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: 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: Many biological seep studies focused on the distribution, structure, nutrition and food web architecture of seep communities as well as on their interaction with the seep geochemistry. However, overall respiration at cold seeps received only little attention. We conducted in-situ oxygen flux measurements in combination with ex-situ oxygen micro-profiles, respiration measurements, as well as rate determinations of microbial methane and sulfate turnover to assess respiration pathways as well as carbon turnover at a seep habitat that was recently discovered alongside the Hikurangi Margin offshore northern New Zealand. This habitat is dominated by dense beds of tube-building, heterotrophic ampharetid polychaetes. Average total oxygen uptake (TOU) from this habitat was very high (83.7 mmol m− 2 day− 1). TOU at a non-seep reference site ranged between 2.7 and 5.8 mmol m− 2 day− 1. About 37% (30.8 mmol m− 2 day− 1) of the average TOU was consumed by ampharetids. Considering mean diffusive oxygen uptake (8.5 mmol m− 2 day− 1) the remaining fraction of ~ 53% of the TOU (44.4 mmol m− 2 day− 1) might be explained by respiration of epibenthic organisms as well as aerobic methane and sulfide oxidation at the sediment–water interface. The strongly negative carbon isotopic signatures (− 52.9 ± 5‰ VPDB) of the ampharetid tissues indicate a methane derived diet. However, carbon production via anaerobic oxidation of methane (AOM) was too low (0.1 mmol C m− 2 day− 1) to cover the mean carbon demand of the ampharetid communities (21 mmol C m− 2 day− 1). Likely, organic carbon generated via aerobic methane oxidation represents their major carbon source. This is in contrast to other seep habitats, where energy bound in methane is partly transferred to sulfide via AOM and finally consumed by sulfide-oxidizing chemoautotrophs providing carbon that subsequently enters the benthic food web.

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.

Description: Gulf of Mexico cold seeps characterized by variable compositions and magnitudes of hydrocarbon seepage were sampled in order to investigate the effects of natural oils, methane, and non-methane hydrocarbons on microbial activity, diversity, and distribution in seafloor sediments. Though some sediments were characterized by relatively high quantities of oil, which may be toxic to some microorganisms, high rates of sulfate reduction (SR, 27.9714.7 mmol m2 d1), anaerobic oxidation of methane (AOM, 16.276.7 mmol m2 d1), and acetate oxidation (2.7470.76 mmol m2 d1) were observed in radiotracer measurements. In many instances, the SR rate was higher than the AOM rate, indicating that non-methane hydrocarbons fueled SR. Analysis of 16S rRNA gene clone libraries revealed phylogenetically diverse communities that were dominated by phylotypes of sulfate-reducing bacteria (SRB) and anaerobic methanotrophs of the ANME-1 and ANME-2 varieties. Another group of archaea form a Gulf of Mexico-specific clade (GOM ARC2) that may be important in brine-influenced, oil-impacted sediments from deeper water. Additionally, species grouping within the uncultivated Deltaproteobacteria clades SEEP-SRB3 and -SRB4, as well as relatives of Desulfobacterium anilini, were observed in relatively higher abundance in the oil-impacted sediments, suggesting that these groups of SRB may be involved in or influenced by degradation of higher hydrocarbons or petroleum byproducts.

Description: Highlights • Fatty acids preserved in an Oligocene whale bone were analysed. • The fatty acid content of the fossil was in the permil range vs. a recent whale vertebra. • Ca. 80% of the n-C16 and n-C18 alkyl moieties were extractable, ca. 20% being bound to kerogen. • Endogenous fatty acids were largely of microbial origin (sulfate reducers, actinobacteria). Abstract The taphonomic and diagenetic processes by which organic substances are preserved in animal remains are not completely known and the originality of putative metazoan biomolecules in fossil samples is a matter of scientific discussion. Here we report on biomarker information preserved in a fossil whale bone from an Oligocene phosphatic limestone (El Cien Fm., Mexico), with a focus on fatty acyl compounds. Extracts were quantitatively analysed using gas chromatography–mass spectrometry (GC–MS) and, to identify macromolecular-linked remains, demineralised extraction residues were subjected to catalytic hydropyrolysis (HyPy). To better recognise potential authentic (i.e. animal-derived) lipids, the data from the ancient bone were compared with those obtained from (i) the adjacent host sediment of the fossil and (ii) a recent whale (Phocoena phocoena) vertebra. In addition, the spatial distribution of organic and inorganic species was observed at the μm level by imaging MS (time-of-flight-secondary ion mass spectrometry, ToF-SIMS). Our results revealed a rather even distribution of hydrocarbon-, O- and N-containing ions in the trabecular network of the ancient bone. A different, more patchy arrangement of organic compounds was evident in the former marrow cavities that were partly cemented by clotted micrites of putative microbial origin. The concentration of fatty acids (FAs) in the ancient bone was in the permil range of the amount extracted from the recent whale vertebra. Endogenous compounds, including monoenoic n-C16 and n-C18 as well as branched FAs, were identified in the fossil bone by comparison with the host sediment. Ca. 80% of the prevalent n-C16 and n-C18 moieties in the ancient bone were extractable as FAs, whereas ca. 20% were covalently bound in the non-saponifiable kerogen fraction. Ample pyrite precipitates, distinctive 10-methyl branched FAs and microbial microborings (“tunneling”) indicate that sulfate reducers and collagen-degrading actinomycetes were central players in the microbial decomposition of the bone. Similarities with reported microbial FA patterns suggest that the FAs in the fossil bone were largely contributed by these microbial “last eaters”. The results highlight some of the degradation and preservation mechanisms during marine FA diagenesis in the “natural laboratory” of bones, and therefore the processes that lead to either degradation, preservation, or introduction of these widespread biomolecules in the fossils of ancient marine animals.

Description: Highlights • Polypropylene and biodegradable plastic bags were incubated in marine sediments. • Bacterial colonization was highest on biodegradable plastic bags. • None of the two bag types showed signs of degradation after 98 days. • Marine sediments probably represent a long-term sink for both types of litter. Abstract To date, the longevity of plastic litter at the sea floor is poorly constrained. The present study compares colonization and biodegradation of plastic bags by aerobic and anaerobic benthic microbes in temperate fine-grained organic-rich marine sediments. Samples of polyethylene and biodegradable plastic carrier bags were incubated in natural oxic and anoxic sediments from Eckernförde Bay (Western Baltic Sea) for 98 days. Analyses included (1) microbial colonization rates on the bags, (2) examination of the surface structure, wettability, and chemistry, and (3) mass loss of the samples during incubation. On average, biodegradable plastic bags were colonized five times higher by aerobic and eight times higher by anaerobic microbes than polyethylene bags. Both types of bags showed no sign of biodegradation during this study. Therefore, marine sediment in temperate coastal zones may represent a long-term sink for plastic litter and also supposedly compostable material.

Description: The degradation and preservation affecting the biomarker record of ancient metazoa are not fully understood. We report on a five month experiment on the fate of fatty acids (FAs) during the degradation of recent whale vertebrae (Phocoena phocoena). Whale bones were analysed for extractable FAs and macromolecularly bound n-acyl compounds. Fresh bone showed extractable FAs dominated by 16: 1 omega 7c, 16:0, 18:1 omega 9c and 18:0. Calculated degradation rate constant (k) values showed a rapid decrease in FA concentration, with k values higher for unsaturated than for saturated compounds (0.08/day for 18: 1 omega 9c, 0.05/day for 16:0). The appearance or increased abundance of distinctive methyl branched (e.g. i/ai-15:0 and -17:0, 10Me-16:0) and hydroxy FAs (e.g. 10OH-16:0 and 10OH-18:0) were observed, providing clear evidence for the microbial degradation of bone organic matter and an input of lipids from specialised bacteria. Catalytic hydropyrolysis (HyPy) of demineralised extraction residues released up to 0.13% of the total n-C-16 and n-C-18 moieties in the degraded bones. This revealed that only a small, yet sizeable, portion of bone-derived fatty acyl units was sequestered into (proto)kerogen during the earliest stages of degradation.

Description: Highlights • Sulphidic event on the shelf resulted in a temporal imbalance of the benthic N cycle. • Bacterial NOx storage is a major source of oxidative power during euxinia. • Peruvian shelf and upper slope sediments are strong recycling sites of fixed N. Abstract Oxygen minimum zones (OMZ) are key regions for fixed nitrogen loss in both the sediments and the water column. During this study, the benthic contribution to N cycling was investigated at ten sites along a depth transect (74–989 m) across the Peruvian OMZ at 12 °S. O2 levels were below detection limit down to ~ 500 m. Benthic fluxes of N2, NO3–, NO2–, NH4+, H2S and O2 were measured using benthic landers. Flux measurements on the shelf were made under extreme geochemical conditions consisting of a lack of O2, NO3– and NO2– in the bottom water and elevated seafloor sulphide release. These particular conditions were associated with a large imbalance in the benthic nitrogen cycle. The sediments on the shelf were densely covered by filamentous sulphur bacteria Thioploca, and were identified as major recycling sites for DIN releasing high amounts of NH4+up to 21.2 mmol m−2 d−1 that were far in excess of NH4+release by ammonification. This difference was attributed to dissimilatory nitrate (or nitrite) reduction to ammonium (DNRA) that was partly being sustained by NO3– stored within the sulphur oxidizing bacteria. Sediments within the core of the OMZ (ca. 200 to 400 m) also displayed an excess flux of N of 3.5 mmol m−2 d−1 mainly as N2. Benthic nitrogen and sulphur cycling in the Peruvian OMZ appears to be particularly susceptible to bottom water fluctuations in O2, NO3−and NO2−, and may accelerate the onset of pelagic euxinia when NO3−and NO2−become depleted.