Katerina Vasileiadou

Katerina Vasileiadou
Hellenic Centre for Marine Research | hcmr · Institute of Marine Biology, Biotechnology and Aquaculture

PhD

About

66
Publications
14,273
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733
Citations
Citations since 2017
16 Research Items
517 Citations
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2017201820192020202120222023020406080100
2017201820192020202120222023020406080100
2017201820192020202120222023020406080100

Publications

Publications (66)
Chapter
Soft bottom benthic communities are among the most important ecosystem components, since they affect biogeochemical cycling and they support the ecosystem’s integrity and health. Undoubtedly, they have earned their place in the current legislation on protection and conservation of biodiversity. However, the descriptors that have been incorporated i...
Article
Full-text available
Several imaging techniques are used in biological and biomedical studies. Micro-computed tomography (micro-CT) is a non-destructive imaging technique that allows the rapid digiti-sation of internal and external structures of a sample in three dimensions and with great resolution. In this review, the strengths and weaknesses of some common imaging t...
Article
Full-text available
Mediterranean ports are sources of significant economic activity and at the same time they act as recipients of considerable anthropogenic disturbance and pollution. Polluted and low-in-oxygen sediments can negatively impact benthic biodiversity and favour recruitment of opportunistic or invasive species. Macrobenthic communities are an important c...
Article
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Chondrichthyes occupy a key position in the phylogeny of vertebrates. The complete sequence of the mitochondrial genome (mitogenome) of four species of sharks and five species of rays was obtained by whole genome sequencing (DNA-seq) in the Illumina HiSeq2500 platform. The arrangement and features of the genes in the assembled mitogenomes were iden...
Article
Full-text available
Urocaridella pulchella Yokeş & Galil, 2006 is a palaemonid cleaner-shrimp of Indo-Pacific origin that was first described from the Mediterranean Sea in 2006. However, limited information is available about its distribution and ecology due to the small size and cryptic habit of the species. We hereby report the first records of U. pulchella in marin...
Article
Full-text available
Background: Environmental DNA and metabarcoding allow the identification of a mixture of species and launch a new era in bio- and eco-assessment. Many steps are required to obtain taxonomically assigned matrices from raw data. For most of these, a plethora of tools are available; each tool's execution parameters need to be tailored to reflect each...
Article
Full-text available
Species distributions are rapidly changing, facilitated by enhanced human migration and globalization over the past several centuries. Increasingly, species are becoming introduced to and established in novel locations that are often well outside their limits for natural dispersal. In marine systems, the anthropogenic transfer of living organisms h...
Poster
Full-text available
PEMA alpha version. PEMA is a metabarcoding pipeline that now supports four marker genes, 16S rRNA (Bacteria), 18S rRNA and COI (Metazoa) and ITS (Fungi). Furthermore, OTU clustering and ASV inference are both provided. Finally, a downstream amplicon analysis of the OTUs/ASVs retrieved, is facilitated by Phyloseq. Thanks to container-based techno...
Preprint
Full-text available
Background: Environmental DNA (eDNA) and metabarcoding, allow the identification of a mixture of individuals and launch a new era in bio- and eco-assessment. A number of steps are required to obtain taxonomically assigned (Molecular) Operational Taxonomic Unit ((M)OTU) tables from raw data. For most of these, a plethora of tools is available; each...
Conference Paper
Full-text available
Metabarcoding is a genetics-NGS-based biodiversity assessment method, that uses marker genes to detect and determine environmental sample community composition. Depending on the targeted group of organisms, specific marker genes are employed. P.E.M.A. is a pipeline for two marker genes, 16S rRNA (microbes) and COI (eukaryotes). As input, P.E.M.A. a...
Poster
Full-text available
Elucidating the role of the environment on the population distribution and gene flow patterns is one of the main challenges of evolutionary biology. Transitional water ecosystems are hosting habitats with temporally and spatially variable conditions, which make them very useful in understanding the mechanisms affecting population establishment. The...
Article
Full-text available
Sulfate‐reducing microorganisms (SRMs) are a phylogenetically and physiologically diverse group of microorganisms, responsible for the dissimilatory reduction of sulfate. SRMs thrive under anaerobic conditions with high availability of organic matter. Such conditions characterize lagoonal ecosystems which experience regular dystrophic crises. The a...
Article
Genetic diversity and population distribution are influenced by environmental factors, yet information is scarce on the interrelations that define dispersal of populations. Transitional water ecosystems are hosting habitats with temporally and spatially variable conditions, which make them very useful in understanding the mechanisms affecting popul...
Article
Full-text available
Background Coastal lagoons are ecosystems of major importance as they host a number of species tolerant to disturbances and they are highly productive. Therefore, these ecosystems should be protected to ensure stability and resilience. The lagoons of Amvrakikos Gulf form one of the most important lagoonal complexes in Greece. The optimal ecological...
Article
Full-text available
The present study examines the genetic diversity (using cytochrome c oxidase subunit I [COI] haplotypes) of polychaete Hediste diversicolor populations in the Amvrakikos Gulf (western Greece) in order to test Cognetti’s hypothesis on the formation of distinct isolated populations of species living in stressed transitional water habitats. To this pu...
Poster
Full-text available
Transitional water ecosystems host a number of habitats with temporally and spatially variable conditions, thus they can be very useful in understanding the mechanisms affecting population establishment. Samples were collected from lagoons located in Amvrakikos Gulf (Western Greece). These ecosystems are characterized by increased hypoxia and high...
Conference Paper
Full-text available
Amvrakikos Gulf wetlands are under protection status from the international Ramsar convention and «Natura 2000». There are at least twenty lagoons in the Gulf, many of which experience anthropogenic stress. In the framework of the current study, samples were collected in spring of 2014 from Logarou (intense fishing activity), Tsopeli (allegedly in...
Conference Paper
Full-text available
Lagoons are naturally enriched habitats, with unstable environmental conditions caused by their confinement from the sea and their shallow depth. Such ecosystems are characterized by increased hypoxia and high concentrations of hydrogen sulfide. The aim of the present study was to examine the sulfate reducing bacterial community in the lagoonal sed...
Conference Paper
Full-text available
Lagoons are enriched habitats, with unstable environmental conditions caused by their constraint from the sea and their shallowness. Τhe frequent fluctuations of the abiotic parameters cause severe changes in the abundance and distribution of organisms; while this relationship has been studied for macrofaunal organisms, only little is known about t...
Poster
Full-text available
En Mer Méditerranée, le coralligène et les herbiers de Posidonies, qui sont de loin les plus étudiés, sont les habitats les plus importants du point de vue biodiversité côtière. Ils sont le milieu principal produisant complexité structurelle et biodiversité. Les récifs coralligènes produisent des biens (ressources alimentaires et matière première,...
Poster
Full-text available
The coralligenous is a typical Mediterranean marine habitat and hosts the highest concentration of biodiversity of this sea. Paradoxically, unlike Posidonia meadows, it is poorly studied. Like the famous tropical coral reefs, it is a complex biogenic habitat, based on encrusting red algae (numerous metazoan phyla also participate to bio-constructio...
Article
Full-text available
The association of organisms to their environments is a key issue in exploring biodiversity patterns. This knowledge has traditionally been scattered, but textual descriptions of taxa and their habitats are now being consolidated in centralized resources. However, structured annotations are needed to facilitate large-scale analyses. Therefore, we d...
Preprint
Full-text available
The association of organisms to their environments is a key issue in exploring biodiversity patterns. This knowledge has traditionally been scattered, but textual descriptions of taxa and their habitats are now being consolidated in centralized resources. However, structured annotations are needed to facilitate large-scale analyses. Therefore, we d...
Article
Full-text available
A new genus and species of Serpulidae (Annelida, Polychaeta) from the Caribbean Sea. Turbocavus secretus (gen. nov. and sp. nov.) is described from shallow hard substrates (0.5-3 m) in wind-sheltered bays of St. John, U.S. Virgin Islands and Curacao, as well as from diving depths (46-49 m) around Bonaire (Leeward Antilles), Caribbean Sea. The new t...
Article
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Species and genetic diversity are often found to co-vary since they are influenced by external factors in similar ways. In this paper, we analyse the genetic differences of the abundant polychaete Hermodice carunculata (Pallas, 1776) during two successive years at two locations in northern Crete (Aegean Sea) and compare them to other populations in...
Article
Full-text available
The loss of species is known to have negative impacts on the integrity of ecosystems, but the details of this relationship are still far from being fully understood. This study investigates how the distribution patterns of polychaete species and their associated biological traits patterns in six Mediterranean coastal lagoons change under computatio...
Data
Full-text available
The study of ecosystem functioning – the role which organisms play in an ecosystem – is becoming increasingly important in marine ecological research. The functional structure of a community can be represented by a set of functional traits assigned to behavioural, reproductive and morphological characteristics. The collection of these traits from t...
Poster
Full-text available
The Mediterranean Sea is hosting almost 10% of the total marine biodiversity in spite of representing less than 1% of the global ocean surface. This regional sea experiences high anthropogenic pressures, such as growing human population density along the coasts, urbanization, (over)harvesting of living and raw resources, extensive maritime traffic,...
Conference Paper
Full-text available
Coastal lagoons are dynamic ecosystems characterized by vigorously changing temporal and spatial conditions. They are an intriguing field for the study of genetic adaptations and community behavior. In these ecosystems, a small number of species is able to tolerate these conditions. Polychaetes are one of the most abundant taxa inhabiting lagoons a...
Article
Full-text available
The exponential growth of the biomedical literature is making the need for efficient, accurate text-mining tools increasingly clear. The identification of named biological entities in text is a central and difficult task. We have developed an efficient algorithm and implementation of a dictionary-based approach to named entity recognition, which we...
Data
Journal selection for the S800 categories. The table provides an overview of the journal selection for the eight categories that make up S800. For each category we selected between one and four journals, from which we randomly picked 100 Medline abstracts in total from the years 2011 and 2012. (DOC)
Data
The SPECIES and ORGANIMS software documentation including library dependencies, an example of how to run the executables, and the description of the output file format. (DOC)
Data
Inter-annotator agreement for the S800 corpus. We quantified the Inter-Annotator-Agreement (IAA) by calculating Cohen's kappa for all pairs of the five curators. Cohen's kappa is defined as kappa = (Po−Pe)/(1-Pe). Po refers the observed probability of agreement between two curators, whereas Pe is the expected probability of agreement by random chan...
Article
Full-text available
Continuous improvements in the resolution of three-dimensional imaging have led to an increased application of these techniques in conventional taxonomic research in recent years. Coupled with an ever increasing research effort in cybertaxonomy, three-dimensional imaging could give a boost to the development of virtual specimen collections, allowin...
Poster
Full-text available
Lagoons are enriched habitats,with unstable environmental conditions caused by their constraint from the sea and their shallowness, hence they are considered as environments in natural disturbance, vulnerable to anthropogenic influences. The frequent changes of the abiotic parameters cause severe changes in the abundance and distribution of organis...
Poster
Full-text available
Lagoons are enriched habitats, with unstable environmental conditions caused by their constraint from the sea and their shallowness; hence, they are considered as environments in natural disturbance, vulnerable to anthropogenic influences. Τhe frequent changes of the abiotic parameters cause severe changes in the abundance and distribution of organ...
Article
Full-text available
AbstractThis paper discusses the design and implementation of a citizen science pilot project, COMBER (Citizens’ Network for the Observation of Marine BiodivERsity, http://www.comber.hcmr.gr), which has been initiated under the ViBRANT EU e-infrastructure. It is designed and implemented for divers and snorkelers who are interested in participating...
Article
Full-text available
This study examines whether or not biogeographical and/or managerial divisions across the European seas can be validated using soft-bottom macrobenthic community data. The faunal groups used were: all macrobenthos groups, polychaetes, molluscs, crustaceans, echinoderms, sipun- culans and the last 5 groups combined. In order to test the discriminati...
Article
Full-text available
Local species diversity may be determined by processes operating locally, such as disturbance, predation and competition, or by regional processes, such as environmental structuring or history. Classical theory focusing on competition predicts that the species combining to form communities will be less similar to each other than they would be if th...
Article
Full-text available
This study examines whether or not biogeographical and/or managerial divisions across the European seas can be validated using soft-bottom macrobenthic community data. The faunal groups used were: all macrobenthos groups, polychaetes, molluscs, crustaceans, echinoderms, sipunculans and the last 5 groups combined. In order to test the discriminating...
Article
Full-text available
A new Streptosyllis species, S. nunezi n. sp., is described from shallow sandy substrates in the Mediterranean and the Canary Islands. The new species is distinguished by a unique combination of characters: teeth of the shafts of the com- pound chaetae covered by hyaline hood; 1-2 lateral tips formed by the hyaline hood covering the blades of the c...

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Projects

Projects (6)
Project
Marine biodiversity hotspots are regions that host high numbers of endemic or endangered species. At the same time, they are threatened by severe habitat loss and are considered as conservation priority regions. Although these areas are of high importance for biodiversity, they are impacted by considerable pressures and suffer substantial degradation. Nowadays, marine hotspots encounter a whole new reality. Habitat loss or fragmentation is more rapid than ever since the demand for natural resources and the construction of coastal and maritime infrastructures is constantly increasing. Great ecological challenges of the modern era such as climate change and invasions of non-indigenous species bring marine hotspots into the spotlight as they are facing an increased risk of destruction. Therefore, research dedicated to elucidating the impacts of these threats on marine biodiversity hotspots can provide very important insights into their protection. This Research Topic, entitled "Marine Biodiversity Hotspots - Challenges and Resilience", intends to increase the available knowledge on, and our understanding of, the different challenges threatening marine hotspots. Effective restoration and protection methods need to be tested in selected case study key areas, and their potential to be applied widely needs to be investigated and reported. Papers on marine biological hotspots under threat that also suggest approaches to address these impacts are encouraged for submission. Suggested approaches should provide effective solutions for the protection and/or restoration of these fragile marine areas and can cover fields such as marine ecology and genetics. This Research Topic also aims to provide guidance for ecosystem managers and other related stakeholders who could benefit from the information in the scientific studies that will be published and promoted in this special issue. Keywords: marine biodiversity hotspots, ecology, genetics, resilience, conservation https://www.frontiersin.org/research-topics/19111/marine-biodiversity-hotspots---challenges-and-resilience
Project
#JMSE_MDPI Special Issue " #Marine #Biodiversity #Observatory Systems" is open for submission! Guest Editors: Dr. Christina Pavloudi, Dr. Katerina Vasileiadou, Dr. Georgios Kotoulas and Dr. Ioulia Santi Deadline: 25 December 2020 More information can be found at http://mdpi.com/si/51781
Project
Regional cooperation for the transnational ecosystem sustainable development (RECONNECT) project aims to develop strategies for sustainable management of Marine Protected Areas (MPAs) and Natura 2000 sites. The study areas are characterised by similar habitats in different countries, which are threatened by common pressures. Creating a transnational cooperative network to confront under a common approach the environmental threats of ecosystems with a high natural and cultural interest, is the overall goal of this project. The establishment of common practices and a joint regional strategy are the main challenges of RECONNECT. The overall objective of the project is to promote efficient management of natural systems which will enhance the competence of local management authorities through the development of a multidisciplinary Decision Support System (DSS). The new transnational holistic approach which will be developed, will change the current protection strategies in the Balkan-Mediterranean area promoting more efficient and accurate management practices. The main outputs of the RECONNECT project will provide information concerning habitat attributes, as well as the essential biodiversity, socio-economic and cultural variables, which will be freely available as tools through a web-based platform. These outputs will be beneficial for (a) local, regional and national authorities by promoting the sustainability of marine ecosystems; (b) management agencies by enhancing their management toolbox; (c) non-governmental organizations (NGOs) by improving their activities through the suggested strategies; and (d) citizens, as their involvement during the project will increase their environmental awareness. The transnational approach that will be used during the project will combine ecological and genetic methodologies for the biodiversity assessment, as well as socio-economic aspects, under the umbrella of a common DSS promoting joint policies and practices. The protection and conservation of areas with high ecological and economical value aims to harmonize the socio-economic and legal framework between the participating countries, something which could not be achieved individually at a national level. The design of new tools such as the DSS and the Handbook of management practices will be developed through the combination of multidisciplinary methodologies targeting to evaluate ecosystem quality and to promote the sustainable conservation of these vulnerable and fragile ecosystems. During its implementation, RECONNECT project will address consistently EU horizontal principles such as sustainable development, equal opportunities and non-discrimination and equality between men and women. More information: http://www.interreg-balkanmed.eu/approved-project/9/