensities suggests that H2 S inactivates an intermediate of the oxygen evolving complex that accumulates with increasing light intensity. We discuss the implications of these three effects of H2 S in the context of cyanobacterial photosynthesis under conditions with diurnally fluctuating light and H2 S concentrations, such as those occurring in microbial mats and biofilms.

Potential rates of ammonia oxidation, denitrification and anammox were measured in a hypersaline microbial mat. Ammonia oxidation and denitrification had potential rates of 0.8 ± 0.4 and 2.0 ± 1.0 nmol N g−1 h−1, respectively, anammox was not detectable. The rate of N2O production under anoxic conditions accounted for ca. 5% of total denitrification. Using qPCR, the ammonia-oxidation (amoA) genes of gammaproteobacteria had the highest copy number. The denitrification genes narG and nirS exhibited comparable estimates. Sequences of nirS gene were novel, whereas nirK sequences were related to sequences from the Rhizobiales group. Sequences of the nosZ gene were the most diverse and clustered with sequences from various genera. Our results demonstrate that the hypersaline mat from Oman harbors nitrifying and denitrifying bacteria with the potential to perform respective processes at detectable rates.

A new diketo-pyrrolo-pyrrole (DPP) indicator dye for optical sensing of carbon dioxide is prepared via a simple one step synthesis from commercially available low cost 'Pigment Orange 73'. The pigment is modified via alkylation of one of the lactam nitrogens with a tert-butylbenzyl group. The indicator dye is highly soluble in organic solvents and in polymers and shows pH-dependent absorption (λ

CO2 leakage alters benthic carbon cycling and leads to shifts in the food web and ecological functioning of local communities., Subseabed CO2 storage is considered a future climate change mitigation technology. We investigated the ecological consequences of CO2 leakage for a marine benthic ecosystem. For the first time with a multidisciplinary integrated study, we tested hypotheses derived from a meta-analysis of previous experimental and in situ high-CO2 impact studies. For this, we compared ecological functions of naturally CO2-vented seafloor off the Mediterranean island Panarea (Tyrrhenian Sea, Italy) to those of nonvented sands, with a focus on biogeochemical processes and microbial and faunal community composition. High CO2 fluxes (up to 4 to 7 mol CO2 m−2 hour−1) dissolved all sedimentary carbonate, and comigration of silicate and iron led to local increases of microphytobenthos productivity (+450%) and standing stocks (+300%). Despite the higher food availability, faunal biomass (−80%) and trophic diversity were substantially lower compared to those at the reference site. Bacterial communities were also structurally and functionally affected, most notably in the composition of heterotrophs and microbial sulfate reduction rates (−90%). The observed ecological effects of CO2 leakage on submarine sands were reproduced with medium-term transplant experiments. This study assesses indicators of environmental impact by CO2 leakage and finds that community compositions and important ecological functions are permanently altered under high CO2.