Potentially Polluting Marine Sites GeoDB: An S-100 Geospatial Database as an Effective Contribution to the Protection of the Marine Environment

Potentially Polluting Marine Sites (PPMS) are objects on, or areas of, the seabed that may release pollution in the future. A rationale for, and design of, a geospatial database to inventory and manipu-late PPMS is presented. Built as an S-100 Product Specification, it is specified through human-readable UML diagrams and implemented through machine-readable GML files, and includes auxiliary information such as pollution-control resources and potentially vulnerable sites in order to support analyses of the core data. The design and some aspects of implementation are presented, along with metadata requirements and structure, and a perspective on potential uses of the database

Multi-Omic Profiling of Melophlus Sponges Reveals Diverse Metabolomic and Microbiome Architectures that Are Non-overlapping with Ecological Neighbors.

Marine sponge holobionts, defined as filter-feeding sponge hosts together with their associated microbiomes, are prolific sources of natural products. The inventory of natural products that have been isolated from marine sponges is extensive. Here, using untargeted mass spectrometry, we demonstrate that sponges harbor a far greater diversity of low-abundance natural products that have evaded discovery. While these low-abundance natural products may not be feasible to isolate, insights into their chemical structures can be gleaned by careful curation of mass fragmentation spectra. Sponges are also some of the most complex, multi-organismal holobiont communities in the oceans. We overlay sponge metabolomes with their microbiome structures and detailed metagenomic characterization to discover candidate gene clusters that encode production of sponge-derived natural products. The multi-omic profiling strategy for sponges that we describe here enables quantitative comparison of sponge metabolomes and microbiomes to address, among other questions, the ecological relevance of sponge natural products and for the phylochemical assignment of previously undescribed sponge identities

Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae.

Natural product screening programs have uncovered molecules from diverse natural sources with various biological activities and unique structures. However, much is yet underexplored and additional information is hidden in these exceptional collections. We applied untargeted mass spectrometry approaches to capture the chemical space and dispersal patterns of metabolites from an in-house library of marine cyanobacterial and algal collections. Remarkably, 86% of the metabolomics signals detected were not found in other available datasets of similar nature, supporting the hypothesis that marine cyanobacteria and algae possess distinctive metabolomes. The data were plotted onto a world map representing eight major sampling sites, and revealed potential geographic locations with high chemical diversity. We demonstrate the use of these inventories as a tool to explore the diversity and distribution of natural products. Finally, we utilized this tool to guide the isolation of a new cyclic lipopeptide, yuvalamide A, from a marine cyanobacterium

Developing a GIS-Database and Risk Index for Potentially Polluting Marine Sites

The increasing availability of geospatial marine data provides an opportunity for hydrographic offices to contribute to the identification of “Potentially Polluting Marine Sites” (PPMS). These include shipwrecks, oil rigs, pipelines, and dumping areas. To adequately assess the environmental risk of these sites, relevant information must be collected and converted into a multi-scale geodatabase suitable for site inventory and geo-spatial analysis. In addition, a Risk Index – representing an assessment of the magnitude of risk associated with any site – can be derived to determine the potential impacts of these PPMS. However, the successful collection and integration of PPMS information requires some effort to ‘normalize’ and standardize the data based on recognized international standards. In particular, there is benefit in structuring the data in conformance with the Universal Hydrographic Data Model (IHO S-100) recently adopted by the International Hydrographic Organization. In this paper, an S-100 compliant product specification for a PPMS geo-spatial database and associated Marine Site Risk Index is proposed which can be used by national hydrographic offices and marine protection agencies

Mare Geneticum : Balancing Governance of Marine Genetic Resources in International Waters

Peer reviewedPublisher PD

MEDIN Feasibility Study : archiving oil and gas industry site survey data

This report was commissioned by the Marine Environmental and Information Network (MEDIN) to investigate the feasibility of collecting oil and gas industry site surveys conducted on the UKCS (UK Continental Shelf) for archive in the MEDIN DAC (Data Archive Centre) network. The archive of three principle data types is explored; information about legacy site surveys, catalogues of information about data products associated with site surveys and actual site survey data, which may include a survey report and enclosures and/or a selection of data e.g. side-scan or multibeam, sample descriptions and seismic profiles. The merits of the collection of these data types are explored alongside the cost implications, from both an oil and gas industry contractor’s and a marine geoscientist’s perspective, thereby enabling MEDIN to better understand and make decisions as to which data to concentrate on. The principles and proposed procedures for carrying out the collection of these data types are outlined however the practical details of these will require agreement should any decision be made to proceed. At this stage a further thorough detailed scope will be required in order to formulate procedures, qualify numbers, define activities, identify resources and plan timescales. The time period for the collection of legacy site surveys will require consideration i.e. how far back it is feasible to collect this information, and whether requests should be phased to include surveys acquired within predetermined time intervals. The size of the actual site survey data holdings, the storage capacity required to archive these and the amount of work involved in processing this data into useable and useful formats will require review. Some of these issues may need to be considered on a case-by-case basis. The procedures themselves will require regular review dependent on the response i.e. the volume, types and condition of data received

Seafloor characterization using airborne hyperspectral co-registration procedures independent from attitude and positioning sensors

The advance of remote-sensing technology and data-storage capabilities has progressed in the last decade to commercial multi-sensor data collection. There is a constant need to characterize, quantify and monitor the coastal areas for habitat research and coastal management. In this paper, we present work on seafloor characterization that uses hyperspectral imagery (HSI). The HSI data allows the operator to extend seafloor characterization from multibeam backscatter towards land and thus creates a seamless ocean-to-land characterization of the littoral zone

System requirement report for Level 2 – national management institutions, for the Bureau of Fisheries and Aquatic Resources in the Philippines

This report presents the findings from a thorough literature review, workshops, and group and individual interviews conducted by STREAM in the Philippines in November and December 2003. The ambitious scope of the report combined with the limited time frame and funding available to compile it necessitated the extensive use of secondary data, including both published and unpublished material written by staff of the agencies / organisations involved, with very limited editing of material used. All possible efforts were made to generate information in participation with the government institutions responsible for managing the fisheries, and all contributors (as well as many other stakeholders) were provided with multiple opportunities to comment on the report content. The contributors are listed on the front page of the report. (Pdf contains 56 pages)

Comparative Genomics of Cyanobacterial Symbionts Reveals Distinct, Specialized Metabolism in Tropical Dysideidae Sponges.

Marine sponges are recognized as valuable sources of bioactive metabolites and renowned as petri dishes of the sea, providing specialized niches for many symbiotic microorganisms. Sponges of the family Dysideidae are well documented to be chemically talented, often containing high levels of polyhalogenated compounds, terpenoids, peptides, and other classes of bioactive small molecules. This group of tropical sponges hosts a high abundance of an uncultured filamentous cyanobacterium, Hormoscilla spongeliae Here, we report the comparative genomic analyses of two phylogenetically distinct Hormoscilla populations, which reveal shared deficiencies in essential pathways, hinting at possible reasons for their uncultivable status, as well as differing biosynthetic machinery for the production of specialized metabolites. One symbiont population contains clustered genes for expanded polybrominated diphenylether (PBDE) biosynthesis, while the other instead harbors a unique gene cluster for the biosynthesis of the dysinosin nonribosomal peptides. The hybrid sequencing and assembly approach utilized here allows, for the first time, a comprehensive look into the genomes of these elusive sponge symbionts.IMPORTANCE Natural products provide the inspiration for most clinical drugs. With the rise in antibiotic resistance, it is imperative to discover new sources of chemical diversity. Bacteria living in symbiosis with marine invertebrates have emerged as an untapped source of natural chemistry. While symbiotic bacteria are often recalcitrant to growth in the lab, advances in metagenomic sequencing and assembly now make it possible to access their genetic blueprint. A cell enrichment procedure, combined with a hybrid sequencing and assembly approach, enabled detailed genomic analysis of uncultivated cyanobacterial symbiont populations in two chemically rich tropical marine sponges. These population genomes reveal a wealth of secondary metabolism potential as well as possible reasons for historical difficulties in their cultivation

Effects of low seawater pH on the marine polychaete Platynereis dumerilii

An important priority for any organism is to maintain internal cellular homeostasis including acidbase balance. Yet, the molecular level impacts of changing environmental conditions, such as low pH, remain uncharacterised. Herein, we isolate partial Na+/H+ exchangers (NHE), carbonic anhydrase (CA), and calmodulin (CaM) genes from a polychaete, Platynereis dumerilii and investigate their relative expression in acidified seawater conditions. mRNA expression of NHE was significantly down-regulated after 1 h and up-regulated after 7 days under low pH treatment (pH 7.8), indicating changes in acid-base transport. Furthermore, the localisation of NHE expression was also altered. A trend of down regulation in CA after 1 h was also observed, suggesting a shift in the CO2 and HCO3- balance. No change in CaM expression was detected after 7 days exposure to acidified seawater. This study provides insight into the molecular level changes taking place following exposure to acidified seawater in a non-calcifying, ubiquitous, organism