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Research Tools and Methods for Marine Species Acquisition and Identification
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Research Tools and Methods for Marine Species Acquisition and Identification

A special issue of Journal of Marine Science and Engineering (ISSN 2077-1312).

Deadline for manuscript submissions: closed (30 September 2015) | Viewed by 56568

Special Issue Editor

Prof. Dr. Angelika Brandt

E-Mail Website
Guest Editor
Biocenter Grindel and Zoological Museum, University of Hamburg, Hamburg, Germany
Interests: systematics; biodiversity research; biogeography; ecology; evolution; deep sea; polar areas; Isopoda (Crustacea Peracarida)

Special Issue Information

Dear Colleagues,

The oceans are the largest ecosystems on Earth and harbor a very high biodiversity. Only a very minor part of this diversity is described and we know that the deeper in the ocean we go the less we know about this environment and the fauna that inhabits it. In addition, the smaller the organisms are the less we know about them.

This bias is still due to the fact that deep-sea areas are not easily accessible and that logistic and financial constraints hamper sampling of these areas. Moreover, we find such a high biodiversity in almost all catches from hadal and abyssal depths that it takes a long time to identify the material and describe the new species, as usually more than 50% of the species from these depths are new to science.

Challenges in deep-sea research that have to be met in future, thus, refer to two issues:

1. Deep-sea sampling

- long wire times

- high expenses for shiptime

- often insufficient specimens due to sampling gear and patchiness of the organisms

2. Species identification

- very high species richness

- no identification guides

- slow species identification and description

- large databases (systematics and biogeography)

Therefore, the present Special Issue is meant to present the most recent advances and challenges and aims in techniques dealing with novel, fast, and efficient sampling and processing of species, for example in the deep sea (or in other marine or terrestrial areas).

Prof. Dr. Angelika Brandt
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Journal of Marine Science and Engineering is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.


Keywords

  • sampling devices
  • autonomous sampling gear
  • underwater observatories
  • identification methods
  • species
  • diversity
  • genetic methods for fast species identification
  • rapid identification or illustration techniques
  • acceleration of species identification

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Published Papers (5 papers)

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Research

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5830 KiB  
Article
Cutting the Umbilical: New Technological Perspectives in Benthic Deep-Sea Research
by Angelika Brandt, Julian Gutt, Marc Hildebrandt, Jan Pawlowski, Jakob Schwendner, Thomas Soltwedel and Laurenz Thomsen
J. Mar. Sci. Eng. 2016, 4(2), 36; https://doi.org/10.3390/jmse4020036 - 20 May 2016
Cited by 51 | Viewed by 11758
Abstract
Many countries are very active in marine research and operate their own research fleets. In this decade, a number of research vessels have been renewed and equipped with the most modern navigation systems and tools. However, much of the research gear used for [...] Read more.
Many countries are very active in marine research and operate their own research fleets. In this decade, a number of research vessels have been renewed and equipped with the most modern navigation systems and tools. However, much of the research gear used for biological sampling, especially in the deep-sea, is outdated and dependent on wired operations. The deployment of gear can be very time consuming and, thus, expensive. The present paper reviews wire-dependent, as well as autonomous research gear for biological sampling at the deep seafloor. We describe the requirements that new gear could fulfil, including the improvement of spatial and temporal sampling resolution, increased autonomy, more efficient sample conservation methodologies for morphological and molecular studies and the potential for extensive in situ real-time studies. We present applicable technologies from robotics research, which could be used to develop novel autonomous marine research gear, which may be deployed independently and/or simultaneously with traditional wired equipment. A variety of technological advancements make such ventures feasible and timely. In proportion to the running costs of modern research vessels, the development of such autonomous devices might be already paid off after a discrete number of pioneer expeditions. Full article
(This article belongs to the Special Issue Research Tools and Methods for Marine Species Acquisition and Identification)
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1305 KiB  
Article
Algal Community Membership of Estuarine Mudflats from the Savannah River, United States
by Kalina M. Manoylov, Yenkang Ellen France, Abeselom Geletu and Joseph N. Dominy
J. Mar. Sci. Eng. 2016, 4(1), 11; https://doi.org/10.3390/jmse4010011 - 22 Feb 2016
Cited by 13 | Viewed by 5581
Abstract
Algae represent a large and diverse group of photosynthetic organisms inhabiting all aquatic habitats. Although the traditional assessment of algal diversity relies mainly on microscopy-based morphological identification, certain limitations exist. In this study, we present a combined molecular and morphological assessment of algal [...] Read more.
Algae represent a large and diverse group of photosynthetic organisms inhabiting all aquatic habitats. Although the traditional assessment of algal diversity relies mainly on microscopy-based morphological identification, certain limitations exist. In this study, we present a combined molecular and morphological assessment of algal diversity in mudflats from the Savannah River Estuary, Georgia. High diversity of diatoms was documented, and less than 20% of the algal community was physiologically active at the time of collection. From the total genomic DNA extracted from the field samples and lab isolates, 18S rDNA sequences were PCR amplified, cloned, sequenced, identified, and then compared to the taxa identified via microscopy. Only a few of the DNA sequences matched documented taxa, and the abundance of particular algal species was limited to morphological analysis. Surprisingly, upon examination of the remaining lysis buffer from the mechanical lysis step of algal cells, diatom species were left intact even in the presence of a detergent indicating that the diatom species resistant to lysis could be easily underrepresented. Generation of additional algal sequences data, tied to accurate taxonomic identification, is essential to current environmental sequencing projects and potentially would allow faster acquisition of algal community structure within these unique environments. Full article
(This article belongs to the Special Issue Research Tools and Methods for Marine Species Acquisition and Identification)
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13905 KiB  
Article
An End-to-End DNA Taxonomy Methodology for Benthic Biodiversity Survey in the Clarion-Clipperton Zone, Central Pacific Abyss
by Adrian G. Glover, Thomas G. Dahlgren, Helena Wiklund, Inga Mohrbeck and Craig R. Smith
J. Mar. Sci. Eng. 2016, 4(1), 2; https://doi.org/10.3390/jmse4010002 - 25 Dec 2015
Cited by 77 | Viewed by 16756
Abstract
Recent years have seen increased survey and sampling expeditions to the Clarion-Clipperton Zone (CCZ), central Pacific Ocean abyss, driven by commercial interests from contractors in the potential extraction of polymetallic nodules in the region. Part of the International Seabed Authority (ISA) regulatory requirements [...] Read more.
Recent years have seen increased survey and sampling expeditions to the Clarion-Clipperton Zone (CCZ), central Pacific Ocean abyss, driven by commercial interests from contractors in the potential extraction of polymetallic nodules in the region. Part of the International Seabed Authority (ISA) regulatory requirements are that these contractors undertake environmental research expeditions to their CCZ exploration claims following guidelines approved by the ISA Legal and Technical Commission (ISA, 2010). Section 9 (e) of these guidelines instructs contractors to “…collect data on the sea floor communities specifically relating to megafauna, macrofauna, meiofauna, microfauna, nodule fauna and demersal scavengers”. There are a number of methodological challenges to this, including the water depth (4000–5000 m), extremely warm surface waters (~28 °C) compared to bottom water (~1.5 °C) and great distances to ports requiring a large and long seagoing expedition with only a limited number of scientists. Both scientists and regulators have recently realized that a major gap in our knowledge of the region is the fundamental taxonomy of the animals that live there; this is essential to inform our knowledge of the biogeography, natural history and ultimately our stewardship of the region. Recognising this, the ISA is currently sponsoring a series of taxonomic workshops on the CCZ fauna and to assist in this process we present here a series of methodological pipelines for DNA taxonomy (incorporating both molecular and morphological data) of the macrofauna and megafauna from the CCZ benthic habitat in the recent ABYSSLINE cruise program to the UK-1 exploration claim. A major problem on recent CCZ cruises has been the collection of high-quality samples suitable for both morphology and DNA taxonomy, coupled with a workflow that ensures these data are made available. The DNA sequencing techniques themselves are relatively standard, once good samples have been obtained. The key to quality taxonomic work on macrofaunal animals from the tropical abyss is careful extraction of the animals (in cold, filtered seawater), microscopic observation and preservation of live specimens, from a variety of sampling devices by experienced zoologists at sea. Essential to the long-term iterative building of taxonomic knowledge from the CCZ is an “end-to-end” methodology to the taxonomic science that takes into account careful sampling design, at-sea taxonomic identification and fixation, post-cruise laboratory work with both DNA and morphology and finally a careful sample and data management pipeline that results in specimens and data in accessible open museum collections and online repositories. Full article
(This article belongs to the Special Issue Research Tools and Methods for Marine Species Acquisition and Identification)
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Review

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1845 KiB  
Review
Methodological Studies on Estimates of Abundance and Diversity of Heterotrophic Flagellates from the Deep-Sea Floor
by Alexandra Schoenle, Alexandra Jeuck, Frank Nitsche, Paul Venter, Dennis Prausse and Hartmut Arndt
J. Mar. Sci. Eng. 2016, 4(1), 22; https://doi.org/10.3390/jmse4010022 - 3 Mar 2016
Cited by 11 | Viewed by 6497
Abstract
Extreme environmental conditions in the deep sea hamper access to protist communities. In combination with the potentially highly diverse species composition, it demands a wide range of methods to be applied at the same time to guarantee a high resolution of quantitative and [...] Read more.
Extreme environmental conditions in the deep sea hamper access to protist communities. In combination with the potentially highly diverse species composition, it demands a wide range of methods to be applied at the same time to guarantee a high resolution of quantitative and qualitative studies of deep-sea heterotrophic flagellates (HF). Within this study, we present a possible combination of several culture-independent and culture-dependent methods available for investigating benthic deep-sea HF communities. Besides live-counting and fixation of HF, we refer to cultivation methods and molecular surveys using next generation sequencing. Laboratory ecological experiments under deep-sea conditions (high pressure, low temperature) could allow the approval of the potential deep-sea origin of sampled HF. The combination of different methods offers a unique possibility to receive detailed information on nanofaunal life in the deep sea. Specific fixation techniques to preserve samples directly at the sampling depth must be applied in further studies to reflect the real biodiversity of the largest habitat on earth. Full article
(This article belongs to the Special Issue Research Tools and Methods for Marine Species Acquisition and Identification)
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1928 KiB  
Review
How Aphia—The Platform behind Several Online and Taxonomically Oriented Databases—Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics
by Leen Vandepitte, Bart Vanhoorne, Wim Decock, Stefanie Dekeyzer, Aina Trias Verbeeck, Lorenzo Bovit, Francisco Hernandez and Jan Mees
J. Mar. Sci. Eng. 2015, 3(4), 1448-1473; https://doi.org/10.3390/jmse3041448 - 1 Dec 2015
Cited by 25 | Viewed by 14965
Abstract
The Aphia platform is an infrastructure designed to capture taxonomic and related data and information, and includes an online editing environment. The latter allows easy access to experts so they can update the content of the database in a timely fashion. Aphia is [...] Read more.
The Aphia platform is an infrastructure designed to capture taxonomic and related data and information, and includes an online editing environment. The latter allows easy access to experts so they can update the content of the database in a timely fashion. Aphia is the core platform that underpins the World Register of Marine Species (WoRMS) and its more than 80 related global, regional and thematic species databases, but it also allows the storage of non-marine data. The content of Aphia can be consulted online, either by individual users or via machine-to-machine interactions. Aphia uses unique and stable identifiers for each available name in the database through the use of Life Science Identifiers (LSIDs). The system not only allows the storage of accepted and unaccepted names, but it also documents the relationships between names. This makes it a very powerful tool for taxonomic quality control, and also allows the linking of different pieces of information through scientific names, both within the Aphia platform and in relation to externally hosted databases. Through these LSIDs, Aphia has become an important player in the field of (marine) biodiversity informatics, allowing interactions between its own taxonomic data and e.g., biogeographic databases. Some applications in the field of biodiversity informatics encompass the coupling of species traits and taxonomy, as well as the creation of diverse, expert validated data products that can be used by policy makers, for example. Aphia also supplies (part of) its content to other data integrators and the infrastructure can be used to host orphan databases in danger of being lost. Full article
(This article belongs to the Special Issue Research Tools and Methods for Marine Species Acquisition and Identification)
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