Isotopic signature of specific biomarkers derived from anaerobic methanotrophic archaea (ANME groups) and sulphate-reducing bacteria (SRB) at different cold seep provinces

Anaerobic methane-oxidizing microbial communities in sediments at cold methane seeps are important factors in controlling methane emission to the ocean and atmosphere. Here, we investigated the distribution and carbon isotopic signature of specific biomarkers derived from anaerobic methanotrophic archaea (ANME groups) and sulphate-reducing bacteria (SRB) responsible for the anaerobic oxidation of methane (AOM) at different cold seep provinces of Hydrate Ridge, Cascadia margin. The special focus was on their relation to in situ cell abundances and methane turnover. In general, maxima in biomarker abundances and minima in carbon isotope signatures correlated with maxima in AOM and sulphate reduction as well as with consortium biomass. We found ANME-2a/DSS aggregates associated with high abundances of sn-2,3-di-O-isoprenoidal glycerol ethers (archaeol, sn-2-hydroxyarchaeol) and specific bacterial fatty acids (C16:1omega5c, cyC17:0omega5,6) as well as with high methane fluxes (Beggiatoa site). The low to medium flux site (Calyptogena field) was dominated by ANME-2c/DSS aggregates and contained less of both compound classes but more of AOM-related glycerol dialkyl glycerol tetraethers (GDGTs). ANME-1 archaea dominated deeper sediment horizons at the Calyptogena field where sn-1,2-di-O-alkyl glycerol ethers (DAGEs), archaeol, methyl-branched fatty acids (ai-C15:0, i-C16:0, ai-C17:0), and diagnostic GDGTs were prevailing. AOM-specific bacterial and archaeal biomarkers in these sediment strata generally revealed very similar d13C-values of around -100 per mill. In ANME-2-dominated sediment sections, archaeal biomarkers were even more 13C-depleted (down to -120 per mill), whereas bacterial biomarkers were found to be likewise 13C-depleted as in ANME-1-dominated sediment layers (d13C: -100 per mill). The zero flux site (Acharax field), containing only a few numbers of ANME-2/DSS aggregates, however, provided no specific biomarker pattern. Deeper sediment sections (below 20 cm sediment depth) from Beggiatoa covered areas which included solid layers of methane gas hydrates contained ANME-2/DSS typical biomarkers showing subsurface peaks combined with negative shifts in carbon isotopic compositions. The maxima were detected just above the hydrate layers, indicating that methane stored in the hydrates may be available for the microbial community. The observed variations in biomarker abundances and 13C-depletions are indicative of multiple environmental and physiological factors selecting for different AOM consortia (ANME-2a/DSS, ANME-2c/DSS, ANME-1) along horizontal and vertical gradients of cold seep settings.

Biogeochemical measurements of cold seep sediments inhabit by vesicomyid clams in the Japan Deep Sea Trench

Vesicomyidae clams harbor sulfide-oxidizing endosymbionts and are typical members of cold seep communities associated with tectonic faults where active venting of fluids and gases takes place. We investigated the central biogeochemical processes that supported a vesicomyid clam colony as part of a locally restricted seep community in the Japan Trench at 5346 m water depth, one of the deepest seep settings studied to date. An integrated approach of biogeochemical and molecular ecological techniques was used combining in situ and ex situ measurements. During the cruise YK06-05 in 2006 with the RV Yokosuka to the Japan Trench, we investigated a clam colony inhabited by Abyssogena phaseoliformis (former known as Calyptogena phaseoliformis) and Isorropodon fossajaponicum (former known as Calyptogena fossajaponica). The targeted sampling and precise positioning of the in situ instruments were achieved with the manned research submersible Shinkai 6500 (JAMSTEC, Nankoku, Kochi, Japan). Sampling was first performed close to the rim of the JTC colony and then at the center. Immediately after sample recovery onboard, the sediment core was sub-sampled for ex situ rate measurements or preserved for later analyses. In sediment of the clam colony, low sulfate reduction (SR) rates (max. 128 nmol ml**-1 d**-1) were coupled to the anaerobic oxidation of methane (AOM). They were observed over a depth range of 15 cm, caused by active transport of sulfate due to bioturbation of the vesicomyid clams. A distinct separation between the seep and the surrounding seafloor was shown by steep horizontal geochemical gradients and pronounced microbial community shifts. The sediment below the clam colony was dominated by anaerobic methanotrophic archaea (ANME-2c) and sulfate-reducing Desulfobulbaceae (SEEP-SRB-3, SEEP-SRB-4). Aerobic methanotrophic bacteria were not detected in the sediment and the oxidation of sulfide seemed to be carried out chemolithoautotrophically by Sulfurovum species. Thus, major redox processes were mediated by distinct subgroups of seep-related microorganisms that might have been selected by this specific abyssal seep environment. Fluid flow and microbial activity was low but sufficient to support the clam community over decades and to build up high biomasses. Hence, the clams and their microbial communities adapted successfully to a low-energy regime and may represent widespread chemosynthetic communities in the Japan Trench.

The HERMES cold-water coral database

The HERMES cold-water coral database is a combination of historical and published sclerectinia cold-water coral occurrences (mainly Lophelia pertusa) and new records of the HERMES project along the European margin. This database will be updated if new findings are reported. New or historical data can be sent to Ben De Mol (mailto:bendemol@ub.edu). Besides geocodes a second category indicates the coral species and if they are sampled alive or dead. If absolute dating is available of the corals this is provide together with the method. Only the framework building cold-water corals are selected: Lophelia pertusa, Madrepora oculata and common cold-water corals often associated with the framework builders like: Desmophyllum sp and Dendrophylia sp. in comments other observed corals are indicated. Another field indicates if the corals are part of a large build-up or solitary. A third category of parameters is referencing to the quality of the represented data. In this category are the following parameters indicated: source of reference, source type (such as Fishermen location, scientific paper, cruise reports). sample code and or name and sample type (e.g. rock dredge, grab, video line). These parameters must allow an assessment of the quality of the described parameters.

Porewater concentrations, pH, single cell number, anaerobic oxidation of methane (AOM) rate, sulfate reduction (SR) rate of samples during METEOR cruise M76/3b at the REGAB cold seep site from the West African margin in 2008

The giant pockmark REGAB (West African margin, 3160 m water depth) is an active methane-emitting cold seep ecosystem, where the energy derived from microbially mediated oxidation of methane supports high biomass and diversity of chemosynthetic communities. Bare sediments interspersed with heterogeneous chemosynthetic assemblages of mytilid mussels, vesicomyid clams and siboglinid tubeworms form a complex seep ecosystem. To better understand if benthic bacterial communities reflect the patchy distribution of chemosynthetic fauna, all major chemosynthetic habitats at REGAB were investigated using an interdisciplinary approach combining porewater geochemistry, in situ quantification of fluxes and consumption of methane, as well bacterial community fingerprinting. This study revealed that sediments populated by different fauna assemblages show distinct biogeochemical activities and are associated with distinct sediment bacterial communities. The methane consumption and methane effluxes ranged over one to two orders of magnitude across habitats, and reached highest values at the mussel habitat, which hosted a different bacterial community compared to the other habitats. Clam assemblages had a profound impact on the sediment geochemistry, but less so on the bacterial community structure. Moreover, all clam assemblages at REGAB were restricted to sediments characterized by complete methane consumption in the seafloor, and intermediate biogeochemical activity. Overall, variations in the sediment geochemistry were reflected in the distribution of both fauna and microbial communities; and were mostly determined by methane flux.

Environmental characteristics and gas composition of Lost Hammer, Canadian Arctic

We report the first microbiological characterization of a terrestrial methane seep in a cryo-environment in the form of an Arctic hypersaline (~24% salinity), subzero (-5 C), perennial spring, arising through thick permafrost in an area with an average annual air temperature of -15 C. Bacterial and archaeal 16S rRNA gene clone libraries indicated a relatively low diversity of phylotypes within the spring sediment (Shannon index values of 1.65 and 1.39, respectively). Bacterial phylotypes were related to microorganisms such as Loktanella, Gillisia, Halomonas and Marinobacter spp. previously recovered from cold, saline habitats. A proportion of the bacterial phylotypes were cultured, including Marinobacter and Halomonas, with all isolates capable of growth at the in situ temperature (-5 C). Archaeal phylotypes were related to signatures from hypersaline deep-sea methane-seep sediments and were dominated by the anaerobic methane group 1a (ANME-1a) clade of anaerobic methane oxidizing archaea. CARD-FISH analyses indicated that cells within the spring sediment consisted of ~84.0% bacterial and 3.8% archaeal cells with ANME-1 cells accounting for most of the archaeal cells. The major gas discharging from the spring was methane (~50%) with the low CH4/C2 + ratio and hydrogen and carbon isotope signatures consistent with a thermogenic origin of the methane. Overall, this hypersaline, subzero environment supports a viable microbial community capable of activity at in situ temperature and where methane may behave as an energy and carbon source for sustaining anaerobic oxidation of methane-based microbial metabolism. This site also provides a model of how a methane seep can form in a cryo-environment as well as a mechanism for the hypothesized Martian methane plumes.

Alkenone analyses of sediment cores from the western Arabian Sea

Records of total organic carbon (TOC) and C37 alkenones were used as indicators for past primary productivity in the western and eastern Arabian Sea. Data from GeoB 3005, an open ocean site in the western Arabian Sea upwelling area, are compared with similar records of GeoB 3007 from the Owen Ridge, Ocean Drilling Program (ODP) Site 723 from the continental margin off Oman and MD 900963 from the eastern Arabian Sea. TOC/C37 alkenone records together with other proxies used to reconstruct upwelling intensity, indicate periods of high productivity in tune with precessional forcing all over the Arabian Sea. Based on their phase-relationship to variations in boreal summer insolation they can be divided into three groups. In the western Arabian Sea the precession-related phasing is different between productivity proxies and those for summer monsoon wind strength and upwelling intensity. TOC and C37 alkenone records from the western Arabian Sea lag the other monsoonal indicators by about 5 kyr, but lead productivity indicators from the eastern Arabian Sea by 3 kyr. Based on the differences in phase relationships associated with the precessional cycling between productivity and monsoonal proxies in the western Arabian Sea it is proposed that the TOC/C37 alkenone signal in the western Arabian Sea document a combined signal of moderate SW monsoon winds and of strengthened and prolonged NE monsoon winds. In the eastern Arabian Sea the phasing hints to coincidence between maximum productivity and stronger NE monsoon winds associated with precession-related maxima in ice volume. In contrast, variations in paleoproductivity at site GeoB 3007 from the Owen Ridge indicate productivity maxima during glacial substages 8.2, 6.2 and 2.2, whereas precessionrelated changes are of only minor importance at this location. The results of frequency analyses confirm that productivity at site GeoB 3007 responds predominantly to glacialinterglacial climate changes, while site GeoB 3005 from the open ocean upwelling region near the Gulf of Aden is dominated by precessional insolation. A possible explanation for the pattern revealed at the Owen Ridge is the periodic NW-SE displacement of the Findlater Jet axis, which separates the region of open ocean upwelling to the northwest from downwelling to the southeast ofthe jet. The carbon isotopes of planktic foraminifera reflect nutrient related d13C variations of dissolved inorganic carbon. The difference between the planktic foraminifera Globigerinoides ruber (w), living in the upper 50 m of the water column, and the deeper Iiving Neogloboquadrina dutertrei (Delta d13Cr-d) of core GeoB 3005 displays nutrient variations in the upwelling area near the Gulf of Aden. The results of cross-spectral analyses between Deltad13Cr-d of GeoB 3005 and proxies for SW monsoon intensity indicate, too, a dissociation of productivity from monsoonal upwelling intensity. Instead, productivity depends mainly on the availability of nutrients, while upwelling intensity of sub-surface water masses seems to be of only secondary importance. Additionally, sea surface temperatures (SSTs) were reconstructed using the unsaturation ratio of C37 alkenones. Alkenone SSTs reflect annual mean temperatures rather than explicitly the season of upwelling. This is evident from alkenone SSTs in a transect of surface sediments extending from the inner Gulf of Aden into the western Arabian Sea. The alkenone-derived SST records of GeoB 3005 from the open ocean upwelling region near the Gulf of Aden and GeoB 3007 from the Owen Ridge reveal similar variations with high SSTs during interglacial and low SSTs during glacial periods. The glacial marine oxygen isotope stage (MIS) 6 remains relatively warm and was not as cold as MIS 3 to 4 and 8 according to the alkenone SST. Similar variation-patterns were reconstructed in the coastal upwelling area off Oman for ODP Site 723 as weIl as in the eastern Arabian Sea for MD 900963, where upwelling is not as pronounced as in the western Arabian Sea. Spectral-analyses indicate that SST changes are in good agreement with the modulation of low-latitude precessional insolation changes by eccentricity. However, they do not show the pronounced cydicity in the precessional frequency band, which is characteristic for variations in paleoproductivity. Although the overall variation pattern is very similar, a dose comparison between the western (GeoB 3005) and the eastern Arabian Sea (MD 900963) shows larger differences between both sites during cold intervals than during periods of warm SSTs. This is attributed to a more effective cooling of surface waters in the western Arabian Sea by prolonged NE monsoon winds during times of expanded Northern Hemisphere ice-sheets, thereby lowering the annual mean SSTs stronger than in the eastern Arabian Sea.

Total organic carbon, delta13C, biomarker, gas compilations and hopanoids analysis from IODP Sites 307-U1317 and 307-U1318

During the Integrated Ocean Drilling Program (IODP) Expedition 307 for the first time a cold-water coral carbonate mound was drilled down through its base into the underlying sediments. In the current study, sample material from within and below Challenger Mound, located in the Belgica carbonate mound province in the Porcupine Basin offshore Ireland, was investigated for its distribution of microbial communities and gas composition using biogeochemical and geochemical approaches to elucidate the question on the initiation of carbonate mounds. Past and living microbial populations are lower in the mound section compared to the underlying sediments or sediments of an upslope reference site. A reason for this might be a reduced substrate feedstock, reflected by low total organic carbon (TOC) contents, in the once coral dominated mound sequence. In contrast, in the reference site a lithostratigraphic sequence with comparatively high TOC contents shows higher abundances of both past and present microbial communities, indicating favourable living conditions from time of sedimentation until today. Composition and isotopic values of gases below the mound base seem to point to a mixed gas of biogenic and thermogenic origin with a higher proportion of biogenic gas. Oil-derived hydrocarbons were not detected at the mound site. This suggests that at least in the investigated part of the mound base the upward flow of fossil hydrocarbons, being one hypothesis for the initiation of the formation of carbonate mounds, seems to be only of minor significance.

Gas, water and volume characteristics during controlled degassing experiments on ODP Leg 164 PCS cores

A pressurized core with CH4 hydrate or dissolved CH4 should evolve gas volumes in a predictable manner as pressure is released over time at isothermal conditions. Incremental gas volumes were collected as pressure was released over time from 29 pressure core sampler (PCS) cores from Sites 994, 995, 996, and 997 on the Blake Ridge. Most of these cores were kept at or near 0ºC with an ice bath, and many of these cores yielded substantial quantities of CH4. Volume-pressure plots were constructed for 20 of these cores. Only five plots conform to expected volume and pressure changes for sediment cores with CH4 hydrate under initial pressure and temperature conditions. However, other evidence suggests that sediment in these five and at least five other PCS cores contained CH4 hydrate before core recovery and gas release. Detection of CH4 hydrate in a pressurized sediment core through volume-pressure relationships is complicated by two factors. First, significant quantities of CH4-poor borehole water fill the PCS and come into contact with the core. This leads to dilution of CH4 concentration in interstitial water and, in many cases, decomposition of CH4 hydrate before a degassing experiment begins. Second, degassing experiments were conducted after the PCS had equilibrated in an ice-water bath (0ºC). This temperature is significantly lower than in situ values in the sediment formation before core recovery. Our results and interpretations for PCS cores collected on Leg 164 imply that pressurized containers formerly used by the Deep Sea Drilling Project (DSDP) and currently used by ODP are not appropriately designed for direct detection of gas hydrate in sediment at in situ conditions through volume-pressure relationships.

Methane fluxes and carbonate deposits at eastern Mediterranean cold seeps

High acoustic seafloor-backscatter signals characterize hundreds of patches of methane-derived authigenic carbonates and chemosynthetic communities associated with hydrocarbon seepage on the Nile Deep Sea Fan (NDSF) in the Eastern Mediterranean Sea. During a high-resolution ship-based multibeam survey covering a ~ 225 km**2 large seafloor area in the Central Province of the NDSF we identified 163 high-backscatter patches at water depths between 1500 and 1800 m, and investigated the source, composition, turnover, flux and fate of emitted hydrocarbons. Systematic Parasound single beam echosounder surveys of the water column showed hydroacoustic anomalies (flares), indicative of gas bubble streams, above 8% of the high-backscatter patches. In echosounder records flares disappeared in the water column close to the upper limit of the gas hydrate stability zone located at about 1350 m water depth due to decomposition of gas hydrate skins and subsequent gas dissolution. Visual inspection of three high-backscatter patches demonstrated that sediment cementation has led to the formation of continuous flat pavements of authigenic carbonates typically 100 to 300 m in diameter. Volume estimates, considering results from high-resolution autonomous underwater vehicle (AUV)-based multibeam mapping, were used to calculate the amount of carbonate-bound carbon stored in these slabs. Additionally, the flux of methane bubbles emitted at one high-backscatter patch was estimated (0.23 to 2.3 × 10**6 mol a**-1) by combined AUV flare mapping with visual observations by remotely operated vehicle (ROV). Another high-backscatter patch characterized by single carbonate pieces, which were widely distributed and interspaced with sediments inhabited by thiotrophic, chemosynthetic organisms, was investigated using in situ measurements with a benthic chamber and ex situ sediment core incubation and allowed for estimates of the methane consumption (0.1 to 1 × 10**6 mol a**-1) and dissolved methane flux (2 to 48 × 10**6 mol a**-1). Our comparison of dissolved and gaseous methane fluxes as well as methane-derived carbonate reservoirs demonstrates the need for quantitative assessment of these different methane escape routes and their interaction with the geo-, bio-, and hydrosphere at cold seeps.