Properties of seawater and particulate matter from a WETLabs ALFA hyperspectral laser spectrofluorometer mounted on the continuous surface water sampling system during the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides continuous measurements made with an Aquatic Laser Fluorescence Analyzer (ALFA) (Chekalyuk et al., 2014), connected in-line to the TARA flow through system during 2013. The ALFA instrument provides dual-wavelength excitation (405 and 514 nm) of laser-stimulated emission (LSE) for spectral and temporal analysis. It offers in vivo fluorescence assessments of phytoplankton pigments, biomass, photosynthetic yield (Fv/Fm), phycobiliprotein (PBP)-containing phytoplankton groups, and chromophoric dissolved organic matter (CDOM) (Chekalyuk and Hafez, 2008; 2013A). Spectral deconvolution (SDC) is used to assess the overlapped spectral bands of aquatic fluorescence constituents and water Raman scattering (R). The Fv/Fm measurements are spectrally corrected for non-chlorophyll fluorescence background produced by CDOM and other constituents (Chekalyuk and Hafez, 2008). The sensor was cleaned weakly following the manufacturer recommended protocol.

Analysis of temporal microbial properties from experimental plots of the Jena experiment (2003-2014)

The study was carried out on the main plots (Main Experiment) of a large grassland biodiversity experiment, the Jena Experiment. In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. This data set consists of standard deviation (SD), mean and stability (stab) of soil microbial basal respiration (µl O2/h/g dry soil) and microbial biomass carbon (µg C/g dry soil). Data were derived by taking soil samples and measuring basal and substrate-induced microbial respiration with an oxygen-consumption apparatus. Samples for calculating the temporal stability were taken every year in May/June from 2003 to 2014, except in 2005. Oxygen consumption of soil microorganisms in fresh soil equivalent to 3.5 g dry weight was measured at 22°C over a period of 24 h. Basal respiration (µlO2/g dry soil/h) was calculated as mean of the oxygen consumption rates of hours 14 to 24 after the start of measurements. Substrate- induced respiration was determined by adding D-glucose to saturate catabolic enzymes of microorganisms according to preliminary studies (4 mg g-1 dry soil solved in 400 µl deionized water). Maximum initial respiratory response (µl O2/g dry soil/h) was calculated as mean of the lowest three oxygen consumption values within the first 10 h after glucose addition. Microbial biomass carbon (µg C/g dry soil) was calculated as 38 × Maximum initial respiratory response according to prelimiray studies.

A global seasonal surface ocean climatology of phytoplankton types based on CHEMTAX analysis of HPLC pigments

Much advancement has been made in recent years in field data assimilation, remote sensing and ecosystem modeling, yet our global view of phytoplankton biogeography beyond chlorophyll biomass is still a cursory taxonomic picture with vast areas of the open ocean requiring field validations. High performance liquid chromatography (HPLC) pigment data combined with inverse methods offer an advantage over many other phytoplankton quantification measures by way of providing an immediate perspective of the whole phytoplankton community in a sample as a function of chlorophyll biomass. Historically, such chemotaxonomic analysis has been conducted mainly at local spatial and temporal scales in the ocean. Here, we apply a widely tested inverse approach, CHEMTAX, to a global climatology of pigment observations from HPLC. This study marks the first systematic and objective global application of CHEMTAX, yielding a seasonal climatology comprised of ~1500 1°x1° global grid points of the major phytoplankton pigment types in the ocean characterizing cyanobacteria, haptophytes, chlorophytes, cryptophytes, dinoflagellates, and diatoms, with results validated against prior regional studies where possible. Key findings from this new global view of specific phytoplankton abundances from pigments are a) the large global proportion of marine haptophytes (comprising 32 ± 5% of total chlorophyll), whose biogeochemical functional roles are relatively unknown, and b) the contrasting spatial scales of complexity in global community structure that can be explained in part by regional oceanographic conditions. These publicly accessible results will guide future parameterizations of marine ecosystem models exploring the link between phytoplankton community structure and marine biogeochemical cycles.

Grain-size analysis and geochemistry of sediment core GeoB13602-1

Grain-size, terrigenous element and rock magnetic remanence data of Quaternary marine sediments retrieved at the NW African continental margin off Gambia (gravity core GeoB 13602-1, 13°32.71' N, 17°50.96'W) were jointly analyzed by end-member (EM) unmixing methods to distinguish and budget past terrigenous fluxes. We compare and cross-validate the identified single-parameter EM systems and develop a numerical strategy to calculate associated multi-parameter EM properties. One aeolian and two fluvial EMs were found. The aeolian EM is much coarser than the fluvial EMs and is associated with a lower goethite/hematite ratio, a higher relative concentration of magnetite and lower Al/Si and Fe/K ratios. Accumulation rates and grain sizes of the fluvial sediment appear to be primarily constrained by shore distance (i.e., sea-level fluctuations) and to a lesser extent by changes in hinterland precipitation. High dust fluxes occurred during the Last Glacial Maximum (LGM) and during Heinrich Stadials (HS) while the fluvial input remained unchanged. Our approach reveals that the LGM dust fluxes were ~7 times higher than today's. However, by far the highest dust accumulation occurred during HS 1 (~300 g m**-2 yr** -1), when dust fluxes were ~80 fold higher than today. Such numbers have not yet been reported for NW Africa, and emphasize strikingly different environmental conditions during HSs. They suggest that deflation rate and areal extent of HSs dust sources were much larger due to retreating vegetation covers. Beyond its regional and temporal scope, this study develops new, in principle, generally applicable strategies for multi-method end-member interpretation, validation and flux budgeting calibration.

Seagrass time-series analysis products, in Moreton Bay, Australia, with links to GeoTIFFs

The spatial and temporal dynamics of seagrasses have been well studied at the leaf to patch scales, however, the link to large spatial extent landscape and population dynamics is still unresolved in seagrass ecology. Traditional remote sensing approaches have lacked the temporal resolution and consistency to appropriately address this issue. This study uses two high temporal resolution time-series of thematic seagrass cover maps to examine the spatial and temporal dynamics of seagrass at both an inter- and intra-annual time scales, one of the first globally to do so at this scale. Previous work by the authors developed an object-based approach to map seagrass cover level distribution from a long term archive of Landsat TM and ETM+ images on the Eastern Banks (~200 km**2), Moreton Bay, Australia. In this work a range of trend and time-series analysis methods are demonstrated for a time-series of 23 annual maps from 1988 to 2010 and a time-series of 16 monthly maps during 2008-2010. Significant new insight was presented regarding the inter- and intra-annual dynamics of seagrass persistence over time, seagrass cover level variability, seagrass cover level trajectory, and change in area of seagrass and cover levels over time. Overall we found that there was no significant decline in total seagrass area on the Eastern Banks, but there was a significant decline in seagrass cover level condition. A case study of two smaller communities within the Eastern Banks that experienced a decline in both overall seagrass area and condition are examined in detail, highlighting possible differences in environmental and process drivers. We demonstrate how trend and time-series analysis enabled seagrass distribution to be appropriately assessed in context of its spatial and temporal history and provides the ability to not only quantify change, but also describe the type of change. We also demonstrate the potential use of time-series analysis products to investigate seagrass growth and decline as well as the processes that drive it. This study demonstrates clear benefits over traditional seagrass mapping and monitoring approaches, and provides a proof of concept for the use of trend and time-series analysis of remotely sensed seagrass products to benefit current endeavours in seagrass ecology.

Multi-temporal shoreline change rates on Taku Atoll

Recent-past shoreline changes on reef islands are now subject to intensified monitoring via remote sensing data. Based on these data, rates of shoreline change calculated from long-term measurements (decadal) are often markedly lower than recent short-term rates (over a number of years). This observation has raised speculations about the growing influence of sea-level rise on reef island stability. This observation, however, can also be explained if we consider two basic principles of geomorphology and sedimentology. For Takú Atoll, Papua New Guinea, we show that natural shoreline fluctuations of dynamic reef islands have a crucial influence on the calculation of short-term rates of change. We analyze an extensive dataset of multitemporal shoreline change rates from 1943 to 2012 and find that differing rates between long- and short-term measurements consistently reflect the length of the observation interval. This relationship appears independent from the study era and indicates that reef islands were equally dynamic during the early periods of analysis, i.e. before the recent acceleration of sea-level rise. Consequently, we suggest that high rates of shoreline change calculated from recent short-term observations may simply result from a change in temporal scale and a shift from geomorphic equilibrium achieved over cyclic time towards an apparent disequilibrium during shorter periods of graded time. This new interpretation of short- and long-term shoreline change rates has important implications for the ongoing discussion about reef island vulnerability, showing that an observed jump from low to high rates of change may be independent from external influences, including but not limited to sea-level rise.

Tie points and goechemical analysis from different Holes of ODP Site 165-1002

The fine-grained sediments of the Cariaco Basin, Venezuela, of the last 130 ky, whose deposition history is well characterized, were analyzed geochemically in order to test the validity of sediment bulk geochemistry as an indicator of detrital provenance. Several binary and ternary diagrams as well as the chemical index of alteration (CIA) were tested for their capacity to discriminate the poorly contrasted detrital sources to the Cariaco Basin, and to describe the temporal evolution of the contributions of these different sources. Most of the diagrams tested did not allow a good discrimination of sources or, when sources were well discriminated, did not allow an interpretation of the temporal variations consistent with the known history. A relatively good discrimination of sources and a consistent interpretation of temporal variations were however obtained using Hf vs. Th and La/Yb vs. Gd/Yb binary diagrams, as well as Ti-Zr-Th, Ti-Zr-La, and Lu-Hf-Th ternary diagrams. Compared to the previous studies of the detrital content of the Cariaco Basin sediments, the geochemical approach permitted the recognition of a sediment contribution eroded from the Unare platform and Gulf of Cariaco during rapid sea level oscillations, and the contribution of Saharan eolian particles during the Younger Dryas-Preboreal and MIS6-5 transition. The choice of plotted elements was determined after considering carrier minerals, so that different elements may be informative in different sedimentary contexts. Overall, mineral sorting during transport appears as a major limit to quantitative estimation of the different contributions. In particular mineral sorting leads to the selective enrichment of elements associated with clays (Al, Rb, Th and LREE) in sediments deposited in the basin. Unless the geochemical effect of mineral sorting can be measured, it appears that quantitative provenance analysis should be performed on fractions of similar grain size instead of bulk sediment.

Geochemical analysis of nine sections from the Nama Group, Namibia

The first appearance of skeletal metazoans in the late Ediacaran (~550 million years ago; Ma) has been linked to the widespread development of oxygenated oceanic conditions, but a precise spatial and temporal reconstruction of their evolution has not been resolved. Here we consider the evolution of ocean chemistry from ~550 to ~541 Ma across shelf-to-basin transects in the Zaris and Witputs Sub-Basins of the Nama Group, Namibia. New carbon isotope data capture the final stages of the Shuram/Wonoka deep negative C-isotope excursion, and these are complemented with a reconstruction of water column redox dynamics utilising Fe-S-C systematics and the distribution of skeletal and soft-bodied metazoans. Combined, these inter-basinal datasets provide insight into the potential role of ocean redox chemistry during this pivotal interval of major biological innovation. The strongly negative d13C values in the lower parts of the sections reflect both a secular, global change in the C-isotopic composition of Ediacaran seawater, as well as the influence of 'local' basinal effects as shown by the most negative d13C values occurring in the transition from distal to proximal ramp settings. Critical, though, is that the transition to positive d13C values postdates the appearance of calcified metazoans, indicating that the onset of biomineralization did not occur under post-excursion conditions. Significantly, we find that anoxic and ferruginous deeper water column conditions were prevalent during and after the transition to positive d13C that marks the end of the Shuram/Wonoka excursion. Thus, if the C isotope trend reflects the transition to global-scale oxygenation in the aftermath of the oxidation of a large-scale, isotopically light organic carbon pool, it was not sufficient to fully oxygenate the deep ocean. Both sub-basins reveal highly dynamic redox structures, where shallow, inner ramp settings experienced transient oxygenation. Anoxic conditions were caused either by episodic upwelling of deeper anoxic waters or higher rates of productivity. These settings supported short-lived and monospecific skeletal metazoan communities. By contrast, microbial (thrombolite) reefs, found in deeper inner- and mid-ramp settings, supported more biodiverse communities with complex ecologies and large skeletal metazoans. These long-lived reef communities, as well as Ediacaran soft-bodied biotas, are found particularly within transgressive systems, where oxygenation was persistent. We suggest that a mid-ramp position enabled physical ventilation mechanisms for shallow water column oxygenation to operate during flooding and transgressive sea-level rise. Our data support a prominent role for oxygen, and for stable oxygenated conditions in particular, in controlling both the distribution and ecology of Ediacaran skeletal metazoan communities.

Multi-temporal mapping of seagrass cover, species and biomass of the Eastern Banks, Moreton Bay, Australia, with links to shapefiles

The spatial and temporal dynamics of seagrasses have been studied from the leaf to patch (100 m**2) scales. However, landscape scale (> 100 km**2) seagrass population dynamics are unresolved in seagrass ecology. Previous remote sensing approaches have lacked the temporal or spatial resolution, or ecologically appropriate mapping, to fully address this issue. This paper presents a robust, semi-automated object-based image analysis approach for mapping dominant seagrass species, percentage cover and above ground biomass using a time series of field data and coincident high spatial resolution satellite imagery. The study area was a 142 km**2 shallow, clear water seagrass habitat (the Eastern Banks, Moreton Bay, Australia). Nine data sets acquired between 2004 and 2013 were used to create seagrass species and percentage cover maps through the integration of seagrass photo transect field data, and atmospherically and geometrically corrected high spatial resolution satellite image data (WorldView-2, IKONOS and Quickbird-2) using an object based image analysis approach. Biomass maps were derived using empirical models trained with in-situ above ground biomass data per seagrass species. Maps and summary plots identified inter- and intra-annual variation of seagrass species composition, percentage cover level and above ground biomass. The methods provide a rigorous approach for field and image data collection and pre-processing, a semi-automated approach to extract seagrass species and cover maps and assess accuracy, and the subsequent empirical modelling of seagrass biomass. The resultant maps provide a fundamental data set for understanding landscape scale seagrass dynamics in a shallow water environment. Our findings provide proof of concept for the use of time-series analysis of remotely sensed seagrass products for use in seagrass ecology and management.

Compilation of sedimentation rates and smear slide analysis of DSDP sites

A history of Mesozoie and Cenozoic palaeoenvironments of the North Atlantie Oeean has been developed based on a detailed analysis of the temporal and spatial distribution of major pelagie sediment facies, of hiatuses. of bulk sediment accumulation rates, and of concentrations and fluxes of the main deep-sea sediment components. The depositional history of the North Atlantic can be subdivided into three major phase: (a) Late Jurassie and Early Cretaceous phase: clastic terrigenous and biogenic pelagic sediment components accumulated rapidly under highly productive surface water masses over the entire occan basin; (b) Late Cretaceous to Early Miocene phase: relatively little terrigenous and pelagic biogenic sediment reached the North Atlantic Ocean floor, intensive hiatus formation occurred at variable rates, and wide stretches of the deep-ocean floor were covered by slowly accumulating terrigenous muds: (c) Middle Miocene to Recent phase: accumulation rates of biogenic and terrigenous deep-sea sediment components increased dramatically up to Quaternary times, rates of hiatus formation and the intensity of deep-water circulation inferred from them seem to have decreased. However, accumulation rate patterns of calcareous pelagic sediment components suggest that large scale reworking and di splacement of deep-sea sediments occurred at a variable rate over wide areas of the North Atlantic during this period.