Fluorescence energy transfer dye-labeled primers for DNA sequencing and analysis.

Fluorescent dye-labeled DNA primers have been developed that exploit fluorescence energy transfer (ET) to optimize the absorption and emission properties of the label. These primers carry a fluorescein derivative at the 5' end as a common donor and other fluorescein and rhodamine derivatives attached to a modified thymidine residue within the primer sequence as acceptors. Adjustment of the donor-acceptor spacing through the placement of the modified thymidine in the primer sequence allowed generation of four primers, all having strong absorption at a common excitation wavelength (488 nm) and fluorescence emission maxima of 525, 555, 580, and 605 nm. The ET efficiency of these primers ranges from 65% to 97%, and they exhibit similar electrophoretic mobilities by gel electrophoresis. With argon-ion laser excitation, the fluorescence of the ET primers and of the DNA sequencing fragments generated with ET primers is 2- to 6-fold greater than that of the corresponding primers or fragments labeled with single dyes. The higher fluorescence intensity of the ET primers allows DNA sequencing with one-fourth of the DNA template typically required when using T7 DNA polymerase. With single-stranded M13mp18 DNA as the template, a typical sequencing reaction with ET primers on a commercial sequencer provided DNA sequences with 99.8% accuracy in the first 500 bases. ET primers should be generally useful in the development of other multiplex DNA sequencing and analysis methods.

Registro de excentricidad de alta frecuencia en los sedimentos continentales de la Cuenca de Guadix (Cordillera Bética, España)

Los sedimentos continentales (Plioceno-Cuaternario) que afloran en el sector central de la Cuenca de Guadix (Sur de España) muestran una ciclicidad de 100 ka consistente en la alternancia de depósitos de abanicos aluviales y sedimentos fluvio-lacustres. Durante el Plioceno y el Pleistoceno la Cuenca de Guadix era endorreica, y se caracterizaba por la existencia de un sistema axial fluvial y una orla marginal de abanicos aluviales transversales. En la zona de estudio, estos sistemas estaban relacionados lateralmente, ocupando de forma alterna el valle axial en el sector central de la Cuenca de Guadix. La edad estimada para la alternancia, ca. 100 ka, cae en la banda de excentricidad de alta frecuencia de Milankovitch. Estas fases podrían interpretarse como el resultado de máximos de excentricidad (inviernos más largos y fríos, con mayor volumen de precipitaciones que favorecerían las progradaciones de los abanicos) o de excentricidad mínima (períodos más secos y fríos, con una cubierta vegetal más escasa en las áreas fuente y, por tanto, un mayor aporte de sedimento por precipitaciones muy concentradas en el tiempo al sistema aluvial). Se muestra cómo los datos paleomagnéticos no son lo suficientemente precisos para proporcionar una buena correlación de las fases de progradación con la curva de excentricidad de Laskar et al. (2004), por lo que se pone en duda su precisión a la hora de determinar el significado climático de la ciclicidad.

(Appendix) Oxygen isotope record and carbonate mineralogy of the top part of ODP Hole 101-633A

Hole 633A was drilled in the southern part of Exuma Sound on the toe-of-slope of the southeastern part of Great Bahama Bank during ODP Leg 101. The top 55 m, collected as a suite of six approximately 9.5-m-long hydraulic piston cores, represents a Pliocene-Pleistocene sequence of periplatform carbonate ooze, a mixture of pelagic calcite (foraminifer and coccolith tests), some pelagic aragonite (pteropod tests), and bank-derived fine aragonite and magnesian calcite. A 1.6-m.y.-long hiatus was identified at 43.75 mbsf using calcareous nannofossil biostratigraphy and magnetostratigraphy. The 43.75-m-thick periplatform sequence above the hiatus is a complete late Pliocene-Quaternary record of the past 2.15 m.y. The d18O curve, primarily based on Globigerinoides sacculifera, clearly displays high-frequency/low-amplitude cycles during the early Pleistocene and low-frequency/high-amplitude cycles during the middle and late Pleistocene. Variations in aragonite content in the fine fraction of the periplatform ooze show a cyclic pattern throughout the Pleistocene, as previously observed in piston cores of the upper Pleistocene. These variations correlate well with the d18O record: high aragonite corresponds to light interglacial d18O values, and vice versa. Comparison of the d18O record and the aragonite curve helps to identify 23 interglacial and glacial oxygen-isotope stages, corresponding to 10.5 aragonite cycles (labeled A to K) commonly established during the middle and late Pleistocene (0.9 Ma-present). Strictly based on the aragonite curve, another 11 aragonite cycles, labeled L to V, were identified for the early Pleistocene (0.9 to 1.6 Ma). Mismatches between the d18O record and the aragonite curve occur mainly at some of the glacial-to-interglacial transitions, where aragonite increases usually lag behind d18O depletion. When one visually connects the minima on the Pleistocene aragonite curve, low-frequency (0.4 to 0.5 m.y.) supercycles seem to be superimposed on the high-frequency cycles. The timing of this supercycle roughly matches the timing of the Pleistocene carbonate preservation supercycles described in the Pacific, Indian, and Atlantic oceans. Mismatches between aragonite and d18O cycles are even more obvious for the late Pliocene (1.6 to 2.15 Ma). Irregular aragonite variations are observed for the late Pliocene, although after the onset of late Pleistocene-like glaciations in the North Atlantic Ocean 2.4 m.y. ago the d18O record has shown a mode of high-frequency/low-amplitude cycles. Initiation of climatically induced aragonite cycles occurs only at the Pliocene-Pleistocene transition, 1.6 m.y. ago. After that time, aragonite cycles are fully developed throughout the Quaternary. The 11-m-thick periplatform sequence below the hiatus represents a lower Pliocene interval between 3.75 and 4.45 Ma. The bottom half (4.25-4.45 Ma) has a fairly constant, high aragonite content (averaging 60%) and high sedimentation rates (28 m/m.y.) and corresponds to the end of the prolonged early Pliocene interglacial interval (4.1-5.0 Ma), established as a worldwide high sea-level stand. The second half (3.75-4.25 Ma), in which aragonite content decreases by successive steps, paralleled by a gradual 5180 enrichment in Globigerinoides sacculifera and low sedimentation rates (10 m/m.y), corresponds to the climatic deterioration established worldwide between 4.1 and 3.8 Ma, to a decrease of carbonate preservation observed in the equatorial Pacific Ocean, and to a global sea-level decline. Dolomite, a ubiquitous secondary component in the lower Pliocene, is interpreted as being authigenic and possibly related to diagenetic transformation of primary bank-derived fine magnesian calcite. Transformation of the primary mineralogical composition of the periplatform ooze was evidently minor, as the sediments have retained a detailed record of the Pliocene-Pleistocene climatic evolution. Clear evidence of diagenetic transformations in the periplatform ooze includes (1) the disappearance of magnesian calcite in the upper 20 m of Hole 633A, (2) the occurrence of calcite overgrowths on foraminiferal tests and microclasts at intermittent chalky core levels, and (3) the ubiquitous presence of authigenic dolomite in the lower Pliocene.

Incubation experiments to examine the production and loss of CH3I in surface seawater

In order to investigate production pathways of methyl iodide and controls on emissions from the surface ocean, a set of repeated in-vitro incubation experiments were performed over an annual cycle in the context of a time-series of in-situ measurements in Kiel Fjord (54.3 N, 10.1E). The incubation experiments revealed a diurnal variation of methyl iodide in samples exposed to natural light, with maxima during day time and losses during night hours. The amplitude of the daily accumulation varied seasonally and was not affected by filtration (0.2µm), consistent with a photochemical pathway for CH3I production. The methyl iodide loss rate during night time correlated with the concentration accumulated during daytime. Daily (24 hour) net production (Pnet) was similar in magnitude between in vitro and in situ mass balances. However, the estimated gross production (Pgross) of methyl iodide ranged from -0.07 to 2.24 pmol/day and were 5 times higher in summer than Pnet calculated from the in-situ study [Shi et al., 2014]. The large excess of Pgross over Pnet revealed by the in-vitro (incubation) experiments in summer is a consequence of large losses of CH3I by as-yet uncharacterized processes (e.g. biological degradation or chemical pathways other than Cl- substitution).

Halogen deposition in polar snow and ice

The atmospheric chemistry of iodine and bromine in polar regions is of interest due to the key role of halogens in many atmospheric processes, particularly tropospheric ozone destruction. Bromine is emitted from the open ocean but is enriched above first-year sea ice during springtime bromine explosion events, whereas iodine is emitted from biological communities hosted by sea ice. It has been previously demonstrated that bromine and iodine are present in Antarctic ice over glacial-interglacial cycles. Here we investigate seasonal variability of bromine and iodine in polar snow and ice, to evaluate their emission, transport and deposition in Antarctica and the Arctic and better understand potential links to sea ice. We find that bromine enrichment (relative to sea salt content) and iodine concentrations in polar ice do vary seasonally in Arctic snow and Antarctic ice and we relate such variability to satellite-based observations of tropospheric halogen concentrations. Peaks of bromine enrichment in Arctic snow and Antarctic ice occur in spring and summer, when sunlight is present. Iodine concentrations are largest in winter Antarctic ice strata, contrary to contemporary observations of summer maxima in iodine emissions.

(Table 1) Concentrations of Os, Ir, Pt and 187Os/188Os ratio in ODP Hole 130-806C samples

New osmium (Os) isotope and platinum group element (PGE) concentration data are used in conjunction with published 3He and Th isotope data to determine the relative proportions of lithogenic, extraterrestrial and hydrogenous iridium (Ir) in a Pacific pelagic carbonate sequence from the Ocean Drilling Program (ODP) Site 806 on the Ontong Java Plateau (OJP). These calculations demonstrate that lithogenic and extraterrestrial contributions to sedimentary Ir budget are minor, while hydrogenous Ir accounts for roughly 85% of the total Ir. Application of analogous partitioning calculations to previously reported data from a North Pacific red clay sequence (LL44-GPC3) yields very similar results. Total Ir burial fluxes at Site 806 and LL44-GPC3 are also similar, 45 and 30 pg/cm**2/kyr, respectively. Average Ir/3He and Ir/xs230Th_initial ratios calculated from the entire Site 806 data set are similar to those reported earlier for Pacific sites. In general, down-core profiles of Ir, 3He and xs230Th_initial, are not well correlated with one another. However, all three data sets show similar variance and yield sediment mass accumulation rate estimates that agree within a factor of two. While these results indicate that Ir concentration has potential as a point-paleoflux tracer in pelagic carbonates, Ir-based paleoflux estimates are likely subject to uncertainties that are similar to those associated with Co-based paleoflux estimates. Consequently, local calibration of Ir flux in space and time will be required to fully assess the potential of Ir as a point paleoflux tracer. Measured 187Os/188Os of the OJP sediments are systematically lower than the inferred 187Os/188Os of contemporaneous seawater and a clear glacial-interglacial 187Os/188Os variation is lacking. Mixing calculations suggest Os contributions from lithogenic sources are insufficient to explain the observed 187Os/188Os variations. The difference between the 187Os/188Os of bulk sediment and that of seawater is interpreted in terms of subtle contributions of unradiogenic Os carried by particulate extraterrestrial material. Down-core variations of 187Os/188Os with Pt/Ir and Os/Ir also point to contributions from extraterrestrial particles. Mixing calculations for each set of several triplicate analyses suggest that the unradiogenic Os end member cannot be characterized by primary extraterrestrial particles of chondritic composition. It is noteworthy that in efforts aimed at determining the effect of extraterrestrial contributions, 187Os/188Os of pelagic carbonates has greater potential compared to abundances of PGE. An attempt has been made for the first time to estimate sediment mass accumulation rates based on amount of extraterrestrial Os in the OJP samples and previously reported extraterrestrial Os flux. Throughout most of the OJP record, Os isotope-based paleoflux estimates are within a factor of two of those derived using other constant flux tracers. Meaningful flux estimates cannot be made during glacial maxima because the OJP sediments do not record the low 187Os/188Os reported previously. We speculate that this discrepancy may be related to focusing of extraterrestrial particles at the OJP, as has been suggested to explain down-core 3He variations.

(Table 1) Concentrations of CaCO3 and organic carbon, organic matter atomic C/N ratios and delta13C values of sediment samples from Site DSDP 594

CaCO3 and total organic carbon concentrations, organic matter C/N and carbon isotope ratios, and sediment accumulation rates in late Quaternary sediments from DSDP Site 594 provide information about glacial-interglacial variations in the delivery of organic matter to the Chatham Rise offshore of southeastern New Zealand. Low C/N ratios and nearly constant organic delta13C values of ?23? indicate that marine production dominates organic matter supply in both glacial and interglacial times during oxygen isotope stages 1 through 6 (0-140 ka) and 17 through 19 (660-790 ka). Increased organic carbon mass accumulation rates in isotope stages 2, 4, 6, and 18 record enhanced marine productivity during glacial maxima. Excursions of organic delta13C values to ca. ?29? in portions of isotope stage 2 suggest that the local concentration of dissolved CO2 was occasionally elevated during the last glacial maximum, probably as a result of short periods of lowered sea-surface temperature. Dilution of carbonates by clastic continental sediment generally increases at this location during glacial maxima, but enhanced delivery of land-derived organic matter does not accompany the increased accumulation of clastic sediments.

(Table 1) Age and sedimentation rates of Pleistocene/Holocene sequences at DSDP Sites 86-580 and 94-611

The recovery from the North Atlantic (Site 611) of a continuous Pleistocene sedimentary record with a siliceous microfaunal component made it possible to compare the high-latitude abundance pattern of the radiolarian species Cycladophora davisiana in the Atlantic with that produced from analyses of a high-latitude record (Site 580) from the northwest Pacific. Previous studies had shown that the late Pleistocene (0-0.45 Ma) abundance variations of this species in these high-latitude regions were similar. Cycladophora davisiana maxima in the North Atlantic record reach abundance levels three to four times higher than C. davisiana maxima registered in sediments from the northwest Pacific site. This difference in magnitude of abundance peaks is most likely an effect of the more northerly location of Site 611 (53°N) compared with that of Site 580 (42°N), since high-latitude time-slice studies have shown a direct relationship between increasing latitude and C. davisiana abundance. Discontinuous preservation of radiolarians in sediments from North Atlantic Site 611 allows only tentative correlation of the North Atlantic and northwest Pacific C. davisiana abundance curves. These correlations are confined to those portions of the cores where ages are tightly constrained by magnetic boundaries, and to intervals with comparable sedimentation rates.

Planktonic foraminiferal abundances and stable isotope ratios in middle Miocene sediments of the North Atlantic and the southwestern Pacific

A three-fold expansion of the Antarctic ice sheet at 13.60, 12.82, and 11.60 Ma has been inferred from delta18O maxima analyzed in planktonic and benthic foraminiferal tests, although accompanying changes in sea surface temperature have not been detailed. We present estimated changes in middle Miocene surface-water temperatures based on analysis of delta18O in planktonic foraminifera collected at mid-latitude Deep Sea Drilling Project sites in the North Atlantic and South Pacific oceans. We also identify periods of ice-sheet growth based on comparisons of benthic and planktonic foraminiferal delta18O values. Our results indicate: (1) a distinct cooling of the sea surface from 13.6 to 13.5 Ma immediately following a peak in ice volume at 13.6 Ma, (2) a cooling of the sea surface during a period of increasing ice volume from 13.2 to 13.0 Ma, and (3) a development of the Antarctic ice sheet during a period of cooling of the sea surface centered at 11.6 Ma.

Dissolved iron measured along surface transects of the CARUSO-EISENEX experiment

Measurements of Fe(II) and H2O2 were carried out in the Atlantic sector of the Southern Ocean during EisenEx, an iron enrichment experiment. Iron was added on three separate occasions, approximately every 8 days, as a ferrous sulfate (FeSO4) solution. Vertical profiles of Fe(II) showed maxima consistent with the plume of the iron infusion. While H2O2 profiles revealed a corresponding minima showing the effect of oxidation of Fe(II) by H2O2, observations showed detectable Fe(II) concentrations existed for up to 8 days after an iron infusion. H2O2 concentrations increased at the depth of the chlorophyll maximum when iron concentrations returned to pre-infusion concentrations (<80 pM) possibly due to biological production related to iron reductase activity. In this work, Fe(II) and dissolved iron were used as tracers themselves for subsequent iron infusions when no further SF6 was added. EisenEx was subject to periods of weak and strong mixing. Slow mixing after the second infusion allowed significant concentrations of Fe(II) and Fe to exist for several days. During this time, dissolved and total iron in the infusion plume behaved almost conservatively as it was trapped between a relict mixed layer and a new rain-induced mixed layer. Using dissolved iron, a value for the vertical diffusion coefficient Kz=6.7±0.7 cm**2/s was obtained for this 2-day period. During a subsequent surface survey of the iron-enriched patch, elevated levels of Fe(II) were found in surface waters presumably from Fe(II) dissolved in the rainwater that was falling at this time. Model results suggest that the reaction between uncomplexed Fe(III) and O2? was a significant source of Fe(II) during EisenEx and helped to maintain high levels of Fe(II) in the water column. This phenomenon may occur in iron enrichment experiments when two conditions are met: (i) When Fe is added to a system already saturated with regard to organic complexation and (ii) when mixing processes are slow, thereby reducing the dispersion of iron into under-saturated waters.

Middle Miocene isotope stratigraphy and paleoceanographic evolution of the northwest and southwest Australian margins (Wombat Plateau and Great Australian Bight)

The benthic stable isotope record from ODP Site 761 (Wombat Plateau, NW Australia, 2179.3 m water depth) documents complete recovery of the middle Miocene delta13C excursion corresponding to the climatic optimum and subsequent expansion of the East Antarctic Ice Sheet. The six main delta13C maxima of the "Monterey Excursion" between 16.4 and 13.6 Ma and the characteristic stepped increase in delta18O between 14.5 and 13.9 Ma are clearly identified. The sedimentary record of the shallower ODP Sites 1126 and 1134 [Great Australian Bight (GAB), SWAustralia, 783.8 and 701 m water depth, respectively] is truncated by several unconformities. However, a composite benthic stable isotope curve for these sites provides a first middle Miocene bathyal record for southwest Australia. The delta18O and delta13C curves for Sites 1126 and 1134 indicate a cooler, better-ventilated water mass at ~700 m water depth in the Great Australian Bight since approximately 16 Ma. This cooler and younger water mass probably originated from a close southern source. Cooling of the bottom water at ~16 Ma started much earlier than at other sites of equivalent paleodepths in the central and western parts of the Indian Ocean. At Site 761, the delta18O curve shows an excellent match with the global sea level curve between ~11.5 and 15.1 Ma, and thus closely reflects changes in global ice volume. Prior to 15.1 Ma, the mismatch between the delta18O curve and the sea level curve indicates that delta18O fluctuations are mainly due to changes in bottom water temperature.

Benthic foraminiferal assemblages and epifaunal isotope record of the Agulhas Plateau

Benthic foraminiferal assemblages and the carbon isotope composition of the epifaunal benthic foraminifera Epistominella exigua and Fontbotia wuellerstorfi have been investigated along core MD02-2589 located at the southern Agulhas Plateau (41°26.03'S, 25°15.30'E, 2660 m water depth). This study aims to evaluate changes in the benthic paleoenvironment and its influence on benthic d13C with a notable focus on E. exigua, a species associated with phytodetritus deposits and poorly studied in isotope paleoceanographic reconstructions. The benthic foraminiferal assemblages (>63 µm) show large fluctuations in species composition suggesting significant changes in the pattern of ocean surface productivity conceivably related to migrations of the Subtropical Convergence (STC) and Subantarctic Front (SAF). Low to moderate seasonality and relatively higher food supply to the seafloor are indicated during glacial marine isotope stages (MIS) 6, 4, and 2 and during MIS 3, probably associated with the northward migration of the SAF and confluence with the more stationary STC above the southern flank of the Agulhas Plateau. The lowest organic carbon supply to the seafloor is indicated from late MIS 5b to MIS 4 as a consequence of increased influence of the Agulhas Front (AF) and/or weakening of the influence of the STC over the region. Episodic delivery of fresh organic matter, similar to modern conditions at the core location, is indicated during MIS 5c-MIS 5e and at Termination I. Comparison of this paleoenvironmental information with the paired d13C records of E. exigua and F. wuellerstorfi suggests that organic carbon offsets d13C of E. exigua from ambient bottom water d13CDIC, while its d13C amplitude, on glacial-interglacial timescales, does not seem affected by changes of organic carbon supply to the seafloor. This suggests that this species calcifies preferentially during the short time span of the year when productivity peaks and phytodetritus is delivered to the seafloor. Therefore E. exigua, while offset from d13CDIC, potentially more faithfully records the amplitude of ambient bottom water d13CDIC changes than F. wuellerstorfi, notably in settings such as the Southern Ocean that experienced substantial changes through time in the organic carbon supply to the seafloor.

Absolute abundances of benthic foraminifers and stable isotopes from the Alvin dives 3709-3712

The presence of gas hydrates on the Blake Ridge diapir, northeastern Atlantic Ocean, offers an opportunity to study the impact of methane seepage on the ecology and geochemistry of benthic foraminifera in the late Holocene. Three push cores, covering a time span of ~ 1000 yrs, were retrieved from three distinct microhabitats at the top of the diapir at a water depth of ~ 2150 m: (i) sediments away from seepage (control core), (ii) sediments overlain by clusters of methanotrophic and thiotrophic bivalves, and (iii) chemoautotrophic microbial mats. The foraminiferal assemblages at the two seep sites are marked by a reduction in benthic foraminiferal species diversity, coupled with a near-absence of agglutinated species. However, an opportunistic population rise in CH4- or H2S-tolerant calcareous species (e.g., Globocassidulina subglobosa and Cassidulina laevigata) that utilize the abundant trophic resources at the seeps has led to an increase in the overall assemblage density there. The delta18O and delta13C values of three species of benthic foraminifera - Gyroidinoides laevigatus, Globocassidulina subglobosa, and Uvigerina peregrina - and the planktonic species Globorotalia menardii were acquired from all three cores. The benthic species from methane seeps yield delta13C values of 0.1 to - 4.2 (per mil VPDB), that are distinctly more 13C-depleted relative to the delta13C of 0.4 to - 1.0 (per mil VPDB) at the control (off seep) site. The species from a mussel-bed site exhibit more negative delta13C values than those from microbial mats, possibly reflecting different food sources and higher rate of anaerobic oxidation of methane. The positive delta13C values in the paired planktonic species suggest that authigenic carbonate precipitation did not overprint the observed 13C depletions. Hence the probable cause of negative delta13C of benthic foraminifera is primary calcification from Dissolved Inorganic Carbon (DIC) containing mixed carbon fractions from (a) highly 13C-depleted, microbially-oxidized methane and (b) a seawater source.