| 1. |
- Abreu, A., et al.
(author)
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Priorities for ocean microbiome research
- 2022
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In: Nature Microbiology. - : Springer Science and Business Media LLC. - 2058-5276. ; 7:7, s. 937-947
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Journal article (peer-reviewed)abstract
- Studying the ocean microbiome can inform international policies related to ocean governance, tackling climate change, ocean acidification and pollution, and can help promote achievement of multiple Sustainable Development Goals. Microbial communities have essential roles in ocean ecology and planetary health. Microbes participate in nutrient cycles, remove huge quantities of carbon dioxide from the air and support ocean food webs. The taxonomic and functional diversity of the global ocean microbiome has been revealed by technological advances in sampling, DNA sequencing and bioinformatics. A better understanding of the ocean microbiome could underpin strategies to address environmental and societal challenges, including achievement of multiple Sustainable Development Goals way beyond SDG 14 'life below water'. We propose a set of priorities for understanding and protecting the ocean microbiome, which include delineating interactions between microbiota, sustainably applying resources from oceanic microorganisms and creating policy- and funder-friendly ocean education resources, and discuss how to achieve these ambitious goals.
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| 2. |
- Anton, Victor, et al.
(author)
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An open-source, citizen science and machine learning approach to analyse subsea movies
- 2021
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In: Biodiversity Data Journal. - 1314-2828. ; 9
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Journal article (peer-reviewed)abstract
- Background The increasing access to autonomously-operated technologies offer vast opportunities to sample large volumes of biological data. However, these technologies also impose novel demands on ecologists who need to apply tools for data management and processing that= are efficient, publicly available and easy to use. Such tools are starting to be developed for wider community and here we present an approach to combine essential analytical functions for analysing large volumes of image data in marine ecological research. New information This paper describes the Koster Seafloor Observatory, an open-source approach to analysing large amounts of subsea movie data for marine ecological research. The approach incorporates three distinct modules to: manage and archive the subsea movies, involve citizen scientists to accurately classify the footage and, finally, train and test machine learning algorithms for detection of biological objects. This modular approach is based on open-source code and allows researchers to customise and further develop the presented functionalities to various types of data and questions related to analysis of marine imagery. We tested our approach for monitoring cold water corals in a Marine Protected Area in Sweden using videos from remotely-operated vehicles (ROVs). Our study resulted in a machine learning model with an adequate performance, which was entirely trained with classifications provided by citizen scientists. We illustrate the application of machine learning models for automated inventories and monitoring of cold water corals. Our approach shows how citizen science can be used to effectively extract occurrence and abundance data for key ecological species and habitats from underwater footage. We conclude that the combination of open-source tools, citizen science systems, machine learning and high performance computational resources are key to successfully analyse large amounts of underwater imagery in the future.
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| 3. |
- Bourlat, Sarah, et al.
(author)
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Feeding ecology of Xenoturbella bocki (phylum Xenoturbellida) revealed by genetic barcoding
- 2008
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In: Molecular Ecology Resources. - 1755-098X. ; 8, s. 18-22
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Journal article (peer-reviewed)abstract
- The benthic marine worm Xenoturbella is frequently contaminated with molluscan DNA, which had earlier caused confusion resulting in a suggested bivalve relationship. In order to find the source of the contaminant, we have used molluscan sequences derived from Xenoturbella and compared them to barcodes obtained from several individuals of the nonmicroscopic molluscs sharing the same environment as Xenoturbella. Using cytochrome oxidase 1, we found the contaminating sequences to be 98% similar to the bivalve Ennucula tenuis. Using the highly variable D1-D2 region of the large ribosomal subunit in Xenoturbella, we found three distinct species of contaminating molluscs, one of which is 99% similar to the bivalve Abra nitida, one of the most abundant bivalves in the Gullmarsfjord where Xenoturbella was found, and another 99% similar to the bivalve Nucula sulcata. These data clearly show that Xenoturbella only contains molluscan DNA originating from bivalves living in the same environment, refuting former hypotheses of a bivalve relationship. In addition, these data suggest that Xenoturbella feeds specifically on bivalve prey from multiple species, possibly in the form of eggs and larvae.
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| 4. |
- Bourlat, Sarah, et al.
(author)
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Genomics in marine monitoring: new opportunities for assessing marine health status.
- 2013
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In: Marine pollution bulletin. - : Elsevier BV. - 1879-3363 .- 0025-326X. ; 74:1, s. 19-31
-
Journal article (peer-reviewed)abstract
- This viewpoint paper explores the potential of genomics technology to provide accurate, rapid, and cost efficient observations of the marine environment. The use of such approaches in next generation marine monitoring programs will help achieve the goals of marine legislation implemented world-wide. Genomic methods can yield faster results from monitoring, easier and more reliable taxonomic identification, as well as quicker and better assessment of the environmental status of marine waters. A summary of genomic methods that are ready or show high potential for integration into existing monitoring programs is provided (e.g. qPCR, SNP based methods, DNA barcoding, microarrays, metagenetics, metagenomics, transcriptomics). These approaches are mapped to existing indicators and descriptors and a series of case studies is presented to assess the cost and added value of these molecular techniques in comparison with traditional monitoring systems. Finally, guidelines and recommendations are suggested for how such methods can enter marine monitoring programs in a standardized manner.
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| 5. |
- Davies, N., et al.
(author)
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Report of the 14th Genomic Standards Consortium Meeting, Oxford, UK, September 17-21, 2012
- 2014
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In: Standards in Genomic Sciences. - : Springer Science and Business Media LLC. - 1944-3277. ; 9:3, s. 1236-1250
-
Journal article (peer-reviewed)abstract
- This report summarizes the proceedings of the 14th workshop of the Genomic Standards Consortium (GSC) held at the University of Oxford in September 2012. The primary goal of the workshop was to work towards the launch of the Genomic Observatories (GOs) Network under the GSC. For the first time, it brought together potential GOs sites, GSC members, and a range of interested partner organizations. It thus represented the first meeting of the GOs Network (GOs1). Key outcomes include the formation of a core group of “champions” ready to take the GOs Network forward, as well as the formation of working groups. The workshop also served as the first meeting of a wide range of participants in the Ocean Sampling Day (OSD) initiative, a first GOs action. Three projects with complementary interests – COST Action ES1103, MG4U and Micro B3 – organized joint sessions at the workshop. A two-day GSC Hackathon followed the main three days of meetings.
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| 6. |
- Davies, Neil, et al.
(author)
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The founding charter of the Genomic Observatories Network
- 2014
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In: GigaScience. - 2047-217X. ; 3:2
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Journal article (peer-reviewed)abstract
- Abstract The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms.An international group of 64 scientists first published the call for a global network of Genomic Observatories in January 2012. The vision for such a network was expanded in a subsequent paper and developed over a series of meetings in Bremen (Germany), Shenzhen (China), Moorea (French Polynesia), Oxford (UK), Pacific Grove (California, USA), Washington (DC, USA), and London (UK). While this community-building process continues, here we express our mutual intent to establish the GOs Network formally, and to describe our shared vision for its future. The views expressed here are ours alone as individual scientists, and do not necessarily represent those of the institutions with which we are affiliated.
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| 7. |
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| 8. |
- Dunn, Casey W, et al.
(author)
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Broad phylogenomic sampling improves resolution of the animal tree of life.
- 2008
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 452:7188, s. 745-9
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Journal article (peer-reviewed)abstract
- Long-held ideas regarding the evolutionary relationships among animals have recently been upended by sometimes controversial hypotheses based largely on insights from molecular data. These new hypotheses include a clade of moulting animals (Ecdysozoa) and the close relationship of the lophophorates to molluscs and annelids (Lophotrochozoa). Many relationships remain disputed, including those that are required to polarize key features of character evolution, and support for deep nodes is often low. Phylogenomic approaches, which use data from many genes, have shown promise for resolving deep animal relationships, but are hindered by a lack of data from many important groups. Here we report a total of 39.9 Mb of expressed sequence tags from 29 animals belonging to 21 phyla, including 11 phyla previously lacking genomic or expressed-sequence-tag data. Analysed in combination with existing sequences, our data reinforce several previously identified clades that split deeply in the animal tree (including Protostomia, Ecdysozoa and Lophotrochozoa), unambiguously resolve multiple long-standing issues for which there was strong conflicting support in earlier studies with less data (such as velvet worms rather than tardigrades as the sister group of arthropods), and provide molecular support for the monophyly of molluscs, a group long recognized by morphologists. In addition, we find strong support for several new hypotheses. These include a clade that unites annelids (including sipunculans and echiurans) with nemerteans, phoronids and brachiopods, molluscs as sister to that assemblage, and the placement of ctenophores as the earliest diverging extant multicellular animals. A single origin of spiral cleavage (with subsequent losses) is inferred from well-supported nodes. Many relationships between a stable subset of taxa find strong support, and a diminishing number of lineages remain recalcitrant to placement on the tree.
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| 9. |
- Faurby, S., et al.
(author)
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Population dynamics of American horseshoe crabs-historic climatic events and recent anthropogenic pressures
- 2010
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In: Molecular Ecology. - 0962-1083. ; 19:15, s. 3088-3100
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Journal article (peer-reviewed)abstract
- Populations of the American horseshoe crab, Limulus polyphemus, have declined, but neither the causes nor the magnitude are fully understood. In order to evaluate historic demography, variation at 12 microsatellite DNA loci surveyed in 1218 L. polyphemus sampled from 28 localities was analysed with Bayesian coalescent-based methods. The analysis showed strong declines in population sizes throughout the species' distribution except in the geographically isolated southern-most population in Mexico, where a strong increase in population size was inferred. Analyses suggested that demographic changes in the core of the distribution occurred in association with the recolonization after the Ice Age and also by anthropogenic effects, such as the past overharvest of the species for fertilizer or the current use of the animals as bait for American eel (Anguilla rostrata) and whelk (Busycon spp.) fisheries. This study highlights the importance of considering both climatic changes and anthropogenic effects in efforts to understand population dynamics-a topic which is highly relevant in the ongoing assessments of the effects of climate change and overharvest.
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| 10. |
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| 11. |
- Fuchs, Judith, 1978, et al.
(author)
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The first comprehensive molecular phylogeny of Bryozoa (Ectoprocta) based on combined analyses of nuclear and mitochondrial genes
- 2009
-
In: Molecular Phylogenetics and Evolution. ; 52, s. 225-233
-
Journal article (peer-reviewed)abstract
- Bryozoa is one of the most puzzling phyla in the animal kingdom and little is known about their evolutionary history. Its phylogenetic position among the Metazoa remains unsettled, as well as its intra-phylum relationships. Here, we present the first comprehensive molecular phylogeny of Bryozoa based on the mitochondrial gene COI and two nuclear genes 18S rDNA and 28S rDNA including 32 species from 23 families. We show that the monophyletic status is supported for the phylum as well as for previously defined bryozoan classes. The 28S rDNA supports a close relationship of Phylactolaemata and Stenolaemata, while partial COI and 18S rDNA show the freshwater Phylactolaemata as basal bryozoans. The Gymnolaemata have generally been divided into soft-bodied forms (Ctenostomata) and hard-bodied species (Cheilostomata). In our analyses all three genes conflict with this assumption and show hard body forms having evolved within Gymnolaemata several times.
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| 12. |
- Fuchs, Judith, 1978, et al.
(author)
-
The first internal molecular phylogeny of the animal phylum Entoprocta.
- 2010
-
In: Molecular Phylogenetics and Evolution. - 1055-7903. ; 56:1, s. 370-379
-
Journal article (peer-reviewed)abstract
- This article provides the first molecular phylogenetic study of the enigmatic invertebrate phylum Entoprocta and was designed to resolve the internal phylogenetic relationships of the taxon. The study is based on partial and combined analyses of the mitochondrial gene cytochrome c oxidase subunit I (COI), as well as the nuclear ribosomal genes 28S rDNA and 18S rDNA. A short morphological character matrix was constructed to trace character evolution along the combined molecular phylogenetic tree. The combined analyses of all three genes strongly support the monophyly of the phylum Entoprocta and a sister group relationship of Entoprocta and Cycliophora, a result which is consistent with a number of previous morphological and molecular assessments. We find evidence for two separate lineages within the Entoprocta, one lineage leading to all recent colonial taxa, Coloniales, another representing the clade of solitary entoprocts, Solitaria. Our study suggests that Loxosomella is a paraphyletic assembly with regard to the genera Loxomitra, Loxosoma, and Loxocorone. The results imply that the ancestral entoproct was a solitary, marine organism with an epizoic life style. The groundplan of the entoproct adult stage probably included a bilobed centralized nervous system, and the larva was assumedly planktonic, with a gut and a ciliated creeping sole.
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| 13. |
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| 14. |
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| 15. |
- González-Talaván, Alberto, et al.
(author)
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Data Refinement Using the BioVeL Portal
- 2014
-
Book (other academic/artistic)abstract
- This document is a practical guide on how to assess the quality of biodiversity datasets, like those accessible through the GBIF Network using BioVeL online workflows portal. The manual takes a practical tutorial-based approach that the reader can repeat using the sample datasets provided. A complement of practical exercises based on real-case scenarios should help users attain the skills demonstrated in the tutorials. The manual also provides a generic introduction about data quality and the use of workflows for those who wish to familiarize themselves with the basic theory behind these practices.
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| 16. |
- Gärdenfors, Ulf, et al.
(author)
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Swedish LifeWatch ─ a biodiversity infrastructure integrating and reusing data from citizen science, monitoring and research
- 2014
-
In: Human Computation. - : Human Computation Institute. - 2330-8001. ; 1, s. 147-163
-
Journal article (peer-reviewed)abstract
- With continued pressure on biodiversity and ever-growing conflicts with human development, qualified systems for scenario modelling, impact assessment and decision support are urgently needed. Such systems must be able to integrate complex models and information from many sources and do so in a flexible and transparent way. To that end, as well as for other complicated and data-intensive biodiversity research purposes, the concept of LifeWatch has emerged. The idea of LifeWatch is to construct e-infrastructure and virtual laboratories by integrating large data sources, computational capacities, and tools for analysis and modelling in an open, serviceoriented architecture. To be efficient and accurate, a continuous inflow of large quantities of data is essential. However, even with new techniques, government-funded monitoring data and research data will not feed the system with up-to-date species information of sufficient scale and resolution. To fill this void, skilled amateur observers (citizen scientists) can contribute to a very valuable extent. After a preparatory phase, a Swedish LifeWatch (SLW) consortium was initiated in 2011. Swedish LifeWatch developed an infrastructure where all components are accessible through open web services. At the SLW Analysis portal, different formats of species and environmental data can be accessed instantly, and integrated, analysed, visualized and downloaded at selected temporal, spatial or taxonomic scales. Swedish LifeWatch currently provides 46 million species observations from eight different databases, all harmonized according to standardized formats and the Dyntaxa taxonomic backbone database. Almost 40 million of these observations were provided by citizens through the online reporting system named the Species Observation System (SOS) or Artportalen. This paper describes this system, as well as the incentives that make it so successful. The citizen science data in the SOS are accessible, together with data from research and monitoring, in the SLW infrastructure, making the latter a powerful instrument for large-scale data extraction, visualization and analysis.
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| 17. |
- Hardisty, Alex, et al.
(author)
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A decadal view of biodiversity informatics: challenges and priorities.
- 2013
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In: BMC ecology. - : Springer Science and Business Media LLC. - 1472-6785. ; 13
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Journal article (peer-reviewed)abstract
- Biodiversity informatics plays a central enabling role in the research community's efforts to address scientific conservation and sustainability issues. Great strides have been made in the past decade establishing a framework for sharing data, where taxonomy and systematics has been perceived as the most prominent discipline involved. To some extent this is inevitable, given the use of species names as the pivot around which information is organised. To address the urgent questions around conservation, land-use, environmental change, sustainability, food security and ecosystem services that are facing Governments worldwide, we need to understand how the ecosystem works. So, we need a systems approach to understanding biodiversity that moves significantly beyond taxonomy and species observations. Such an approach needs to look at the whole system to address species interactions, both with their environment and with other species.It is clear that some barriers to progress are sociological, basically persuading people to use the technological solutions that are already available. This is best addressed by developing more effective systems that deliver immediate benefit to the user, hiding the majority of the technology behind simple user interfaces. An infrastructure should be a space in which activities take place and, as such, should be effectively invisible.This community consultation paper positions the role of biodiversity informatics, for the next decade, presenting the actions needed to link the various biodiversity infrastructures invisibly and to facilitate understanding that can support both business and policy-makers. The community considers the goal in biodiversity informatics to be full integration of the biodiversity research community, including citizens' science, through a commonly-shared, sustainable e-infrastructure across all sub-disciplines that reliably serves science and society alike.
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| 18. |
- Hardisty, Alex R., et al.
(author)
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BioVeL: A virtual laboratory for data analysis and modelling in biodiversity science and ecology
- 2016
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In: BMC Ecology. - : Springer Science and Business Media LLC. - 1472-6785. ; 16
-
Journal article (peer-reviewed)abstract
- © 2016 The Author(s).Background: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as "Web services") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust "in silico" science. However, use of this approach in biodiversity science and ecology has thus far been quite limited. Results: BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on-line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible 'virtual laboratory', free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity. Conclusions: Our work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.
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| 19. |
- Hejnol, A, et al.
(author)
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Assessing the root of bilaterian animals with scalable phylogenomic methods
- 2009
-
In: Proceedings of the Royal Society B. ; 276:1677, s. 4261-4270
-
Journal article (peer-reviewed)abstract
- A clear picture of animal relationships is a prerequisite to understand how the morphological and ecological diversity of animals evolved over time. Among others, the placement of the acoelomorph flatworms, Acoela and Nemertodermatida, has fundamental implications for the origin and evolution of various animal organ systems. Their position, however, has been inconsistent in phylogenetic studies using one or several genes. Furthermore, Acoela has been among the least stable taxa in recent animal phylogenomic analyses, which simultaneously examine many genes from many species, while Nemertodermatida has not been sampled in any phylogenomic study. New sequence data are presented here from organisms targeted for their instability or lack of representation in prior analyses, and are analysed in combination with other publicly available data. We also designed new automated explicit methods for identifying and selecting common genes across different species, and developed highly optimized supercomputing tools to reconstruct relationships from gene sequences. The results of the work corroborate several recently established findings about animal relationships and provide new support for the placement of other groups. These new data and methods strongly uphold previous suggestions that Acoelomorpha is sister clade to all other bilaterian animals, find diminishing evidence for the placement of the enigmatic Xenoturbella within Deuterostomia, and place Cycliophora with Entoprocta and Ectoprocta. The work highlights the implications that these arrangements have for metazoan evolution and permits a clearer picture of ancestral morphologies and life histories in the deep past.
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| 20. |
- Karlsson, Rikard, et al.
(author)
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Analysis of potential distribution and impacts for two species of alien crabs in Northern Europe
- 2019
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In: Biological Invasions. - : Springer Science and Business Media LLC. - 1387-3547 .- 1573-1464. ; 21:10, s. 3109-3119
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Journal article (peer-reviewed)abstract
- The Asian shore crab (Hemigrapsus sanguineus) and the brush-clawed shore crab (H. takanoi) both originate from east Asia but have in recent years established viable populations throughout coastal European waters. The two species are highly competitive and canoccur in very high densities. Both species have been linked to the decrease of otherwise abundant native species such as the European shore crab (Carcinus maenas) and the common periwinkle (Littorina littorea). As both crabs are relatively new in European coastal waters, little is known about the full distribution range that may be achieved by these crabs and the ecological impact that may follow with an invasion of coastal habitats. In this study we investigated the potential distribution of Hemigrapsus in coastal waters of Northern Europe and the potential impact on the native competitor C. maenas. To this end we collected crabs on the Swedish west coast and on Helgoland and used these for behavioural experiments. We also collected new observation records of both species in Sweden and used these occurrences for building ecological niche models. We report that the potential distribution range of both H. sanguineus and H. takanoi extends from western Sweden to eastern Ireland (east–west) and southern Norway to western France (north–south). We also found evidence that H. takanoi can establish viable populations in nutrient-rich inshore areas of the western and southern Baltic Sea and that competition by H. sanguineus is likely to affect abundances of C. maenas in the areas where these species co-occur. © 2019, The Author(s).
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| 21. |
- Kissling, W. Daniel, et al.
(author)
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Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale
- 2018
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In: Biological Reviews. - : Wiley. - 1464-7931 .- 1469-185X. ; 93:1, s. 600-625
-
Journal article (peer-reviewed)abstract
- © 2017 Cambridge Philosophical Society. Much biodiversity data is collected worldwide, but it remains challenging to assemble the scattered knowledge for assessing biodiversity status and trends. The concept of Essential Biodiversity Variables (EBVs) was introduced to structure biodiversity monitoring globally, and to harmonize and standardize biodiversity data from disparate sources to capture a minimum set of critical variables required to study, report and manage biodiversity change. Here, we assess the challenges of a 'Big Data' approach to building global EBV data products across taxa and spatiotemporal scales, focusing on species distribution and abundance. The majority of currently available data on species distributions derives from incidentally reported observations or from surveys where presence-only or presence-absence data are sampled repeatedly with standardized protocols. Most abundance data come from opportunistic population counts or from population time series using standardized protocols (e.g. repeated surveys of the same population from single or multiple sites). Enormous complexity exists in integrating these heterogeneous, multi-source data sets across space, time, taxa and different sampling methods. Integration of such data into global EBV data products requires correcting biases introduced by imperfect detection and varying sampling effort, dealing with different spatial resolution and extents, harmonizing measurement units from different data sources or sampling methods, applying statistical tools and models for spatial inter- or extrapolation, and quantifying sources of uncertainty and errors in data and models. To support the development of EBVs by the Group on Earth Observations Biodiversity Observation Network (GEO BON), we identify 11 key workflow steps that will operationalize the process of building EBV data products within and across research infrastructures worldwide. These workflow steps take multiple sequential activities into account, including identification and aggregation of various raw data sources, data quality control, taxonomic name matching and statistical modelling of integrated data. We illustrate these steps with concrete examples from existing citizen science and professional monitoring projects, including eBird, the Tropical Ecology Assessment and Monitoring network, the Living Planet Index and the Baltic Sea zooplankton monitoring. The identified workflow steps are applicable to both terrestrial and aquatic systems and a broad range of spatial, temporal and taxonomic scales. They depend on clear, findable and accessible metadata, and we provide an overview of current data and metadata standards. Several challenges remain to be solved for building global EBV data products: (i) developing tools and models for combining heterogeneous, multi-source data sets and filling data gaps in geographic, temporal and taxonomic coverage, (ii) integrating emerging methods and technologies for data collection such as citizen science, sensor networks, DNA-based techniques and satellite remote sensing, (iii) solving major technical issues related to data product structure, data storage, execution of workflows and the production process/cycle as well as approaching technical interoperability among research infrastructures, (iv) allowing semantic interoperability by developing and adopting standards and tools for capturing consistent data and metadata, and (v) ensuring legal interoperability by endorsing open data or data that are free from restrictions on use, modification and sharing. Addressing these challenges is critical for biodiversity research and for assessing progress towards conservation policy targets and sustainable development goals.
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| 22. |
- Kjeldsen, Kasper Urup, et al.
(author)
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Two types of endosymbiotic bacteria in the enigmatic marine worm Xenoturbella.
- 2010
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In: Applied and Environmental Microbiology. - 1098-5336. ; 76:8, s. 2657-2662
-
Journal article (peer-reviewed)abstract
- Two types of endosymbiotic bacteria were identified in the gastrodermis of the marine invertebrate Xenoturbella bocki (Xenoturbellida, Bilateria). While previously described Chlamydia-like endosymbionts were rare, Gammaproteobacteria distantly related to other endosymbionts and pathogens were abundant. The endosymbionts should be considered when interpreting the poorly understood ecology and evolution of Xenoturbella.
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| 23. |
- Koureas, Dimitrios, et al.
(author)
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Community engagement : The ‘last mile’ challenge for European research e-infrastructures
- 2016
-
In: Research Ideas and Outcomes. - : Pensoft Publishers. - 2367-7163. ; 2
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Journal article (peer-reviewed)abstract
- Europe is building its Open Science Cloud; a set of robust and interoperable e-infrastructures with the capacity to provide data and computational solutions through cloud-based services. The development and sustainable operation of such e-infrastructures are at the forefront of European funding priorities. The research community, however, is still reluctant to engage at the scale required to signal a Europe-wide change in the mode of operation of scientific practices. The striking differences in uptake rates between researchers from different scientific domains indicate that communities do not equally share the benefits of the above European investments. We highlight the need to support research communities in organically engaging with the European Open Science Cloud through the development of trustworthy and interoperable Virtual Research Environments. These domain-specific solutions can support communities in gradually bridging technical and socio-cultural gaps between traditional and open digital science practice, better diffusing the benefits of European e-infrastructures.
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| 24. |
- Laugen, Ane T, et al.
(author)
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The Pacific Oyster (Crassostrea gigas) Invasion in Scandinavian Coastal Waters: Impact on Local Ecosystem Services
- 2015
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In: Biological Invasions in Changing Ecosystems: Vectors, Ecological Impacts, Management and Predictions.. - Warsaw : DE GRUYTER OPEN. - 9783110438666 ; , s. 232-257
-
Book chapter (peer-reviewed)abstract
- Shellfish have always played an important role in subsistence and income for coastal communities. Shallow-water bivalve beds are easily accessible and have been exploited and overexploited for centuries. Depletion of stocks has lead to farming and aquaculture of many species. Few species, if any, have been as popular and successful as the the Pacific oyster (C. gigas). Its highly efficient filter feeding, high growth rates, massive repoductive output, and tolerance of a large range of abiotic conditions, has not only made it one of the world’s 20 most cultured species, but also one of the most invasive. This chapter tracks the Pacific oyster on its way towards the North-eastern corner of its European distribution, predicts its future distribution, and discusses the implications for local ecosystems.
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| 25. |
- Leidenberger, Sonja, et al.
(author)
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Evaluating the potential of ecological niche modelling as a component in marine non-indigenous species risk assessments
- 2015
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In: Marine Pollution Bulletin. - : Elsevier. - 0025-326X .- 1879-3363. ; 97:1-2, s. 470-487
-
Journal article (peer-reviewed)abstract
- Marine biological invasions have increased with the development of global trading, causing the homogenization of communities and the decline of biodiversity. A main vector is ballast water exchange from shipping. This study evaluates the use of ecological niche modelling (ENM) to predict the spread of 18 non-indigenous species (NIS) along shipping routes and their potential habitat suitability (hot/cold spots) in the Baltic Sea and Northeast Atlantic. Results show that, contrary to current risk assessment methods, temperature and sea ice concentration determine habitat suitability for 61% of species, rather than salinity (11%). We show high habitat suitability for NIS in the Skagerrak and Kattegat, a transitional area for NIS entering or leaving the Baltic Sea. As many cases of NIS introduction in the marine environment are associated with shipping pathways, we explore how ENM can be used to provide valuable information on the potential spread of NIS for ballast water risk assessment.
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| 26. |
- Martaeng, Rasmus, 1997, et al.
(author)
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Phylogeographic study using autonomous reef monitoring structures indicates fast range expansion of the invasive bryozoan Juxtacribrilina mutabilis
- 2023
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In: Hydrobiologia. - : Springer Science and Business Media LLC. - 0018-8158 .- 1573-5117. ; 850, s. 4115-26
-
Journal article (peer-reviewed)abstract
- This is a phylogeographical study of Juxtacribrilina mutabilis, a recently described bryozoan from Japan with sightings in Sweden, Norway, and Maine (US), to test how fast and far it has expanded across Europe in recent years. J. mutabilis settles easily on ship hulls, making it a useful model organism for studying long-distance invasion pathways. The study was conducted using Autonomous Reef Monitoring Structures (ARMS) to monitor the entire European coastline and Svalbard for J. mutabilis using DNA metabarcoding. During the time between its first sighting in Europe 2008 and the last ARMS retrieval 2020, the data shows how J. mutabilis has gained a pan-European distribution, being genetically identified in 14 new distinct locations. Presence/absence of barcodes were confirmed by image-based identification in 74% of the samples. Fourteen haplotypes never reported before were discovered in a 264 bp region of the cytochrome oxidase I gene. Two haplotypes (HP1 and HP3) occurred frequently and geographically widely dispersed, indicating intercontinental connectivity. Two locations, Koster and Getxo showed particularly high genetic diversity with similar haplotype networks suggesting continuous gene flow across oceanographically unlinked regions. Given the recent description of J. mutabilis and the relatively few historical encounters, the genetic diversity described here suggests an unusually fast range expansion within the last two decades. Such global spreading events of fouling organisms may become more common in the future as a result of more frequent and interconnected ship traffic.
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| 27. |
- Mathew, Cherian, et al.
(author)
-
A semi-automated workflow for biodiversity data retrieval, cleaning, and quality control
- 2014
-
In: Biodiversity Data Journal. - 1314-2836 .- 1314-2828. ; 2:e4221, s. 1-12
-
Journal article (peer-reviewed)abstract
- The compilation and cleaning of data needed for analyses and prediction of species distributions is a time consuming process requiring a solid understanding of data formats and service APIs provided by biodiversity informatics infrastructures. We designed and implemented a Taverna-based Data Refinement Workflow which integrates taxonomic data retrieval, data cleaning, and data selection into a consistent, standards-based, and effective system hiding the complexity of underlying service infrastructures. The workflow can be freely used both locally and through a web-portal which does not require additional software installations by users.
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| 28. |
- Mathew, C, et al.
(author)
-
Data Refinement Workflow
- 2012
-
In: http://www.myexperiment.org/packs/267.html.
-
Other publication (other academic/artistic)abstract
- The Taxonomic Data Refinement Workflow provides an environment for preparing observational and specimen data sets for use in scientific analyses such as: species distribution analysis,species richness and diversity studies, species occurrence studiesh, historical analysis, and other spatio-temporal analyses. This pack contains: - The Taxonomic Data Refinement (Integrated) Workflow (.t2flow file) - Its (version) dependent libraries - Relevant documentation, including diagrammatic representation of the workflow - Example data files , including input and output data. For more information on BioVeL's Data Refinement Workflow, please click here" with a link to http://www.biovel.eu/index.php/workflows/data-refinement-wf This workflow has been created by the Biodiversity Virtual e-Laboratory (BioVeL : http://www.biovel.eu/) project. BioVeL is funded by the EU’s Seventh Framework Program, grant no. 283359
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| 29. |
- Mohammadi, Z., et al.
(author)
-
Unidirectional Introgression and Evidence of Hybrid Superiority over Parental Populations in Eastern Iranian Plateau Population of Hares (Mammalia: Lepus Linnaeus, 1758)
- 2020
-
In: Journal of Mammalian Evolution. - : Springer Science and Business Media LLC. - 1064-7554 .- 1573-7055. ; 27:4, s. 723-743
-
Journal article (peer-reviewed)abstract
- Hares from Iran can be divided into three morphological groups, with Lepus europaeus inhabiting the western parts of Iran. Hares from lowland areas along the southeastern corner of the Caspian Sea are morphologically similar to both L. tolai and L. tibetanus, but diagnosis is complicated by a lack of taxonomic agreement. Mitochondrial DNA suggests L. tibetanus rather than L. tolai, although comparative material is not incontestable. The third group, in more xeric habitats of eastern Iran, shows a mixture of traits characteristic of both the west Iranian L. europaeus and the Golestan population, the southeast Caspian Sea. Mitochondrial and nuclear loci reveal conflicting patterns, where hares from eastern Iran cluster with L. europaeus based on mtDNA, but with the Golestan population based on nuclear transferrin, suggesting a mixed ancestry. Ecological niche modeling indicates that the preferred habitat of the Golestan population is more restricted than that of the other two groups. Pure L. europaeus occur in areas of high seasonality, low temperature, and high precipitation, whereas the population in eastern Iran inhabits areas characterized by high contrast in daily temperatures and the highest isothermality in eastern Iran. Parts of the range of this population are also indicated to correspond to the fundamental niche of L. europaeus, yet both parental forms appear to be absent from this area occupied by individuals of apparent mixed ancestry. This suggests that the population of mixed ancestry may have selective advantages over the parental forms, and that the absence of the latter from this area may be due to competitive exclusion. As the population of mixed ancestry thus appears to be self-sustaining, incipient speciation of a stabilized hybrid may be implied. © 2019, Springer Science+Business Media, LLC, part of Springer Nature.
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| 30. |
- Moosbrugger, Martin, et al.
(author)
-
The placental analogue and the pattern of sexual reproduction in the cheilostome bryozoan Bicellariella ciliata (Gymnolaemata).
- 2012
-
In: Frontiers in zoology. - : Springer Science and Business Media LLC. - 1742-9994. ; 9:1
-
Journal article (peer-reviewed)abstract
- ABSTRACT: Background: Matrotrophy or extraembryonic nutrition – transfer of nutrients from mother to embryo during gestation – is well known and thoroughly studied among vertebrates, but still poorly understood in invertebrates. The current paper focuses on the anatomy and ultrastructure of the oogenesis and placentotrophy as well as formation of the brood chamber (ovicell) in the cheilostome bryozoan Bicellariella ciliata (Linnaeus, 1758). Our research aimed to combine these aspects of the sexual reproduction into an integral picture, highlighting the role of the primitive placenta-like system in the evolution of bryozoan reproductive patterns. Results: Follicular and nutrimentary provisioning of the oocyte occur during oogenesis. Small macrolecithal oocytes are produced, and embryos are nourished in the ovicell via a simple placental analogue (embryophore). Every brooding episode is accompanied by the hypertrophy of the embryophore, which collapses after larval release. Nutrients are released and uptaken by exocytosis (embryophore) and endocytosis (embryo). Embryos lack specialized area for nutrient uptake, which occurs through the whole epidermal surface. The volume increase between the ripe oocyte and the larva is ca. 10-fold. Conclusions: The ovicell is a complex organ (not a special polymorph as often thought) consisting of an ooecium (protective capsule) and an ooecial vesicle (plugging the entrance to the brooding cavity) that develop from the distal and the fertile zooid correspondingly. Combination of macrolecithal oogenesis and extraembryonic nutrition allows attributing B. ciliata to species with reproductive pattern IV. However, since its oocytes are small, this species represents a previously undescribed variant of this pattern, which appears to represent a transitional state from the insipient matrotrophy (with large macrolecithal eggs) to substantial one (with small microlecithal ones). Altogether, our results substantially added and corrected the data obtained by the previous authors, providing a new insight in our understanding of the evolution of matrotrophy in invertebrates.
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| 31. |
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| 32. |
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| 33. |
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| 34. |
- Nilsson Sköld, Helen, 1970, et al.
(author)
-
Stem Cells in Asexual Reproduction of Marine Invertebrates
- 2009
-
In: Stem Cells in Marine Organisms. - Netherlands : Springer. - 9789048127665 ; , s. 105-137
-
Book chapter (other academic/artistic)abstract
- While sexual reproduction is conserved and almost ubiquitous, asexual reproduction in forms of parthenogenesis or agametic cloning from somatic tissue is less conserved. The phylogeny shows that agametic cloning is widespread but scattered with many different modes for asexual formation of a new animal. This suggests that independent forms of cloning have evolved later from sexual ancestors between and within different phyla. Here, we present an overview of agametic cloning in the marine animal kingdom and discuss molecular and evolutionary aspects of somatic stem cell usage for asexual cloning. The molecular tissue characterizations and the relative role of different stem cells involved in agametic cloning are only at its beginning with whole phyla largely uncovered. An emerging hypothesis is that the first somatic stem cells used in cloning were also able to form a germ-line and that the more limited lineage specific stem cells are derived. We discuss advantages and problems with agametic cloning from somatic tissue and propose that the levels of stem cell potential held in the tissue can have large consequences for the reproductive life cycle strategies and long-term fitness in clonal animals and strains. We finally describe suitable molecular experimental approaches for future research on this topic.
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| 35. |
- Obst, Matthias, 1974, et al.
(author)
-
A Marine Biodiversity Observation Network for Genetic Monitoring of Hard-Bottom Communities (ARMS-MBON)
- 2020
-
In: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 7
-
Journal article (peer-reviewed)abstract
- Marine hard-bottom communities are undergoing severe change under the influence of multiple drivers, notably climate change, extraction of natural resources, pollution and eutrophication, habitat degradation, and invasive species. Monitoring marine biodiversity in such habitats is, however, challenging as it typically involves expensive, non-standardized, and often destructive sampling methods that limit its scalability. Differences in monitoring approaches furthermore hinders inter-comparison among monitoring programs. Here, we announce a Marine Biodiversity Observation Network (MBON) consisting of Autonomous Reef Monitoring Structures (ARMS) with the aim to assess the status and changes in benthic fauna with genomic-based methods, notably DNA metabarcoding, in combination with image-based identifications. This article presents the results of a 30-month pilot phase in which we established an operational and geographically expansive ARMS-MBON. The network currently consists of 20 observatories distributed across European coastal waters and the polar regions, in which 134 ARMS have been deployed to date. Sampling takes place annually, either as short-term deployments during the summer or as long-term deployments starting in spring. The pilot phase was used to establish a common set of standards for field sampling, genetic analysis, data management, and legal compliance, which are presented here. We also tested the potential of ARMS for combining genetic and image-based identification methods in comparative studies of benthic diversity, as well as for detecting non-indigenous species. Results show that ARMS are suitable for monitoring hard-bottom environments as they provide genetic data that can be continuously enriched, re-analyzed, and integrated with conventional data to document benthic community composition and detect non-indigenous species. Finally, we provide guidelines to expand the network and present a sustainability plan as part of the European Marine Biological Resource Centre (www.embrc.eu).
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| 36. |
- Obst, Matthias, 1974, et al.
(author)
-
A new species of Cycliophora from the mouthparts of the American lobster, Homarus americanus (Nephropidae, Decapoda)
- 2006
-
In: Organisms Diversity and Evolution. - : Elsevier BV. - 1439-6092 .- 1618-1077. ; 6:2, s. 83-97
-
Journal article (peer-reviewed)abstract
- The present study describes a new species of Cycliophora with the aid of light- and electron microscopy. The animals live attached or free-living on the mouth appendages of the American lobster, Homarus americanus. Individuals occur in dense clusters of up to several thousand individuals. The new species is named Symbion americanus sp. nov. according to the name of its host; it can be distinguished from the previously described species Symbion pandora by the presence of a posterior pair of retractable tubular appendages or toes in the Prometheus larva. Morphological variation among cycliophorans on H. americanus collected in different localities seems to be high. In several sexual populations of S. americanus, older feeding individuals with a female typically have 5-13 rings of cuticular scars and a thicker cuticle. Moreover, attached Prometheus larvae frequently contain three males, chordoid cysts possess a distal appendix, and chordoid larval morphology varies among localities. These differences in morphology might indicate the existence of cryptic species. The presence of toes in the Prometheus larva could support a cycliophoran relationship with rotiferan taxa, although additional ultrastructural studies are needed. Considering that the genus Homarus is at least 60 My years old, and with regard to its history of speciation, it seems possible that the two Symbion species separated during the Pleistocene. © 2005 Gesellschaft für Biologische Systematik.
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| 37. |
- Obst, Matthias, 1974
(author)
-
Deep Relations in Nordic and Baltic Biodiversity e-Infrastructures (DeepDive)
- 2019
-
In: Biodiversity Information Science and Standards. - : Pensoft Publishers. - 2535-0897.
-
Conference paper (peer-reviewed)abstract
- The vision of the DeepDive program (https://neic.no/deepdive) is to establish a regional infrastructure network consisting of Nordic and Baltic data centers and information systems and to provide seamlessly operating regional data services, tools, and virtual laboratories. The program is funded by the Nordic e-Infrastructure Collaboration (https://neic.no) and was launched in 2017. Here we present some of the results and outcomes from the technical collaborations in the network. We will show examples of integration of biodiversity data services and portals though common Application Programming Interfaces (APIs) and Graphical User Interfaces (GUIs), describe our program to foster a biodiversity informatics community in the region, and explain advances in system interoperability that have been achieved over the past three years. We will also highlight the technical plans for further development and long-term sustainability of our Nordic and Baltic e-infrastructure network and make suggestions for further linkage to international information systems and ESFRI infrastructures.
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| 38. |
- Obst, Matthias, 1974, et al.
(author)
-
Marine long-term biodiversity assessment suggests loss of rare species in the Skagerrak and Kattegat region
- 2018
-
In: Marine Biodiversity. - : Springer Science and Business Media LLC. - 1867-1616 .- 1867-1624. ; 48:4, s. 2165-2176
-
Journal article (peer-reviewed)abstract
- © 2017 The Author(s) Studies of cumulative and long-term effects of human activities in the ocean are essential for developing realistic conservation targets. Here, we report the results of a recent national marine biodiversity inventory along the Swedish West coast between 2004 and 2009. The expedition revisited many historical localities that have been sampled with the same methods in the early twentieth century. We generated comparable datasets from our own investigation and the historical data to compare species richness, abundance, and geographic distribution of diversity. Our analysis indicates that the benthic ecosystems in the region have lost a large part of its original species richness over the last seven decades. We find evidence that especially rare species have disappeared. This process has caused a more homogenized community structure in the region and diminished historical biodiversity hotspots. We argue that the contemporary lack of rare species in the benthic ecosystems of the Kattegat and Skagerrak offers less opportunity to respond to environmental perturbations in the future and suggest improving the poor representation of rare species in the region. The study shows the value of biodiversity inventories as well as natural history collections in investigations of accumulated effects of anthropogenic activities and for re-establishing species-rich, productive, and resilient ecosystems.
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| 39. |
- Obst, Matthias, 1974, et al.
(author)
-
Molecular phylogeny of extant horseshoe crabs (Xiphosura, Limulidae) indicates Paleogene diversification of Asian species
- 2012
-
In: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903. ; 62:1, s. 21-26
-
Journal article (peer-reviewed)abstract
- Horseshoe crabs are marine invertebrates well known for their exceptionally low rates of diversification during their entire evolutionary history. Despite the low species diversity in the group, the phylogenetic relationships among the extant species, especially among the three Asian species are still unresolved. Here we apply a new set of molecular genetic data in combination with a wide geographic sampling of the intra-specific diversity to reinvestigate the evolutionary history among the four living limulid xiphosurans. Our analysis of the intraspecific diversity reveals low levels of connectivity among Carci- noscorpius rotundicauda lineages, which can be explained by the estuarine-bound ecology of this species. Moreover, a clear genetic break across the Thai–Malay Peninsula suggests the presence of cryptic species in C. rotundicauda. The limulid phylogeny finds strong support for a monophyletic genus Tachypleus and a diversification of the three Asian species during the Paleogene period, with speciation events well sepa- rated in time by several million years. The tree topology suggests that the three Asian species originated in central South East Asia from a marine stem group that inhabited the shallow coastal waters between the Andaman Sea, Vietnam, and Borneo. In this region C. rotundicauda probably separated from the Tachypleus stem group by invading estuarine habitats, while Tachypleus tridentatus most likely migrated northeast along the Southern coast of China and towards Japan.
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| 40. |
- Obst, Matthias, 1974, et al.
(author)
-
Skönhet under luppen
- 2007
-
In: Flora och Fauna. ; 102:4, s. 16-22
-
Journal article (other academic/artistic)
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| 41. |
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| 42. |
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| 43. |
- Orr, Russell J.S., et al.
(author)
-
A molecular phylogeny of historical and contemporary specimens of an under-studied micro-invertebrate group
- 2021
-
In: Ecology and Evolution. - : Wiley. - 2045-7758. ; 11:1, s. 309-320
-
Journal article (peer-reviewed)abstract
- © 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. Resolution of relationships at lower taxonomic levels is crucial for answering many evolutionary questions, and as such, sufficiently varied species representation is vital. This latter goal is not always achievable with relatively fresh samples. To alleviate the difficulties in procuring rarer taxa, we have seen increasing utilization of historical specimens in building molecular phylogenies using high throughput sequencing. This effort, however, has mainly focused on large-bodied or well-studied groups, with small-bodied and under-studied taxa under-prioritized. Here, we utilize both historical and contemporary specimens, to increase the resolution of phylogenetic relationships among a group of under-studied and small-bodied metazoans, namely, cheilostome bryozoans. In this study, we pioneer the sequencing of air-dried cheilostomes, utilizing a recently developed library preparation method for low DNA input. We evaluate a de novo mitogenome assembly and two iterative methods, using the sequenced target specimen as a reference for mapping, for our sequences. In doing so, we present mitochondrial and ribosomal RNA sequences of 43 cheilostomes representing 37 species, including 14 from historical samples ranging from 50 to 149years old. The inferred phylogenetic relationships of these samples, analyzed together with publicly available sequence data, are shown in a statistically well-supported 65 taxa and 17 genes cheilostome tree, which is also the most broadly sampled and largest to date. The robust phylogenetic placement of historical samples whose contemporary conspecifics and/or congenerics have been sequenced verifies the appropriateness of our workflow and gives confidence in the phylogenetic placement of those historical samples for which there are no close relatives sequenced. The success of our workflow is highlighted by the circularization of a total of 27 mitogenomes, seven from historical cheilostome samples. Our study highlights the potential of utilizing DNA from micro-invertebrate specimens stored in natural history collections for resolving phylogenetic relationships among species.
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| 44. |
- Orr, Russell J.S., et al.
(author)
-
Paleozoic origins of cheilostome bryozoans and their parental care inferred by a new genome-skimmed phylogeny
- 2022
-
In: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 8:13
-
Journal article (peer-reviewed)abstract
- Phylogenetic relationships and the timing of evolutionary events are essential for understanding evolution on longer time scales. Cheilostome bryozoans are a group of ubiquitous, species-rich, marine colonial organisms with an excellent fossil record but lack phylogenetic relationships inferred from molecular data. We present genome-skimmed data for 395 cheilostomes and combine these with 315 published sequences to infer relationships and the timing of key events among c. 500 cheilostome species. We find that named cheilostome genera and species are phylogenetically coherent, rendering fossil or contemporary specimens readily delimited using only skeletal morphology. Our phylogeny shows that parental care in the form of brooding evolved several times independently but was never lost in cheilostomes. Our fossil calibration, robust to varied assumptions, indicates that the cheilostome lineage and parental care therein could have Paleozoic origins, much older than the first known fossil record of cheilostomes in the Late Jurassic.
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| 45. |
- Rettig, Katharina, et al.
(author)
-
A bayesian network to inform the management of key species in Kosterhavet National Park under contrasting storylines of environmental change
- 2022
-
In: Estuarine, Coastal and Shelf Science. - : Elsevier BV. - 0272-7714 .- 1096-0015. ; 280
-
Journal article (peer-reviewed)abstract
- Global climate change and related land use changes are expected to impose unprecedented pressures on coastal biodiversity and ecosystem processes. To sustainably manage coastal ecosystems, it is crucial to predict the consequences of human activities for coastal ecosystems and identify areas for directed abatement measures. Empirical data together with expert knowledge and evidence from the literature were integrated into a Bayesian Belief Network (BBN) for a marine protected area, the Kosterhavet National Park off the Swedish west coast. The variability and interactions of anthropogenic pressures and two key ecosystem components, eelgrass meadows and northern shrimp stock, were tested under four storylines of environmental change. The results show that of the influential drivers of environmental change, only three variables (bottom trawling, leisure boating and aquaculture) are manageable within the national park itself. Scenario analysis suggested that notable gains of both ecosystem components were most likely under a storyline of sustainable development, assuming a radiative forcing of 4.5W/m2 by 2100 in concert with a preventive cooperation among neighboring countries and a tighter restriction of commercial and recreational uses in the park area. The findings suggest that the sustainable management of eelgrass meadows and northern shrimp stock in Kosterhavet National Park requires both local measures at the scale of the park's water bodies and, to a greater part, also regional measures, e.g., to reduce nutrient influx from adjacent water bodies. In conclusion, this approach can help practitioners to make more informed management decisions and foresee the effects of routes of socio-economic development.
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| 46. |
- Santi, I., et al.
(author)
-
European marine omics biodiversity observation network: a strategic outline for the implementation of omics approaches in ocean observation
- 2023
-
In: Frontiers in Marine Science. ; 10
-
Journal article (peer-reviewed)abstract
- Marine ecosystems, ranging from coastal seas and wetlands to the open ocean, accommodate a wealth of biological diversity from small microorganisms to large mammals. This biodiversity and its associated ecosystem function occurs across complex spatial and temporal scales and is not yet fully understood. Given the wide range of external pressures on the marine environment, this knowledge is crucial for enabling effective conservation measures and defining the limits of sustainable use. The development and application of omics-based approaches to biodiversity research has helped overcome hurdles, such as allowing the previously hidden community of microbial life to be identified, thereby enabling a holistic view of an entire ecosystem's biodiversity and functioning. The potential of omics-based approaches for marine ecosystems observation is enormous and their added value to ecosystem monitoring, management, and conservation is widely acknowledged. Despite these encouraging prospects, most omics-based studies are short-termed and typically cover only small spatial scales which therefore fail to include the full spatio-temporal complexity and dynamics of the system. To date, few attempts have been made to establish standardised, coordinated, broad scaled, and long-term omics observation networks. Here we outline the creation of an omics-based marine observation network at the European scale, the European Marine Omics Biodiversity Observation Network (EMO BON). We illustrate how linking multiple existing individual observation efforts increases the observational power in large-scale assessments of status and change in biodiversity in the oceans. Such large-scale observation efforts have the added value of cross-border cooperation, are characterised by shared costs through economies of scale, and produce structured, comparable data. The key components required to compile reference environmental datasets and how these should be linked are major challenges that we address.
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| 47. |
- Schander, C, 1960, et al.
(author)
-
The fauna of hydrothermal vents on the Mohn Ridge (North Atlantic)
- 2010
-
In: Marine Biology Research. - 1745-1000. ; 6:2, s. 155-171
-
Journal article (peer-reviewed)abstract
- The macrofauna of the newly discovered hydrothermal vent field on the Mohn Ridge at 71 degrees N was investigated. Samples were collected during the cruise BIODEEP 2006 using the ROV 'Bathysaurus'. A total of 180 species-level taxa were identified. The region contains very few vent-endemic species, but some species of Porifera, Crustacea and Mollusca may be vent-associated. Dense aggregations of motile non-vent species such as Heliometra glacialis and Gorgonocephalus eucnemis surrounded the vent area, but the area in general only held small numbers of sedentary animals. Calcareous sponges comprised an unusually high portion of the sponge species found and they constitute one of the first pioneers among the sessile invertebrates settling on these vents. Possible explanations for the structure of the fauna in the region are discussed.
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| 48. |
- Schreiber, Lars, et al.
(author)
-
Description of Endozoicomonas ascidiicola sp nov., isolated from Scandinavian ascidians
- 2016
-
In: Systematic and Applied Microbiology. - : Elsevier BV. - 0723-2020 .- 1618-0984. ; 39:5, s. 313-318
-
Journal article (peer-reviewed)abstract
- Two gram-negative, facultative anaerobic, chemoorganoheterotrophic, motile and rod-shaped bacteria, strains AVMARTO5(T) and KASP37, were isolated from ascidians (Tunicata, Ascidiaceae) of the genus Ascidiella collected at Gullmarsfjord, Sweden. The strains are the first cultured representatives of an ascidian-specific lineage within the genus Endozoicomonas (Gammaproteobacteria, Oceanospirillales, Hahellaceae). Both strains feature three distinct 16S rRNA gene paralogs, with identities of 98.9-99.1% (AVMARTO5(T)) and 97.7-98.8% (KASP37) between paralogs. The strains are closely related to Endozoicomonas atrinae and Endozoicomonas elysicola, with which they share 97.3-98.0% 16S rRNA gene sequence identity. Digital DNA-DNA hybridization, average nucleotide identity, and tetra-nucleotide correlation analysis indicate that both strains belong to a single species distinct from their closest relatives. Both strains feature similar DNA G + C contents of 46.70 mol%(AVMARTO5T) and 44.64 mol%(KASP37).The fatty acid patterns of AVMARTO5(T) and KASP37 are most similar to those of Endozoicomonas euniceicola and Endozoicomonas gorgoniicola. Based on the polyphasic approach, we propose the species Endozoicomonas ascidiicola sp. nov. to accommodate the newly isolated strains. E. ascidiicola sp. nov. is represented by the type strain AVMARTO5(T) (=DSM 100913(T) = LMG 29095(T)) and strain KASP37 (=DSM 100914= LMG 29096).
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| 49. |
- Schreiber, L., et al.
(author)
-
Endozoicomonas Are Specific, Facultative Symbionts of Sea Squirts
- 2016
-
In: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 7
-
Journal article (peer-reviewed)abstract
- Ascidians are marine filter feeders and harbor diverse microbiota that can exhibit a high degree of host-specificity. Pharyngeal samples of Scandinavian and Mediterranean ascidians were screened for consistently associated bacteria by culture-dependent and-independent approaches. Representatives of the Endozoicomonas (Gammaproteobacteria, Hahellaceae) Glade were detected in the ascidian species Ascidiella aspersa, Ascidiella scabra, Botryllus schlosseri, Ciona intestinalis, Styela clava, and multiple Ascidia/Ascidiella spp. In total, Endozoicomonas was detected in more than half of all specimens screened, and in 25-100% of the specimens for each species. The retrieved Endozoicomonas 16S rRNA gene sequences formed an ascidian-specific subclade, whose members were detected by fluorescence in situ hybridization (FISH) as extracellular microcolonies in the pharynx. Two strains of the ascidian-specific Endozoicomonas subclade were isolated in pure culture and characterized. Both strains are chemoorganoheterotrophs and grow on mucin (a mucus glycoprotein). The strains tested negative for cytotoxic or antibacterial activity. Based on these observations, we propose ascidian-associated Endozoicomonas to be commensals, living off the mucus continuously secreted into the pharynx. Members of the ascidian-specific Endozoicomonas subclade were also detected in seawater from the Scandinavian sampling site, which suggests acquisition of the symbionts by horizontal transmission. The combined results indicate a host-specific, yet facultative symbiosis between ascidians and Endozoicomonas.
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| 50. |
- Skriver Hansen, Andreas, 1983, et al.
(author)
-
Synthesizing knowledge and evidence to inform the management of coastal seas’ biodiversity and NCPs – a case study from Sweden
- 2022
-
In: Presentation given at ECSA 59, 5-8 September 2022, Kursaal, San Sebastian, Spain. - Essen : University of Duisburg Essen, Faculty of Biology, Aquatic Ecology.
-
Conference paper (other academic/artistic)abstract
- While being among the most productive ecosystems on earth, coastal ecosystems are heavily impacted by anthropogenic causes on land and at sea. Fisheries, nutrient discharges from land uses and global climate change, for example, adversely affect coastal seas’ biodiversity, functioning and related nature’s contributions to people (NCPs). Data and knowledge of particular cause-effect relationships in these complex systems is often insufficient or missing. Therefore, a coupled model framework was developed that allows the combination of evidence from environmental monitoring data, literature, expert knowledge and stakeholder interviews and thereby enables the exploration of causal relations between human-induced environmental change, biodiversity and NCPs. The framework was applied to the Kosterhavet National Park in Sweden. First, a Bayesian Belief Network (BBN) was built to link anthropogenic land and sea uses and climate change via abiotic and biotic cause-and-effect relationships to two ecological key species in the national park: eelgrass (Zostera marina) and northern shrimp (Pandalus borealis). Subsequently, social-cultural and social-economic cause-and-consequence chains were developed, to derive the potential implications of changes in eelgrass coverage and shrimp stock on human well-being. It was shown that the sustainable management of the two target species in Kosterhavet National Park requires local management in the park (e.g. recreational use and fishery) and regional management across coastal water bodies (e.g. nutrient management). Significant declines in eelgrass and northern shrimp were found to impact the people’s place attachment, tradition, knowledge and identity more than their regional economy. The coupled model framework is currently implemented as an online tool to facilitate its application and support decision making.
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