Marine Science/Ocean Life Related Journals

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The following are the scientific journals we recommend and periodically review for information concerning marine life... pleasecontact us with any suggestions or comments.

Directory of Open Access Journals

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American Fisheries Society

The American Fisheries Society publishes a suite of journals for aquatic resource professionals. These journals—Transactions of the American Fisheries Society, featuring papers on basic fisheries science; North American Journal of Fisheries Management, covering management research, experiences, and recommendations; North American Journal of Aquaculture, providing guidance for those who breed and raise aquatic animals; and Journal of Aquatic Animal Health, focusing on health maintenance and disease treatment—are available to AFS members, institutions, and libraries in both print and electronic formats.

Animal Conservation

A Journal of Ecology, Evolution and Genetics. Animal Conservation provides a forum for rapid publication of novel, peer-reviewed research into conservation of animal species and their habitats. The focus is on rigorous studies of an empirical or theoretical nature. Studies may relate to populations, species, or communities but should have broad conservation significance. A central theme is to publish important new ideas and findings from evolutionary biology and ecology that contribute towards the scientific basis of conservation biology. Subjects covered by the journal include behaviour and population biology; wildlife disease and epidemiology; evolutionary ecology and genetics; systematic biology and phylogenetics; biodiversity and biogeography; management (including translocation and sustainable use). The journal is essential reading for conservation biologists, policy-makers and students.

Animal Ecology

The Journal of Animal Ecology first appeared in 1932. It publishes the best in original research on any aspect of animal ecology. Recently it has published papers on population ecology, behavioural ecology, community ecology, physiological ecology and evolutionary ecology. Field, laboratory and theoretical studies based upon terrestrial, freshwater or marine systems are all published. The editors are keen to promote all these traditional areas and also to encourage publication of papers in new and emerging fields such as molecular ecology.

Aquaculture

An international journal devoted to research on the exploration, improvement and management of all aquatic food resources, both floristic and faunistic, from freshwater, brackish and marine environments, related directly or indirectly to human consumption.

Aquatic Conservation: Marine and Freshwater Ecosystems

Aquatic Conservation: Marine and Freshwater Ecosystems is an international journal dedicated to publishing original papers that relate specifically to freshwater, brackish or marine habitats and encouraging work that spans these ecosystems. This journal provides a forum in which all aspects of the conservation of aquatic biological resources can be presented and discussed, enabling greater cooperation and efficiency in solving problems in aquatic resource conservation. The publication of both practical studies in conservation as well as theoretical considerations of the underlying principles is encouraged. Contributions are accepted from as wide a geographical range as possible to ensure a broad representation of conservation issues in both developed and developing countries. The journal also publishes short communications, review articles, discussions and book reviews.

Aquatic Conservation: Marine and Freshwater Ecosystems serves as a focus for scientists in research institutes, universities, industry, nature conservation organizations and all levels of government as well as aquatic habitat and fishery managers and policy makers concerned with these issues.

Aquatic Sciences - Research Across Boundaries

Aquatic Sciences - Research Across Boundaries (AS) publishes original research, overviews, and reviews dealing with aquatic (both freshwater and marine) systems and their boundaries, including the impact of human activities on these systems. ASspans the range from molecular-level mechanistic studies to investigations at the whole ecosystem scale. AS seeks articles presenting research across disciplinary and environmental boundaries, that is (i) studies examining interactions among geological, microbial, biological, chemical, physical, hydrological, and societal processes, and (ii) studies assessing land-water, air-water, benthic-pelagic, river-ocean, lentic-lotic, and groundwater-surface water interactions.

Aquatic Toxicology

Aquatic Toxicology publishes original scientific papers dealing with the mechanisms of toxicity in aquatic environments and theunderstanding of responses to toxic agents at community, species, tissue, cellular and subcellular level, including aspects of uptake, metabolism and excretion of toxicants; understanding effects of toxic substances on aquatic ecosystems; toxicant-induced alterations in organisms as evinced, for example, through biochemical and physiological reactions, including adaptive responses; the development of procedures and techniques that significantly advance the understanding of processes and events that produce toxic effects; in-depth studies of human health aspects of aquatic toxicology. Chemical and other identification of toxicants will be considered when related to the understanding of perturbations in life processes. Reports of laboratory and field investigations may be accepted; however, the findings should contribute to the understanding of processes and mechanisms.

Biogeosciences

Biogeosciences (BG) is an international scientific journal dedicated to the publication and discussion of research articles, short communications and review papers on all aspects of the interactions between the biological, chemical and physical processes in terrestrial or extraterrestrial life with the geosphere, hydrosphere and atmosphere. The objective of the journal is to cut across the boundaries of established sciences and achieve an interdisciplinary view of these interactions. Experimental, conceptual and modeling approaches are welcome.

Biological Bulletin

The Biological Bulletin publishes outstanding experimental research on the full range of biological topics and organisms, from the fields of Neurobiology, Behavior, Physiology, Ecology, Evolution, Development and Reproduction, Cell Biology, Biomechanics, Symbiosis, and Systematics. Published since 1897 by the Marine Biological Laboratory (MBL) in Woods Hole, Massachusetts,The Biological Bulletin is one of America's oldest, peer-reviewed scientific journals.

Biological Conservation

Biological Conservation has as its main purpose the widest dissemination of original papers dealing with the preservation of wildlife and the conservation or wise use of biological and allied natural resources. It is concerned with plants and animals and their habitats in a changing and increasingly man–dominated biosphere – in fresh and salt waters as well as on land and in the atmosphere. Biological Conservation publishes field studies, analytical and modeling studies and review articles. While its main basis is ecological the journal aims at fostering other relevant aspects of biological conservation and hopes thereby to encourage more research and publication of work which contributes to our knowledge and understanding of wildlife communities and their value to mankind.

The journal's coverage of the discipline of conservation ecology is relevant to universities and research institutes while the emphasis on the practical application of the research results is important to all land managers, from those dealing with landscape design problems to those whose concern is nature reserve management.

Biology

Journal of Biology is an international journal that publishes biological research articles of exceptional interest, together with associated commentary. Original research articles that are accepted for publication are published in full on the web within two weeks, are immediately made freely available to all, and are also distributed in a print edition sent to several thousand life scientists. Articles from the full spectrum of biology are appropriate for consideration, provided they are of outstanding interest and importance. (As a guide, the journal will consider articles of a standard similar to those published in Nature, Science or Cell.)

Conservation Genetics

Conservation Genetics promotes the conservation of genetic diversity by providing a forum where data and ideas can be presented, facilitating the further development of this field of study. Contributions come from researchers in a variety of fields including population genetics, molecular ecology and biology, evolutionary biology, and systematics, to name just a few. Conservation issues are multifaceted and incorporate diverse disciplines. This journal will focus on genetic and evolutionary applications to the problems of conservation, while reflecting the diversity of concerns that are relevant to conservation biology. Papers are accepted in the following categories: full research papers, review papers, short communications, and short methodological notes (including lab methods, computer programs & models, and PCR primers).

Continental Shelf Research

Continental Shelf Research publishes articles dealing with the physical oceanography, sedimentology, geology, chemistry, biology and ecology of the shallow marine environment, from coastal and estuarine water out to the shelf break. Papers that are published present results from both fundamental, original research as well as applied, or directed research.

Emphasis is placed on interdisciplinary process-oriented contributions, and encouragement is given to the publication of the results of innovative experimental studies with more general applicability. Continental Shelf Research publishes occasional review articles. It also includes a section on Notes, Instrumentation and Methods. Furthermore, papers are open for written discussion for up to three months following publication and both the discussion and the author's response are published.

Coral Reefs - Journal of the International Society for Reef Studies

This journal supplies a focal point for the hitherto scattered literature in this rapidly expanding field of reef studies, publishing analytical and theoretical papers on both modern and ancient reefs. It encourages the search for generalizations about reef structure and dynamics, and reflects the growing awareness among reef workers of the importance of experimentation, modeling, quantification and applied science in reef studies. Papers published in the journal deal with population dynamics and community ecology of reef organisms, energy and nutrient flows, biogeochemical cycles, physiology of calcification, reef response to natural and anthropogenic stress, behavioral ecology, sedimentology, diagenesis, reef structure and morphology, evolutionary ecology of the reef biota, paleoceanography of coral reefs and coral islands and the science which underpins reef management. The journal is also open to review articles, notes and perspectives on major scientific problems concerning coral reefs.

Crustacean Biology

The Journal of Crustacean Biology contains papers of broad interest dealing with any aspect of crustacean biology, biographies of notable carcinologists, notices of business transacted at meetings of

The Crustacean Society, book reviews of works on Crustacea, and pertinent announcements. Papers will be published in English only, but abstracts or summaries in French, German, Portuguese, or Spanish may be added when appropriate. Descriptions of single new species may be accepted if accompanied by significant information on zoogeography, ecology, phylogenetic relationships, or other biological concerns.

Crustaceana

Crustaceana is the foremost journal in the world on crustacean research. Including the latest papers from all branches of zoology, it gives up-to-date information on aspects such as taxonomy, zoogeography, ecology, physiology, anatomy, genetics, palaeontology and biometry, and covers all groups of crustacea. Boasting a large international circulation, Crustaceana takes care to supply its readers with an abstract of each article in both English and another congress language.

Current Biology

Current Biology publishes articles in any area of biology, provided that the research clearly represents an important advance of especially broad interest to biologists. Articles must be written and illustrated in a way that is appropriate for nonspecialist readers. Articles should normally occupy 4-10 pages of the journal; there are about 900 words or 40 references to a full page. Brevity is a virtue except when it is at the expense of essential information. Current Biology also publishes Reports: short papers reporting results that are of genuinely broad interest but that for one reason or another do not make a sufficiently complete story to justify publication as a full Article. Authors are welcome to suggest that their paper be considered as a Report if they feel it is suitable for that format. Reports should occupy no more than five pages of the journal.

Deep Sea Research Part I: Oceanographic Research Papers

Deep-Sea Research Part I: Oceanographic Research Papers is devoted to the publication of the results of original scientific research, the solution of instrumental problems, and new laboratory methods in the marine sciences. It is unique in the field of oceanography in its interdisciplinary approach covering a wide variety of subjects related to the geological, physical, mathematical, chemical and biological aspects of the ocean, the sea floor and the boundary layer between the atmosphere and the ocean. Papers that are particularly timely or topical may receive accelerated editorial response and publication as Rapid Response Papers.

Deep Sea Research Part II: Topical Studies in Oceanography

Deep-Sea Research Part II: Topical Studies in Oceanography publishes topical issues from the many international and interdisciplinary projects which are undertaken in oceanography. Besides these special issues from projects, the journal publishes collections of papers presented at conferences. The special issues regularly have electronic annexes of non-text material (numerical data, images, images, video, etc.) which are published with the special issues in ScienceDirect. Deep-Sea Research Part II was split off as a separate journal devoted to topical issues in 1993. Its companion journal Deep-Sea Research Part I: Oceanographic Research Papers, publishes the regular research papers in this area.

Dynamics of Atmospheres and Oceans

The journal exists for the publication of research articles on the fluid dynamics of atmospheres and oceans and their interactions, on related basic dynamical processes, and on climatic and biogeochemical problems in which the fluid dynamics play an essential role. Theoretical, numerical, observational and laboratory studies are all welcome.

Earth & Planetary Science Letters

Since its first appearance in 1966, Earth and Planetary Science Letters has built up an enviable reputation. Its successful formula of presenting high-quality research articles with minimal delay has made it one of the most important sources of information in its field. The articles published reflect the great impact made on research in the geosciences by the use of successful research methods from other disciplines such as chemistry, physics, and mathematics. It also covers research into all aspects of lunar studies, plate tectonics, ocean floor spreading, and continental drift, as well as basic studies of the physical, chemical and mechanical properties of the Earth's crust and mantle, the atmosphere and the hydrosphere.

Mid 2002 a new section of short reviews called Frontiers was introduced within Earth and Planetary Science Letters. These high profile papers are written by leading experts and published as the opening pages to regular EPSL issues. The papers fill an important niche of fast communications that bring the scientific community up-to-speed on interesting new areas of science.

EcoHealth

Ecosystem change has far reaching implications for health and sustainability at local, regional and global scales. EcoHealth is a new international journal focused on the integration of knowledge at the interface between ecological and health sciences.

EcoHealth builds on the foundation laid by the complementary journals Ecosystem Health and the Global Change and Human Health. By merging these two journals and linking with the Consortium for Conservation Medicine, the journal provides an authoritative forum for research and practice that integrates human, wildlife and ecosystem health. The focus on human and wildlife health reflects their centrality as criterion for humankind's search for a sustainable future.

Ecology & Society

Ecology and Society is an electronic, peer-reviewed, multi-disciplinary journal devoted to the rapid dissemination of current research. Manuscript submission, peer review, and publication are all handled on the Internet. Content of the journal ranges from the applied to the theoretical. In general, papers should cover topics relating to the ecological, political, and social foundations for sustainable social-ecological systems. Specifically, the journal publishes articles that present research findings on the following issues: (a) the management, stewardship and sustainable use of ecological systems, resources and biological diversity at all levels, (b) the role natural systems play in social and political systems and conversely, the effect of social, economic and political institutions on ecological systems and services, and (c) the means by which we can develop and sustain desired ecological, social and political states.

Ecosystems

The study and management of ecosystems represent the most dynamic field of contemporary ecology. Ecosystem research bridges fundamental ecology and environmental ecology and environmental problem-solving, and spans boundaries of scale, discipline and perspective. Ecosystems features a distinguished team of editors-in-chief and an outstanding international editorial board, and is seen worldwide as a vital home for publishing significant research as well as editorials, mini-reviews and special features.

Ecotoxicology

Ecotoxicology is an international journal devoted to the publication of fundamental research on the effects of toxic chemicals on populations, communities and terrestrial, freshwater and marine ecosystems. It aims to elucidate mechanisms and processes whereby chemicals exert their effects on ecosystems and the impact caused at the population or community level. The journal is not biased with respect to taxon or biome, and papers that indicate possible new approaches to regulation and control of toxic chemicals and those aiding in formulating ways of conserving threatened species are particularly welcome. Studies on individuals should demonstrate linkage to population effects in clear and quantitative ways. Laboratory studies must show a clear linkage to specific field situations. The journal includes not only original research papers but technical notes and review articles, both invited and submitted. A strong, broadly based editorial board ensures as wide an international coverage as possible.

Environmental Biology of Fishes

Environmental Biology of Fishes is an international journal which publishes original studies on the ecology, life history, epigenetics, behavior, physiology, morphology, systematics and evolution of marine and freshwater fishes and fishlike organisms. empirical and theoretical papers are published that deal with the relationship between fishes and their external and internal environment, whether natural or unnatural. In particular, the journal concentrates on papers which advance the scholarly understanding of life and which draw on a variety of disciplines in reaching this understanding. Relevant concepts in biology and philosophy of science are also published.

Environmental Biology of Fishes publishes editorials, invited editorials, full papers, brief communications, rapid communications, essays, invited reviews, critical book reviews, translation proposals, and editorial comment and announcements.

Occasional issues are dedicated to the proceedings of relevant and topical conferences, which may also appear in a hardcover edition in the companion series Developments in Environmental Biology of Fishes.

Environmental Policy and Law

This international journal has created to encourage and develop the exchange of information and experience on all legal, administrative and policy matters relevant to the human and natural environment: air, water and soil pollution as well as waste management; the conservation of flora and fauna; protected areas and land-use control; development and conservation of the world's non-renewable resources.

In short, all aspects included in the concept of sustainable development. For more than two decades Environmental Policy and Law has assumed the role of the leading international forum for policy and legal matters relevant to this field. Environmental Policy and Law is divided into sections for easy accessibility. These sections cover the activities of the United Nations and its specialized agencies, other international developments, regional activities within the framework of CARICOM, OAU, ASEAN, etc., and developments at the national level from all over the world. An important and distinctive feature is the publication of selected documents appearing with the minimum of delay, which are not easily accessible, such as the resolutions from non-public meetings of parliamentarians, guidelines or draft conventions not yet published or newly concluded agreements.

Environmental Policy and Law fills a gap left by other publications. Subscribers are politicians, government officials at the highest level of decision-making, academics, scientists, practicing lawyers, firms, and private persons wishing to keep up to date on contemporary policies and practices.

Environmental Pollution

Environmental Pollution is an international journal that addresses issues relevant to the nature, distribution and ecological effects of all types and forms of chemical pollutants in air, soil and water. The Editors welcome articles based on original research, findings from re–examination and interpretation of existing data and reviews of important issues. In addition, the journal also publishes articles on new methods of detection, study and remediation of environmental pollutants.

Estuarine, Coastal & Shelf Science

Estuarine, Coastal and Shelf Science is an international multidisciplinary journal devoted to the analysis of saline water phenomena ranging from the outer edge of the continental shelf to the upper limits of the tidal zone. The journal provides a unique forum, unifying the multidisciplinary approaches to the study of the oceanography of estuaries, coastal zones, and continental shelf seas. It features original papers and short communications treating such disciplines as zoology, botany, geology, sedimentology, physical oceanography, numerical models, and chemical processes.

Experimental Marine Biology and Ecology

The Journal provides a forum for work on the biochemistry, physiology, behavior, and genetics of marine plants and animals in relation to their ecology; all levels of biological organization will be considered, including studies of ecosystems and ecological modeling. The main emphasis of the Journal lies in experimental work, both from the laboratory and the field. Descriptive studies will, however, be acceptable if they elucidate general ecological principles. Papers describing important new techniques, methods and apparatus will also be considered. All papers will be refereed by experts before acceptance for publication. In all cases proofs will be sent to authors. The editors, referees, and publisher will make every effort to expedite publication and the co-publication of authors in this task is welcomed.

Fish Biology

The Journal of Fish Biology is a leading international journal for scientists engaged in all aspects of fish and fisheries research, both freshwater and marine. The journal publishes high-quality papers relevant to the central theme of fish biology and aims to bring together under one cover an overall picture of the research in progress and to provide international communication among researchers in many disciplines with a common interest in the biology of fish.

Research Areas Include: Aquaculture; Behavior; Biochemistry; Diseases; Distribution; Ecology; Genetics; Growth; Immunology; Migration; Morphology; Parasitology; Physiology; Pollution; Population studies; Reproduction; Taxonomy; Toxicology.

Fish & Shellfish Immunology

Fish and Shellfish Immunology rapidly publishes high-quality, peer-refereed contributions in the expanding fields of fish and shellfish immunology. It presents studies on the basic mechanisms of both the specific and non-specific defense systems, the cells, tissues, and humoral factors involved, their dependence on environmental and intrinsic factors, response to pathogens, response to vaccination, and applied studies on the development of specific vaccines for use in the aquaculture industry.

Fisheries & Aquatic Sciences (Canadian Journal of)

Published continuously since 1901 (under various titles), this monthly journal is the primary publishing vehicle for the multidisciplinary field of aquatic sciences. The Journal has been ranked by ISI as one of the top three journals in its field for the past decade. It publishes perspectives (syntheses, critiques, and re-evaluations), discussions (comments and replies), articles, and rapid communications, on cells, organisms, populations, ecosystems, or processes that affect aquatic systems, to amplify, modify, question, or redirect accumulated knowledge in the field of fisheries and aquatic science.

Geobiology

The Virtual Journal of Geobiology is available exclusively on the Web. It is a virtual journal in that it lists articles with a geobiological component recently published in a wide range of Elsevier Science journals. The articles are personally selected by the editor, Professor Lee Kump, on the basis of their potential to highlight interesting and important developments in the area of geobiology.

Geobiology is emerging as a new subject at the many interfaces between modern biology and the various fields of Earth and space sciences. Yet, there remains uncertainty and discussion about the origin of the current interest in this area. Has it to do with fashion or obtaining research funding, with breaking down barriers between traditional disciplines, or with attempts to revitalise Earth and planetary sciences in the universities? Is it a dynamic new field, a new name for an old subject, or just a short-lived excitement that will soon die away?

Hydrobiologia

Hydrobiologia publishes original articles in the fields of fundamental limnology and marine biology. A wide range of papers is published, including ecology, physiology, biogeography, methodology and taxonomy. Applied (technological) papers are also published, provided they are of general interest and not solely technical in nature. Occasionally very long papers, reviews and special issues are published at the invitation of the Editors, as are the proceedings of relevant, specialized symposia, e.g. Seaweed Symposia; Saline Lakes Symposia; Sediment/Water Interactions Symposia; Rotifer Symposia; Aquatic Oligochaete Biology Symposia; Turbellaria Symposia; Symposia on Copepoda and Cladocera; Tropical Limnology/high-latitude Limnology Symposia; and recently North Sea-Estuaries Interactions; Phosphorus in Freshwater Ecosystems and Expected Effects of Climatic Change on Marine Coastal Ecosystems. Purely descriptive work, whether limnological, ecological or taxonomic, can only be considered if it is firmly embedded in a larger biological framework.

ICES Journal of Marine Science

The ICES Journal of Marine Science publishes articles, short communications, and critical reviews that contribute to our scientific understanding of marine systems and the impact of human activities. The Journal serves as a foundation for scientific advice across the broad spectrum of management and conservation issues related to the marine environment. Oceanography, marine habitats, living resources, and related management topics constitute the key elements of papers eligible for publication. Integrated studies that bridge gaps between traditional disciplines are particularly welcome. The scope of the Journal has been broadened to include economic, social, and public administration studies to the extent that they are directly related to management of the seas and are of general interest to marine scientists. Proceedings of ICES-sponsored symposia constitute an integral part of the Journal and observe the standards set for regular papers.

Invertebrate Pathology

The Journal of Invertebrate Pathology presents original research articles and notes on the induction and pathogenesis of diseases of invertebrates, including the suppression of diseases in beneficial species, and the use of diseases in controlling undesirable species. In addition, the journal publishes the results of physiological, morphological, genetic, immunological and ecological studies as related to the etiologic agents of diseases of invertebrates.

JMBA - Journal of the Marine Biological Association of the United Kingdom

JMBA is an international journal with a worldwide distribution publishing original research on all aspects of marine biology. It includes current international research developments and features much of the pioneering work taking place today on major issues concerning marine organisms and their environment. Subjects covered include: ecological surveys and population studies of oceanic, coastal and shore communities; physiology and experimental biology; taxonomy, morphology and life history of marine animals and plants; and chemical and physical oceanographic work which relates closely to the biological environment. Papers are also published on the rapidly developing techniques employed at sea for the sampling, recording, capture and observation of marine organisms, and chemical analyses of sea water. JMBA is produced from a working marine laboratory by scientists actively involved in research.

Limnology & Oceanography

Limnology and Oceanography publishes original articles about all aspects of limnology and oceanography. The journal's unifying theme is the understanding of aquatic ecosystems. Submissions are judged on the originality of their data, interpretations, and ideas, and on the degree to which they can be generalized beyond the particular aquatic ecosystem examined. Laboratory and modeling studies must demonstrate relevance to natural environments; typically this means that they are bolstered by substantial "real world" data. Few purely theoretical papers are accepted for review; authors are strongly advised to include such materials in more complete papers that use the new theory to elucidate important features of aquatic ecosystems.

Marine & Freshwater Research

Marine & Freshwater Research bridges subject field divisions in the marine, estuarine and freshwater sciences, making it a truly interdisciplinary aquatic science journal. Papers are selected for their originality, significance and potential interest to our broad audience.

Marine Biology

The Editors of Marine Biology invite and will consider for publication original contributions to the following fields of research: Plankton research: Studies on the biology, physiology, biochemistry and genetics of plankton organisms both under laboratory and field conditions. Biological and biochemical oceanography. Environment-organism and organism-organism interrelationships. Experimental biology: Research on metabolic rates and routes in microorganisms, plants and animals. Respiration; nutrition; life cycles. Molecular biology, biochemistry, physiology and behavior: Biochemical research on marine organisms; photosynthesis; permeability; osmoregulation; ionregulation; active transport; adaptation; analyses of environmental effects on functions (tolerances, rates and efficiencies of metabolism, growth and reproduction) and structures; migrations; orientation; general behavior. Biosystem research: Experimental biosystems and microcosms. Energy budgets: flow routes and balance sheets of energy and matter in the marine environment. Interspecific interrelationships, food webs. Dynamics and structures of microbial, plant and animal populations. Use, management and protection of living marine resources. Effects of man on marine life, including pollution. Evolution: Investigations on speciation, population genetics, and biological history of the oceans. Theoretical biology related to the marine environment: Concepts and models of quantification and mathematical formulation; system analysis; information theory. Methods: Apparatus and techniques employed in marine biological research; underwater exploration and experimentation.

Marine Biology Research

Marine Biology Research aims to provide practitioners and academics with a forum for ideas and discussion on all areas of marine biology and oceanography. The journal will cover a broad range of topics, including: Ecology, Behaviour, Benthic dynamics, Biodiversity, Ecosystem functioning, Environment, Evolution, Phylogeny, Physiology, Taxonomy. Applied aspects (environment, fisheries) of marine biological research, which contribute to general biological insight, will also be covered.

Marine Biotechnology

Articles describing the molecular biology, genetics, cell biology, and biochemistry of any aquatic prokaryote or eukaryote will be considered. Papers on biotechnological applications should address fundamental questions or demonstrate novel technical developments. Work on marine natural products will also be considered when it meets these criteria. The journal will publish articles describing innovative molecular techniques for the study and manipulation (including transgenesis) of marine and freshwater organisms or research pertaining to industrial applications (aquaculture/mariculture) of aquatic organisms.

Marine Chemistry

Marine Chemistry is an international medium for the publication of original studies and occasional reviews in the field of chemistry in the marine environment, with emphasis on the dynamic approach. The journal endeavors to cover all aspects, from chemical processes to theoretical and experimental work, and, by providing a central channel of communication, to speed the flow of information in this relatively new and rapidly expanding discipline.

Marine Ecology Progress Series

MEPS serves as a worldwide forum for all aspects of marine ecology, fundamental and applied. The journal covers: microbiology, botany, zoology, ecosystem research, biological oceanography, ecological aspects of fisheries and aquaculture, pollution, environmental protection, conservation, resource management.

Marine Environmental Research

Marine Environmental Research publishes original research papers on chemical, physical, and biological interactions in the oceans and coastal waters. The journal serves as a forum for new information on biology, chemistry, and toxicology and syntheses that advance understanding of marine environmental processes. Submission of multidisciplinary studies is encouraged. Studies that utilize experimental approaches to clarify the roles of anthropogenic and natural causes of changes in marine ecosystems are especially welcome, as are those studies that represent new developments of a theoretical or conceptual aspect of marine science. All papers published in this journal are reviewed by qualified peers prior to acceptance and publication.

Marine Geology, Geochemistry and Geophysics

Since 1964 this international journal has been reporting on developments in the fields of marine geology, geochemistry and geophysics. Marine Geology provides regular access to original studies and comprehensive reviews and, in addition, has a special "letters section" which ensures particularly rapid publication of short papers.

Marine Micropaleontology

Marine Ornithology: an International Journal of Seabird Science and Conservation

Marine Ornithology presents peer reviewed contributions concerning international seabird science and conservation. The African Seabird Group, the Pacific Seabird Group, the Australasian Seabird Group, the Seabird Group, and the Dutch Seabird Group have jointly managed and published Marine Ornithology: an International Journal of Seabird Science and Conservation since 2003.

Marine Pollution Bulletin

Marine Pollution Bulletin is concerned with the rational use of maritime and marine resources in estuaries, the seas and oceans, as well as with documenting marine pollution and introducing new forms of measurement and analysis. A wide range of topics are discussed as news, comment, reviews and research reports, not only on effluent disposal and pollution control, but also on the management, economic aspects and protection of the marine environment in general. A distinctive feature of Marine Pollution Bulletin is the number of different categories of articles which are published. Papers (Reports) form the core of the journal, while Baselines document measurements which are expected to have value in the future. Reviews are generally invited by the editors on subjects which cross traditional lines, but suggestions for topics are welcomed. Viewpoints are a less formal forum for scientists to comment freely on matters of relevant national and international importance. Other sections of the Bulletin include News, New Products, Conference Reports, Conference Diary, Correspondence and Book Reviews. Two volumes are published annually, one of which contains a series of special issues on topics of particular current interest. The importance and influence of these special issues, which address the major marine environmental concerns of our time, is increasingly being recognised not just by the wider scientific community, but also by environmental policy makers at national and international level.

Marine Systems

The purpose of this journal is to provide a medium of exchange for those engaged in marine research where there exists an interplay between geology, chemistry, biology, and physics. The Journal of Marine Systems therefore welcomes original and state-of-the-art contributions on all aspects of marine sciences. Preference is given to papers which extend beyond the limit of a single discipline and which follow the rationale of system analysis.

Marine Technology Society Journal

The Marine Technology Society Journal is an international, peer reviewed quarterly. It offers a selection of original contributions by professionals involved in ocean science, engineering, technology and policy. Each issue includes book reviews and commentary. To further enrich the dialogue among a wide range of readers of varying disciplines, the MTS Journal has inaugurated a new comment and reply section called Crosstalk. Readers are invited to submit a comment, question, or clarification in response to papers, reports, or commentaries printed in the Journal.

Microbial Ecology

Microbial Ecology is an international journal whose aim is the advancement and dissemination of information describing the interactions between microorganisms and the biotic and abiotic components of their environments. Microbial Ecology features articles of original research and brief reviews.

National Academy of Sciences (Proceedings - PNAS)

PNAS is one of the world's most-cited multidisciplinary scientific serials. Since its establishment in 1914, it continues to publish cutting-edge research reports, commentaries, reviews, perspectives, colloquium papers, and actions of the Academy. Coverage in PNAS spans the biological, physical, and social sciences. PNAS is published weekly in print, and daily online in PNAS Early Edition.

Natural History

The Journal of Natural History is an international journal publishing original research, reviews, opinions and correspondence in systematics and evolutionary and interactive biology. The traditional features of the journal, taxonomic works in entomology and zoology, have been maintained, providing a scientific basis for the application of systematics in biological control, agriculture, aquaculture, and medical and veterinary zoology. The journal also publishes papers on cladistics, experimental taxonomy, parasitology, ecology, behavior and the interaction of organisms with their environment. The editors are supported by an international editorial board and a large panel of referees.

Nature

To serve scientists through prompt publication of significant advances in any branch of science, and to provide a forum for the reporting and discussion of news and issues concerning science. Second, to ensure that the results of science are rapidly disseminated to the public throughout the world, in a fashion that conveys their significance for knowledge, culture and daily life.Nature online - the homepage of the International weekly journal of science, and the flagship product of the Nature family of journals

Ocean & Coastal Management

Ocean & Coastal Management is an international journal dedicated to the study of all aspects of ocean and coastal management at local, regional, national and international levels. The Editors encourage articles involving analytical approaches, development of theory, and improvement of management practice. Comparative studies (e.g. subnational, cross–national, to other policy areas) are especially encouraged.

Ocean Science

Ocean Science (OS) is a new international and free to web scientific journal dedicated to the publication and discussion of research articles, short communications and review papers on all aspects of ocean science, experimental, theoretical and laboratory. The primary objective is to publish a very high quality scientific journal with free web based access for researchers and other interested people throughout the world.

Oceanologia

The journal Oceanologia publishes original papers on marine research with the emphasis on fundamental aspects. Papers dealing with processes in the marine environment are preferred to purely descriptive ones; they should contribute to the understanding of the functioning of marine ecosystems, including their abiotic aspects.

Oceanus (WHOI)

Oceanus is both an online magazine and a semiannual print magazine published by Woods Hole Oceanographic Institution. It explores Earth's last frontier, delivering news and commentary on the meaning and value of ocean research, engineering, and education at WHOI.

Paleoceanography

Paleoceanography focuses on original contributions dealing with the marine sedimentary record from the present ocean basins and margins and from exposures of ancient marine sediments on the continents. Approaches include sedimentology; isotope geochemistry; paleontology; seismic stratigraphy; physical, chemical, and biological oceanography; marine geology and geophysics; Quaternary geology; and modeling. Contributions are global and regional rather than local; and cover all ages (Precambrian to the Quaternary, including modern analogs).

Plankton Research

Journal of Plankton Research publishes innovative papers that significantly advance the field of plankton research. All kinds of marine, brackish and freshwater plankton are considered: viruses, bacteria, fungi, phytoplankton, and zooplankton, including meroplankton and ichthyoplankton.

Population Ecology

Population Ecology publishes original research articles and reviews on various aspects of population ecology, from the individual to the community level. Among the specific fields included are population dynamics and distribution, evolutionary ecology, ecological genetics, theoretical models, conservation biology, agroecosystem studies, and bioresource management. brief notes on both empirical and theoretical investigations, as well as comments on previously published papers, are published as Notes and Comments. Discussions on new concepts, analyses, and data are published in Forum. Special Features, collections of research articles and reviews organized by the editors, are published periodically and focus on specific research topics.

Progress in Oceanography

Progress in Oceanography publishes the longer, more comprehensive papers that most oceanographers feel are necessary, on occasion, to do justice to their work. Contributions are generally either a review of an aspect of oceanography or a treatise on an expanding oceanographic subject. The articles cover the entire spectrum of disciplines within the science of oceanography. Occasionally volumes are devoted to collections of papers and conference proceedings of exceptional interest. Essential reading for all oceanographers.

Review of Hydrobiology

A Journal Covering all Aspects of Limnology and Marine Biology. Throughout the decades, the development of water ecology has been reflected in this journal: the analysis and assessment of biological structures in water in their interconnection with the internal and external cycle of materials. Today the articles reflect the journal's title: Hydrobiology - the science of life processes in water. It is international, forming the basis for relevant decisions in politics and society, since mankind is dependent on water in so many ways. An international team of scientists guarantees the international character and comprehensive coverage of this journal.

Science

Science is a weekly, peer-reviewed journal that publishes significant original scientific research, plus reviews and analyses of current research and science policy. Our offices in Washington, D.C., and Cambridge, U.K., welcome submissions from all fields of science and from any source.

Science of the Total Environment

The journal is primarily an international medium for the publication of research into those changes in the environment caused by man's activities. Specifically, it is concerned with the changes in the natural level and distribution of chemical elements and compounds which may affect the well-being of the living world, and ultimately harm man himself. emphasis is given to applied environmental chemistry and environmental health.

Sea Research

The Journal of Sea Research is an international and multidisciplinary periodical on marine research, with an emphasis on marine ecosystems. This field should be seen in its widest sense, including both biotic and abiotic aspects of all types of marine and estuarine systems, benthic as well as pelagic. Apart from quality, the main criterion for selection of papers will be whether they contribute to the understanding of the functioning of marine systems. As several subdisciplines add to this aim, manuscripts are welcome from the fields of marine biology, marine geology, marine chemistry, and physical oceanography, provided they are not only descriptive. Although the emphasis is on fundamental research, papers describing important and relevant new techniques, methods and apparatus will also be considered.

Systematics and Biodiversity

Systematics and Biodiversity is an international life science journal devoted to whole-organism biology, especially systematics and taxonomic biodiversity. It emphasizes the importance and multi-disciplinary significance of systematics. It records the diversity of organisms through descriptive taxonomic papers. The underlying basis of biodiversity is addressed directly and indirectly, through studies of taxonomic relationships, and of growth, form, adaptation and function, and through analysis and synthesis of biodiversity patterns in time and space, especially with respect to environmental and human factors. Coverage also includes relevant theory and methodology, and conservation biology.

Theoretical Biology

The Journal of Theoretical Biology is the leading forum for theoretical papers that give insight into biological processes. It covers a very wide range of topics and is of interest to biologists in many areas of research. Many of the papers make use of mathematics, and an effort is made to make the papers intelligible to biologists as a whole. Experimental material bearing on theory is acceptable. Comment on theoretical issues or on papers published in the journal is welcomed in the form of Letters to the Editors. The Journal of Theoretical Biology now operates receiving offices in San Diego and London ensuring faster publication times for papers.

The ScientificWorld

A 'Journal of many Journals', TheScientificWorldJOURNAL is organized as a matrix of overlapping Domains. Each Domain has its own Editorial Board of distinguished scientists acting as Editors and Board Members. Articles published inTheScientificWorldJOURNAL are published simultaneously in all relevant Domains to promote inter-disciplinary exchange. Domains within related subject areas are organized into Clusters (Cell Biology, Environmental/Ecological Sciences, Genetics/Genomics/Proteomics, Pharmacology/Pharmaceutics, and Physiological/Health Sciences).

Trends in Ecology & Evolution

Now the highest-cited journal in Ecology and Evolutionary Biology, Trends in Ecology & Evolution contains polished, concise and readable reviews, opinions and letters in all areas of ecology and evolutionary science. It serves as an invaluable source of information for researchers, lecturers, teachers, field workers and students. Trends in Ecology & Evolution keeps these scientists informed of new developments and ideas across the full range of ecology and evolutionary biology - from the pure to the applied, and from molecular to global. Now, more than ever before, is it necessary for life scientists to be aware of research from a wide range of disciplines, especially in the face of the gathering momentum of global environmental change and destruction. More than any other journal, Trends in Ecology & Evolution is the major forum for coverage of all the important issues concerning organisms and their environments.

Water, Air, & Soil Pollution - An International Journal of Environmental Pollution

Water, Air, & Soil Pollution (WASP) is an international, interdisciplinary journal on all aspects of pollution and solutions to pollution in the biosphere. This includes chemical, physical and biological processes affecting flora, fauna, water, air and soil in relation to environmental pollution. Because of its scope, the subject areas are diverse and include all aspects of pollution sources, transport, deposition, accumulation, acid precipitation, atmospheric pollution, metals, aquatic pollution including marine pollution and ground water, waste water, pesticides, soil pollution, sewage, sediment pollution, forestry pollution, effects of pollutants on humans, vegetation, fish, aquatic species, micro-organisms, animals, ecological implications of pollution and pollution models. Water, Air, & Soil Pollution also publishes manuscripts on methods used in the study of environmental pollutants, environmental toxicology, environmental biology, environmental engineering related to pollution, biodiversity as influenced by pollution, environmental biotechnology as applied to pollution (e.g. bioremediation), environmental modeling and biorestoration of polluted environments. Water, Air, & Soil Pollution publishes research letters (short communications of significant research generally not exceeding six journal pages), regular papers, reviews and book reviews. Special and topical issues are published in the companion journal Water, Air, & Soil Pollution: Focus.

Water, Air, & Soil Pollution: Focus

Water, Air, & Soil Pollution: Focus (WAFO) is a companion journal to Water, Air, & Soil Pollution. Water, Air, & Soil Pollution is an international, interdisciplinary journal on all aspects of pollution and solutions to pollution in the biosphere. This includes chemical, physical and biological processes affecting flora, fauna, water, air and soil in relation to environmental pollution. Because of its scope, the subject areas are diverse and include all aspects of pollution sources, transport, deposition, accumulation, acid precipitation, atmospheric pollution, metals, aquatic pollution including marine pollution and ground water, waste water, pesticides, soil pollution, sewage, sediment pollution, forestry pollution, effects of pollutants on humans, vegetation, fish, aquatic species, micro-organisms, animals, ecological implications of pollution and pollution models. Water, Air, & Soil Pollution also publishes manuscripts on methods used in the study of environmental pollutants, environmental toxicology, environmental biology, environmental engineering related to pollution, biodiversity as influenced by pollution, environmental biotechnology as applied to pollution (e.g. bioremediation), environmental modeling and biorestoration of polluted environments. WAFO publishes special and topical issues where WASP publishes research letters (short communications of significant research generally not exceeding six journal pages), regular papers, reviews and book reviews. The scientific scopes of both journals are the same.

Wetlands Ecology & Management

(as of 2000, incorporating 'Mangroves and Salt Marshes')

Wetlands Ecology and Management is an international journal that publishes original articles in the field of wetlands ecology, the science of the structure and functioning of wetlands for their transformation, utilization, preservation and management on a sustainable basis. The journal covers both pure and applied science dealing with biological, physical and chemical aspects of freshwater, brackish and marine coastal wetlands. The journal aims to encourage the exchange of information between environmental managers, local and national authorities and scientists by providing a forum for papers dealing with scientifically-based management issues around all types of wetlands.

Besides original research papers, discussion papers and short reports, the journal will occasionally include invited review papers on topical subjects. Book reviews, notices of scientific meetings and special issues, arising from chosen scientific symposia or workshops, or as a collection of papers on special topics, will also be published.

WWW Journal of Biology

The primary purpose of this journal is to create an open forum for rapid interactive peer reviewed information exchange in the biological sciences. The journal encourages articles from both plant and animal biological sciences. In general the journal is open to quality articles from any discipline of the biological sciences.

Zoology

Since its foundation in 1830, the traditional aims of the Journal of Zoology have been to publish research on taxonomy and on descriptions of new species of animals. However, with the proliferation of specialist journals, which cater for these important but specialist topics, the Editors have redirected the focus of the Journal to publish hypothesis-driven research that will be of greater interest to the general reader in zoology. Apart from the exclusion of papers of only specialist interest, the Journal will continue to publish original research and reviews within the whole field of zoology, and it will continue to provide information on the latest trends and developments in this ever-expanding subject.

The latest from PLoS ONE: Marine and Aquatic Sciences

PLoS ONE - Category Marine and Aquatic Sciences

Rhodolith Beds Are Major CaCO3 Bio-Factories in the Tropical South West Atlantic

by Gilberto M. Amado-Filho, Rodrigo L. Moura, Alex C. Bastos, Leonardo T. Salgado, Paulo Y. Sumida, Arthur Z. Guth, Ronaldo B. Francini-Filho, Guilherme H. Pereira-Filho, Douglas P. Abrantes, Poliana S. Brasileiro, Ricardo G. Bahia, Rachel N. Leal, Les Kaufman, Joanie A. Kleypas, Marcos Farina, Fabiano L. Thompson
Rhodoliths are nodules of non-geniculate coralline algae that occur in shallow waters (<150 m depth) subjected to episodic disturbance. Rhodolith beds stand with kelp beds, seagrass meadows, and coralline algal reefs as one of the world's four largest macrophyte-dominated benthic communities. Geographic distribution of rhodolith beds is discontinuous, with large concentrations off Japan, Australia and the Gulf of California, as well as in the Mediterranean, North Atlantic, eastern Caribbean and Brazil. Although there are major gaps in terms of seabed habitat mapping, the largest rhodolith beds are purported to occur off Brazil, where these communities are recorded across a wide latitudinal range (2°N - 27°S). To quantify their extent, we carried out an inter-reefal seabed habitat survey on the Abrolhos Shelf (16°50′ - 19°45′S) off eastern Brazil, and confirmed the most expansive and contiguous rhodolith bed in the world, covering about 20,900 km². Distribution, extent, composition and structure of this bed were assessed with side scan sonar, remotely operated vehicles, and SCUBA. The mean rate of CaCO₃production was estimated from in situ growth assays at 1.07 kg m⁻² yr⁻¹, with a total production rate of 0.025 Gt yr⁻¹, comparable to those of the world's largest biogenic CaCO₃ deposits. These gigantic rhodolith beds, of areal extent equivalent to the Great Barrier Reef, Australia, are a critical, yet poorly understood component of the tropical South Atlantic Ocean. Based on the relatively high vulnerability of coralline algae to ocean acidification, these beds are likely to experience a profound restructuring in the coming decades.
Habitat Selection and Temporal Abundance Fluctuations of Demersal Cartilaginous Species in the Aegean Sea (Eastern Mediterranean)

by Christos D. Maravelias, George Tserpes, Maria Pantazi, Panagiota Peristeraki
Predicting the occurrence of keystone top predators in a multispecies marine environment, such as the Mediterranean Sea, can be of considerable value to the long-term sustainable development of the fishing industry and to the protection of biodiversity. We analysed fisheries independent scientific bottom trawl survey data of two of the most abundant cartilaginous fish species (Scyliorhinus canicula, Raja clavata) in the Aegean Sea covering an 11-year sampling period. The current findings revealed a declining trend in R. clavata and S. canicula abundance from the late ′90 s until 2004. Habitats with the higher probability of finding cartilaginous fish present were those located in intermediate waters (depth: 200–400 m). The present results also indicated a preferential species' clustering in specific geographic and bathymetric regions of the Aegean Sea. Depth appeared to be one of the key determining factors for the selection of habitats for all species examined. With cartilaginous fish species being among the more biologically sensitive fish species taken in European marine fisheries, our findings, which are based on a standardized scientific survey, can contribute to the rational exploitation and management of their stocks by providing important information on temporal abundance trends and habitat preferences.
Energetic Plasticity Underlies a Variable Response to Ocean Acidification in the Pteropod, Limacina helicina antarctica

by Brad A. Seibel, Amy E. Maas, Heidi M. Dierssen
Ocean acidification, caused by elevated seawater carbon dioxide levels, may have a deleterious impact on energetic processes in animals. Here we show that high PCO₂ can suppress metabolism, measured as oxygen consumption, in the pteropod, L. helicina forma antarctica, by ∼20%. The rates measured at 180–380 µatm (MO₂ = 1.25 M^−0.25, p = 0.007) were significantly higher (ANCOVA, p = 0.004) than those measured at elevated target CO₂ levels in 2007 (789–1000 µatm, = 0.78 M^−0.32, p = 0.0008; Fig. 1). However, we further demonstrate metabolic plasticity in response to regional phytoplankton concentration and that the response to CO₂ is dependent on the baseline level of metabolism. We hypothesize that reduced regional Chl a levels in 2008 suppressed metabolism and masked the effect of ocean acidification. This effect of food limitation was not, we postulate, merely a result of gut clearance and specific dynamic action, but rather represents a sustained metabolic response to regional conditions. Thus, pteropod populations may be compromised by climate change, both directly via CO₂-induced metabolic suppression, and indirectly via quantitative and qualitative changes to the phytoplankton community. Without the context provided by long-term observations (four seasons) and a multi-faceted laboratory analysis of the parameters affecting energetics, the complex response of polar pteropods to ocean acidification may be masked or misinterpreted.
De Novo Transcriptomic Analysis of an Oleaginous Microalga: Pathway Description and Gene Discovery for Production of Next-Generation Biofuels

by LingLin Wan, Juan Han, Min Sang, AiFen Li, Hong Wu, ShunJi Yin, ChengWu Zhang
Background
Eustigmatos cf. polyphem is a yellow-green unicellular soil microalga belonging to the eustimatophyte with high biomass and considerable production of triacylglycerols (TAGs) for biofuels, which is thus referred to as an oleaginous microalga. The paucity of microalgae genome sequences, however, limits development of gene-based biofuel feedstock optimization studies. Here we describe the sequencing and de novo transcriptome assembly for a non-model microalgae species, E. cf. polyphem, and identify pathways and genes of importance related to biofuel production.
Results
We performed the de novo assembly of E. cf. polyphem transcriptome using Illumina paired-end sequencing technology. In a single run, we produced 29,199,432 sequencing reads corresponding to 2.33 Gb total nucleotides. These reads were assembled into 75,632 unigenes with a mean size of 503 bp and an N50 of 663 bp, ranging from 100 bp to >3,000 bp. Assembled unigenes were subjected to BLAST similarity searches and annotated with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology identifiers. These analyses identified the majority of carbohydrate, fatty acids, TAG and carotenoids biosynthesis and catabolism pathways in E.cf. polyphem.
Conclusions
Our data provides the construction of metabolic pathways involved in the biosynthesis and catabolism of carbohydrate, fatty acids, TAG and carotenoids in E. cf. polyphem and provides a foundation for the molecular genetics and functional genomics required to direct metabolic engineering efforts that seek to enhance the quantity and character of microalgae-based biofuel feedstock.
Habitat and Scale Shape the Demographic Fate of the Keystone Sea Urchin Paracentrotus lividus in Mediterranean Macrophyte Communities

by Patricia Prado, Fiona Tomas, Stefania Pinna, Simone Farina, Guillem Roca, Giulia Ceccherelli, Javier Romero, Teresa Alcoverro
Demographic processes exert different degrees of control as individuals grow, and in species that span several habitats and spatial scales, this can influence our ability to predict their population at a particular life-history stage given the previous life stage. In particular, when keystone species are involved, this relative coupling between demographic stages can have significant implications for the functioning of ecosystems. We examined benthic and pelagic abundances of the sea urchin Paracentrotus lividus in order to: 1) understand the main life-history bottlenecks by observing the degree of coupling between demographic stages; and 2) explore the processes driving these linkages. P. lividus is the dominant invertebrate herbivore in the Mediterranean Sea, and has been repeatedly observed to overgraze shallow beds of the seagrass Posidonia oceanica and rocky macroalgal communities. We used a hierarchical sampling design at different spatial scales (100 s, 10 s and <1 km) and habitats (seagrass and rocky macroalgae) to describe the spatial patterns in the abundance of different demographic stages (larvae, settlers, recruits and adults). Our results indicate that large-scale factors (potentially currents, nutrients, temperature, etc.) determine larval availability and settlement in the pelagic stages of urchin life history. In rocky macroalgal habitats, benthic processes (like predation) acting at large or medium scales drive adult abundances. In contrast, adult numbers in seagrass meadows are most likely influenced by factors like local migration (from adjoining rocky habitats) functioning at much smaller scales. The complexity of spatial and habitat-dependent processes shaping urchin populations demands a multiplicity of approaches when addressing habitat conservation actions, yet such actions are currently mostly aimed at managing predation processes and fish numbers. We argue that a more holistic ecosystem management also needs to incorporate the landscape and habitat-quality level processes (eutrophication, fragmentation, etc.) that together regulate the populations of this keystone herbivore.
Capturing Single Cell Genomes of Active Polysaccharide Degraders: An Unexpected Contribution of Verrucomicrobia

by Manuel Martinez-Garcia, David M. Brazel, Brandon K. Swan, Carol Arnosti, Patrick S. G. Chain, Krista G. Reitenga, Gary Xie, Nicole J. Poulton, Monica Lluesma Gomez, Dashiell E. D. Masland, Brian Thompson, Wendy K. Bellows, Kai Ziervogel, Chien-Chi Lo, Sanaa Ahmed, Cheryl D. Gleasner, Chris J. Detter, Ramunas Stepanauskas
Microbial hydrolysis of polysaccharides is critical to ecosystem functioning and is of great interest in diverse biotechnological applications, such as biofuel production and bioremediation. Here we demonstrate the use of a new, efficient approach to recover genomes of active polysaccharide degraders from natural, complex microbial assemblages, using a combination of fluorescently labeled substrates, fluorescence-activated cell sorting, and single cell genomics. We employed this approach to analyze freshwater and coastal bacterioplankton for degraders of laminarin and xylan, two of the most abundant storage and structural polysaccharides in nature. Our results suggest that a few phylotypes of Verrucomicrobia make a considerable contribution to polysaccharide degradation, although they constituted only a minor fraction of the total microbial community. Genomic sequencing of five cells, representing the most predominant, polysaccharide-active Verrucomicrobia phylotype, revealed significant enrichment in genes encoding a wide spectrum of glycoside hydrolases, sulfatases, peptidases, carbohydrate lyases and esterases, confirming that these organisms were well equipped for the hydrolysis of diverse polysaccharides. Remarkably, this enrichment was on average higher than in the sequenced representatives of Bacteroidetes, which are frequently regarded as highly efficient biopolymer degraders. These findings shed light on the ecological roles of uncultured Verrucomicrobia and suggest specific taxa as promising bioprospecting targets. The employed method offers a powerful tool to rapidly identify and recover discrete genomes of active players in polysaccharide degradation, without the need for cultivation.
Can Thermoclines Be a Cue to Prey Distribution for Marine Top Predators? A Case Study with Little Penguins

by Laure Pelletier, Akiko Kato, André Chiaradia, Yan Ropert-Coudert
The use of top predators as bio-platforms is a modern approach to understanding how physical changes in the environment may influence their foraging success. This study examined if the presence of thermoclines could be a reliable signal of resource availability for a marine top predator, the little penguin (Eudyptula minor). We studied weekly foraging activity of 43 breeding individual penguins equipped with accelerometers. These loggers also recorded water temperature, which we used to detect changes in thermal characteristics of their foraging zone over 5 weeks during the penguin’s guard phase. Data showed the thermocline was detected in the first 3 weeks of the study, which coincided with higher foraging efficiency. When a thermocline was not detected in the last two weeks, foraging efficiency decreased as well. We suggest that thermoclines can represent temporary markers of enhanced food availability for this top-predator to which they must optimally adjust their breeding cycle.
Plant Products Affect Growth and Digestive Efficiency of Cultured Florida Pompano (Trachinotus carolinus) Fed Compounded Diets

by Gregory P. Lech, Robert C. Reigh
Costs of compounded diets containing fish meal as a primary protein source can be expected to rise as fish meal prices increase in response to static supply and growing demand. Alternatives to fish meal are needed to reduce production costs in many aquaculture enterprises. Some plant proteins are potential replacements for fish meal because of their amino acid composition, lower cost and wide availability. In this study, we measured utilization of soybean meal (SBM) and soy protein concentrate (SPC) by Florida pompano fed compounded diets, to determine the efficacy of these products as fish meal replacements. We also calculated apparent digestibility coefficients (ADCs) for canola meal (CM), corn gluten meal (CGM), and distillers dried grains with solubles (DDGS), following typical methods for digestibility trials. Juvenile Florida pompano were fed fish-meal-free diets containing graded levels of SBM and SPC, and weight gain was compared to a control diet that contained SBM, SPC, and fish meal. Fish fed diets that contained 25–30 percent SBM in combination with 43–39 percent SPC had weight gain equivalent to fish fed the control diet with fish meal, while weight gain of fish fed other soy combinations was significantly less than that of the control group. Apparent crude protein digestibility of CGM was significantly higher than that of DDGS but not significantly different from CM. Apparent energy digestibility of DDGS was significantly lower than CGM but significantly higher than CM. Findings suggested that composition of the reference diet used in a digestibility trial affects the values of calculated ADCs, in addition to the chemical and physical attributes of the test ingredient.
Excreted Thiocyanate Detects Live Reef Fishes Illegally Collected Using Cyanide—A Non-Invasive and Non-Destructive Testing Approach

by Marcela C. M. Vaz, Teresa A. P. Rocha-Santos, Rui J. M. Rocha, Isabel Lopes, Ruth Pereira, Armando C. Duarte, Peter J. Rubec, Ricardo Calado
Cyanide fishing is a method employed to capture marine fish alive on coral reefs. They are shipped to markets for human consumption in Southeast Asia, as well as to supply the marine aquarium trade worldwide. Although several techniques can be used to detect cyanide in reef fish, there is still no testing method that can be used to survey the whole supply chain. Most methods for cyanide detection are time-consuming and require the sacrifice of the sampled fish. Thiocyanate anion (SCN−) is a metabolite produced by the main metabolic pathway for cyanide anion (CN⁻) detoxification. Our study employed an optical fiber (OF) methodology (analytical time <6 min) to detect SCN− in a non-invasive and non-destructive manner. Our OF methodology is able to detect trace levels (>3.16 µg L⁻¹) of SCN⁻ in seawater. Given that marine fish exposed to cyanide excrete SCN− in the urine, elevated levels of SCN− present in the seawater holding live reef fish indicate that the surveyed specimens were likely exposed to cyanide. In our study, captive-bred clownfish (Amphiprion clarkii) pulse exposed for 60 s to either 12.5 or 25 mg L⁻¹of CN⁻ excreted up to 6.96±0.03 and 9.84±0.03 µg L⁻¹ of SCN⁻, respectively, during the 28 days following exposure. No detectable levels of SCN⁻ were recorded in the water holding control organisms not exposed to CN⁻, or in synthetic seawater lacking fish. While further research is necessary, our methodology can allow a rapid detection of SCN⁻ in the holding water and can be used as a screening tool to indicate if live reef fish were collected with cyanide.
Phocid Seal Leptin: Tertiary Structure and Hydrophobic Receptor Binding Site Preservation during Distinct Leptin Gene Evolution

by John A. Hammond, Chris Hauton, Kimberley A. Bennett, Ailsa J. Hall
The cytokine hormone leptin is a key signalling molecule in many pathways that control physiological functions. Although leptin demonstrates structural conservation in mammals, there is evidence of positive selection in primates, lagomorphs and chiropterans. We previously reported that the leptin genes of the grey and harbour seals (phocids) have significantly diverged from other mammals. Therefore we further investigated the diversification of leptin in phocids, other marine mammals and terrestrial taxa by sequencing the leptin genes of representative species. Phylogenetic reconstruction revealed that leptin diversification was pronounced within the phocid seals with a high dN/dS ratio of 2.8, indicating positive selection. We found significant evidence of positive selection along the branch leading to the phocids, within the phocid clade, but not over the dataset as a whole. Structural predictions indicate that the individual residues under selection are away from the leptin receptor (LEPR) binding site. Predictions of the surface electrostatic potential indicate that phocid seal leptin is notably different to other mammalian leptins, including the otariids. Cloning the grey seal leptin binding domain of LEPR confirmed that this was structurally conserved. These data, viewed in toto, support a hypothesis that phocid leptin divergence is unlikely to have arisen by random mutation. Based upon these phylogenetic and structural assessments, and considering the comparative physiology and varying life histories among species, we postulate that the unique phocid diving behaviour has produced this selection pressure. The Phocidae includes some of the deepest diving species, yet have the least modified lung structure to cope with pressure and volume changes experienced at depth. Therefore, greater surfactant production is required to facilitate rapid lung re-inflation upon surfacing, while maintaining patent airways. We suggest that this additional surfactant requirement is met by the leptin pulmonary surfactant production pathway which normally appears only to function in the mammalian foetus.
Transcriptomics of In Vitro Immune-Stimulated Hemocytes from the Manila Clam Ruditapes philippinarum Using High-Throughput Sequencing

by Rebeca Moreira, Pablo Balseiro, Josep V. Planas, Berta Fuste, Sergi Beltran, Beatriz Novoa, Antonio Figueras
Background
The Manila clam (Ruditapes philippinarum) is a worldwide cultured bivalve species with important commercial value. Diseases affecting this species can result in large economic losses. Because knowledge of the molecular mechanisms of the immune response in bivalves, especially clams, is scarce and fragmentary, we sequenced RNA from immune-stimulated R. philippinarum hemocytes by 454-pyrosequencing to identify genes involved in their immune defense against infectious diseases.
Methodology and Principal Findings
High-throughput deep sequencing of R. philippinarum using 454 pyrosequencing technology yielded 974,976 high-quality reads with an average read length of 250 bp. The reads were assembled into 51,265 contigs and the 44.7% of the translated nucleotide sequences into protein were annotated successfully. The 35 most frequently found contigs included a large number of immune-related genes, and a more detailed analysis showed the presence of putative members of several immune pathways and processes like the apoptosis, the toll like signaling pathway and the complement cascade. We have found sequences from molecules never described in bivalves before, especially in the complement pathway where almost all the components are present.
Conclusions
This study represents the first transcriptome analysis using 454-pyrosequencing conducted on R. philippinarumfocused on its immune system. Our results will provide a rich source of data to discover and identify new genes, which will serve as a basis for microarray construction and the study of gene expression as well as for the identification of genetic markers. The discovery of new immune sequences was very productive and resulted in a large variety of contigs that may play a role in the defense mechanisms of Ruditapes philippinarum.
Effect of Sub-Lethal Exposure to Ultraviolet Radiation on the Escape Performance of Atlantic Cod Larvae (Gadus morhua)

by Yuichi Fukunishi, Howard I. Browman, Caroline M. F. Durif, Reidun M. Bjelland, Anne Berit Skiftesvik
The amount of ultraviolet (UV) radiation reaching the earth's surface has increased due to depletion of the ozone layer. Several studies have reported that UV radiation reduces survival of fish larvae. However, indirect and sub-lethal impacts of UV radiation on fish behavior have been given little consideration. We observed the escape performance of larval cod (24 dph, SL: 7.6±0.2 mm; 29 dph, SL: 8.2±0.3 mm) that had been exposed to sub-lethal levels of UV radiation vs. unexposed controls. Two predators were used (in separate experiments): two-spotted goby (Gobiusculus flavescens; a suction predator) and lion's mane jellyfish (Cyanea capillata; a “passive" ambush predator). Ten cod larvae were observed in the presence of a predator for 20 minutes using a digital video camera. Trials were replicated 4 times for goby and 5 times for jellyfish. Escape rate (total number of escapes/total number of attacks ×100), escape distance and the number of larvae remaining at the end of the experiment were measured. In the experiment with gobies, in the UV-treated larvae, both escape rate and escape distance (36%, 38±7.5 mm respectively) were significantly lower than those of control larvae (75%, 69±4.7 mm respectively). There was a significant difference in survival as well (UV: 35%, Control: 63%). No apparent escape response was observed, and survival rate was not significantly different, between treatments (UV: 66%, Control: 74%) in the experiment with jellyfish. We conclude that the effect and impact of exposure to sub-lethal levels of UV radiation on the escape performance of cod larvae depends on the type of predator. Our results also suggest that prediction of UV impacts on fish larvae based only on direct effects are underestimations.
Are We Predicting the Actual or Apparent Distribution of Temperate Marine Fishes?

by Jacquomo Monk, Daniel Ierodiaconou, Euan Harvey, Alex Rattray, Vincent L. Versace
Planning for resilience is the focus of many marine conservation programs and initiatives. These efforts aim to inform conservation strategies for marine regions to ensure they have inbuilt capacity to retain biological diversity and ecological function in the face of global environmental change – particularly changes in climate and resource exploitation. In the absence of direct biological and ecological information for many marine species, scientists are increasingly using spatially-explicit, predictive-modeling approaches. Through the improved access to multibeam sonar and underwater video technology these models provide spatial predictions of the most suitable regions for an organism at resolutions previously not possible. However, sensible-looking, well-performing models can provide very different predictions of distribution depending on which occurrence dataset is used. To examine this, we construct species distribution models for nine temperate marine sedentary fishes for a 25.7 km² study region off the coast of southeastern Australia. We use generalized linear model (GLM), generalized additive model (GAM) and maximum entropy (MAXENT) to build models based on co-located occurrence datasets derived from two underwater video methods (i.e. baited and towed video) and fine-scale multibeam sonar based seafloor habitat variables. Overall, this study found that the choice of modeling approach did not considerably influence the prediction of distributions based on the same occurrence dataset. However, greater dissimilarity between model predictions was observed across the nine fish taxa when the two occurrence datasets were compared (relative to models based on the same dataset). Based on these results it is difficult to draw any general trends in regards to which video method provides more reliable occurrence datasets. Nonetheless, we suggest predictions reflecting the species apparent distribution (i.e. a combination of species distribution and the probability of detecting it). Consequently, we also encourage researchers and marine managers to carefully interpret model predictions.
Discrimination of Juvenile Yellowfin (Thunnus albacares) and Bigeye (T. obesus) Tunas using Mitochondrial DNA Control Region and Liver Morphology

by Ivane R. Pedrosa-Gerasmio, Ricardo P. Babaran, Mudjekeewis D. Santos
Yellowfin tuna, Thunnus albacares (Bonnaterre, 1788) and bigeye tuna, Thunnus obesus (Lowe, 1839) are two of the most economically important tuna species in the world. However, identification of their juveniles, especially at sizes less than 40 cm, is very difficult, often leading to misidentification and miscalculation of their catch estimates. Here, we applied the mitochondrial DNA control region D-loop, a recently validated genetic marker used for identifying tuna species (Genus Thunnus), to discriminate juvenile tunas caught by purse seine and ringnet sets around fish aggregating devices (FADs) off the Southern Iloilo Peninsula in Central Philippines. We checked individual identifications using the Neighbor-Joining Method and compared results with morphometric analyses and the liver phenotype. We tested 48 specimens ranging from 13 to 31 cm fork length. Morpho-meristic analyses suggested that 12 specimens (25%) were bigeye tuna and 36 specimens (75%) were yellowfin tuna. In contrast, the genetic and liver analyses both showed that 5 specimens (10%) were bigeye tuna and 43 (90%) yellowfin tuna. This suggests that misidentification can occur even with highly stringent morpho-meristic characters and that the mtDNA control region and liver phenotype are excellent markers to discriminate juveniles of yellowfin and bigeye tunas.
Symbiodinium Transcriptomes: Genome Insights into the Dinoflagellate Symbionts of Reef-Building Corals

by Till Bayer, Manuel Aranda, Shinichi Sunagawa, Lauren K. Yum, Michael K. DeSalvo, Erika Lindquist, Mary Alice Coffroth, Christian R. Voolstra, Mónica Medina
Dinoflagellates are unicellular algae that are ubiquitously abundant in aquatic environments. Species of the genusSymbiodinium form symbiotic relationships with reef-building corals and other marine invertebrates. Despite their ecologic importance, little is known about the genetics of dinoflagellates in general and Symbiodinium in particular. Here, we used 454 sequencing to generate transcriptome data from two Symbiodinium species from different clades (clade A and clade B). With more than 56,000 assembled sequences per species, these data represent the largest transcriptomic resource for dinoflagellates to date. Our results corroborate previous observations that dinoflagellates possess the complete nucleosome machinery. We found a complete set of core histones as well as several H3 variants and H2A.Z in one species. Furthermore, transcriptome analysis points toward a low number of transcription factors in Symbiodinium spp. that also differ in the distribution of DNA-binding domains relative to other eukaryotes. In particular the cold shock domain was predominant among transcription factors. Additionally, we found a high number of antioxidative genes in comparison to non-symbiotic but evolutionary related organisms. These findings might be of relevance in the context of the role that Symbiodinium spp. play as coral symbionts. Our data represent the most comprehensive dinoflagellate EST data set to date. This study provides a comprehensive resource to further analyze the genetic makeup, metabolic capacities, and gene repertoire of Symbiodinium and dinoflagellates. Overall, our findings indicate that Symbiodinium possesses some unique characteristics, in particular the transcriptional regulation in Symbiodinium may differ from the currently known mechanisms of eukaryotic gene regulation.
Swim-Training Changes the Spatio-Temporal Dynamics of Skeletogenesis in Zebrafish Larvae (Danio rerio)

by Ansa W. Fiaz, Karen M. Léon-Kloosterziel, Gerrit Gort, Stefan Schulte-Merker, Johan L. van Leeuwen, Sander Kranenbarg
Fish larvae experience many environmental challenges during development such as variation in water velocity, food availability and predation. The rapid development of structures involved in feeding, respiration and swimming increases the chance of survival. It has been hypothesized that mechanical loading induced by muscle forces plays a role in prioritizing the development of these structures. Mechanical loading by muscle forces has been shown to affect larval and embryonic bone development in vertebrates, but these investigations were limited to the appendicular skeleton. To explore the role of mechanical load during chondrogenesis and osteogenesis of the cranial, axial and appendicular skeleton, we subjected zebrafish larvae to swim-training, which increases physical exercise levels and presumably also mechanical loads, from 5 until 14 days post fertilization. Here we show that an increased swimming activity accelerated growth, chondrogenesis and osteogenesis during larval development in zebrafish. Interestingly, swim-training accelerated both perichondral and intramembranous ossification. Furthermore, swim-training prioritized the formation of cartilage and bone structures in the head and tail region as well as the formation of elements in the anal and dorsal fins. This suggests that an increased swimming activity prioritized the development of structures which play an important role in swimming and thereby increasing the chance of survival in an environment where water velocity increases. Our study is the first to show that already during early zebrafish larval development, skeletal tissue in the cranial, axial and appendicular skeleton is competent to respond to swim-training due to increased water velocities. It demonstrates that changes in water flow conditions can result into significant spatio-temporal changes in skeletogenesis.
Mobility, Expansion and Management of a Multi-Species Scuba Diving Fishery in East Africa

by Hampus Eriksson, Maricela de la Torre-Castro, Per Olsson
Background
Scuba diving fishing, predominantly targeting sea cucumbers, has been documented to occur in an uncontrolled manner in the Western Indian Ocean and in other tropical regions. Although this type of fishing generally indicates a destructive activity, little attention has been directed towards this category of fishery, a major knowledge gap and barrier to management.
Methodology and Principal Findings
With the aim to capture geographic scales, fishing processes and social aspects the scuba diving fishery that operate out of Zanzibar was studied using interviews, discussions, participant observations and catch monitoring. The diving fishery was resilient to resource declines and had expanded to new species, new depths and new fishing grounds, sometimes operating approximately 250 km away from Zanzibar at depths down to 50 meters, as a result of depleted easy-access stock. The diving operations were embedded in a regional and global trade network, and its actors operated in a roving manner on multiple spatial levels, taking advantage of unfair patron-client relationships and of the insufficient management in Zanzibar.
Conclusions and Significance
This study illustrates that roving dynamics in fisheries, which have been predominantly addressed on a global scale, also take place at a considerably smaller spatial scale. Importantly, while proposed management of the sea cucumber fishery is often generic to a simplified fishery situation, this study illustrates a multifaceted fishery with diverse management requirements. The documented spatial scales and processes in the scuba diving fishery emphasize the need for increased regional governance partnerships to implement management that fit the spatial scales and processes of the operation.
Demersal Fish Assemblages and Spatial Diversity Patterns in the Arctic-Atlantic Transition Zone in the Barents Sea

by Edda Johannesen, Åge S. Høines, Andrey V. Dolgov, Maria Fossheim
Direct and indirect effects of global warming are expected to be pronounced and fast in the Arctic, impacting terrestrial, freshwater and marine ecosystems. The Barents Sea is a high latitude shelf Sea and a boundary area between arctic and boreal faunas. These faunas are likely to respond differently to changes in climate. In addition, the Barents Sea is highly impacted by fisheries and other human activities. This strong human presence places great demands on scientific investigation and advisory capacity. In order to identify basic community structures against which future climate related or other human induced changes could be evaluated, we analyzed species composition and diversity of demersal fish in the Barents Sea. We found six main assemblages that were separated along depth and temperature gradients. There are indications that climate driven changes have already taken place, since boreal species were found in large parts of the Barents Sea shelf, including also the northern Arctic area. When modelling diversity as a function of depth and temperature, we found that two of the assemblages in the eastern Barents Sea showed lower diversity than expected from their depth and temperature. This is probably caused by low habitat complexity and the distance to the pool of boreal species in the western Barents Sea. In contrast coastal assemblages in south western Barents Sea and along Novaya Zemlya archipelago in the Eastern Barents Sea can be described as diversity “hotspots”; the South-western area had high density of species, abundance and biomass, and here some species have their northern distribution limit, whereas the Novaya Zemlya area has unique fauna of Arctic, coastal demersal fish. (see Information S1 for abstract in Russian).
Structural and Functional Characterization of Mature Forms of Metalloprotease E495 from Arctic Sea-Ice Bacterium Pseudoalteromonas sp. SM495

by Hai-Lun He, Jun Guo, Xiu-Lan Chen, Bin-Bin Xie, Xi-Ying Zhang, Yong Yu, Bo Chen, Bai-Cheng Zhou, Yu-Zhong Zhang
E495 is the most abundant protease secreted by the Arctic sea-ice bacterium Pseudoalteromonas sp. SM495. As a thermolysin family metalloprotease, E495 was found to have multiple active forms in the culture of strain SM495. E495-M (containing only the catalytic domain) and E495-M-C1 (containing the catalytic domain and one PPC domain) were two stable mature forms, and E495-M-C1-C2 (containing the catalytic domain and two PPC domains) might be an intermediate. Compared to E495-M, E495-M-C1 had similar affinity and catalytic efficiency to oligopeptides, but higher affinity and catalytic efficiency to proteins. The PPC domains from E495 were expressed as GST-fused proteins. Both of the recombinant PPC domains were shown to have binding ability to proteins C-phycocyanin and casein, and domain PPC1 had higher affinity to C-phycocyanin than domain PPC2. These results indicated that the domain PPC1 in E495-M-C1 could be helpful in binding protein substrate, and therefore, improving the catalytic efficiency. Site-directed mutagenesis on the PPC domains showed that the conserved polar and aromatic residues, D26, D28, Y30, Y/W65, in the PPC domains played key roles in protein binding. Our study may shed light on the mechanism of organic nitrogen degradation in the Arctic sea ice.
Impairment of the Bacterial Biofilm Stability by Triclosan

by Helen V. Lubarsky, Sabine U. Gerbersdorf, Cédric Hubas, Sebastian Behrens, Francesco Ricciardi, David M. Paterson
The accumulation of the widely-used antibacterial and antifungal compound triclosan (TCS) in freshwaters raises concerns about the impact of this harmful chemical on the biofilms that are the dominant life style of microorganisms in aquatic systems. However, investigations to-date rarely go beyond effects at the cellular, physiological or morphological level. The present paper focuses on bacterial biofilms addressing the possible chemical impairment of their functionality, while also examining their substratum stabilization potential as one example of an important ecosystem service. The development of a bacterial assemblage of natural composition – isolated from sediments of the Eden Estuary (Scotland, UK) – on non-cohesive glass beads (<63 µm) and exposed to a range of triclosan concentrations (control, 2 – 100 µg L⁻¹) was monitored over time by Magnetic Particle Induction (MagPI). In parallel, bacterial cell numbers, division rate, community composition (DGGE) and EPS (extracellular polymeric substances: carbohydrates and proteins) secretion were determined. While the triclosan exposure did not prevent bacterial settlement, biofilm development was increasingly inhibited by increasing TCS levels. The surface binding capacity (MagPI) of the assemblages was positively correlated to the microbial secreted EPS matrix. The EPS concentrations and composition (quantity and quality) were closely linked to bacterial growth, which was affected by enhanced TCS exposure. Furthermore, TCS induced significant changes in bacterial community composition as well as a significant decrease in bacterial diversity. The impairment of the stabilization potential of bacterial biofilm under even low, environmentally relevant TCS levels is of concern since the resistance of sediments to erosive forces has large implications for the dynamics of sediments and associated pollutant dispersal. In addition, the surface adhesive capacity of the biofilm acts as a sensitive measure of ecosystem effects.
Housekeeping Mutualisms: Do More Symbionts Facilitate Host Performance?

by Adrian C. Stier, Michael A. Gil, C. Seabird McKeon, Sarah Lemer, Matthieu Leray, Suzanne C. Mills, Craig W. Osenberg
Mutualisms often involve one host supporting multiple symbionts, whose identity, density and intraguild interactions can influence the nature of the mutualism and performance of the host. However, the implications of multiple co-occurring symbionts on services to a host have rarely been quantified. In this study, we quantified effects of decapod symbionts on removal of sediment from their coral host. Our field survey showed that all common symbionts typically occur as pairs and never at greater abundances. Two species, the crab Trapezia serenei and the shrimp Alpheus lottini, were most common and co-occurred more often than expected by chance. We conducted a mesocosm experiment to test for effects of decapod identity and density on sediment removal. Alone, corals removed 10% of sediment, but removal increased to 30% and 48% with the presence of two and four symbionts, respectively. Per-capita effects of symbionts were independent of density and identity. Our results suggest that symbiont density is restricted by intraspecific competition. Thus, increased sediment removal from a coral host can only be achieved by increasing the number of species of symbionts on that coral, even though these species are functionally equivalent. Symbiont diversity plays a key role, not through added functionality but by overcoming density limitation likely imposed by intraspecific mating systems.
Reproductive Schedules in Southern Bluefin Tuna: Are Current Assumptions Appropriate?

by Karen Evans, Toby A. Patterson, Howard Reid, Shelton J. Harley
Southern bluefin tuna (SBT) appear to comprise a single stock that is assumed to be both mixed across its distribution and having reproductive adults that are obligate, annual spawners. The putative annual migration cycle of mature SBT consists of dispersed foraging at temperate latitudes with migration to a single spawning ground in the tropical eastern Indian Ocean. Spawning migrations have been assumed to target two peaks in spawning activity; one in September-October and a second in February-March. SBT of sizes comparable to that of individuals observed on the spawning ground were satellite tagged in the Tasman Sea region (2003–2008) and demonstrated both migrations to the spawning grounds and residency in the Tasman Sea region throughout the whole year. All individuals undertaking apparent spawning migrations timed their movements to coincide with the second recognised spawning peak or even later. These observations suggest that SBT may demonstrate substantial flexibility in the scheduling of reproductive events and may even not spawn annually as currently assumed. Further, the population on the spawning grounds may be temporally structured in association with foraging regions. These findings provide new perspectives on bluefin population and spatial dynamics and warrant further investigation and consideration of reproductive schedules in this species.
Characterization of Common Carp Transcriptome: Sequencing, De Novo Assembly, Annotation and Comparative Genomics

by Peifeng Ji, Guiming Liu, Jian Xu, Xumin Wang, Jiongtang Li, Zixia Zhao, Xiaofeng Zhang, Yan Zhang, Peng Xu, Xiaowen Sun
Background
Common carp (Cyprinus carpio) is one of the most important aquaculture species of Cyprinidae with an annual global production of 3.4 million tons, accounting for nearly 14% of the freshwater aquaculture production in the world. Due to the economical and ecological importance of common carp, genomic data are eagerly needed for genetic improvement purpose. However, there is still no sufficient transcriptome data available. The objective of the project is to sequence transcriptome deeply and provide well-assembled transcriptome sequences to common carp research community.
Result
Transcriptome sequencing of common carp was performed using Roche 454 platform. A total of 1,418,591 clean ESTs were collected and assembled into 36,811 cDNA contigs, with average length of 888 bp and N50 length of 1,002 bp. Annotation was performed and a total of 19,165 unique proteins were identified from assembled contigs. Gene ontology and KEGG analysis were performed and classified all contigs into functional categories for understanding gene functions and regulation pathways. Open Reading Frames (ORFs) were detected from 29,869 (81.1%) contigs with an average ORF length of 763 bp. From these contigs, 9,625 full-length cDNAs were identified with sequence length from 201 bp to 9,956 bp. Comparative analysis revealed that 27,693(75.2%) contigs have significant similarity to zebrafish Refseq proteins, and 24,371(66.2%), 24,501(66.5%) and 25,025(70.0%) to teraodon, medaka and three-spined stickleback refseq proteins. A total of 2,064 microsatellites were initially identified from 1,730 contigs, and 1,639 unique sequences had sufficient flanking sequences on both sides for primer design.
Conclusion
The transcriptome of common carp had been deep sequenced, de novo assembled and characterized, providing the valuable resource for better understanding of common carp genome. The transcriptome data will facilitate future functional studies on common carp genome, and gradually apply in breeding programs of common carp, as well as closely related other Cyprinids.
The Effects of Spatially Heterogeneous Prey Distributions on Detection Patterns in Foraging Seabirds

by Octavio Miramontes, Denis Boyer, Frederic Bartumeus
Many attempts to relate animal foraging patterns to landscape heterogeneity are focused on the analysis of foragers movements. Resource detection patterns in space and time are not commonly studied, yet they are tightly coupled to landscape properties and add relevant information on foraging behavior. By exploring simple foraging models in unpredictable environments we show that the distribution of intervals between detected prey (detection statistics) is mostly determined by the spatial structure of the prey field and essentially distinct from predator displacement statistics. Detections are expected to be Poissonian in uniform random environments for markedly different foraging movements (e.g. Lévy and ballistic). This prediction is supported by data on the time intervals between diving events on short-range foraging seabirds such as the thick-billed murre (Uria lomvia). However, Poissonian detection statistics is not observed in long-range seabirds such as the wandering albatross (Diomedea exulans) due to the fractal nature of the prey field, covering a wide range of spatial scales. For this scenario, models of fractal prey fields induce non-Poissonian patterns of detection in good agreement with two albatross data sets. We find that the specific shape of the distribution of time intervals between prey detection is mainly driven by meso and submeso-scale landscape structures and depends little on the forager strategy or behavioral responses.
Accuracy of Using Visual Identification of White Sharks to Estimate Residency Patterns

by David G. Delaney, Ryan Johnson, Marthán N. Bester, Enrico Gennari
Determining the residency of an aquatic species is important but challenging and it remains unclear what is the best sampling methodology. Photo-identification has been used extensively to estimate patterns of animals' residency and is arguably the most common approach, but it may not be the most effective approach in marine environments. To examine this, in 2005, we deployed acoustic transmitters on 22 white sharks (Carcharodon carcharias) in Mossel Bay, South Africa to quantify the probability of detecting these tagged sharks by photo-identification and different deployment strategies of acoustic telemetry equipment. Using the data collected by the different sampling approaches (detections from an acoustic listening station deployed under a chumming vessel versus those from visual sightings and photo-identification), we quantified the methodologies' probability of detection and determined if the sampling approaches, also including an acoustic telemetry array, produce comparable results for patterns of residency. Photo-identification had the lowest probability of detection and underestimated residency. The underestimation is driven by various factors primarily that acoustic telemetry monitors a large area and this reduces the occurrence of false negatives. Therefore, we propose that researchers need to use acoustic telemetry and also continue to develop new sampling approaches as photo-identification techniques are inadequate to determine residency. Using the methods presented in this paper will allow researchers to further refine sampling approaches that enable them to collect more accurate data that will result in better research and more informed management efforts and policy decisions.
Aragonite Precipitation by “Proto-Polyps” in Coral Cell Cultures

by Tali Mass, Jeana L. Drake, Liti Haramaty, Yair Rosenthal, Oscar M. E. Schofield, Robert M. Sherrell, Paul G. Falkowski
The mechanisms of coral calcification at the molecular, cellular and tissue levels are poorly understood. In this study, we examine calcium carbonate precipitation using novel coral tissue cultures that aggregate to form “proto-polyps”. Our goal is to establish an experimental system in which calcification is facilitated at the cellular level, while simultaneously allowing in vitromanipulations of the calcifying fluid. This novel coral culturing technique enables us to study the mechanisms of biomineralization and their implications for geochemical proxies. Viable cell cultures of the hermatypic, zooxanthellate coral,Stylophora pistillata, have been maintained for 6 to 8 weeks. Using an enriched seawater medium with aragonite saturation state similar to open ocean surface waters (Ω_arag∼4), the primary cell cultures assemble into “proto-polyps” which form an extracellular organic matrix (ECM) and precipitate aragonite crystals. These extracellular aragonite crystals, about 10 µm in length, are formed on the external face of the proto-polyps and are identified by their distinctive elongated crystallography and X-ray diffraction pattern. The precipitation of aragonite is independent of photosynthesis by the zooxanthellae, and does not occur in control experiments lacking coral cells or when the coral cells are poisoned with sodium azide. Our results demonstrate thatproto-polyps, aggregated from primary coral tissue culture, function (from a biomineralization perspective) similarly to whole corals. This approach provides a novel tool for investigating the biophysical mechanism of calcification in these organisms.
Groundwater Nitrogen Pollution and Assessment of Its Health Risks: A Case Study of a Typical Village in Rural-Urban Continuum, China

by Yang Gao, Guirui Yu, Chunyan Luo, Pei Zhou
Protecting groundwater from nitrogen contamination is an important public-health concern and a major national environmental issue in China. In this study, we monitored water quality in 29 wells from 2009 to 2010 in a village in Shanghai city, whick belong to typical rural-urban continuum in China. The total N and NO₃-N exhibited seasonal changes, and there were large fluctuations in NH₄-N in residential areas, but without significant seasonal patterns. NO₂-N in the water was not stable, but was present at high levels. Total N and NO₃-N were significantly lower in residential areas than in agricultural areas. The groundwater quality in most wells belonged to Class III and IV in the Chinese water standard, which defines water that is unsuitable for human consumption. Our health risk assessments showed that NO₃-N posed the greatest carcinogenic risk, with risk values ranging from 19×10⁻⁶ to 80×10⁻⁶, which accounted for more than 90% of the total risk in the study area.
Global Assessment of Extinction Risk to Populations of Sockeye Salmon Oncorhynchus nerka

by Peter S. Rand, Matthew Goslin, Mart R. Gross, James R. Irvine, Xanthippe Augerot, Peter A. McHugh, Victor F. Bugaev
Background
Concern about the decline of wild salmon has attracted the attention of the International Union for the Conservation of Nature (IUCN). The IUCN applies quantitative criteria to assess risk of extinction and publishes its results on the Red List of Threatened Species. However, the focus is on the species level and thus may fail to show the risk to populations. The IUCN has adapted their criteria to apply to populations but there exist few examples of this type of assessment. We assessed the status of sockeye salmon Oncorhynchus nerka as a model for application of the IUCN population-level assessments and to provide the first global assessment of the status of an anadromous Pacific salmon.
Methods/Principal Findings
We found from demographic data that the sockeye salmon species is not presently at risk of extinction. We identified 98 independent populations with varying levels of risk within the species' range. Of these, 5 (5%) are already extinct. We analyzed the risk for 62 out of 93 extant populations (67%) and found that 17 of these (27%) are at risk of extinction. The greatest number and concentration of extinct and threatened populations is in the southern part of the North American range, primarily due to overfishing, freshwater habitat loss, dams, hatcheries, and changing ocean conditions.
Conclusions/Significance
Although sockeye salmon are not at risk at the species-level, about one-third of the populations that we analyzed are at risk or already extinct. Without an understanding of risk to biodiversity at the level of populations, the biodiversity loss in salmon would be greatly underrepresented on the Red List. We urge government, conservation organizations, scientists and the public to recognize this limitation of the Red List. We also urge recognition that about one-third of sockeye salmon global population diversity is at risk of extinction or already extinct.
Interspecific Hybridization Increased in Congeneric Flatfishes after the Prestige Oil Spill

by Victor Crego-Prieto, Jose L. Martinez, Agustin Roca, Eva Garcia-Vazquez
Marine species with relatively low migratory capacity are threatened by habitat alterations derived from human activities. In November 2002 the tanker Prestige sank off the Spanish northwest coast releasing 70,000 tons of fuel and damaging biota in the area. Despite efforts to clean the damaged areas, fuel remnants have affected marine species over the last nine years. This study is focused on two flatfish, Lepidorhombus boscii (four-spotted megrim) and L. whiffiagonis (megrim), whose spawning areas are located at the edge of the continental platform. We have analyzed megrim samples from North Spanish and French waters obtained before and after the oil spill. Genotypes at the nuclear marker 5S rDNA indicate a significant increase in interspecific hybridization after the Prestige accident, likely due to forced spawning overlap. The mitochondrial D-Loop region was employed for determining the direction of hybrid crosses, which were most frequently L. boscii female x L. whiffiagonismale. Reduced ability of L. boscii females to select conspecific mates would explain such asymmetric hybridization. To our knowledge this is the first time that increased hybridization between fish species can be associated to an oil spill. These results illustrate the potential long-term effect of petrol wastes on wild fish species.
Phylogeny and Diversification Patterns among Vesicomyid Bivalves

by Carole Decker, Karine Olu, Regina L. Cunha, Sophie Arnaud-Haond
Vesicomyid bivalves are among the most abundant and diverse symbiotic taxa in chemosynthetic-based ecosystems: more than 100 different vesicomyid species have been described so far. In the present study, we investigated the phylogenetic positioning of recently described vesicomyid species from the Gulf of Guinea and their western Atlantic and Pacific counterparts using mitochondrial DNA sequence data. The maximum-likelihood (ML) tree provided limited support for the recent taxonomic revision of vesicomyids based on morphological criteria; nevertheless, most of the newly sequenced specimens did not cluster with their morphological conspecifics. Moreover, the observed lack of geographic clustering suggests the occurrence of independent radiations followed by worldwide dispersal. Ancestral character state reconstruction showed a significant correlation between the characters “depth” and “habitat” and the reconstructed ML phylogeny suggesting possible recurrent events of ‘stepwise speciation’ from shallow to deep waters in different ocean basins. This is consistent with genus or species bathymetric segregation observed from recent taxonomic studies. Altogether, our results highlight the need for ongoing re-evaluation of the morphological characters used to identify vesicomyid bivalves.

Minggu, 22 April 2012

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