• European Marine Science
• Other dataset type close
• ABYSS close
• DE close
• English close

We aimed to explore the community composition and turnover of eukaryotic and bacterial microorganisms associated with ice-associated and sinking algal aggregates, as well as their similarity to potential source communities of sea ice, water and deep-sea sediments using Illumina tag sequencing. We sampled algae aggregates growing in melt ponds on sea ice, deposited algae aggregates at the seafloor in more than 4000 m water depth, sea ice, upper water column, sediment surface and the gut content of holothurians feeding on the deposits. For Illumina sequencing, the Amplicon libraries of the bacterial V4-V6 region of the 16S rRNA gene and the eukaryotic V4 region of the 18S rRNA gene were generated according to the protocol recommended by Illumina (16S Metagenomic Sequencing Library Preparation, Part # 15044223, Rev. B). For Bacteria we selected the S-D-Bact-0564-a-S-15 and S-*Univ-1100-a-A-15 primer pair based on a primer evaluation by Klindworth et al. (2013, doi:10.1093/nar/gks808) and for Eukaryota the TAReukFWD1 and TAReukREV3 primers (Stoeck et al., 2010; doi:10.1111/j.1365-294X.2009.04480.x). Libraries were sequenced on an Illumina MiSeq platform in 2x300 cycles paired end runs. For Sequence data cleaning & processin, we used cutadapt (v. 1.8.1; Martin, 2011; doi:10.14806/ej.17.1.200) for the removal of primer sequences and a custom awk script to ensure the correct orientation of reads prior to merging. For merging forward and reverse reads we used pear (v. 0.9.5; Zhang et al., 2014; doi:10.1093/bioinformatics/btt593) and trimmed and quality filtered all sequences using trimmomatic (v. 0.32; Bolger et al., 2014; doi:10.1093/bioinformatics/btu170). We reassured correct formatting of the fastq files with bbmap (v. 34.00; B. Bushnell - sourceforge.net/projects/bbmap) before clustering the reads into OTUs by applying a local clustering threshold of d=1 and the fastidious option in swarm (v. 2.1.1; Mahé et al., 2015; doi:10.7717/peerj.1420). Subsequently, we used the SINA aligner (v. 1.2.10; Pruesse et al., 2012; doi:10.1093/bioinformatics/bts252) to align and classify the seed sequence of each OTU with the SILVA SSU database release 123 (Quast et al., 2013; doi:10.1093/nar/gks1219). OTUs that were classified as chloroplasts, mitochondria, archaea, or those that could not be classified at domain level were removed from further analysis. OTUs that were classified as bacteria within the eukaryotic dataset and vice versa, were removed as well. Furthermore, we removed all absolute singletons, OTUs that were only represented by a single sequence across the complete dataset. Filtering and removal of absolute singletons resulted in a final number of 8,869 bacterial and 7,627 eukaryotic OTUs. All further analyses were performed on these processed OTU abundance tables. Supplement to: Rapp, Josephine Z; Fernández-Méndez, Mar; Bienhold, Christina; Boetius, Antje (2018): Effects of ice-algal aggregate export on the connectivity of bacterial core communities in the central Arctic Ocean. Frontiers in Microbiology, 9

Sea-ice diatoms are known to accumulate in large aggregates in and under the sea ice including melt ponds. In the Arctic, they can contribute substantially to particle export when sinking from the ice. The role and regulation of microbial aggregation in the highly seasonal, nutrient- and light-limited Arctic sea-ice ecosystem is not yet well understood, and may vary in relation to the fate of the Arctic sea-ice cover. To elucidate the mechanism controlling the formation and export of algal aggregates from sea ice, we investigated samples taken in late summer 2011 and 2012, during two cruises to the Eurasian Basin of the Central Arctic Ocean. Dense, spherical aggregates composed mainly of pennate diatoms, and filamentous aggregates formed by Melosira arctica were found in different degradation stages, with carbon to Chlorophyll a ratios ranging from 110 to 66700, and carbon to nitrogen molar ratios of 8-35 and 9-40, respectively. Fresh sub-ice algal aggregate densities ranged between 1 and 17 aggregates/m**2, corresponding to a net primary production of 0.4-40 mg C/m**2/d, contributing 3-80% of total biomass and up to 94% of total production at a local scale. A key factor controlling buoyancy of the aggregates was light intensity, regulating photosynthetic oxygen production and flotation by gas bubbles trapped within the mucous matrix, even at low ambient nutrient concentrations. Our data was used to evaluate the factors regulating the distribution and importance of the Arctic algal aggregates as carbon source for pelagic and benthic communities. Supplement to: Fernández-Méndez, Mar; Wenzhöfer, Frank; Peeken, Ilka; Sørensen, Heidi L; Glud, Ronnie N; Boetius, Antje; Vopel, Kay (2014): Composition, Buoyancy Regulation and Fate of Ice Algal Aggregates in the Central Arctic Ocean. PLoS ONE, 9(9), e107452

In a multidisciplinary ex situ experiment, benthic bacterial deep-sea communities from 2,500 m water depth at the Long-Term Ecological Research Observatory HAUSGARTEN (stationPS93/050-5 and 6), were retrieved using a TV-guided multiple corer. Surface sediments (0 - 2 cm) of 16 cores were mixed with sterile filtered deep-sea water to a final sediment dilution of 3.5 fold. The slurries were split and supplemented with five different types of habitat-related detritus: chitin, as the most abundant biopolymer in the oceans, and four different naturally occurring Arctic algae species, i.e. Thalassiosira weissflogii, Emiliania huxleyi, Bacillaria sp. and Melosira arctica. Incubations were performed in five replicates, at in situ temperature and at atmospheric pressure, as well as at in situ pressure of 250 atm. At the start of the incubation and after 23 days, changes in key community functions, i.e. extracellular enzymatic activity, oxygen respiration and secondary production of biomass (bacterial cell numbers and biomass), were assessed along with changes in the bacterial community composition based on 16S rRNA gene and 16S rRNA Illumina sequencing. In summary, differences in community structure and in the uptake and remineralization of carbon in the different treatments suggest an effect of organic matter quality on bacterial diversity as well as on carbon turnover at the seafloor. Supplement to: Hoffmann, Katy; Hassenrück, Christiane; Salman-Carvalho, Verena; Holtappels, Moritz; Bienhold, Christina (2017): Response of bacterial communities to different detritus compositions in Arctic deep-sea sediments. Frontiers in Microbiology, 8, 266