Publications

Abstract Background Isolation of marine microorganisms is fundamental to gather information about their physiology, ecology and genomic content. To date, most of the bacterial isolation efforts have focused on the photic ocean leaving the deep ocean less explored. We have created a marine culture collection of heterotrophic bacteria (MARINHET) using a standard marine medium comprising a total of 1561 bacterial strains, and covering a variety of oceanographic regions from different seasons and years, from 2009 to 2015. Specifically, our marine collection contains isolates from both photic (817) and aphotic layers (744), including the mesopelagic (362) and the bathypelagic (382), from the North Western Mediterranean Sea, the North and South Atlantic Ocean, the Indian, the Pacific, and the Arctic Oceans. We described the taxonomy, the phylogenetic diversity and the biogeography of a fraction of the marine culturable microorganisms to enhance our knowledge about which heterotrophic marine isolates are recurrently retrieved across oceans and along different depths. Results The partial sequencing of the 16S rRNA gene of all isolates revealed that they mainly affiliate with the classes Alphaproteobacteria (35.9%), Gammaproteobacteria (38.6%), and phylum Bacteroidetes (16.5%). In addition, Alteromonas and Erythrobacter genera were found the most common heterotrophic bacteria in the ocean growing in solid agar medium. When comparing all photic, mesopelagic, and bathypelagic isolates sequences retrieved from different stations, 37% of them were 100% identical. This percentage increased up to 59% when mesopelagic and bathypelagic strains were grouped as the aphotic dataset and compared to the photic dataset of isolates, indicating the ubiquity of some bacterial isolates along different ocean depths. Finally, we isolated three strains that represent a new species, and the genome comparison and phenotypic characterization of two of these strains (ISS653 and ISS1889) concluded that they belong to a new species within the genus Mesonia . Conclusions Overall, this study highlights the relevance of culture-dependent studies, with focus on marine isolated bacteria from different oceanographic regions and depths, to provide a more comprehensive view of the culturable marine bacteria as part of the total marine microbial diversity.

Studies focusing on marine macrophyte metabarcoding from environmental samples are scarce, due to the lack of a universal barcode for these taxa, and to their poor representation in DNA databases. Here, we searched for a short barcode able to identify marine macrophytes from tissue samples; then, we created a DNA reference library which was used to identify macrophytes in eDNA from coastal sediments. Barcoding of seagrasses, mangroves and marine macroalgae (Chlorophyta, Rhodophyta and Phaeophyceae) was tested using 18 primer pairs from six barcoding genes: the plant barcodes rbcL, matK and trnL, plus the genes ITS2, COI and 18S. The 18S gene showed the highest universality among marine macrophytes, amplifying 95%-100% of samples; amplification performance of the other barcodes was limited. Taxonomy was assigned using a phylogeny-based approach to create an 18S DNA reference library. Macrophyte tissue sequences were accurately identified within their phyla (88%), order (76%), genus (71%) and species (23%). Nevertheless, out of 86 macrophytes tested, only 48% and 15% had a reference sequence at genus and at species level, respectively. Identification at these levels can be improved by more inclusive reference libraries. Using the 18S mini-barcode and the reference library, we recovered eDNA from 21 marine macrophytes in sediments, demonstrating the barcode's ability to trace primary producers that contribute to blue carbon. We expect this barcode to also be useful for other ecological questions, such as tracing macro primary producers in marine food webs.

In harsh habitats, community structure is believed to be controlled primarily by physical factors while biological interactions are considered to be of little relevance. However, evidence of avoidance behaviors between the life stages of some species suggests otherwise. A long-standing hypothesis from sandy beaches suggests that avoidance between adults and juveniles dictates some aspects of their ecology, but this has not been explicitly tested. Here, we used a field survey to document the diel activity of adults and juveniles of the talitrid amphipod Americorchestia longicornis . We then used laboratory experiments to assess the influence of adults on the activity of juveniles and to measure juvenile mortality rates in the presence and absence of adults, with and without food. In the field, we found clear differences in the diel activity of adults and juveniles. Adults were active throughout the night but not in daylight, whereas juvenile activity peaked at dusk and dawn. Similar patterns of activity were recorded in laboratory tanks that included both stages. However, when adults were excluded, juveniles shifted towards night activity, suggesting that the pattern of activity observed in the field is a mechanism to avoid larger conspecifics. In separate trials, predation by adults was a significant driver of juvenile mortality, regardless of initial juvenile density and food availability. Altogether, these results suggest that segregation between amphipod life stages is driven by the avoidance of direct interactions, specifically, cannibalism. This likely influences the role played by these amphipods, both as prey and as processors of stranded seaweeds.

Abstract Bio‐logging data obtained by tagging animals are key to addressing global conservation challenges. However, the many thousands of existing bio‐logging datasets are not easily discoverable, universally comparable, nor readily accessible through existing repositories and across platforms, slowing down ecological research and effective management. A set of universal standards is needed to ensure discoverability, interoperability and effective translation of bio‐logging data into research and management recommendations. We propose a standardisation framework adhering to existing data principles (FAIR: Findable, Accessible, Interoperable and Reusable; and TRUST: Transparency, Responsibility, User focus, Sustainability and Technology) and involving the use of simple templates to create a data flow from manufacturers and researchers to compliant repositories, where automated procedures should be in place to prepare data availability into four standardised levels: (a) decoded raw data, (b) curated data, (c) interpolated data and (d) gridded data. Our framework allows for integration of simple tabular arrays (e.g. csv files) and creation of sharable and interoperable network Common Data Form (netCDF) files containing all the needed information for accuracy‐of‐use, rightful attribution (ensuring data providers keep ownership through the entire process) and data preservation security. We show the standardisation benefits for all stakeholders involved, and illustrate the application of our framework by focusing on marine animals and by providing examples of the workflow across all data levels, including filled templates and code to process data between levels, as well as templates to prepare netCDF files ready for sharing. Adoption of our framework will facilitate collection of Essential Ocean Variables (EOVs) in support of the Global Ocean Observing System (GOOS) and inter‐governmental assessments (e.g. the World Ocean Assessment), and will provide a starting point for broader efforts to establish interoperable bio‐logging data formats across all fields in animal ecology.

Abstract Aim Marine forests of brown macroalgae create essential habitats for coastal species and support invaluable ecological services. Here, we provide the first global analysis of species richness and endemicity of both the kelp and fucoid biomes. Location Global. Time period Contemporary. Major taxa studied Marine forests of brown macroalgae, formed by kelp (here defined as orders Laminariales, Tilopteridales and Desmarestiales) and fucoid (order Fucales), inhabiting subtidal and intertidal environments. Methods We coupled a large dataset of macroalgal observations (420 species, 1.01 million records) with a high‐resolution dataset of relevant environmental predictors (i.e., light, temperature, salinity, nitrate, wave energy and ice coverage) to develop stacked species distribution models (stacked SDMs) and yield estimates of global species richness and endemicity. Results Temperature and light were the main predictors shaping the distribution of subtidal species, whereas wave energy, temperature and salinity were the main predictors of intertidal species. The highest regional species richness for kelp was found in the north‐east Pacific (maximum 32 species) and for fucoids in south‐east Australia (maximum 53 species), supporting the hypothesis that these regions were the evolutionary sources of global colonization by brown macroalgae. Locations with low species richness coincided between kelp and fucoid, occurring mainly at higher latitudes (e.g., Siberia) and the Baltic Sea, where extensive ice coverage and low‐salinity regimes prevail. Regions of high endemism for both groups were identified in the Galapagos Islands, Antarctica, South Africa and East Russia. Main conclusions We estimated the main environmental drivers and limits shaping the distribution of marine forests of brown macroalgae and mapped biogeographical centres of species richness and endemicity, which largely coincided with the expectation from previous evolutionary hypotheses. The mapped biodiversity patterns can serve as new baselines for planning and prioritizing locations for conservation, management and climate change mitigation strategies, flagging threatened marine forest regions under different climate change scenarios.

Ocean warming reduces O 2 solubility and increases organismal O 2 demand, endangering marine life. Coastal ecosystems, however, experience O 2 supersaturation during peak daytime temperatures due to metabolic cycles. Recent discoveries show that this environmental supersaturation can reduce the vulnerability of tropical species to warming by satisfying their oxygen requirements. To test whether this also occurs within the cnidarian holobiont, we elevated internal O 2 in Cassiopea andromeda at nighttime (i.e. holobiont respiration prevails on Symbiodniaceae O 2 production) relying on bell pulsation for ventilation, then experimentally subjected them to thermal stress (+1°C day -1 ). Though ecologically unrealistic, this approach verified our hypothesis and eliminated confounding factors. Holobionts were exposed to either constant levels of 100% air saturation (100AS) or nighttime supersaturation (NSS; where 100% air saturation transitioned to O 2 supersaturation at nighttime). At sublethal temperatures, supersaturation mitigated reductions in holobiont size of ~ 10.37% (-33.418% ± 0.345 under 100AS vs -23.039% ± 0.687 under NSS). Supersaturation alleviated chlorophyll- a loss by 42.73% until 34°C, when counteraction of this process could not be sustained due to excessive thermal stress. Supersaturation also enriched potentially beneficial bacterial taxa of the microbiome and selected a more consistent bacterial community. Although modest, the detected effects show that a O 2 surplus increased the resistance of the holobionts to thermal stress.