Description: During Earth’s history, precipitation of calcium carbonate by heterotrophic microbes has substantially contributed to the genesis of copious amounts of carbonate sediment and its subsequent lithification. Previous work identified the microbial sulfur and nitrogen cycle as principal pathways involved in the formation of marine calcium carbonate deposits. While substantial knowledge exists for the importance of the sulfur cycle, specifically sulfate reduction, with regard to carbonate formation, information about carbonate genesis connected to the microbial nitrogen cycle is dissatisfactory. In addition to the established pathways for carbonate mineral formation, also the potential of microbial carbonic anhydrase, a carbonate-relevant, zinc-containing enzyme, is receiving currently increased attention. However, also in this field knowledge is scarce and fragmentary. Here we demonstrate microbial carbonate precipitation as a direct result of the interplay between the microbial nitrogen cycle and a microbially produced enzyme. Using Alcanivorax borkumensis as a model organism, our experiments depict precipitation of a peloidal carbonate matrix within days to weeks, induced by simultaneous ammonification and extracellular carbonic anhydrase activity. The precipitates show similar morphology, mineralogy, δ44/40Ca, and δ88/86Sr to analogs of modern carbonate peloids. The obtained Sr/Ca partition coefficient DSr showed no clear deviation from inorganic carbonate phases, indicating that microbially mediated carbonate precipitation, indeed, follows the principles of physico-chemical precipitation. The observed relative enrichment of the precipitates in zinc might help to constrain zinc variations in natural carbonate archives. Our study demonstrates that ammonification, due to intense microbial organic matter degradation, and carbonic anhydrase may play a substantial role for calcium carbonate precipitation in paleo- and recent shallow marine environments.

Description: The earliest diagenetic post-mortem exposure of biogenic carbonates at the sea floor and in the uppermost sediment column results in the colonization of hard-part surfaces by bacterial communities. Some of the metabolic redox processes related to these communities have the potential to alter carbonate shell properties, and hence affect earliest diagenetic pathways with significant consequences for archive data. During a three-month in vitro study, shell subsamples of the ocean quahog Arctica islandica (Linnaeus, 1767) were incubated in natural anoxic sediment slurries and bacterial culture medium of the heterotrophic Shewanella sediminisHAW-EB3. Bulk analyses of the liquid media from the Shewanella sediminis incubation revealed an over ten-fold increase in total alkalinity, dissolved inorganic carbon and ΩAragonite, and the alteration of the Mg/Ca, Mg/Sr and Sr/Ca ratios relative to control incubations without cultures. Ion ratios were most affected in the incubation with anoxic sediment, depicting a 25% decrease in Mg/Ca relative to the control. Shell sample surfaces that were exposed to both incubations displayed visible surface dissolution features, and an 8 wt% loss in calcium content. No such alteration features were detected in control shells. Apparently, alteration of shell carbonate properties was induced by microbially driven decomposition of shell intercrystalline organic constituents and subsequent opening of pathways for pore fluid-crystal exchange. This study illustrates the potential influence of benthic bacterial metabolism on biogenic carbonate archives during the initial stages of diagenetic alteration within a relatively short experimental duration of only three months. These results suggest that foremost the biological effect of bacterial cation adsorption on divalent cation ratios has the potential to complicate proxy interpretation. Results shown here highlight the necessity to consider bacterial metabolic activities in marine sediments for the interpretation of palaeo-environmental proxies from shell carbonate archives.

Description: Highlights • A new bentho-pelagic transport mechanism of microorganisms is hypothesized • A bubble transport hypothesis was tested using a new gas bubble-collecting device • Bubble-mediated transport rate of methanotrophs was quantified at a gas vent • The Bubble Transport Mechanism may influence the pelagic methane sink Abstract The importance of methanotrophic microorganisms in the sediment and water column for balancing marine methane budgets is well accepted. However, whether methanotrophic populations are distinct for benthic and pelagic environments or are the result of exchange processes between the two, remains an area of active research. We conducted a field pilot study at the Rostocker Seep site (Coal Oil Point seep field, offshore California, USA) to test the hypothesis that bubble-mediated transport of methane-oxidizing microorganisms from the sediment into the water column is quantifiable. Measurements included dissolved methane concentration and showed a strong influence of methane seepage on the water-column methane distribution with strongly elevated sea surface concentrations with respect to atmospheric equilibrium (saturation ratio ~17,000%). Using Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD FISH) analysis, aerobic methane oxidizing bacteria (MOB) were detected in the sediment and the water column, whereas anaerobic methanotrophs (ANME-2) were detected exclusively in the sediment. Critical data for testing the hypothesis were collected using a novel bubble catcher that trapped naturally emanating seep gas bubbles and any attached particles approximately 15 cm above the seafloor. Bubble catcher experiments were carried out directly above a natural bubble seep vent and at a nearby reference site, for which an “engineered” nitrogen bubble vent without sediment contact was created. Our experiments indicate the existence of a “Bubble Transport Mechanism”, which transports MOB from the sediment into the water column. In contrast, ANME-2 were not detected in the bubble catcher. The Bubble Transport Mechanism could have important implications for the connectivity between benthic and pelagic methanotrophic communities at methane seep sites.

Description: Highlights • High abundance of active anaerobic methanotrophs in sediments of the blowout crater suggests adaptation to methane seepage within at most two decades. • Fast exchange processes in permeable surface sediments prevent sulfate depletion and probably methane-derived carbonate precipitation. • Methane seepage impacts isotopic and assemblage composition of benthic foraminifera. Abstract Methane emissions from marine sediments are partly controlled by microbial anaerobic oxidation of methane (AOM). AOM provides a long-term sink for carbon through precipitation of methane-derived authigenic carbonates (MDAC). Estimates on the adaptation time of this benthic methane filter as well as on the establishment of related processes and communities after an onset of methane seepage are rare. In the North Sea, considerable amounts of methane have been released since 20 years from a man-made gas blowout offering an ideal natural laboratory to study the effects of methane seepage on initially “pristine” sediment. Sediment cores were taken from the blowout crater and a reference site (50 m distance) in 2011 and 2012, respectively, to investigate porewater chemistry, the AOM community and activity, the presence of authigenic carbonates, and benthic foraminiferal assemblages. Potential AOM activity (up to 3060 nmol cm−3 sediment d−1 or 375 mmol m−2 d−1) was detected only in the blowout crater up to the maximum sampling depth of 18 cm. CARD-FISH analyzes suggest that monospecific ANME-2 aggregates were the only type of AOM organisms present, showing densities (up to 2.2*107 aggregates cm−3) similar to established methane seeps. No evidence for recent MDAC formation was found using stable isotope analyzes (δ13C and δ18O). In contrast, the carbon isotopic signature of methane was recorded by the epibenthic foraminifer Cibicides lobatulus (δ13C −0.66‰). Surprisingly, the foraminiferal assemblage in the blowout crater was dominated by Cibicides and other species commonly found in the Norwegian Channel and fjords, indicating that these organisms have responded sensitively to the specific environmental conditions at the blowout. The high activity and abundance of AOM organisms only at the blowout site suggests adaptation to a strong increase in methane flux in the order of at most two decades. High gas discharge dynamics in permeable surface sediments facilitate fast sulfate replenishing and stimulation of AOM. The accompanied prevention of total alkalinity build-up in the porewater thereby appears to inhibit the formation of substantial methane-derived authigenic carbonate at least within the given time window.

Description: Methane hydrate is an icelike substance that is stable at high pressure and low temperature in continental margin sediments. Since the discovery of a large number of gas flares at the landward termination of the gas hydrate stability zone off Svalbard, there has been concern that warming bottom waters have started to dissociate large amounts of gas hydrate and that the resulting methane release may possibly accelerate global warming. Here, we can corroborate that hydrates play a role in the observed seepage of gas, but we present evidence that seepage off Svalbard has been ongoing for at least three thousand years and that seasonal fluctuations of 1-2°C in the bottom-water temperature cause periodic gas hydrate formation and dissociation, which focus seepage at the observed sites.

Description: Microbial aerobic methane oxidation (MOx) is intrinsically coupled to the production of carbon dioxide, favoring carbonate dissolution. Recently, microbial organic polymers were shown to be able to induce carbonate dissolution. To discriminate between different mechanisms causing calcite dissolution, experiments were conducted in the presence of solid calcite with (1) actively growing cells (2) starving cells, and (4) dead cells of the methanotrophic bacterium Methylosinus trichosporium under brackish conditions (salinity 10) near calcite saturation (saturation state (Ω) 1.76 to 2.22). Total alkalinity and the amount of dissolved calcium markedly increased in all experiments containing M. trichosporium cells. After initial system equilibration, similar calcite dissolution rates, ranging between 14.9 (dead cells) and 29.6 μmol l−1 d−1 (actively growing cells), were observed. While concentrations of transparent exopolymer particles declined with time in the presence of actively growing and starving cells, they increased in experiments with dead cells. Scanning electron microscopy images of calcite crystals revealed visible surface corrosion after exposure to live and dead M. trichosporium cells. The results of this study indicate a strong potential for microbial MOx to affect calcite stability negatively, facilitating calcite dissolution. In addition to CO2 production by methanotrophically active cells, we suggest that the release of acidic or Ca2+-chelating organic carbon compounds from dead cells could also enhance calcite dissolution.

Description: Highlights: • The Giant Gjallar Vent is still active in terms of fluid migration and faulting. • The Base Pleistocene Unconformity acts as a seal to upward fluid migration. • Seal bypass in at least one location leads to a new phase of fluid venting. The Giant Gjallar Vent (GGV), located in the Vøring Basin off mid-Norway, is one of the largest (~ 5 × 3 km) vent systems in the North Atlantic. The vent represents a reactivated former hydrothermal system that formed at about 56 Ma. It is fed by two pipes of 440 m and 480 m diameter that extend from the Lower Eocene section up to the Base Pleistocene Unconformity (BPU). Previous studies based on 3D seismic data differ in their interpretations of the present activity of the GGV, describing the system as buried and as reactivated in the Upper Pliocene. We present a new interpretation of the GGV’s reactivation, using high-resolution 2D seismic and Parasound data. Despite the absence of geochemical and hydroacoustic indications for fluid escape into the water column, the GGV appears to be active because of various seismic anomalies which we interpret to indicate the presence of free gas in the subsurface. The anomalies are confined to the Kai Formation beneath the BPU and the overlying Naust Formation, which are interpreted to act as a seal to upward fluid migration. The seal is breached by focused fluid migration at one location where an up to 100 m wide chimney-like anomaly extends from the BPU up to the seafloor. We propose that further overpressure build-up in response to sediment loading and continued gas ascent beneath the BPU will eventually lead to large-scale seal bypass, starting a new phase of venting at the GGV.

Description: Sulfate-reducing bacteria are known to mediate dolomite formation under hypersaline conditions, but details of the crystal nucleation process are still poorly constrained. Our laboratory study demonstrates for the first time that Desulfobulbus mediterraneus, a marine sulfate-reducing bacterium, mediates primary precipitation of Mg-rich dolomite under anoxic conditions in media replicating modern seawater chemistry at low temperature (21 °C). Precipitation of crystals was associated with extracellular polymeric substances in a monospecific biofilm, providing templates for nucleation by altering the molar Mg/Ca ratio. After initial nucleation of single nanospherulites (∼50 nm), growth was mediated by aggregation, resulting in spherulites of ∼2–3 μm in diameter. Nucleation led to differences in Mg/Ca ratios and δ44/40Ca values among the organic material (i.e., biofilm including cells and extracellular polymeric substances; 0.87 ± 0.01 [2 SD] and 0.48‰ ± 0.11‰ [2 SE], respectively), the crystals (1.02 ± 0.11 [2 SD] and 〈−0.08‰ ± 0.24‰ [2 SE], respectively), and the liquid bulk medium after mineral precipitation (4.53 ± 0.04 [2 SD] and 1.10‰ ± 0.24‰ [2 SE], respectively). These data indicate a two-step fractionation process involved in the sequestration of Ca from the solution into the crystal lattice of the mineral precipitated. Our results demonstrate the capability of extracellular polymeric substances to overcome kinetic inhibition, fostering the formation of kinetically less favorable Mg-rich dolomite, and they also question the applicability of the Ca isotopic system as a proxy for paleogeochemistry of seawater.

Description: Subduction of the oceanic Cocos plate offshore Costa Rica causes strong advection of methane-charged fluids. Presented here are the first direct measurements of microbial anaerobic oxidation of methane (AOM) and sulfate reduction (SR) rates in sediments from the two mounds, applying radiotracer techniques in combination with numerical modeling. In addition, analysis of carbonate δ18O, δ13C, and 87Sr / 86Sr signatures constrain the origin of the carbonate-precipitating fluid. Average rates of microbial activities showed differences with a factor of 4.8 to 6.3 between Mound 11 [AOM 140.71 (±40.84 SD); SR 117.25 (±82.06 SD) mmol m−2 d−1, respectively] and Mound 12 [AOM 22.37 (±0.85 SD); SR 23.99 (±5.79 SD) mmol m−2 d−1, respectively]. Modeling results yielded flow velocities of 50 cm a−1 at Mound 11 and 8–15 cm a−1 at Mound 12. Analysis of oxygen and carbon isotope variations of authigenic carbonates from the two locations revealed higher values for Mound 11 (δ18O: 4.7 to 5.9‰, δ13C: −21.0 to −29.6‰), compared to Mound 12 (δ18O: 4.1 to 4.5‰, δ13C: −45.7 to −48.9‰). Analysis of carbonates 87Sr / 86Sr indicated temporal changes of deep-source fluid admixture at Mound 12. The present study is in accordance with previous work supporting considerable differences of methane flux between the two Mounds. It also strengthens the hypothesis of a predominantly deep fluid source for Mound 11 versus a rather shallow source of biogenic methane for Mound 12. The results demonstrate that methane-driven microbial activity is a valid ground truthing tool for geophysical measurements of fluid advection and constraining of recent methane fluxes in the study area. The study further shows that the combination of microbial rate measurements, numerical modeling, and authigenic carbonate analysis provide a suitable approach to constrain temporal and spatial variations of methane charged fluid flow at the Pacific Costa Rican margin.

Description: Two ∼6 m long sediment cores were collected along the ∼300 m isobath on the Alaskan Beaufort Sea continental margin. Both cores showed distinct sulfate-methane transition zones (SMTZ) at 105 and 120 cm below seafloor (cmbsf). Sulfate was not completely depleted below the SMTZ but remained between 30 and 500 μM. Sulfate reduction and anaerobic oxidation of methane (AOM) determined by radiotracer incubations were active throughout the methanogenic zone. Although a mass balance could not explain the source of sulfate below the SMTZ, geochemical profiles and correlation network analyses of biotic and abiotic data suggest a cryptic sulfur cycle involving iron, manganese and barite. Inhibition experiments with molybdate and 2-bromoethanesulfonate (BES) indicated decoupling of sulfate reduction and AOM and competition between sulfate reducers and methanogens for substrates. While correlation network analyses predicted coupling of AOM to iron reduction, the addition of manganese or iron did not stimulate AOM. Since none of the classical archaeal anaerobic methanotrophs (ANME) were abundant, the involvement of unknown or unconventional phylotypes in AOM is conceivable. The resistance of AOM activity to inhibitors implies deviation from conventional enzymatic pathways. This work suggests that the classical redox cascade of electron acceptor utilization based on Gibbs energy yields does not always hold in diffusion-dominated systems, and instead biotic processes may be more strongly coupled to mineralogy.