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1. Ballast water has been identified as a leading vector for introduction of non-indigenous species (NIS). Recently, the International Maritime Organization (IMO) implemented management standards – D-2 – where all large, commercial ships trading internationally are required to adopt an approved treatment system using technologies such as ultraviolet radiation or chlorination. However, current management regulations are based only on the total abundance of viable taxa transported (i.e., total propagule pressure), largely ignoring species richness (i.e., colonization pressure).2. To determine the efficacy of chlorine treatment in reducing invasion risks and changes in transported biological communities inside ballast tanks, we used DNA metabarcoding-based approaches to estimate colonization pressure (here, the number of species/Operational Taxonomic Units (OTUs) introduced) and relative propagule pressure (relative abundance of each species/OTU) of zooplankton communities in control and chlorine treated tanks during four transatlantic voyages. 3. Our study demonstrated that transport itself did not significantly reduce colonization pressure of zooplankton species, nor did chlorine treatment. Chlorine treatment altered community structure by reducing relative propagule pressure of some taxa such as Mollusca and Rotifera, while increasing relative propagule pressure of some Oligohymenophorea and Copepoda species.4. Synthesis and applications. Chlorine treatment may not reduce invasion risks as much as previously thought. Reduction in total propagule pressure does not mean reduction in abundance of all species equally. While some taxa might experience drastically reduced abundance, others might not change at all or increase due to hatching from dormant stages initiated by chlorine exposure. Therefore, management strategies should consider changes in total propagule pressure and colonization pressure when forecasting risk of new invasions. We therefore recommend adopting new approaches, such as DNA metabarcoding-based methods, to assess the whole biodiversity discharged from ballast water. As species responses to chlorine treatment are variable and affected by concentration, we also recommend a combination of different technologies to reduce introduction risks of aquatic organisms. Supplement to: Lin, Yaping; Zhan, Aibin; Hernandez, Marco R; Paolucci, Esteban; MacIsaac, Hugh J; Briski, Elizabeta (2020): Can chlorination of ballast water reduce biological invasions? Journal of Applied Ecology, 57(2), 331-343 The zip file includes:1. raw_data_clean.fasta: Raw sequence reads of zooplankton in ballast water samples2. raw_data.fasta: OTU representative sequences3. OTU_table.xlsx: OTU table

Table S1 The locations of the 20 pet shops surveyed across Northern Ireland :

Supplement to: Callbeck, Cameron; Lavik, Gaute; Ferdelman, Timothy G; Fuchs, Bernhard M; Gruber-Vodicka, Harald R; Hach, Philipp F; Littmann, Sten; Schoffelen, Niels J; Kalvelage, Tim; Thomsen, Soeren; Schunck, Harald; Löscher, Carolin R; Schmitz, Ruth A; Kuypers, Marcel MM (2018): Oxygen minimum zone cryptic sulfur cycling sustained by offshore transport of key sulfur oxidizing bacteria. The data set includes, sulfide and sulfur concentrations, SUP05 cell densities, as well as denitrification and carbon fixation rates (based on 15N- and 13C-labelled in situ incubation experiments). The transect extends from the sulfidic upper shelf into the sulfide-free offshore oxygen minimum zone.

AbstractDinoflagellates possess many unique cellular characteristics with unresolved evolutionary histories including nuclei with greatly expanded genomes and chromatin packaged using histone-like proteins and dinoflagellate-viral nucleoproteins instead of histones, highly reduced mitochondrial genomes with extensive RNA editing, a mix of photosynthetic and cryptic secondary plastids, and tertiary plastids. Resolving the evolutionary origin of these traits requires understanding their ancestral states and early intermediates. Several deep-branching dinoflagellate lineages are good candidates for such reconstruction, however they tend to be delicate and environmentally sparse, so such analyses are not always simple. Here, we employ transcriptome sequencing from manually-isolated and microscopically documented cells to resolve the placement of two cells of one such genus, Abedinium, collected by ROV in deep waters off the coast of Monterey Bay. One cell corresponds to the only described species, A. dasypus, while the second cell is distinct and formally described as Abedinium folium, sp. nov. Abedinium has classically been assigned to the deep-branching dinoflagellates subgroup Noctilucea, which is weakly supported by phylogenetic analyses of the single characterized gene from any member of the genus, small subunit ribosomal RNA (SSU rRNA). However, a phylogenetic analysis based on 221 proteins from the transcriptome places Abedinium in a distinct lineage, separate from and basal to the Noctilucea and the rest of the core dinoflagellates. The transcriptome also contains evidence of a cryptic plastid functioning in the biosynthesis of isoprenoids, iron-sulfur clusters, and heme, a mitochondrial genome with all three expected protein-coding genes (cob, cox1, and cox3), and the presence of some but not all dinoflagellate-specific chromatin packaging proteins.

Over broad thermal gradients, the effect of temperature on aerobic respiration and photosynthesis rates explains variation in community structure and function. Yet for local communities, temperature dependent trophic interactions may dominate effects of warming. We tested the hypothesis that food chain length modifies the temperature-dependence of ecosystem fluxes and community structure. In a multi-generation aquatic food web experiment, increasing temperature strengthened a trophic cascade, altering the effect of temperature on estimated mass-corrected ecosystem fluxes. Compared to consumer-free and 3-level food chains, grazer-algae (2-level) food chains responded most strongly to the temperature gradient. Temperature altered community structure, shifting species composition and reducing zooplankton density and body size. Still, food chain length did not alter the temperature dependence of net ecosystem fluxes. We conclude that locally, food chain length interacts with temperature to modify community structure, but only temperature, not food chain length influenced net ecosystem fluxes. Supplement to: Garzke, Jessica; Connor, Stephanie J; Sommer, Ulrich; O'Connor, Mary I (2019): Trophic interactions modify the temperature dependence of community biomass and ecosystem function. PLoS Biology, 17(6), e2006806

Marine alveolates (MALVs) are diverse and widespread early-branching dinoflagellates, but most knowledge of the group comes from a few cultured species that are generally not abundant in natural samples, or from diversity analyses of PCR-based environmental SSU rRNA gene sequences. To more broadly examine MALV genomes, we generated single cell genome sequences from seven individually isolated cells. Genes expected of heterotrophic eukaryotes were found, with interesting exceptions like presence of proteorhodopsin and vacuolar H+-pyrophosphatase. Phylogenetic analysis of concatenated SSU and LSU rRNA gene sequences provided strong support for the paraphyly of MALV lineages. Dinoflagellate viral nucleoproteins were found only in MALV groups that branched as sister to dinokaryotes. Our findings indicate that multiple independent origins of several characteristics early in dinoflagellate evolution, such as a parasitic life style, underlie the environmental diversity of MALVs, and suggest they have more varied trophic modes than previously thought. MALV contigsContigs of seven Marine Alveolate (MALV) cells in FASTA format. Contigs were generated using SPAdes assembler; contaminating sequences were removed as described in the publication.MALV_contigs.zip

In April and May 2019, we compiled the “BenBio” part of the “BenBioDen database” following the “Preferred Reporting Items for Systematic reviews and Meta-Analyses” (PRISMA) Statement for systematic reviews and meta-analyses. In the first PRISMA step, the “Identification” step, we identified 1,373 articles in the Web of Science using the key words “marine meiofauna biomass”, “marine macrofauna biomass”, “marine megafauna biomass”, “marine meiobenth* biomass”, “marine macrobenth* biomass”, “marine megabenth* biomass”, “nematode biomass”, and “benthic ‘standing stock’”. We located an additional 201 publications based on expert knowledge. A search of the PANGAEA® Data Publisher (https://www.pangaea.de/) identified 1,488 datasets representing 148 publications using the key words “meiofauna biomass”, “macrofauna biomass” and “megafauna biomass”. Further 30 datasets were found in the EOL data archive (http://data.eol.ucar.edu/), through citations in review papers, and based on expert knowledge. After removing duplicates, we screened the titles and abstracts of 1,445 studies in PRISMA step 2 (“Screening”; Fig. 1A). This step excluded 951 studies because they did not report biomass values. In the Eligibility step, we assessed full texts of 494 studies for eligibility and excluded 110 studies because they did not report biomass, the publications or data were not accessible, or they did not report benthic biomass in appropriate units (g WW m-2, g DW m-2, g AFDW m-2, g or mol C m-2). Further reasons for excluding full texts included combining benthic biomass for several size classes, reporting benthic biomass for particular taxa rather than the whole size class, presenting biomass for faunal assemblages and/ or a group of sampling stations rather than for individual stations, not presenting primary research or lacking geographical details about sampling stations. We also excluded studies that estimated benthic biomass using modelling approaches, that conducted manipulative experiments, or did not report benthic biomass as single values, means or median values, but instead as ranges. The final “BenBio” part included 384 studies from which we extracted 11,792 georeferenced benthic biomass entries. The Benthos Density, i.e. “BenDen”, part of the “BenBioDen” database was established in July and August 2019 following the PRISMA Statement for systematic reviews and meta-analyses. In the Identification step, we found 2,515 articles in the Web of Science using the key words “meiofauna abundance”, “meiobenthos abundance”, “macrofauna abundance”, “macrobenthos abundance”, “megafauna abundance”, “megabenthos abundance”, “meiofauna Arctic Ocean”, “meiofauna Atlantic Ocean”, “meiofauna Black Sea”, “meiofauna Gulf of Mexico”, “meiofauna Indian Ocean”, “meiofauna Mediterranean Sea”, “meiofauna Pacific Ocean”, “meiofauna Southern Ocean”, “meiofauna Red Sea”, “meiofauna Pacific Ocean”, “megafauna Southern Ocean”, “megafauna Red Sea”, “megafauna Pacific Ocean”, “megafauna Mediterranean Sea”, “megafauna Indian Ocean”, “megafauna Black Sea”, “megafauna Gulf of Mexico”, “megafauna Atlantic Ocean”, “megafauna Arctic Ocean”, “macrofauna Arctic Ocean”, “macrofauna Atlantic Ocean”, “macrofauna Black Sea”, “macrofauna Southern Ocean”, “macrofauna Red Sea”, “macrofauna Pacific Ocean”, “macrofauna Gulf of Mexico”, “macrofauna Indian Ocean”, and “macrofauna Mediterranean Sea”. Expert knowledge identified a further 232 publications. Consulting PANGAEA® Data Publisher (https://www.pangaea.de/) identified 1,549 datasets from 172 publications using the key words “meiofauna abundance”, “macrofauna abundance” and “megafauna abundance”. Expert knowledge or unpublished datasets added a further 21 datasets. After removal of duplicates, the “Screening” step filtered 2,086 titles and abstracts and excluded 1,133 studies because they did not report benthic densities. The third PRISMA step assessed 953 studies and excluded 353 studies because they did not report metazoan meiobenthic, macrobenthic, or invertebrate megabenthic densities or they combined multiple size classes or sampling stations. We excluded other studies in the database that reported experimental studies, were inaccessible, or reported densities in a unit other than ind. m-2 or a unit that could be converted to ind. m-2, or reported densities for specific taxa instead of the entire size class. Studies were also excluded when they reported meta-studies or reviews rather than primary research, presented results of models, lacked sufficient geographical detail about sampling locations, or reported fauna associated with whale falls. The final “BenDen” part consisted of 600 studies from which we extracted 51,559 georeferenced benthic density records. For 12% (BioBen part) and 4% (BioDen part) of all data records, no exact sampling location in geographical coordinates (latitude, longitude) was indicated. For these cases, we approximated the coordinates of the sampling locations using Google Maps based on information about sampling area or based on maps presented in the original publications. We labelled these data records as ‘approximated location’. For studies that presented biomasses in several units, such as WM and DM, we report the data only once (preferred units: WM > DM > AFDM > C). The authors of this study intended to report all data records in the ‘raw’ units in which benthic fauna was measured initially. Whenever unknown conversion factors precluded calculating biomass back to ‘raw’ units, we noted this issue in the database using the label ‘converted data’ and listed references for the individual biomass conversion factors in the database. The authors of the various studies compiled in this database sometimes used different lower and upper limits (in mm) for mesh sizes of nets and/ or sieves to define the size class. Whenever an original study reported a lower and/ or upper limit mesh size, we included this information in the database as ‘sieve mesh size (mm) lower limit’ and ‘sieve mesh size (mm) upper limit’. Studies lacking this information were scored as NA. For those studies that reported data as mean or median ± error terms, we incorporated only mean or median values into the database. In all cases that did not report benthic biomasses and/ or densities in the text or in tables, but presented them in figures, we extracted biomass and/ or density values from these figures using ImageJ. Benthic fauna refers to all fauna that live in or on the seafloor, which researchers typically divide into size classes meiobenthos (32/ 64 µm – 0.5/ 1 mm), macrobenthos (250 µm – 1 cm), and megabenthos (> 1 cm). Benthic fauna play important roles in bioturbation activity, mineralization of organic matter, and in marine food webs. Evaluating their role in these ecosystem functions requires knowledge of their global distribution and biomass. We therefore established the BenBioDen database, the largest open-access database for marine benthic biomass and density data compiled so far. In total, it includes 11,792 georeferenced benthic biomass and 51,559 benthic density records from 384 and 600 studies, respectively. We selected all references following the procedure for systematic reviews and meta-analyses, and report biomass records as grams of wet mass, dry mass, or ash-free dry mass, or carbon per m2 and as abundance records as individuals per m2. This database provides a point of reference for future studies on the distribution and biomass of benthic fauna.

Geodia species north of 60°N in the Atlantic appeared in the literature for the first time when Bowerbank described Geodia barretti and G. macandrewii in 1858 from western Norway. Since then, a number of species have been based on material from various parts of the region: G. simplex, Isops phlegraei, I. pallida, I. sphaeroides, Synops pyriformis, G. parva, G. normani, G. atlantica, Sidonops mesotriaena (now called G. hentscheli), and G. simplicissima. In addition to these 12 nominal species, four species described from elsewhere are claimed to have been identified in material from the northeast Atlantic, namely G. nodastrella and G. cydonium (and its synonyms Cydonium muelleri and Geodia gigas). In this paper, we revise the boreo-arctic Geodia species using morphological, molecular, and biogeographical data. We notably compare northwest and northeast Atlantic specimens. Biological data (reproduction, biochemistry, microbiology, epibionts) for each species are also reviewed. Our results show that there are six valid species of boreo-arctic Atlantic Geodia while other names are synonyms or mis-identifications. Geodia barretti, G. atlantica, G. macandrewii, and G. hentscheli are well established and widely distributed. The same goes for Geodia phlegraei, but this species shows a striking geographical and bathymetric variation, which led us to recognize two species, G. phlegraei and G. parva (here resurrected). Some Geodia are arctic species (G. hentscheli, G. parva), while others are typically boreal (G. atlantica, G. barretti, G. phlegraei, G. macandrewii). No morphological differences were found between specimens from the northeast and northwest Atlantic, except for G. parva. The Folmer cytochrome oxidase subunit I (COI) fragment is unique for every species and invariable over their whole distribution range, except for G. barretti which had two haplotypes. 18S is unique for four species but cannot discriminate G. phlegraei and G. parva. Two keys to the boreo-arctic Geodia are included, one based on external morphology, the other based on spicule morphology. Geodia boreo-arctic distributionThis excel file includes locality records for all six species of boreo-arctic Geodia examined by us in various campaigns/museums collections and from the litterature. This file includes geographical coordinates, museum collection or reference, temperature and salinity when available. When the latitude/longitude information was missing but the locality was given, we reconstructed the geographic coordinates using Google Earth. Temperature ranges for each species were obtained from the campaigns in which bottom temperatures were recorded (e.g. Ingolf Exp., BIOICE, BIOFAR, PA1994, PA2010-009) and from the literature.Geodia_boreo-arctic_distribution.xlsList of Geodia specimens examinedList of boreo-arctic Geodia specimens identified for this study and used to build the distribution maps: In cases where we have many samples from approximately the same locality only a minor number of records are listed; the number in parentheses is the number of specimens caught at each station.List of Geodia specimens.docx

1. Environmental stress can influence species traits and performance considerably. Using a seaweed-snail system from NW (Nova Scotia) and NE (Helgoland) Atlantic rocky shores, we examined how physical stress (wave exposure) modulates traits in the seaweed Fucus vesiculosus and indirectly in its main consumer, the periwinkle Littorina obtusata. 2. In both regions, algal tissue toughness increased with wave exposure. Reciprocal-transplant experiments showed that tissue toughness adjusts plastically to the prevailing level of wave exposure. 3. Choice experiments tested the feeding preference of snails from sheltered, exposed, and very exposed habitats for algae from such wave exposures. Snails from exposed and very exposed habitats consumed algal tissues at similar rates irrespective of the exposure of origin of the algae. However, snails from sheltered habitats consumed less algal tissues from very exposed habitats than tissues from sheltered and exposed habitats. Choice assays using reconstituted algal food (triturated during preparation) identified high thallus toughness as the explanation for the low preference of snails from sheltered habitats for algae from very exposed habitats. 4. Ultrastructural analyses of radulae indicated that rachidian teeth were longest and the number of cusps in lateral teeth (grazing-relevant traits) was highest in snails from very exposed habitats, suggesting that radulae are best suited to rupture tough algal tissues in such snails. 5. No-choice feeding experiments revealed that these radular traits are also phenotypically plastic, as they adjust to the toughness of the algal food. 6. Synthesis. This study indicates that the observed plasticity in the feeding ability of snails is mediated by wave exposure through phenotypic plasticity in the tissue toughness of algae. Thus, plasticity in consumers and their resource species may reduce the potential effects of physical stress on their interaction. Measurements on the rocky shores in Tor Bay, Nova Scotia, Canada (between 45.10644-45.11153 N and 61.21160-61.21700 W) and Helgoland (Helgoland (Bunker: 54.18806 N, 7.87436 E; Augusta Mole: 54.18931 N 7.89972 E; Nord-Ost Hafen, 54.18311 N, 7.88947 E, and Südhafen, 54.17819 N, 7.89417 E) to quantify1. maximum water velocity2. puncture force of Fucus vesiculosus thalli from sites of different wave exposure3. Littorina obtusata consumption of Fucus vesiculosus (fresh (both shores) and reconsituted (only Nova Scotia) from sites of different wave exposure 4. morphological traits (central teeth cusp length, number of cusps on lateral teeth) of field collected Littorina obtusata radula from different sites of wave exposure (only Nova Scotia) 5. morphological traits (central teeth cusp length, number of cusps on lateral teeth) of the Littorina obtusata radula from different sites of wave exposure feed with Fucus vesiculosus from different sites of wave exposre (only Nova Scotia) Supplement to: Molis, Markus; Scrosati, Ricardo A; El-Belely, Ehab F; Lesniowski, Thomas; Wahl, Martin (2015): Wave-induced changes in seaweed toughness entail plastic modifications in snail traits maintaining consumption efficacy. Journal of Ecology, 103(4), 851-859