Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Seagrass and associated benthic community data derived from field surveys at Low Isles, Great Barrier Reef, conducted July-August, 1997

The distribution of seagrass and associated benthic communities on the reef and lagoon of Low Isles, Great Barrier Reef, was mapped between the 29 July and 29 August 1997. For this survey, observers walked or free-dived at survey points positioned approximately 50 m apart along a series of transects. Visual estimates of above-ground seagrass biomass and % cover of each benthos and substrate type were recorded at each survey point. A differential handheld global positioning system (GPS) was used to locate each survey point (accuracy ±3m). A total of 349 benthic survey points were examined. To assist with mapping meadow/habitat type boundaries, an additional 177 field points were assessed and a georeferenced 1:12,000 aerial photograph (26th August 1997) was used as a secondary source of information. Bathymetric data (elevation below Mean Sea Level) measured at each point assessed and from Ellison (1997) supplemented information used to determine boundaries, particularly in the subtidal lagoon. 127.8 ±29.6 hectares was mapped. Seagrass and associated benthic community data was derived by haphazardly placing 3 quadrats (0.25m**2) at each survey point. Seagrass above ground biomass (standing crop, grams dry weight (g DW m**-2)) was determined within each quadrat using a non-destructive visual estimates of biomass technique and the seagrass species present identified. In addition, the cover of all benthos was measured within each of the 3 quadrats using a systematic 5 point method. For each quadrat, frequency of occurrence for each benthic category was converted to a percentage of the total number of points (5 per quadrat). Data are presented as the average of the 3 quadrats at each point. Polygons of discrete seagrass meadow/habitat type boundaries were created using the on-screen digitising functions of ArcGIS (ESRI Inc.), differentiated on the basis of colour, texture, and the geomorphic and geographical context. The resulting seagrass and benthic cover data of each survey point and for each seagrass meadow/habitat type was linked to GPS coordinates, saved as an ArcMap point and polygon shapefile, respectively, and projected to Universal Transverse Mercator WGS84 Zone 55 South.

Decade Wind and Wave Data for NW Iberia, Cabo Sillerio

Seafloor sediment mobilization on the inner Northwest Iberian continental shelf is caused largely by ocean surface waves. The temporal and spatial variability in the wave height, wave period, and wave direction has a profound effect on local sediment mobilization, leading to distinct sediment mobilization scenarios. Six grain-size specific sediment mobilization scenarios, representing seasonal average and storm conditions, were simulated with a physics-based numerical model. Model inputs included meteorological and oceanographic data in conjunction with seafloor grain-size and the shelf bathymetric data. The results show distinct seasonal variations, most importantly in wave height, leading to sediment mobilization, specifically on the inner shelf shallower than 30 m water depth where up to 49% of the shelf area is mobilized. Medium to severe storm events are modeled to mobilize up to 89% of the shelf area above 150 m water depth. The frequency of each of these seasonal and storm-related sediment mobilization scenarios is addressed using a decade of meteorological and oceanographic data. The temporal and spatial patterns of the modeled sediment mobilization scenarios are discussed in the context of existing geological and environmental processes and conditions to assist scientific, industrial and environmental efforts that are directly affected by sediment mobilization. Examples, where sediment mobilization plays a vital role, include seafloor nutrient advection, recurrent arrival of oil from oil-spill-laden seafloor sediment, and bottom trawling impacts.

Stable Water Isotopologue data collected during HCCT-2010

Cloud samples for the isotopic analysis were collected in the framework of the Hill Cap Cloud Thuringia 2010 (HCCT-2010) campaign on Schmücke (50° 39'N/ 10° 46'E, 937 m a.s.l.; Germany) in September and October 2010 with a three-stage Caltech Active Strand Cloudwater Collector (CASCC) during 13 different cloud events with a temporal resolution of 1 to 3 hours. In a first step, we ensured that no additional fractionation occurred during sampling with the CASCC. The d values of the three sizes classes of the CASCC (4 µm to 16 µm, 16 µm to 22 µm and >22 µm) did not differ significantly, revealing that the cloud droplets of different sizes quickly equilibrate their delta value with the one of the surrounding vapor. delta values in the cloud droplets varied from -77 per mil to -15 per mil in d2H and from -12.1 per mil to -3.9 per mil in d18O and were fitted by d2H =7.8*d18O +13*10**-3. delta values decreased with temperature as well as towards the end of the campaign, representing a seasonal trend which is known from d values in precipitation. The deuterium excess of the cloud samples was generally higher than the Local Meteoric Water Line of the closest GNIP (Global Network of Isotopes in Precipitation) station. Rain decreases its deuterium excess during falling through an unsaturated air column, while the cloud droplets conserve the deuterium excess of the initial evaporation and thus have been found to be a good indicator for the airmass source region: higher deuterium excess was measured for polar air masses and lower deuterium excess for Mediterranean air masses. Changes in d values during one cloud event were up to 3.6 per mil (d2H) and 0.23 per mil (d18O), except for frontal passages, which were associated with increases of ~6 per mil per hour (d2H) and ~0.6 per mil per hour (d18O). Using a box model, we showed that the influence of condensation only was able to explain the variation in the isotope signal of two cloud passages. Consequently, we deduced that the water vapor "feeding" the cloud advected the measured changes. A trajectory analysis and moisture source diagnostic revealed that it is very likely that the variations were either related to rain out along the trajectories or to meteorological changes in the moisture source region. This was the first study using stable water isotopologues in cloud water manifesting their potential in the context of atmospheric water vapor circulation.

Geochemical data and magnetic measurements of IODP Expedition 308, Hole U1319A from the Gulf of Mexico

A 160 m mostly turbiditic late Pleistocene sediment sequence (IODP Expedition 308, Hole U1319A) from the Brazos-Trinity intraslope basin system off Texas was investigated with paleo- and rock magnetic methods. Numerous layers depleted in iron oxides and enriched by the ferrimagnetic iron-sulfide mineral greigite (Fe3S4) were detected by diagnostic magnetic properties. From the distribution of these layers, their stratigraphic context and the present geochemical zonation, we develop two conceptual reaction models of greigite formation in non-steady depositional environments. The "sulfidization model" predicts single or twin greigite layers by incomplete transformation of iron monosulfides with polysulfides around the sulfate methane transition (SMT). The "oxidation model" explains greigite formation by partial oxidation of iron monosulfides near the iron redox boundary during periods of downward shifting oxidation fronts. The stratigraphic record provides evidence that both these greigite formation processes act here at typical depths of about 12-14 mbsf and 3-4 mbsf. Numerous "fossil" greigite layers most likely preserved by rapid upward shifts of the redox zonation denote past SMT and sea floor positions characterized by stagnant hemipelagic sedimentation conditions. Six diagenetic stages from a pristine magnetite-dominated to a fully greigite-dominated magnetic mineralogy were differentiated by combination of various hysteresis and remanence parameters.

Environmental context of selected samples from the Tara Oceans Expedition (2009-2013)

The present data set provides contextual environmental data for samples from the Tara Oceans Expedition (2009-2013) that were selected for publication in a special issue of the SCIENCE journal (see related references below). The data set provides calculated averages of mesaurements made at the sampling location and depth, calculated averages from climatologies (AMODIS, VGPM) and satellite products.

Environmental context of a compilation about the distribution of large protists from the Infrakingdom Rhizaria in the global ocean

The present data set provides environmental context to a worldwide compilation from 11 oceanographic expeditions during which an underwater vision profiler (UVP) was deployed in situ to determine the vertical distribution plankton larger than 600 µm, belonging to the Infrakingdom Rhizaria.

Contextual classification of full waveform lidar data in the Wadden Sea

The classification of airborne lidar data is a relevant task in different disciplines. The information about the geometry and the full waveform can be used in order to classify the 3D point cloud. In Wadden Sea areas the classification of lidar data is of main interest for the scientific monitoring of coastal morphology and habitats, but it becomes a challenging task due to flat areas with hardly any discriminative objects. For the classification we combine a Conditional Random Fields framework with a Random Forests approach. By classifying in this way, we benefit from the consideration of context on the one hand and from the opportunity to utilise a high number of classification features on the other hand. We investigate the relevance of different features for the lidar points in coastal areas as well as for the interaction of neighbouring points.

Environmental conditions and habitats of GOS sites and bottle data of HOT-ALOHA station

The Global Ocean Sampling (GOS) expedition is currently the largest and geographically most comprehensive metagenomic dataset, including samples from the Atlantic, Pacific, and Indian Oceans. This study makes use of the wide range of environmental conditions and habitats encompassed within the GOS sites in order to investigate the ecological structuring of bacterial and archaeal taxon ranks. Community structures based on taxonomically classified 16S ribosomal RNA (rRNA) gene fragments at phylum, class, order, family, and genus rank levels were examined using multivariate statistical analysis, and the results were inspected in the context of oceanographic environmental variables and structured habitat classifications. At all taxon rank levels, community structures of neritic, oceanic, estuarine biomes, as well as other exotic biomes (salt marsh, lake, mangrove), were readily distinguishable from each other. A strong structuring of the communities with chlorophyll a concentration and a weaker yet significant structuring with temperature and salinity were observed. Furthermore, there were significant correlations between community structures and habitat classification. These results were used for further investigation of one-to-one relationships between taxa and environment and provided indications for ecological preferences shaped by primary production for both cultured and uncultured bacterial and archaeal clades.

Biodiversity context of all samples from 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 biodiversity context to all samples from the Tara Oceans Expedition (2009-2013), including various diversity indexes calculated for the sampling location using satellite and model climatologies (Darwin project, Physat) and results from the sequencing of Tara Oceans samples.

Environmental context of all samples from the Tara Oceans Expedition (2009-2013), about depth specific features

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 environmental context to all samples from the Tara Oceans Expedition (2009-2013), including calculated averages of mesaurements made concurrently at the sampling location and depth, and calculated averages from climatologies (AMODIS, VGPM) and satellite products.

Registry of samples and environmental context from the Ocean Sampling Day 2014

The Ocean Sampling Day (OSD) is a simultaneous sampling campaign of the world's oceans which took place (for the first time) on the summer solstice (June 21st) in the year 2014. These cumulative samples, related in time, space and environmental parameters, provide insights into fundamental rules describing microbial diversity and function and contribute to the blue economy through the identification of novel, ocean-derived biotechnologies. We see OSD data as a reference data set for generations of experiments to follow in the coming decade. The present data set includes a description of each sample collected during the Ocean Sampling Day 2014 and provides contextual environmental data measured concurrently with the collection of water samples for genomic analyses.

Environmental context of all samples from the Tara Oceans Expedition (2009-2013), about mesoscale features

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 environmental context to all samples from the Tara Oceans Expedition (2009-2013), about mesoscale features related to the sampling date, time and location. Includes calculated averages of mesaurements made concurrently at the sampling location and depth, and calculated averages from climatologies (AMODIS, VGPM) and satellite products.

Maize Stress DIESI-MS Data and R Script

Climatic change is an increasing challenge for agriculture that is driving the development of suitable crops in order to ensure supply for both human nutrition and animal feed. In this context, it is increasingly important to understand the biochemical responses of cells to environmental cues at the whole system level, an aim that is being brought closer by advances in high throughput, cost-efficient plant metabolomics. To support molecular breeding activities, we have assessed the economic, technical and statistical feasibility of using direct mass spectrometry methods to evaluate the physiological state of maize (Zea mays L.) plants grown under different stress conditions.

Stickleback F2 generation transgenerational plasticity experiment: egg and body size data

Nongenetic inheritance mechanisms such as transgenerational plasticity (TGP) can buffer populations against rapid environmental change such as ocean warming. Yet, little is known about how long these effects persist and whether they are cumulative over generations. Here, we tested for adaptive TGP in response to simulated ocean warming across parental and grandparental generations of marine sticklebacks. Grandparents were acclimated for two months during reproductive conditioning, whereas parents experienced developmental acclimation, allowing us to compare the fitness consequences of short-term vs. prolonged exposure to elevated temperature across multiple generations. We found that reproductive output of F1 adults was primarily determined by maternal developmental temperature, but carry-over effects from grandparental acclimation environments resulted in cumulative negative effects of elevated temperature on hatching success. In very early stages of growth, F2 offspring reached larger sizes in their respective paternal and grandparental environment down the paternal line, suggesting that other factors than just the paternal genome may be transferred between generations. In later growth stages, maternal and maternal granddam environments strongly influenced offspring body size, but in opposing directions, indicating that the mechanism(s) underlying the transfer of environmental information may have differed between acute and developmental acclimation experienced by the two generations. Taken together, our results suggest that the fitness consequences of parental and grandparental TGP are highly context dependent, but will play an important role in mediating some of the impacts of rapid climate change in this system.