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.

Composition of sediment pore water and isotopes in carbonate and benthic foraminifera at DSDP Holes 68-501, 69-505 and Site 69-504

Two sites on the southern flank of the Costa Rica Rift were drilled on DSDP Legs 68 and 69, one on crust 3.9 m.y. old and the other on crust 5.9 m.y. old. The basement of the younger site is effectively cooled by the circulation of seawater. The basement of the older site has been sealed by sediment, and an interval in the uppermost 560 meters of basement recently reheated to temperatures of 60 to 120°C. Although the thickness of the sediments at the two sites is similar (150-240 m versus 270 m), the much rougher basement topography at the younger Site 505 produces occasional basement outcrops, through which 80 to 90% of the total heat loss apparently occurs by advection of warm seawater. This seawater has been heated only slightly, however; the temperature at the base of the sediments is only 9°C. Changes in its composition due to reaction with the basement basalts are negligible, as indicated by profiles of sediment pore water chemistry. Bacterial sulfate reduction in the sediments produces a decrease in SO4 (and Ca) and an increase in alkalinity (and Sr and NH3) as depth increases to an intermediate level, but at deeper levels these trends reverse, and all of these species plus Mg, K, Na, and chlorinity approach seawater values near basement. Si, however, is higher, and Li may be lower. At the older site, Site 501/504, where heat loss is entirely by conduction, the temperature at the sediment/basement contact is 59°C. Sediment pore water chemistry is heavily affected by reaction with the basaltic basement, as indicated by large decreases in d18O, Mg, alkalinity, Na, and K and an increase in Ca with increasing depth. The size of the changes in d18O, Mg, alkalinity, Ca, Sr, and SO4 varies laterally over 500 meters, indicating lateral gradients in pore water chemistry that are nearly as large as the vertical gradients. The lateral gradients are believed to result from similar lateral gradients in the composition of the basement formation water, which propagate upward through the sediments by diffusion. A model of the d18O profile suggests that the basement at Site 501/504 was sealed off from advection about 1 m.y. ago, so that reaction rates began to dominate the basement pore water chemistry. A limestone-chert diagenetic front began to move upward through the lower sediments less than 200,000 yr. ago.

Geochemistry and radiolarian distribution of sediment core MD96-2073

A combination of changes in the species composition of the radiolarian populations, and in the sediment chemical composition (content and mass accumulation rates of carbonate, organic carbon, and selected major and trace elements, with special attention paid to Ba) is used to reconstruct the variations in upwelling activity over the last 250 kyr in the Socotra gyre area (Somali-Socotra upwelling system, NW Indian Ocean). In the Socotra gyre (Core MD 962073 at 10°N), the variations in upwelling intensity are reconstructed by the upwelling radiolarian index (URI) while the thermocline/surface radiolarian index (TSRI) testifies to productivity variations during non-upwelling intervals. Despite an origin related both to marine and terrigenous inputs, the geochemical records of organic carbon, silica, and trace elements (Ba, P, Cu, and Zn) normalized to Al are controlled by the variations in surface paleoproductivity. The data indicate a continuous increase in upwelling intensity during the last 250 kyr with a maximum activity within the MIS 3, while high productivity periods in between the upwelling seasons occurred both during glacial and interglacial intervals. A comparison of our data with published observations from another gyre of the Somalian upwelling area located at 5°N in the Somali gyre area shows differences regarding periods of upwelling activity and their geochemical imprint. Three hypotheses are proposed to explain these differences: (1) changes in the planktonic community, resulting in more silica-rich deposits in the Socotra gyre, and more carbonate-rich deposits in the Somali gyre, that are controlled by differences in the source water of the upwelling; (2) a more important terrigenous input in the southern gyre; and (3) a different location of the sites relative to the geographic distribution of the upwelling gyres and hydrologic fronts.

Data files of figures 1, 2 and 3

We investigated optimal conditions for characterization of bioactivity of lytic compound(s) excreted by Alexandrium tamarense based on a cell-bioassay system. Allelochemical response of the cryptophyte Rhodomonas salina indicated the presence oflytic compound(s) in a reliable and reproducible way and allows for quantification of this lytic effect. The parameters tested were the incubation time of putatively lytic extracts or fractions with the target organism R. salina, different techniques for cell harvest from A. tamarense cultures and the optimal harvest time. A three hour incubation time was found to be optimal to yield a rapid response while accurately estimating effective concentration (ECso) values. Harvest of A. tamarense cultures by filtration resulted in loss of lytic activity in most cases and centrifugation was most efficient in terms of recovery of lytic activity. Maximum yield of extracellular lytic activity of A. tamarense cultures was achieved in the stationary phase. Such optimized bioassay guided fractionation techniques are a valuable asset in the isolation and eventual stmctural elucidation of the unknown lytic substances.

Combined metabolome and proteome analysis of the mantle tissue from Pacific oyster Crassostrea gigas exposed to elevated pCO2

Ocean acidification (OA) has been found to affect an array of normal physiological processes in mollusks, especially posing a significant threat to the fabrication process of mollusk shell. In the current study, the impact of exposure to elevated pCO2 condition was investigated in mantle tissue of Crassostrea gigas by an integrated metabolomic and proteomic approach. Analysis of metabolome and proteome revealed that elevated pCO2 could affect energy metabolism in oyster C. gigas, marked by differentially altered ATP, succinate, MDH, PEPCK and ALDH levels. Moreover, the up-regulated calponin-2, tropomyosins and myosin light chains indicated that elevated pCO2 probably caused disturbances in cytoskeleton structure in mantle tissue of oyster C. gigas. This work demonstrated that a combination of proteomics and metabolomics could provide important insights into the effects of OA at molecular levels.

Proteomic and metabolomic responses of Pacific oyster Crassostrea gigas to elevated pCO2 exposure

The gradually increased atmospheric CO2 partial pressure (pCO2) has thrown the carbonate chemistry off balance and resulted in decreased seawater pH in marine ecosystem, termed ocean acidification (OA). Anthropogenic OA is postulated to affect the physiology of many marine calcifying organisms. However, the susceptibility and metabolic pathways of change in most calcifying animals are still far from being well understood. In this work, the effects of exposure to elevated pCO2 were characterized in gills and hepatopancreas of Crassostrea gigas using integrated proteomic and metabolomic approaches. Metabolic responses indicated that high CO2 exposure mainly caused disturbances in energy metabolism and osmotic regulation marked by differentially altered ATP, glucose, glycogen, amino acids and organic osmolytes in oysters, and the depletions of ATP in gills and the accumulations of ATP, glucose and glycogen in hepatopancreas accounted for the difference in energy distribution between these two tissues. Proteomic responses suggested that OA could not only affect energy and primary metabolisms, stress responses and calcium homeostasis in both tissues, but also influence the nucleotide metabolism in gills and cytoskeleton structure in hepatopancreas. This study demonstrated that the combination of proteomics and metabolomics could provide an insightful view into the effects of OA on oyster C. gigas. BIOLOGICAL SIGNIFICANCE: The gradually increased atmospheric CO2 partial pressure (pCO2) has thrown the carbonate chemistry off balance and resulted in decreased seawater pH in marine ecosystem, termed ocean acidification (OA). Anthropogenic OA is postulated to affect the physiology of many marine calcifying organisms. However, the susceptibility and metabolic pathways of change in most calcifying animals are still far from being understood. To our knowledge, few studies have focused on the responses induced by pCO2 at both protein and metabolite levels. The pacific oyster C. gigas, widely distributed throughout most of the world's oceans, is a model organism for marine environmental science. In the present study, an integrated metabolomic and proteomic approach was used to elucidate the effects of ocean acidification on Pacific oyster C. gigas, hopefully shedding light on the physiological responses of marine mollusk to the OA stress.