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 By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived.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.

Bacterial production in the eastern Mediteranean Sea in October 2008 during SES_GR2

The HCMR_SES_LAGRANGIAN_GR2_ MICROBIAL PARAMETERS dataset is based on samples collected in the framework of the project SESAME, in the North Aegean Sea during October 2008. The objectives were to measure the standing stocks and calculate the production of the microbial compartment of the food web, describe the vertical distribution pattern and characterize its structure and function through the water column as influenced by the BSW. Bacterial production was estimated by the 3H-leucine method (Kirchman et al. 1986, Kirchman 1993). At each depth, duplicate samples and a control were incubated with 20 nM L-[4,5 3H]-leucine. Samples were incubated in the dark, at in situ temperature.

Bacterial production in the eastern Mediterranean Sea in March and April 2008 during SES_GR1

The dataset is based on samples collected in the framework of the project SESAME, in the Ionian, Libyan and Aegean Sea during March- April 2008. The objectives were to measure the standing stocks and calculate the production of the microbial compartment of the food web, describe the vertical distribution pattern and characterize its structure and function through the water column. Bacterial production was estimated by the 3H-leucine method (Kirchman et al. 1986, Kirchman 1993). At each depth, duplicate samples and a control were incubated with 20 nM L-[4,5 3H]-leucine. Samples were incubated in the dark, at in situ temperature.

Bacterial production in the eastern Mediteranean Sea in August and September 2008 during SES_GR2

The SES_GR2_MICROBIAL PARAMETERS dataset is based on samples collected in the framework of the project SESAME, in the Ionian, Libyan and Aegean Sea during August-September 2008. The objectives were to measure the standing stocks and calculate the production of the microbial compartment of the food web, describe the vertical distribution pattern and characterize its structure and function through the water column. Bacterial production was estimated by the 3H-leucine method (Kirchman et al. 1986, Kirchman 1993). At each depth, duplicate samples and a control were incubated with 20 nM L-[4,5 3H]-leucine. Samples were incubated in the dark, at in situ temperature.

Thalassiosira weissflogii attachment assay and phylogenetic affiliation of bacterial isolates from samples of the German Wadden Sea

Aggregation of algae, mainly diatoms, is an important process in marine systems leading to the settling of particulate organic carbon predominantly in the form of marine snow. Exudation products of phytoplankton form transparent exopolymer particles (TEP), which acts as the glue for particle aggregation. Heterotrophic bacteria interacting with phytoplankton may influence TEP formation and phytoplankton aggregation. This bacterial impact has not been explored in detail. We hypothesized that bacteria attaching to Thalassiosira weissflogii might interact in a yet-to-be determined manner, which could impact TEP formation and aggregate abundance. The role of individual T. weissflogii-attaching and free-living new bacterial isolates for TEP production and diatom aggregation was investigated in vitro. T. weissflogii did not aggregate in axenic culture, and striking differences in aggregation dynamics and TEP abundance were observed when diatom cultures were inoculated with either diatom-attaching or free-living bacteria. The data indicated that free-living bacteria might not influence aggregation whereas bacteria attaching to diatom cells may increase aggregate formation. Interestingly, photosynthetically inactivated T. weissflogii cells did not aggregate regardless of the presence of bacteria. Comparison of aggregate formation, TEP production, aggregate sinking velocity and solid hydrated density revealed remarkable differences. Both, photosynthetically active T. weissflogii and specific diatom-attaching bacteria were required for aggregation. It was concluded that interactions between heterotrophic bacteria and diatoms increased aggregate formation and particle sinking and thus may enhance the efficiency of the biological pump.

Bacterial production in the Aegean Sea in April 2008 during SES_GR1

The HCMR_SES_LAGRANGIAN_GR1_ MICROBIAL PARAMETERS dataset is based on samples collected in the framework of the project SESAME, in the North Aegean Sea during April 2008. The objectives were to measure the standing stocks and calculate the production of the microbial compartment of the food web, describe the vertical distribution pattern and characterize its structure and function through the water column as influenced by the BSW. Bacterial production was estimated by the 3H-leucine method (Kirchman et al. 1986, Kirchman 1993). At each depth, duplicate samples and a control were incubated with 20 nM L-[4,5 3H]-leucine. Samples were incubated in the dark, at in situ temperature.

Small Changes in pH Have Direct Effects on Marine Bacterial Community Composition: A Microcosm Approach

As the atmospheric CO2 concentration rises, more CO2 will dissolve in the oceans, leading to a reduction in pH. Effects of ocean acidification on bacterial communities have mainly been studied in biologically complex systems, in which indirect effects, mediated through food web interactions, come into play. These approaches come close to nature but suffer from low replication and neglect seasonality. To comprehensively investigate direct pH effects, we conducted highly-replicated laboratory acidification experiments with the natural bacterial community from Helgoland Roads (North Sea). Seasonal variability was accounted for by repeating the experiment four times (spring, summer, autumn, winter). Three dilution approaches were used to select for different ecological strategies, i.e. fast-growing or low-nutrient adapted bacteria. The pH levels investigated were in situ seawater pH (8.15-8.22), pH 7.82 and pH 7.67, representing the present-day situation and two acidification scenarios projected for the North Sea for the year 2100. In all seasons, both automated ribosomal intergenic spacer analysis and 16S ribosomal amplicon pyrosequencing revealed pH-dependent community shifts for two of the dilution approaches. Bacteria susceptible to changes in pH were different members of Gammaproteobacteria, Flavobacteriaceae, Rhodobacteraceae, Campylobacteraceae and further less abundant groups. Their specific response to reduced pH was often context-dependent. Bacterial abundance was not influenced by pH. Our findings suggest that already moderate changes in pH have the potential to cause compositional shifts, depending on the community assembly and environmental factors. By identifying pH-susceptible groups, this study provides insights for more directed, in-depth community analyses in large-scale and long-term experiments.