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Philosophical Transactions of the Royal... Sep 2016The ocean constitutes one of the vastest and richest biomes on our planet. Most recent estimations, all based on indirect approaches, suggest that there are millions of... (Review)
Review
The ocean constitutes one of the vastest and richest biomes on our planet. Most recent estimations, all based on indirect approaches, suggest that there are millions of marine eukaryotic species. Moreover, a large majority of these are small (less than 1 mm), cryptic and still unknown to science. However, this knowledge gap, caused by the lack of diagnostic morphological features in small organisms and the limited sampling of the global ocean, is currently being filled, thanks to new DNA-based approaches. The molecular technique of PCR amplification of homologous gene regions combined with high-throughput sequencing, routinely used to census unculturable prokaryotes, is now also being used to characterize whole communities of marine eukaryotes. Here, we review how this methodological advancement has helped to better quantify the magnitude and patterns of marine eukaryotic diversity, with an emphasis on taxonomic groups previously largely overlooked. We then discuss obstacles remaining to achieve a global understanding of marine eukaryotic diversity. In particular, we argue that 18S variable regions do not provide sufficient taxonomic resolution to census marine life, and suggest combining broad eukaryotic surveys targeting the 18S rRNA region with more taxon-focused analyses of hypervariable regions to improve our understanding of the diversity of species, the functional units of marine ecosystems.This article is part of the themed issue 'From DNA barcodes to biomes'.
Topics: Aquatic Organisms; Biodiversity; Conservation of Natural Resources; DNA Barcoding, Taxonomic; Eukaryota; Marine Biology; Oceans and Seas
PubMed: 27481783
DOI: 10.1098/rstb.2015.0331 -
GigaScience Aug 2021High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing...
High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade's experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility's future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned.
Topics: Aquaculture; Biotechnology; Computing Methodologies; Marine Biology; Software
PubMed: 34405237
DOI: 10.1093/gigascience/giab053 -
Proceedings of the National Academy of... Oct 2010The marine realm represents 70% of the surface of the biosphere and contains a rich variety of organisms, including more than 34 of the 36 living phyla, some of which... (Review)
Review
The marine realm represents 70% of the surface of the biosphere and contains a rich variety of organisms, including more than 34 of the 36 living phyla, some of which are only found in the oceans. The number of marine species used by humans is growing at unprecedented rates, including the rapid domestication of marine species for aquaculture and the discovery of natural products and genes of medical and biotechnological interest in marine biota. The rapid growth in the human appropriation of marine genetic resources (MGRs), with over 18,000 natural products and 4,900 patents associated with genes of marine organisms, with the latter growing at 12% per year, demonstrates that the use of MGRs is no longer a vision but a growing source of biotechnological and business opportunities. The diversification of the use of marine living resources by humans calls for an urgent revision of the goals and policies of marine protected areas, to include the protection of MGRs and address emerging issues like biopiracy or benefit sharing. Specific challenges are the protection of these valuable resources in international waters, where no universally accepted legal framework exists to protect and regulate the exploitation of MGRs, and the unresolved issues on patenting components of marine life. Implementing steps toward the protection of MGRs is essential to ensure their sustainable use and to support the flow of future findings of medical and biotechnological interest.
Topics: Animals; Biodiversity; Conservation of Natural Resources; Ecosystem; Genetics; Humans; Marine Biology; Oceans and Seas; Patents as Topic
PubMed: 20837523
DOI: 10.1073/pnas.0911897107 -
Marine Drugs Apr 2020Marine fungi have been studied since the first record of the species () on the rhizome of the sea grass by Durieu and Montagne in 1846 [1], butthey have largely been...
Marine fungi have been studied since the first record of the species () on the rhizome of the sea grass by Durieu and Montagne in 1846 [1], butthey have largely been neglected, even though it is estimated that there are greater than 10,000 marinefungal species [...].
Topics: Animals; Biological Products; Fungi; Marine Biology
PubMed: 32349436
DOI: 10.3390/md18050230 -
Current Biology : CB Jun 2011
Topics: Animals; Antarctic Regions; Biodiversity; Marine Biology; Seasons
PubMed: 21683895
DOI: 10.1016/j.cub.2011.04.012 -
Marine Drugs Feb 2022When I started to work on marine natural products some thirty years ago I was attracted to this fascinating field of science by the exotic environment, the colourful...
When I started to work on marine natural products some thirty years ago I was attracted to this fascinating field of science by the exotic environment, the colourful shapes of (mostly) marine invertebrates and their complex ecological interactions [...].
Topics: Aquatic Organisms; Biological Products; Marine Biology
PubMed: 35323460
DOI: 10.3390/md20030161 -
Natural Product Reports Feb 2011The years 2000 through mid-2010 marked a transformational period in understanding of the biosynthesis of marine natural products. During this decade the field emerged... (Review)
Review
The years 2000 through mid-2010 marked a transformational period in understanding of the biosynthesis of marine natural products. During this decade the field emerged from one largely dominated by chemical approaches to understanding biosynthetic pathways to one incorporating the full force of modern molecular biology and bioinformatics. Fusion of chemical and biological approaches yielded great advances in understanding the genetic and enzymatic basis for marine natural product biosynthesis. Progress was particularly pronounced for marine microbes, especially actinomycetes and cyanobacteria. During this single decade, both the first complete marine microbial natural product biosynthetic gene cluster sequence was released as well as the first entire genome sequence for a secondary metabolite-rich marine microbe. The decade also saw tremendous progress in recognizing the key role of marine microbial symbionts of invertebrates in natural product biosynthesis. Application of genetic and enzymatic knowledge led to genetic engineering of novel “unnatural” natural products during this time, as well as opportunities for discovery of novel natural products through genome mining. The current review highlights selected seminal studies from 2000 through to June 2010 that illustrate breakthroughs in understanding of marine natural product biosynthesis at the genetic, enzymatic, and small-molecule natural product levels. A total of 154 references are cited.
Topics: Biological Products; Marine Biology; Molecular Structure
PubMed: 21170424
DOI: 10.1039/c0np90032j -
Integrative and Comparative Biology Oct 2021Climate and ocean literacy are two of the most important challenges facing society today. However, many students lack exposure to these topics upon entering college. As...
Climate and ocean literacy are two of the most important challenges facing society today. However, many students lack exposure to these topics upon entering college. As a result, these students must rely on learning climate literacy and ocean conservation through experiences outside of those provided in the traditional undergraduate classroom. To fill this gap, we initiated a marine science professional development program to expose undergraduate students to ocean literacy principles and climate change concepts through marine ecology research and educational outreach. This study evaluates the effects of our undergraduate experiential learning for individuals involved in our research team, our educational outreach team, or both. Clemson University alumni that participated in our program were surveyed to determine educational and professional gains in three areas related to: (1) knowledge; (2) careers; and (3) attitudes. Multiple linear and logistic regressions were used to understand the relationships between gains and program type, mentor experience, and duration of program enrollment. In addition, we evaluated demographic covariates including age, ideology, and gender. Our study found that perceived knowledge of marine science and science communication skills increased with positive mentor experience. Alumni that rated their experience with their mentors highly also indicated that the program was important to their careers after graduation. Students who participated in any program for a prolonged period were more likely to indicate that marine science was important to their careers. These students were also more likely to continue their education. Additionally, we saw that a sense of belonging and identity in science, as well as the understanding of climate change threat on the marine environment, all increased with longer program involvement, more than the type of experience (research versus outreach). Overall, we found that both the research and outreach programs offered opportunities for advancements in knowledge, careers, and attitudes. These results provide evidence that experiential learning has the potential to increase student engagement and understanding of climate change and ocean literacy communication as well as a sense of belonging in science-oriented fields.
Topics: Adult; Female; Humans; Learning; Male; Marine Biology; Minority Groups; Problem-Based Learning; Students; Universities; Young Adult
PubMed: 34043781
DOI: 10.1093/icb/icab104 -
GigaScience 2015Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine...
Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.
Topics: Biodiversity; Database Management Systems; Marine Biology; Metagenomics; Oceans and Seas
PubMed: 26097697
DOI: 10.1186/s13742-015-0066-5 -
Journal of Travel Medicine Dec 1998Envenomation both from jellyfish and other marine animals causes human deaths and severe morbidity in many countries in the world having tropical, or subtropical waters.... (Review)
Review
Envenomation both from jellyfish and other marine animals causes human deaths and severe morbidity in many countries in the world having tropical, or subtropical waters. In part II the world distribution of venomous marine vertebrates is discussed, together with simple first aid and effective medical treatment. Suggestions are made for the awareness and prevention of marine envenomation. With travel becoming more popular than ever, general practitioners and travel medicine consultants must routinely advise their patients on the worldwide hazards of marine envenomation.
Topics: Animals; Bites and Stings; Global Health; Humans; Marine Biology; Travel; Vertebrates
PubMed: 9876198
DOI: 10.1111/j.1708-8305.1998.tb00510.x