(Table S1) Molecular analyses and morphological comparisons of deep-sea clams

Large vesicomyid clams are common inhabitants of sulphidic deep-sea habitats such as hydrothermal vents, hydrocarbon seeps and whale-falls. Yet, the species- and genus-level taxonomy of these diverse clams has been unstable due to insufficiencies in sampling and absence of detailed taxonomic studies that would consistently compare molecular and morphological characters. To clarify uncertainties about species-level assignments, we examined DNA sequences from mitochondrial cytochrome-c-oxidase subunit I (COI) in conjunction with morphological characters. New and published COI sequences were used to create a molecular database for 44 unique evolutionary lineages corresponding to species. Overall, the congruence between molecular and morphological characters was good. Several discrepancies due to synonymous species designations were recognized, and acceptable species names were rectified with published COI sequences in cases where morphological specimens were available. We identified seven species with trans-Pacific distributions, and two species with Indo-Pacific distributions. Presently, 27 species have only been documented from one region, which might reflect limited ranges, or insufficient geographical sampling. Vesicomyids exhibit the greatest species diversity along the northwest Pacific ridge systems and in the eastern Pacific, along the western America margin, where depth zonation typically results in segregation of closely related species. The broad distributions of several vesicomyid species suggest that their required chemosynthetic habitats might be more common than previously recognized and occur along most continental margins.

Molecular and biochemical analyses of wounding in mesocarp of peach (Prunus persica L. Batsch) ripe fruits

The physiological and molecular responses of ripe fruit to wounding were evaluated in two peach (Prunus persica) varieties ('Glohaven', GH, melting and 'BigTop', BT, slow melting nectarine) by comparing mesocarp samples from wedges (as in minimal processing) and whole fruit as the control. Slight differences between the two varieties were detected in terms of ethylene production, whereas total phenol and flavonoid concentrations, and PPO and POD enzyme activities showed a general increase in wounded GH but not in BT. This was associated with the better appearance of the BT wedges at the end of the experimental period (72 h). Microarray (genome-wide ?PEACH3.0) analysis revealed that a total number of 2218 genes were differentially expressed (p < 0.01, log2 fold change expression ratio >1 or <-1) in GH 24 h after wounding compared to the control. This number was much lower (1208) in BT. According to the enrichment analysis, cell wall, plasma membrane, response to stress, secondary metabolic processes, oxygen binding were the GO categories over-represented among the GH up-regulated genes, whereas plasma membrane and response to endogenous stimulus were the categories over-represented among the down-regulated genes. Only 32 genes showed a common expression trend in the two varieties 24 h after wounding, whereas a total of 512 genes (with highly represented transcription factors), displayed opposite behavior. Quantitative RT-PCR analysis confirmed the microarray data for 18 out of a total of 20 genes selected. Specific WRKY, AP2/ERF and HSP20 genes were markedly up-regulated in wounded GH, indicating the activation of regulatory and signaling mechanisms probably related to different hormone categories. Compared to BT, the expression of specific genes involved in phenylpropanoid and triterpenoid biosynthetic pathways showed a more pronounced induction in GH, highlighting the difference between the two peach varieties in terms of molecular responses to wounding in the mesocarp tissue.

Geochemical and nannofossil analyses of Cenomanian/Turonian sediments of DSDP Hole 75-530A

One of the key objectives of Deep Sea Drilling Project (DSDP) Leg 75 was to shed light on the underlying causes of Cretaceous oceanic anoxia in the South Atlantic by addressing two major hypotheses: productivity productivity-driven anoxia vs. enhanced ocean stratification leading to preservation of organic matter and black shale deposition. Here we present a detailed geochemical dataset from sediments deposited during the Cenomanian/Turonian (C/T) transition and the global oceanic anoxic event 2 (OAE 2) at DSDP Site 530A, located off-shore Namibia (southeast Angola Basin, north of Walvis Ridge). To characterise the succession of alternating black and green shales at this site and to reconstruct the evolution of their paleoenvironmental setting, we have combined data derived from investigations on bulk organic matter, biomarkers and the inorganic fraction. The location of the C/T boundary itself is biostratigraphically not well constrained due to the carbonate-poor (but organic matter-rich) facies of these sediments. The bulk d13Corg record and compound-specific d13C data, in combination with published as well as new biostratigraphic data, enabled us to locate more precisely the C/T boundary at DSDP Site 530A. The compound-specific d13C record is the first of this kind reported from C/T black shales in the South Atlantic. It is employed for paleoenvironmental reconstructions and chemostratigraphic correlation to other C/T sections in order to discuss the paleoceanographic aspects and implications of the observations at DSDP Site 530A in a broader context, e.g., with regard to the potential trigger mechanisms of OAE 2, global changes in black shale deposition and climate. On a stratigraphic level, an approximation and monitoring of the syndepositional degree of oxygen depletion within the sediments/bottom waters in comparison to the upper water column is achieved by comparing normalised concentrations of redox-sensitive trace elements with the abundance of highly source specific molecular compounds. These biomarkers are derived from photoautotrophic and simultaneously anoxygenic green sulphur bacteria (Chlorobiacea) and are interpreted as paleoindicators for events of photic zone euxinia. In contrast to a number of other OAE 2 sections that are characterised by continuous black shale sequences, DSDP Site 530A represents a highly dynamic setting where newly deposited black shales were repeatedly exposed to conditions of subtle bottom water re-oxidation, presumably leading to their progressive alteration into green shales. The frequent alternation between both facies and the related anoxic to slight oxygenated conditions can be best explained by variations in vertical extent of an oxygen minimum zone in response to changes in a highly productive western continental margin setting driven by upwelling.

Investigation of cell fate decision in Schizosaccharomyces pombe by ncRNA annotation and statistical analyses

Studies in the fission yeast Schizosaccharomyces pombe (S. pombe) have done much to inform the view of heterochromatin and its control by the RNA interference (RNAi) machinery. Using cDNA synthesised from poly(A)-enriched RNA samples, numerous novel ncRNA loci were discovered, and the 50 and 30 ends of many other genes were refined in previous studies. Although some of these transcripts may encode novel proteins the function of the majority is yet to be determined. The authors have used strand-specific deep sequencing of RNA, irrespective of poly(A) status, to reveal a highly structured antisense programme that modulates gene expression to dictate cell fate decisions during sexual differentiation. They show that an extensive and elaborate array of ncRNA production accompanies sexual differentiation in the fission yeast S. pombe. Experimental manipulation suggests that these transcripts specifically regulate the function of the target genes.

Major cellular and physiological impacts of ocean acidification on a reef building coral

As atmospheric levels of CO2 increase, reef-building corals are under greater stress from both increased sea surface temperatures and declining sea water pH. To date, most studies have focused on either coral bleaching due to warming oceans or declining calcification due to decreasing oceanic carbonate ion concentrations. Here, through the use of physiology measurements and cDNA microarrays, we show that changes in pH and ocean chemistry consistent with two scenarios put forward by the Intergovernmental Panel on Climate Change (IPCC) drive major changes in gene expression, respiration, photosynthesis and symbiosis of the coral, Acropora millepora, before affects on biomineralisation are apparent at the phenotype level. Under high CO2 conditions corals at the phenotype level lost over half their Symbiodinium populations, and had a decrease in both photosynthesis and respiration. Changes in gene expression were consistent with metabolic suppression, an increase in oxidative stress, apoptosis and symbiont loss. Other expression patterns demonstrate upregulation of membrane transporters, as well as the regulation of genes involved in membrane cytoskeletal interactions and cytoskeletal remodeling. These widespread changes in gene expression emphasize the need to expand future studies of ocean acidification to include a wider spectrum of cellular processes, many of which may occur before impacts on calcification.

Zircons, isotope ratios and element analyses from tonalite and oxide gabbro of the mid-ocean ridge from ODP Hole 176-735B

A limiting factor in the accuracy and precision of U/Pb zircon dates is accurate correction for initial disequilibrium in the 238U and 235U decay chains. The longest-lived-and therefore most abundant-intermediate daughter product in the 235U isotopic decay chain is 231Pa (T1/2 = 32.71 ka), and the partitioning behavior of Pa in zircon is not well constrained. Here we report high-precision thermal ionization mass spectrometry (TIMS) U-Pb zircon data from two samples from Ocean Drilling Program (ODP) Hole 735B, which show evidence for incorporation of excess 231Pa during zircon crystallization. The most precise analyses from the two samples have consistent Th-corrected 206Pb/238U dates with weighted means of 11.9325 ± 0.0039 Ma (n = 9) and 11.920 ± 0.011 Ma (n = 4), but distinctly older 207Pb/235U dates that vary from 12.330 ± 0.048 Ma to 12.140 ± 0.044 Ma and 12.03 ± 0.24 to 12.40 ± 0.27 Ma, respectively. If the excess 207Pb is due to variable initial excess 231Pa, calculated initial (231Pa)/(235U) activity ratios for the two samples range from 5.6 ± 1.0 to 9.6 ± 1.1 and 3.5 ± 5.2 to 11.4 ± 5.8. The data from the more precisely dated sample yields estimated DPazircon/DUzircon from 2.2-3.8 and 5.6-9.6, assuming (231Pa)/(235U) of the melt equal to the global average of recently erupted mid-ocean ridge basaltic glasses or secular equilibrium, respectively. High precision ID-TIMS analyses from nine additional samples from Hole 735B and nearby Hole 1105A suggest similar partitioning. The lower range of DPazircon/DUzircon is consistent with ion microprobe measurements of 231Pa in zircons from Holocene and Pleistocene rhyolitic eruptions (Schmitt (2007; doi:10.2138/am.2007.2449) and Schmitt (2011; doi:10.1146/annurev-earth-040610-133330)). The data suggest that 231Pa is preferentially incorporated during zircon crystallization over a range of magmatic compositions, and excess initial 231Pa may be more common in zircons than acknowledged. The degree of initial disequilibrium in the 235U decay chain suggested by the data from this study, and other recent high precision datasets, leads to resolvable discordance in high precision dates of Cenozoic to Mesozoic zircons. Minor discordance in zircons of this age may therefore reflect initial excess 231Pa and does not require either inheritance or Pb loss.

(Table 1) Chemical and isotopic analyses of Rajmahal Traps and Ninetyeast Ridge volcanics

The hypothesis that hotspots are the sources of many continental flood basalts is evaluated geochemically for the proposed Rajmahal Traps-Ninetyeast Ridge-Kerguelen hotspot system. It appears that the Kerguelen hotspot did not directly feed Rajmahal magmas, although it may have provided a source of heat for Rajmahal activity.

Element contents, sulfur and oxygen isotopes, and molecular biomarkers of phosphatic crust samples from the Chimbote Platform of the shelf off Peru

Authigenic phosphatic laminites enclosed in phosphorite crusts from the shelf off Peru (10°01' S and 10°24' S) consist of carbonate fluorapatite layers, which contain abundant sulfide minerals including pyrite (FeS2) and sphalerite (ZnS). Low d34Spyrite values (average -28.8 per mill) agree with bacterial sulfate reduction and subsequent pyrite formation. Stable sulfur isotopic compositions of sulfate bound in carbonate fluorapatite are lower than that of sulfate from ambient sea water, suggesting bacterial reoxidation of sulfide by sulfide-oxidizing bacteria. The release of phosphorus and subsequent formation of the autochthonous phosphatic laminites are apparently caused by the activity of sulfate-reducing bacteria and associated sulfide-oxidizing bacteria. Following an extraction-phosphorite dissolution-extraction procedure, molecular fossils of sulfate-reducing bacteria (mono-O-alkyl glycerol ethers, di-O-alkyl glycerol ethers, as well as the short-chain branched fatty acids i/ai-C15:0, i/ai-C17:0 and 10MeC16:0) are found to be among the most abundant compounds. The fact that these molecular fossils of sulfate-reducing bacteria are distinctly more abundant after dissolution of the phosphatic laminite reveals that the lipids are tightly bound to the mineral lattice of carbonate fluorapatite. Moreover, compared with the autochthonous laminite, molecular fossils of sulfate-reducing bacteria are: (1) significantly less abundant and (2) not as tightly bound to the mineral lattice in the other, allochthonous facies of the Peruvian crusts consisting of phosphatic coated grains. These observations confirm the importance of sulfate-reducing bacteria in the formation of the phosphatic laminite. Model calculations highlight that organic matter degradation by sulfate-reducing bacteria has the potential to liberate sufficient phosphorus for phosphogenesis.

Iridium contents and microprobe analyses of DSDP Leg 77 samples

Restudy of Deep Sea Drilling Project Sites 536 and 540 in the southeast Gulf of Mexico gives evidence for a giant wave at Cretaceous-Tertiary boundary time. Five units are recognized: (1) Cenomanian limestone underlies a hiatus in which the five highest Cretaceous stages are missing, possibly because of catastrophic K-T erosion. (2) Pebbly mudstone, 45 m thick, represents a submarine landslide possibly of K-T age. (3) Current-bedded sandstone, more than 2.5 m thick, contains anomalous iridium, tektite glass, and shocked quartz; it is interpreted as ejecta from a nearby impact crater, reworked on the deep-sea floor by the resulting tsunami. (4) A 50-cm interval of calcareous mudstone containing small Cretaceous planktic foraminifera and the Ir peak is interpreted as the silt-size fraction of the Cretaceous material suspended by the impact-generated wave. (5) Calcareous mudstone with basal Tertiary forams and the uppermost tail of the Ir anomaly overlies the disturbed interval, dating the impact and wave event as K-T boundary age. Like Beloc in Haiti and Mimbral in Mexico, Sites 536 and 540 are consistent with a large K-T age impact at the nearby Chicxulub crater.

Carbon and carbonate analyses of DSDP Leg 27 samples

Leg 27 sediments were analyzed for total carbon and acid-insoluble (organic) carbon using a LECO acid-base Analyzer. The 3-cc sediment samples were first dried at 105°-110°C and then ground to a homogeneous powder. The ground sediment was redried and two samples, a 0.1-g and a 0.5-g sample, were then weighed into LECO clay crucibles. The 0.5-g sample was acidified with diluted hydrochloric acid and washed with distilled water. The sample was then dried and analyzed for acid-insoluble carbon, listed in the table as "organic" carbon. The 0.1-g sample was analyzed for total carbon without further treatment. If the result showed less than 10% CaCO3, an additional 0.5-g sample was analyzed for greater accuracy. The calcium carbon percentages were calculated as follows: (% total C-% organic C) * 8.33 = % CaCO3. Although other carbonates may be present, all acid-soluble carbon was calculated as calcium carbonate. All results are given in weight percent.

Carbonate mineralogical and isotopic analyses of TV-guided grab samples and TV-guided box corer samples from the Shumagin area

Methane seepage leads to Mg-calcite and aragonite precipitation at a depth of 4,850 m on the Aleutian accretionary margin. Stromatolitic and oncoid growth structures imply encrustation of microorganisms (microbial mats) in the host sediment with a unique growth direction downward into the sediment, forming crust-shaped lithologies. Biomarker investigations of the residue after carbonate dissolution show strong enrichments in crocetane and archaeol, which contain extremely low d13C values. This indicates the presence of methane-consuming archaea, and d13C values of -42 to -51 per mill PDB indicate that methane is the carbon source for the carbonate crusts. Thus, it appears that stromatolitic encrustations of methanotrophic anaerobic archaea probably occurs in a consortium with sulphate-reducing bacteria and that carbonate precipitation proceeds downward into the sediment, where ascending cold fluids provide a methane source. Strontium and oxygen isotope analyses as well as 14C ages of the carbonates suggest that the fluids come from deep within the sediment and that carbonate precipitation began about 3,000 years ago.