Microbial processes and element cycling from micro- to meso-scale : from single cells and aggregates to the whole water column perspective.

Microorganisms are important drivers of the carbon, nitrogen, and sulfur cycles on earth. They can adapt to various substrates and, thus, inhabit ecological niches too extreme for higher lifeforms, such as sub- and anoxic or even sulfidic waters. They follow a wide range of ecological strategies with variable levels of specialization to their environment. In the highly stratified water column of the Baltic Sea, respiration of organic matter in combination with sluggish ventilation causes the formation of anoxic zones. Here, organic material is decomposed anaerobically, which leads to the increased production of hydrogen sulfide – a highly toxic compound for higher lifeforms (e.g. multicellular organisms). The transition zone between sulfidic and suboxic conditions, the redox zone, is inhabited by two chemolithoautotrophic key organisms, both with the same ability to detoxify hydrogen sulfide via oxidation with nitrate. Interestingly, both organisms show an overlapping abundance. While the gammaproteobacterial SUP05 clade is most abundant in the suboxic zone, the epsilonproteobacterial Sulfurimonas GD17 subgroup dominates the sulfidic zone. This led to the question of how these two organisms can survive within the same habitat although they exhibit the same substrate requirements. In Paper I, I coupled phylogenetic identification with single-cell uptake measurements of SUP05 and Sulfurimonas GD17 in environmental samples from the Gotland Deep redox zone. I was able to identify niche separation due to different substrate utilization strategies: SUP05 is streamlined, non-motile, and slowly utilizing; essentially a K-strategist, adapted to low substrate conditions and omnipresent in most of the oxygen minimum zones worldwide. In contrast, Sulfurimonas GD17 is a fast utilizing r-strategist, specialized for high and fluctuating substrate conditions, which uses chemotactic behavior to move into regions of favorable substrate conditions. Together they drive a highly efficient detoxification machinery in the Baltic Sea redox zone. Remarkable microbial strategies which influence matter cycling can be found in other pelagic environments as well. Sinking particles are considered an important potential habitat for pelagic microorganisms due to their substrate richness and structural heterogeneity, as well as their omnipresence in the world oceans. Within individual porous particles, it is theorized that innumerable redox gradients should exist at the microscale, whose attributes in aggregate would drive and control significant elemental fluxes globally. However, marine particles still represent a major black box in microbial ecology due to their fragile nature, which makes them inaccessible for detailed micro-scale observations. Therefore, I present in Paper II a cryogel-based embedding and slicing approach, which enables detailed microscopic investigations of the microbial community within the intact particle structure. The approach is compatible with most structural and phylogenetic staining protocols, such as for different extracellular exopolymers and microbial identification using various fluorescent in situhybridization (FISH) protocols. It also allows the three-dimensional reconstruction of whole aggregates as well as precise porosity calculations and is, moreover, applicable to sediment traps for undisturbed in situ samplings. As Paper I clearly illustrates, cellular abundance and species distribution must be accompanied by cellular activity measurements to fully describe an organism’s ecological role. In Paper III, I therefore present an optimized embedding and slicing method based on soft and hard plastic resins, which enables single-cell uptake measurements using modern nano-scale secondary ion mass spectrometer (NanoSIMS) measurements across the complex microzone structures of marine particles. Embedded specimens were characterized by low outgassing and ablation properties within the ultra-high vacuum chamber (i.e. good conditions for NanoSIMS), but high secondary ion yields. Moreover, critical aspects of cellular biogeochemistry, such as the potential use of alternative electron acceptors by microorganisms, could be identified within particles for the first time, visible as 34S and 15N enrichments from stable isotope labelled sulfate and nitrate in single cells. Staining properties for structural compounds similar to those in Paper II, enabled three-dimensional reconstruction and porosity calculations as well. The combination of both methods presented in Paper II and Paper III opens up new ways to investigate the microbial ecology and their interaction with the particle structure in terms of phylogeny and activity. The influence of the particle-associated microbial community on matter cycling at larger scales depends both on particle structure (above) and on particle abundance and distribution in the water column. To scale up results measured by the methods developed above, we need to identify and measure the distributions of fragile particles at high vertical resolution, without physical distortion. In Paper IV, I present a coupled study of optical particle quantification, physical particle characterization, as well as molecular sequencing in the region of Fram Strait. Calculated particle sinking trajectories and microbial genetic source tracking revealed a strong vertical connectivity between the observed microbial communities. This connectivity was most pronounced in areas with sea ice coverage, where almost half of the particle-associated communities in the deep sea were linked to surface-derived microbes. In turn, it could be concluded that further sea ice decline in the Arctic Ocean may reduce vertical microbial connectivity, which possibly alters current biogeochemical cycling. This study exemplifies the huge potential of optical quantification coupled to microbiological and molecular methods for multiscale particle investigations. The abundance and sinking behavior of particles are highly influenced by biological processes, including microbial degradation and remineralization, as well as grazing and repackaging by zooplankton. However, physical forcing, particularly on the sub-meso and mesoscale, critically shape particle distributions in the water column. In Paper V, I present a combined investigation of optical particle counting and classification as well as Acoustic Doppler Current Profiler (ADCP) based current velocity measurements in a cyclonic eddy of the South Atlantic. I observed vertical propagation of presumably wind-driven inertial wave energy following the vorticity field at the eddy perimeter, a process known as ‘inertial chimney’ effect. The resulting zone of increased horizontal shear in the upper 1500 m caused increased upward vertical nutrient flux, supporting enhanced primary production and intensified particle formation in surface eddy. I could show that particles > 0.5 mm in diameter generally followed the relative vorticity field, leading to a sub-surface V-shape of the particle distribution that has not previously been observed. Repackaging and fragmentation by copepods in combination with low carbon-specific degradation led to a threefold increased carbon flux to the deep sea in the center of the eddy. I concluded that cyclonic eddies must regularly cause increased deep carbon export events, in the oligotrophic South Atlantic gyre, and globally. Global matter cycles, including entire pelagic food webs, are affected by the microbial dynamics of sinking particles. These, in turn, are shaped by a wide variety of physical and biological processes ranging from the microscale to mesoscale. Sinking particles and their complex communities thus represent a biogeochemical link between small- and large-scale processes. My work highlights how the global impacts of particle-associated microbial communities can only be understood through investigations using interdisciplinary approaches at multiple scales. In my thesis, I used cutting-edge methodologies to investigate microbial processes at the micro-scale, and built strategies to integrate these processes into a broader understanding of microbial dynamics at oceanographic scales of relevance to the global ocean

Combining Field and Imaging Spectroscopy to Map Soil Organic Carbon in a Semiarid Environment

Semiarid regions are especially vulnerable to climate change and human-induced land-use changes and are of major importance in the context of necessary carbon sequestration and ongoing land degradation. Topsoil properties, such as soil carbon content, provide valuable indicators to these processes, and can be mapped using imaging spectroscopy (IS). In semiarid regions, this poses difficulties because models are needed that can cope with varying land surface and soil conditions, consider a partial vegetation coverage, and deal with usually low soil organic carbon (SOC) contents. We present an approach that aims at addressing these difficulties by using a combination of field and IS to map SOC in an extensively used semiarid ecosystem. In hyperspectral imagery of the HyMap sensor, the influence of nonsoil materials, i.e., vegetation, on the spectral signature of soil dominated image pixels was reduced and a residual soil signature was calculated. The proposed approach allowed this procedure up to a vegetation coverage of 40% clearly extending the mapping capability. SOC quantities are predicted by applying a spectral feature-based SOC prediction model to image data of residual soil spectra. With this approach, we could significantly increase the spatial extent for which SOC could be predicted with a minimal influence of a vegetation signal compared to previous approaches where the considered area was limited to a maximum of, e.g., 10% vegetation coverage. As a regional example, the approach was applied to a 320 km2 area in the Albany Thicket Biome, South Africa, where land cover and landuse changes have occurred due to decades of unsustainable land management. In the generated maps, spatial SOC patterns were interpreted and linked to geomorphic features and land surface processes, i.e., areas of soil erosion. It was found that the chosen approach supported the extraction of soil-related spectral image information in the semiarid region with highly varying land cover. However, the quantitative prediction of SOC contents revealed a lack in absolute accuracy

Combining Field and Imaging Spectroscopy to Map Soil Organic Carbon in a Semiarid Environment

Semiarid regions are especially vulnerable to climate change and human-induced land-use changes and are of major importance in the context of necessary carbon sequestration and ongoing land degradation. Topsoil properties, such as soil carbon content, provide valuable indicators to these processes, and can be mapped using imaging spectroscopy (IS). In semiarid regions, this poses difficulties because models are needed that can cope with varying land surface and soil conditions, consider a partial vegetation coverage, and deal with usually low soil organic carbon (SOC) contents. We present an approach that aims at addressing these difficulties by using a combination of field and IS to map SOC in an extensively used semiarid ecosystem. In hyperspectral imagery of the HyMap sensor, the influence of nonsoil materials, i.e., vegetation, on the spectral signature of soil dominated image pixels was reduced and a residual soil signature was calculated. The proposed approach allowed this procedure up to a vegetation coverage of 40% clearly extending the mapping capability. SOC quantities are predicted by applying a spectral feature-based SOC prediction model to image data of residual soil spectra. With this approach, we could significantly increase the spatial extent for which SOC could be predicted with a minimal influence of a vegetation signal compared to previous approaches where the considered area was limited to a maximum of, e.g., 10% vegetation coverage. As a regional example, the approach was applied to a 320 km2 area in the Albany Thicket Biome, South Africa, where land cover and landuse changes have occurred due to decades of unsustainable land management. In the generated maps, spatial SOC patterns were interpreted and linked to geomorphic features and land surface processes, i.e., areas of soil erosion. It was found that the chosen approach supported the extraction of soil-related spectral image information in the semiarid region with highly varying land cover. However, the quantitative prediction of SOC contents revealed a lack in absolute accuracy

Turbulent mixing and the formation of an intermediate nepheloid layer above the Siberian continental shelf break

Intermediate nepheloid layers (INLs) form important pathways for the cross-slope transport and vertical export of particulate matter, including carbon. While intermediate maxima in particle settling fluxes have been reported in the Eurasian Basin of the Arctic Ocean, direct observations of turbid INLs above the continental slope are still lacking. In this study, we provide the first direct evidence of an INL, coinciding with enhanced mid-water turbulent dissipation rates, over the Laptev Sea continental slope in summer 2018. Current velocity data show a period of enhanced downslope flow with depressed isopcynals, suggesting that the enhanced turbulent dissipation is probably the consequence of the presence of an unsteady lee wave. Similar events occur mostly during ice free periods, suggesting an increasing frequency of episodic cross-slope particle transport in the future. The discovery of the INL and the episodic generation mechanism provide new insights into particle transport dynamics in this rapidly changing environment

Evaluating higher education teaching performance using combined analytic hierarchy process and data envelopment analysis

Evaluating higher education teaching performance is complex as it involves consideration of both objective and subjective criteria. The student evaluation of teaching (SET) is used to improve higher education quality. However, the traditional approaches to considering students’ responses to SET questionnaires for improving teaching quality have several shortcomings. This study proposes an integrated approach to higher education teaching evaluation that combines the analytical hierarchy process (AHP) and data envelopment analysis (DEA). The AHP allows consideration of the varying importance of each criterion of teaching performance, while DEA enables the comparison of tutors on teaching as perceived by students with a view to identifying the scope for improvement by each tutor. The proposed teaching evaluation method is illustrated using data from a higher education institution in Greece

Publisher Correction: Carbon dioxide sink in the Arctic Ocean from cross-shelf transport of dense Barents Sea water

In the version of this article initially published, author Cora Hörstmann was wrongly listed with a second affiliation with the Department of Ecoscience–Applied Marine Ecology and Modelling, Aarhus University rather than the Mediterranean Institute of Oceanography (MIO), Marseille, France. Furthermore, references 83–97, now found in the Supplementary Tables caption, were wrongly cited in the Data Availability section. The errors have been corrected in the HTML and PDF versions of the article

A vast icefish breeding colony discovered in the Antarctic

A breeding colony of notothenioid icefish (Neopagetopsis ionah, Nybelin 1947) of globally unprecedented extent has been discovered in the southern Weddell Sea, Antarctica. The colony was estimated to cover at least �240 km2 of the eastern flank of the Filchner Trough, comprised of fish nests at a density of 0.26 nests per square meter, representing an estimated total of �60 million active nests and associated fish biomass of >60,000 tonnes. The majority of nests were each occupied by 1 adult fish guarding 1,735 eggs (±433 SD). Bot- tom water temperatures measured across the nesting colony were up to 2�C warmer than the surrounding bottom waters, indicating a spatial correlation between the modified Warm Deep Water (mWDW) upflow onto the Weddell Shelf and the active nesting area. Historical and concurrently collected seal movement data indicate that this concentrated fish biomass may be utilized by predators such as Weddell seals (Lep- tonychotes weddellii, Lesson 1826). Numerous degraded fish carcasses within and near the nesting colony suggest that, in death as well as life, these fish provide input for local food webs and influence local biogeo- chemical processing. To our knowledge, the area surveyed harbors the most spatially expansive continuous fish breeding colony discovered to date globally at any depth, as well as an exceptionally high Antarctic sea- floor biomass. This discovery provides support for the establishment of a regional marine protected area in the Southern Ocean under the Convention on the Conservation of Antarctic Marine Living Resources (CCAMLR) umbrella

Global Distribution of Zooplankton Biomass Estimated by In Situ Imaging and Machine Learning

Zooplankton plays a major role in ocean food webs and biogeochemical cycles, and provides major ecosystem services as a main driver of the biological carbon pump and in sustaining fish communities. Zooplankton is also sensitive to its environment and reacts to its changes. To better understand the importance of zooplankton, and to inform prognostic models that try to represent them, spatially-resolved biomass estimates of key plankton taxa are desirable. In this study we predict, for the first time, the global biomass distribution of 19 zooplankton taxa (1-50 mm Equivalent Spherical Diameter) using observations with the Underwater Vision Profiler 5, a quantitative in situ imaging instrument. After classification of 466,872 organisms from more than 3,549 profiles (0-500 m) obtained between 2008 and 2019 throughout the globe, we estimated their individual biovolumes and converted them to biomass using taxa-specific conversion factors. We then associated these biomass estimates with climatologies of environmental variables (temperature, salinity, oxygen, etc.), to build habitat models using boosted regression trees. The results reveal maximal zooplankton biomass values around 60 degrees N and 55 degrees S as well as minimal values around the oceanic gyres. An increased zooplankton biomass is also predicted for the equator. Global integrated biomass (0-500 m) was estimated at 0.403 PgC. It was largely dominated by Copepoda (35.7%, mostly in polar regions), followed by Eumalacostraca (26.6%) Rhizaria (16.4%, mostly in the intertropical convergence zone). The machine learning approach used here is sensitive to the size of the training set and generates reliable predictions for abundant groups such as Copepoda (R2 approximate to 20-66%) but not for rare ones (Ctenophora, Cnidaria, R2 < 5%). Still, this study offers a first protocol to estimate global, spatially resolved zooplankton biomass and community composition from in situ imaging observations of individual organisms. The underlying dataset covers a period of 10 years while approaches that rely on net samples utilized datasets gathered since the 1960s. Increased use of digital imaging approaches should enable us to obtain zooplankton biomass distribution estimates at basin to global scales in shorter time frames in the future

Retinal Microcirculation as a Correlate of a Systemic Capillary Impairment After Severe Acute Respiratory Syndrome Coronavirus 2 Infection

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), affects the pulmonary systems via angiotensin-converting enzyme-2 (ACE-2) receptor, being an entry to systemic infection. As COVID-19 disease features ACE-2 deficiency, a link to microcirculation is proposed. Optical coherence tomography angiography (OCT-A) enables non-invasive analysis of retinal microvasculature. Thus, an impaired systemic microcirculation might be mapped on retinal capillary system. As recent OCT-A studies, analyzing microcirculation in two subdivided layers, yielded contrary results, an increased subdivision of retinal microvasculature might offer an even more fine analysis. The aim of the study was to investigate retinal microcirculation by OCT-A after COVID-19 infection in three subdivided layers (I). In addition, short-term retinal affections were monitored during COVID-19 disease (II). Considering (I), a prospective study (33 patientspost−COVID and 28 controls) was done. Macula and peripapillary vessel density (VD) were scanned with the Spectralis II. Macula VD was measured in three layers: superficial vascular plexus (SVP), intermediate capillary plexus (ICP), and deep capillary plexus (DCP). Analysis was done by the EA-Tool, including an Anatomical Positioning System and an analysis of peripapillary VD by implementing Bruch's membrane opening (BMO) landmarks. Overall, circular (c1, c2, and c3) and sectorial VD (s1-s12) was analyzed. Considering (II), in a retrospective study, 29 patients with severe complications of COVID-19 infection, hospitalized at the intensive care unit, were monitored for retinal findings at bedside during hospitalization. (I) Overall (p = 0.0133) and circular (c1, p = 0.00257; c2, p = 0.0067; and c3, p = 0.0345). VD of the ICP was significantly reduced between patientspost−COVID and controls, respectively. Overall (p = 0.0179) and circular (c1, p = 0.0189) peripapillary VD was significantly reduced between both groups. Subgroup analysis of hospitalized vs. non-hospitalized patientspost−COVID yielded a significantly reduced VD of adjacent layers (DCP and SVP) with increased severity of COVID-19 disease. Clinical severity parameters showed a negative correlation with VD (ICP) and peripapillary VD. (II) Funduscopy yielded retinal hemorrhages and cotton wool spots in 17% of patients during SARS-CoV-2 infection. As VD of the ICP and peripapillary regions was significantly reduced after COVID-19 disease and showed a link to clinical severity markers, we assume that the severity of capillary impairment after COVID-19 infection is mapped on retinal microcirculation, visualized by non-invasive OCT-A