Strengthening Europe's Capability in Biological Ocean Observations

This publication is primarily aimed at stakeholders involved in ocean observing, spanning diverse roles from commissioning, managing, funding and coordinating, to developing, implementing, or advising on, ocean observation programmes. Such programmes will have strategic and policy drivers but their main purpose may vary from predominantly researchdriven scientific purposes to environmental monitoring for providing data and reporting to legally-binding regulations or directives. The main focus is on European capabilities but set in a global context with the various actors spanning a variety of geographical scales from national to regional and European. Key stakeholder organizations include environmental or other agencies; marine research institutions, their researchers and operators; international and regional ocean observing initiatives and programmes; national, regional and European policy makers and their advisors; national stations for observations; etc.). It will also be of interest to the wider marine and maritime research and policy community. The main aim of the publication is to increase the relevance of current (and future) European biological ocean observation capacity to strengthen global efforts towards our understanding of the ocean and enhance marine biodiversity conservation, for maintaining a healthy ocean for healthy societies. This document explains why biological ocean observations are needed to assess progress against national and international conservation targets, the Sustainable Development Goals (SDGs), the Blue Growth agenda and to contribute to key EU directives including the Marine Strategy Framework Directive (MSFD). To achieve this, the publication highlights the need of biological ocean observations to reflect clearly defined hypotheses about potential causes of change, including the combined impacts of local and global drivers, and to support the management of our impacts on the ocean. Additionally, it calls for flexible biological ocean observing programmes to capture the relevant drivers operating at multiple spatial scales, by networking and integration of ongoing monitoring programmes, methodological standardization and appropriate policies of data integration and dissemination. It then presents key variables, elements and information products to inform on the status and trends of marine biodiversity

Building capacities for ’omics’ observations in the ocean at high spatiotemporal resolution

Analyzing the distributions and activities of marine organisms with metagenomic, metatranscriptomic, and other ‘omic’ techniques holds great potential in the observation of marine biodiversity and functions. When applied to microbial communities, such approaches are able to capture the multi-faceted responses of marine microbes to natural and anthropogenic pressures and the connected impacts on element cycling including fixation of inorganic carbon and dinitrogen. Ocean time-series and regular transects have delivered a strong foundation of knowledge of marine biogeochemistry. However, the imperative of characterizing the organisms that underly elemental cycles in times of rapid global change is hindered by the low resolution of human- and ship-based observation programs. The benefit of introducing omics-based investigations into ocean observation efforts has been recognized by several institutions and projects running observing programs (e.g., PAP, HAUSGARTEN, CPR, Tara Oceans) and by international initiatives and networks in the field (e.g., GOOS, MBON, LTER, NEON, GLOMICON). In order to establish omics observations as a component of routine observation of the open ocean there is a strong need for technologies that allow for unattended sampling with autonomous platforms as well as for automated shipbased sampling that may be carried out with research vessels and ships of opportunity. Activities to build capacities for omics-based observations were carried out in the framework of the EU FP7 projects AtlantOS and EnviGuard, with a focus on unicellular planktonic organisms that are poorly – or not at all – identified by morphology-based taxonomic techniques,. These efforts focused on the development and validation of new sampling technologies, on the investigation of the performance of different preservatives available to store samples, in situ, for the period of sampler deployments, and on the application of omics methods to samples collected with off-the shelf sampling equipment. In this context, this presentation introduces the new ‘AUTOmated FIltration system for marine Microbes’ / AUTOFIM and ‘Marine Autonomous Plankton Sampler’ / MAPS samplers, informs about the approach and first outcomes of a comparison of both standard preservatives and specific agents for molecular studies, and shows some examples of omics observations carried out in Fram Strait by means of particle traps and moored water samplers as part of the FRAM observatory infrastructure in the HAUSGARTEN area

Metatranscriptomics reveal differences in in situ energy and nitrogen metabolism among hydrothermal vent snail symbionts

Despite the ubiquity of chemoautotrophic symbioses at hydrothermal vents, our understanding of the influence of environmental chemistry on symbiont metabolism is limited. Transcriptomic analyses are useful for linking physiological poise to environmental conditions, but recovering samples from the deep sea is challenging, as the long recovery times can change expression profiles before preservation. Here, we present a novel, in situ RNA sampling and preservation device, which we used to compare the symbiont metatranscriptomes associated with Alviniconcha, a genus of vent snail, in which specific host–symbiont combinations are predictably distributed across a regional geochemical gradient. Metatranscriptomes of these symbionts reveal key differences in energy and nitrogen metabolism relating to both environmental chemistry (that is, the relative expression of genes) and symbiont phylogeny (that is, the specific pathways employed). Unexpectedly, dramatic differences in expression of transposases and flagellar genes suggest that different symbiont types may also have distinct life histories. These data further our understanding of these symbionts' metabolic capabilities and their expression in situ, and suggest an important role for symbionts in mediating their hosts' interaction with regional-scale differences in geochemistry

Transcriptional responses of Trichodesmium to natural inverse gradients of Fe and P availability

The filamentous diazotrophic cyanobacterium Trichodesmium is responsible for a significant fraction of marine di-nitrogen (N2) fixation. Growth and distribution of Trichodesmium and other diazotrophs in the vast oligotrophic subtropical gyres is influenced by iron (Fe) and phosphorus (P) availability, while reciprocally influencing the biogeochemistry of these nutrients. Here we use observations across natural inverse gradients in Fe and P in the North Atlantic subtropical gyre (NASG) to demonstrate how Trichodesmium acclimates in situ to resource availability. Transcriptomic analysis identified progressive upregulation of known iron-stress biomarker genes with decreasing Fe availability, and progressive upregulation of genes involved in the acquisition of diverse P sources with decreasing P availability, while genes involved in N2 fixation were upregulated at the intersection under moderate Fe and P availability. Enhanced N2 fixation within the Fe and P co-stressed transition region was also associated with a distinct, consistent metabolic profile, including the expression of alternative photosynthetic pathways that potentially facilitate ATP generation required for N2 fixation with reduced net oxygen production. The observed response of Trichodesmium to availability of both Fe and P supports suggestions that these biogeochemically significant organisms employ unique molecular, and thus physiological responses as adaptations to specifically exploit the Fe and P co-limited niche they construct

Strengthening Europe’s capability in biological ocean observations

This publication is primarily aimed at stakeholders involved in ocean observing, spanning diverse roles from commissioning, managing, funding and coordinating, to developing, implementing, or advising on, ocean observation programmes. Such programmes will have strategic and policy drivers but their main purpose may vary from predominantly researchdriven scientific purposes to environmental monitoring for providing data and reporting to legally-binding regulations or directives. The main focus is on European capabilities but set in a global context with the various actors spanning a variety of geographical scales from national to regional and European. Key stakeholder organizations include environmental or other agencies; marine research institutions, their researchers and operators; international and regional ocean observing initiatives and programmes; national, regional and European policy makers and their advisors; national stations for observations; etc.). It will also be of interest to the wider marine and maritime research and policy community. The main aim of the publication is to increase the relevance of current (and future) European biological ocean observation capacity to strengthen global efforts towards our understanding of the ocean and enhance marine biodiversity conservation, for maintaining a healthy ocean for healthy societies. This document explains why biological ocean observations are needed to assess progress against national and international conservation targets, the Sustainable Development Goals (SDGs), the Blue Growth agenda and to contribute to key EU directives including the Marine Strategy Framework Directive (MSFD). To achieve this, the publication highlights the need of biological ocean observations to reflect clearly defined hypotheses about potential causes of change, including the combined impacts of local and global drivers, and to support the management of our impacts on the ocean. Additionally, it calls for flexible biological ocean observing programmes to capture the relevant drivers operating at multiple spatial scales, by networking and integration of ongoing monitoring programmes, methodological standardization and appropriate policies of data integration and dissemination. It then presents key variables, elements and information products to inform on the status and trends of marine biodiversity. The Future Science Brief finishes by recommending priorities for enhancing relevant and integrated current biological ocean observing capacity in Europe

Differential effects of nitrate, ammonium, and urea as N sources for microbial communities in the North Pacific Ocean

Nitrogen (N) is the major limiting nutrient for phytoplankton growth and productivity in large parts of the world's oceans. Differential preferences for specific N substrates may be important in controlling phytoplankton community composition. To date, there is limited information on how specific N substrates influence the composition of naturally occurring microbial communities. We investigated the effect of nitrate ( math formula), ammonium ( math formula), and urea on microbial and phytoplankton community composition (cell abundances and 16S rRNA gene profiling) and functioning (photosynthetic activity, carbon fixation rates) in the oligotrophic waters of the North Pacific Ocean. All N substrates tested significantly stimulated phytoplankton growth and productivity. Urea resulted in the greatest (>300%) increases in chlorophyll a (<0.06 μg L−1 and ∼0.19 μg L−1 in the control and urea addition, respectively) and productivity (<0.4 μmol C L−1 d−1 and ∼1.4 μmol C L−1 d−1 in the control and urea addition, respectively) at two experimental stations, largely due to increased abundances of Prochlorococcus (Cyanobacteria). Two abundant clades of Prochlorococcus, High Light I and II, demonstrated similar responses to urea, suggesting this substrate is likely an important N source for natural Prochlorococcus populations. In contrast, the heterotrophic community composition changed most in response to math formula. Finally, the time and magnitude of response to N amendments varied with geographic location, likely due to differences in microbial community composition and their nutrient status. Our results provide support for the hypothesis that changes in N supply would likely favor specific populations of phytoplankton in different oceanic regions and thus, affect both biogeochemical cycles and ecological processes

Expression and Putative Function of Innate Immunity Genes under in situ Conditions in the Symbiotic Hydrothermal Vent Tubeworm Ridgeia piscesae

The relationships between hydrothermal vent tubeworms and sulfide-oxidizing bacteria have served as model associations for understanding chemoautotrophy and endosymbiosis. Numerous studies have focused on the physiological and biochemical adaptations that enable these symbioses to sustain some of the highest recorded carbon fixation rates ever measured. However, far fewer studies have explored the molecular mechanisms underlying the regulation of host and symbiont interactions, specifically those mediated by the innate immune system of the host. To that end, we conducted a series of studies where we maintained the tubeworm, Ridgeia piscesae, in high-pressure aquaria and examined global and quantitative changes in gene expression via high-throughput transcriptomics and quantitative real-time PCR (qPCR). We analyzed over 32,000 full-length expressed sequence tags as well as 26 Mb of transcript sequences from the trophosome (the organ that houses the endosymbiotic bacteria) and the plume (the gas exchange organ in contact with the free-living microbial community). R. piscesae maintained under conditions that promote chemoautotrophy expressed a number of putative cell signaling and innate immunity genes, including pattern recognition receptors (PRRs), often associated with recognizing microbe-associated molecular patterns (MAMPs). Eighteen genes involved with innate immunity, cell signaling, cell stress and metabolite exchange were further analyzed using qPCR. PRRs, including five peptidoglycan recognition proteins and a Toll-like receptor, were expressed significantly higher in the trophosome compared to the plume. Although PRRs are often associated with mediating host responses to infection by pathogens, the differences in expression between the plume and trophosome also implicate similar mechanisms of microbial recognition in interactions between the host and symbiont. We posit that regulation of this association involves a molecular “dialogue” between the partners that includes interactions between the host’s innate immune system and the symbiont