Anna Lichtschlag

Biological and chemical sulfide oxidation in a Beggiatoa inhabited marine sediment

The ecological niche of nitrate-storing Beggiatoa, and their contribution to the removal of sulfide were investigated in coastal sediment. With microsensors a clear suboxic zone of 2–10 cm thick was identified, where neither oxygen nor free sulfide was detectable. In this zone most of the Beggiatoa were found, where they oxidize sulfide with internally stored nitrate. The sulfide input into the suboxic zone was dominated by an upward sulfide flux from deeper sediment, whereas the local production in the suboxic zone was much smaller. Despite their abundance, the calculated sulfide-oxidizing capacity of the Beggiatoa could account for only a small fraction of the total sulfide removal in the sediment. Consequently, most of the sulfide flux into the suboxic layer must have been removed by chemical processes, mainly by precipitation with Fe2+ and oxidation by Fe(III), which was coupled with a pH increase. The free Fe2+ diffusing upwards was oxidized by Mn(IV), resulting in a strong pH decrease. The nitrate storage capacity allows Beggiatoa to migrate randomly up and down in anoxic sediments with an accumulated gliding distance of 4 m before running out of nitrate. We propose that the steep sulfide gradient and corresponding high sulfide flux, a typical characteristic of Beggiatoa habitats, is not needed for their metabolic performance, but rather used as a chemotactic cue by the highly motile filaments to avoid getting lost at depth in the sediment. Indeed sulfide is a repellant for Beggiatoa.

Niche differentiation among mat-forming, sulfide-oxidizing bacteria at cold seeps of the Nile Deep Sea Fan (Eastern Mediterranean Sea)

Sulfidic muds of cold seeps on the Nile Deep Sea Fan (NDSF) are populated by different types of mat-forming sulfide-oxidizing bacteria. The predominant sulfide oxidizers of three different mats were identified by microscopic and phylogenetic analyses as (i) Arcobacter species producing cotton-ball-like sulfur precipitates, (ii) large filamentous sulfur bacteria including Beggiatoa species, and (iii) single, spherical Thiomargarita species. High resolution in situ microprofiles revealed different geochemical settings selecting for the different mat types. Arcobacter mats occurred where oxygen and sulfide overlapped above the seafloor in the bottom water interface. Filamentous sulfide oxidizers were associated with steep gradients of oxygen and sulfide in the sediment. A dense population of Thiomargarita was favored by temporarily changing supplies of oxygen and sulfide in the bottom water. These results indicate that the decisive factors in selecting for different mat-forming bacteria within one deep-sea province are spatial or temporal variations in energy supply. Furthermore, the occurrence of Arcobacter spp.-related 16S rRNA genes in the sediments below all three types of mats, as well as on top of brine lakes of the NDSF, indicates that this group of sulfide oxidizers can switch between different life modes depending on the geobiochemical habitat setting.

Quantification of the effects of ocean acidification on sediment microbial communities in the environment: the importance of ecosystem approaches

To understand how ocean acidification (OA) influences sediment microbial communities, naturally CO2-rich sites are increasingly being used as OA analogues. However, the characterization of these naturally CO2-rich sites is often limited to OA-related variables, neglecting additional environmental variables that may confound OA effects. Here, we used an extensive array of sediment and bottom water parameters to evaluate pH effects on sediment microbial communities at hydrothermal CO2 seeps in Papua New Guinea. The geochemical composition of the sediment pore water showed variations in the hydrothermal signature at seep sites with comparable pH, allowing the identification of sites that may better represent future OA scenarios. At these sites, we detected a 60% shift in the microbial community composition compared with reference sites, mostly related to increases in Chloroflexi sequences. pH was among the factors significantly, yet not mainly, explaining changes in microbial community composition. pH variation may therefore often not be the primary cause of microbial changes when sampling is done along complex environmental gradients. Thus, we recommend an ecosystem approach when assessing OA effects on sediment microbial communities under natural conditions. This will enable a more reliable quantification of OA effects via a reduction of potential confounding effects.

A novel, mat-forming Thiomargarita population associated with a sulfidic fluid flow from a deep-sea mud volcano

A mat-forming population of the giant sulfur bacterium Thiomargarita was discovered at the flank of the mud volcano Amon on the Nile Deep Sea Fan in the Eastern Mediterranean Sea. All cells were of a spherical and vacuolated phenotype and internally stored globules of elemental sulfur. With a diameter of 24-65 µm, Thiomargarita cells from the Eastern Mediterranean were substantially smaller than cells of previously described populations. A 16S rRNA gene fragment was amplified and could be assigned to the Thiomargarita-resembling cells by fluorescence in situ hybridization. This sequence is monophyletic with published Thiomargarita sequences but sequence similarities are only about 94%, indicating a distinct diversification. In the investigated habitat, highly dynamic conditions favour Thiomargarita species over other sulfur-oxidizing bacteria. In contrast to Thiomargarita namibiensis populations, which rely on periodic resuspension from sulfidic sediment into the oxygenated water column, Thiomargarita cells at the Amon mud volcano seem to remain stationary at the sediment surface while environmental conditions change around them due to periodic brine flow.

Hypoxia causes preservation of labile organic matter and changes seafloor microbial community composition (Black Sea)

Hypoxia enhances organic matter preservation in marine sediments by changing benthic communities, bioturbation, and burial rates. Bottom-water oxygen supply is a key factor governing the biogeochemistry and community composition of marine sediments. Whether it also determines carbon burial rates remains controversial. We investigated the effect of varying oxygen concentrations (170 to 0 μM O2) on microbial remineralization of organic matter in seafloor sediments and on community diversity of the northwestern Crimean shelf break. This study shows that 50% more organic matter is preserved in surface sediments exposed to hypoxia compared to oxic bottom waters. Hypoxic conditions inhibit bioturbation and decreased remineralization rates even within short periods of a few days. These conditions led to the accumulation of threefold more phytodetritus pigments within 40 years compared to the oxic zone. Bacterial community structure also differed between oxic, hypoxic, and anoxic zones. Functional groups relevant in the degradation of particulate organic matter, such as Flavobacteriia, Gammaproteobacteria, and Deltaproteobacteria, changed with decreasing oxygenation, and the microbial community of the hypoxic zone took longer to degrade similar amounts of deposited reactive matter. We conclude that hypoxic bottom-water conditions—even on short time scales—substantially increase the preservation potential of organic matter because of the negative effects on benthic fauna and particle mixing and by favoring anaerobic processes, including sulfurization of matter.

Meiobenthos of the Oxic/Anoxic Interface in the Southwestern Region of the Black Sea: Abundance and Taxonomic Composition

The Black Sea contains the World’s largest body of anoxic water. Based on new and published data, we describe trends among selected protozoan and metazoan meiofaunal taxa at water depths of 120–240 m in the northwestern part of the Black Sea near the submarine Dnieper Canyon. This transect spans the transition between increasingly hypoxic but non-sulfidic bottom water and the deeper anoxic/sulfidic zone, the boundary between these two domains being located at approximately 150–180 m depth. This transition zone supports a rich rose-Bengal-stained fauna. Among the protozoans, gromiids are common only at 120 and 130 m. All other groups exhibit more or less distinct abundance maxima near the base of the hypoxic zone. Foraminifera peak sharply at ∼160 m while ciliates are most abundant at 120, 160–190, and 240 m, where they are possibly associated with concentrations of bacterial cells. The three most abundant metazoan taxa also exhibit maxima in the hypoxic zone, the nematodes and polychaetes at 160 m, and the harpacticoid copepods at 150 m. Most of the polychaetes belong to two species, Protodrilus sp. and Vigtorniella zaikai, the larvae of which are widely distributed in severely hypoxic water just above the anoxic/sulfidic zone of the Black Sea. Both protozoans and metazoans are usually concentrated in the 0–1 cm layer of the sediment, except at the shallowest (120–130 m) site where deeper layers may yield a substantial proportion of the assemblage. The concentration of nematodes in the 3–5 cm layer at 120 m is particularly notable. Our data suggest that some benthic species can tolerate anoxic/sulfidic conditions in the Black Sea. An important caveat is that anoxia or severe hypoxia may lead to the corpses of nonindigenous organisms being preserved in our samples. However, we argue that the morphological integrity of specimens, the high population densities (associated with high bacterial concentrations in the case of ciliates), the presence of taxa often found in hypoxic settings, and the presence of all life stages (including gravid females) among nematodes and harpacticoids, suggests that at least some of the organisms are indigenous. Further comparative studies of shallow- and deep-water meiobenthic communities in the Black Sea are necessary in order to establish which species are characteristic and indicative of hypoxic/anoxic conditions.

Distribution and Composition of Thiotrophic Mats in the Hypoxic Zone of the Black Sea (150-170 m Water Depth, Crimea Margin)

At the Black Sea chemocline, oxygen- and sulfide-rich waters meet and form a niche for thiotrophic pelagic bacteria. Here we investigated an area of the Northwestern Black Sea off Crimea close to the shelf break, where the chemocline reaches the seafloor at around 150–170 m water depth, to assess whether thiotrophic bacteria are favored in this zone. Seafloor video transects were carried out with the submersible JAGO covering 20 km2 on the region between 110 and 200 m depth. Around the chemocline we observed irregular seafloor depressions, covered with whitish mats of large filamentous bacteria. These comprised 25–55% of the seafloor, forming a belt of 3 km width around the chemocline. Cores from the mats obtained with JAGO showed higher accumulations of organic matter under the mats compared to mat-free sediments. The mat-forming bacteria were related to Beggiatoa-like large filamentous sulfur bacteria based on 16S rRNA sequences from the mat, and visual characteristics. The microbial community under the mats was significantly different from the surrounding sediments and enriched with taxa affiliated with polymer degrading, fermenting and sulfate reducing microorganisms. Under the mats, higher organic matter accumulation, as well as higher remineralization and radiotracer-based sulfate reduction rates were measured compared to outside the mat. Mat-covered and mat-free sediments showed similar degradability of the bulk organic matter pool, suggesting that the higher sulfide fluxes and subsequent development of the thiotrophic mats in the patches are consequences of the accumulation of organic matter rather than its qualitative composition. Our observations suggest that the key factors for the distribution of thiotrophic mat-forming communities near to the Crimean shelf break are hypoxic conditions that (i) repress grazers, (ii) enhance the accumulation and degradation of labile organic matter by sulfate-reducers, and (iii) favor thiotrophic filamentous bacteria which are adapted to exploit steep gradients in oxygen and sulfide availability; in addition to a specific seafloor topography which may relate to internal waves at the shelf break.

Novel observations of Thiobacterium, a sulfur-storing Gammaproteobacterium producing gelatinous mats

The genus Thiobacterium includes uncultivated rod-shaped microbes containing several spherical grains of elemental sulfur and forming conspicuous gelatinous mats. Owing to the fragility of mats and cells, their 16S ribosomal RNA genes have not been phylogenetically classified. This study examined the occurrence of Thiobacterium mats in three different sulfidic marine habitats: a submerged whale bone, deep-water seafloor and a submarine cave. All three mats contained massive amounts of Thiobacterium cells and were highly enriched in sulfur. Microsensor measurements and other biogeochemistry data suggest chemoautotrophic growth of Thiobacterium. Sulfide and oxygen microprofiles confirmed the dependence of Thiobacterium on hydrogen sulfide as energy source. Fluorescence in situ hybridization indicated that Thiobacterium spp. belong to the Gammaproteobacteria, a class that harbors many mat-forming sulfide-oxidizing bacteria. Further phylogenetic characterization of the mats led to the discovery of an unexpected microbial diversity associated with Thiobacterium.

Best Practice Guidance for Environmental Risk Assessment for offshore CO2 geological storage

Carbon dioxide (CO2) separated from natural gas has been stored successfully below the seabed off Norway for almost two decades. Based on these experiences several demonstration projects supported by the EU and its member states are now setting out to store CO2 captured at power plants in offshore geological formations. The ECO2 project was triggered by these activities and funded by the EU to assess the environmental risks associated with the sub-seabed storage of CO2 and to provide guidance on environmental practices. ECO2 conducted a comprehensive offshore field programme at the Norwegian storage sites Sleipner and Snohvit and at several natural CO2 seepage sites in order to identify potential pathways for CO2 leakage through the overburden, monitor seep sites at the seabed, track and trace the spread of CO2 in ambient bottom waters, and study the response of benthic biota to CO2. ECO2 identified a rich variety of geological structures in the broader vicinity of the storage sites that may have served as conduits for gas release in the geological past and located a seabed fracture and several seeps and abandoned wells where natural gas and formation water are released into the marine environment. Even though leakage may occur if these structures are not avoided during site selection, observations at natural seeps, release experiments, and numerical modelling revealed that the footprint at the seabed where organisms would be impacted by CO2 is small for realistic leakage scenarios. ECO2 conducted additional studies to assess and evaluate the legal framework and the public perception of CO2 storage below the seabed. The following guidelines and recommendations for environmental practices are based on these experiences.

Mineralogical and geochemical analysis of Fe-phases in drill-cores from the Triassic Stuttgart Formation at Ketzin CO2 storage site before CO2 arrival

Abstract Reactive iron (Fe) oxides and sheet silicate-bound Fe in reservoir rocks may affect the subsurface storage of CO2 through several processes by changing the capacity to buffer the acidification by CO2 and the permeability of the reservoir rock: (1) the reduction of three-valent Fe in anoxic environments can lead to an increase in pH, (2) under sulphidic conditions, Fe may drive sulphur cycling and lead to the formation of pyrite, and (3) the leaching of Fe from sheet silicates may affect silicate diagenesis. In order to evaluate the importance of Fe-reduction on the CO2 reservoir, we analysed the Fe geochemistry in drill-cores from the Triassic Stuttgart Formation (Schilfsandstein) recovered from the monitoring well at the CO2 test injection site near Ketzin, Germany. The reservoir rock is a porous, poorly to moderately cohesive fluvial sandstone containing up to 2–4 wt% reactive Fe. Based on a sequential extraction, most Fe falls into the dithionite-extractable Fe-fraction and Fe bound to sheet silicates, whereby some Fe in the dithionite-extractable Fe-fraction may have been leached from illite and smectite. Illite and smectite were detected in core samples by X-ray diffraction and confirmed as the main Fe-containing mineral phases by X-ray absorption spectroscopy. Chlorite is also present, but likely does not contribute much to the high amount of Fe in the silicate-bound fraction. The organic carbon content of the reservoir rock is extremely low (<0.3 wt%), thus likely limiting microbial Fe-reduction or sulphate reduction despite relatively high concentrations of reactive Fe-mineral phases in the reservoir rock and sulphate in the reservoir fluid. Both processes could, however, be fuelled by organic matter that is mobilized by the flow of supercritical CO2 or introduced with the drilling fluid. Over long time periods, a potential way of liberating additional reactive Fe could occur through weathering of silicates due to acidification by CO2.