C. Arvanitidis

C. Arvanitidis
Hellenic Centre for Marine Research | hcmr · Institute of Marine Biology, Biotechnology and Aquaculture

PhD

About

367
Publications
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4,517
Citations

Publications

Publications (367)
Article
Full-text available
Historical biodiversity documents comprise an important link to the long-term data life cycle and provide useful insights on several aspects of biodiversity research and management. However, because of their historical context, they present specific challenges, primarily time- and effort-consuming in data curation. The data rescue process requires...
Article
Full-text available
Although more than 600 marine caves have been recorded so far along the Greek coasts of the Aegean Sea (Eastern Mediterranean), only a few have been systematically studied for their biodiversity. In this study, the benthic communities of six marine caves within a Protected Area of South-Eastern Aegean were studied for the first time, both qualitati...
Preprint
The landscape of biodiversity data infrastructures and organisations is complex and fragmented. Many occupy specialised niches representing narrow segments of the multidimensional biodiversity informatics space, while others operate across a broad front but differ from others by data type(s) handled, their geographic scope and the life cycle phase(...
Article
Full-text available
BiCIKL is an European Union Horizon 2020 project that will initiate and build a new European starting community of key research infrastructures, establishing open science practices in the domain of biodiversity through provision of access to data, associated tools and services at each separate stage of and along the entire research cycle. BiCIKL wi...
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
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Digitisation of specimens (e.g. zoological, botanical) can provide access to advanced morphological and anatomical information and promote new research opportunities. The micro-CT technology may support the development of "virtual museums" or "virtual laboratories" where digital 3D imaging data are shared widely and freely. There is currently a lac...
Article
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Micro-computed tomography (micro-CT) is a promising novel medical imaging modality that allows for non-destructive volumetric imaging of surgical tissue specimens at high spatial resolution. The aim of this study is to provide a comprehensive assessment of the clinical applications of micro-CT for the tissue-based diagnosis of lung diseases. This s...
Article
The BiCIKL Project is born from a vision that biodiversity data are most useful if they are viewed as a network of data that can be integrated and viewed from different starting points. BiCIKL’s goal is to realize that vision by linking biodiversity data infrastructures, particularly for literature, molecular sequences, specimens, nomenclature and...
Article
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The Horizon 2020 project Bi odiversity C ommunity I ntegrated K nowledge L ibrary (BiCIKL) (started 1st of May 2021, duration 3 years) will build a new European community of key research infrastructures, researchers, citizen scientists and other stakeholders in biodiversity and life sciences. Together, the BiCIKL 14 partners will solidify open scie...
Article
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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
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High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational cha...
Article
Background Micro-computed tomography (micro-CT) constitutes an emerging imaging technique, which can be utilized in cardiovascular medicine to study in-detail the microstructure of heart and vessels. This paper aims to systematically review the clinical utility of micro-CT in cardiovascular imaging and propose future applications of micro-CT imagin...
Article
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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...
Data
Scientific knowledge and methodology is undergoing transition from plain manuscript documents to multimedia-rich manuscripts linked to accompanying data. Organized datasets add value to a manuscript by being directly linked and available in reusable format [4]. The benefit of these add-on value could be multiplied once such data get repeatedly upda...
Article
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Background: Angiographic detection of thrombus in STEMI is associated with adverse outcomes. However, routine thrombus aspiration failed to demonstrate the anticipated benefit. Hence, management of high coronary thrombus burden remains challenging. We sought to assess for the first time extracted thrombotic material characteristics utilizing micro-...
Article
Full-text available
This study investigates the trophic diversity of fishes living in a meadow of Caulerpa prolifera on a bimonthly basis between May 2006 and April 2007 in a semi-enclosed coastal marine ecosystem of the Mediterranean Sea (Elounda Bay, Crete Island). The study area is shallow and protected from waves, and it is covered by a C. prolifera bed, character...
Article
Full-text available
Marine hard-bottom communities are undergoing severe change under the influenceof multiple drivers, notably climate change, extraction ofnatural resources, pollutionand eutrophication, habitat degradation, and invasive species. Monitoring marinebiodiversity in such habitats is, however, challenging as it typically involves expensive,non-standardize...
Article
Full-text available
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-standa...
Article
Full-text available
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-standa...
Article
Full-text available
• 1. The coralligenous habitat was studied at the large Mediterranean scale, by applying a standardized, non‐destructive photo‐sampling protocol, developed in the framework of the CIGESMED project. • 2. The results provided evidence to support the following statements: (a) the assemblage pattern is not homogeneously distributed across the four Medi...
Article
The goal of this paper is to propose a screening method for assessing the environmental risk to aquatic systems in harbours worldwide. A semi-quantitative method is based on environmental pressures, environmental conditions and societal response. The method is flexible enough to be applied to 15 harbours globally distributed through a multinational...
Article
The present study aimed to compare anthropogenic impacts in three Mediterranean ports (Cagliari-Italy, Heraklion-Greece, El-Kantatoui-Tunisia) employing benthic macrofaunal indices, used in the context of the European Water Framework Directive. Sampling stations were selected within ports according to sector usage categorization and sampled over th...
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...
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...
Article
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The emblematic sponge Spongia officinalis is currently threatened by recurrent mortality incidents in its native habitats. Elevated temperature has been indicated as a major triggering factor, but the molecular mechanisms recruited for the organism's response to thermal shifts are yet unknown. Here, we experimentally tested the effect of exposure t...
Article
The anabolic effect of exercise on muscles and bones is well documented. In teleost fish exercise has been shown to accelerate skeletogenesis, to increase the bone volume, and to change the shape of vertebral bodies. Still, increased swimming has also been reported to induce malformations of the teleost vertebral column, particularly lordosis. This...
Article
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The Panhellenic Symposium of Oceanography and Fisheries was firstly launched in Athens, 35 years ago sparked by the enthusiasm of the Greek aquatic scientists, massively supported by the voluntary contribution of the Hellenic Centre for Marine Research (HCMR) employees. Over the last three decades, the Symposium established and flourished as the fo...
Article
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Objectives: We report a transcriptome acquisition for the bath sponge Spongia officinalis, a non-model marine organism that hosts rich symbiotic microbial communities. To this end, a pipeline was developed to efficiently separate between bacterial expressed genes from those of eukaryotic origin. The transcriptome was produced to support the assess...
Article
Estimating the potential environmental risks of worldwide coastal recreational navigation on water quality is an important step towards designing a sustainable global market. This study proposes the creation of a global atlas of the environmental risk of marinas on water quality by applying the Marina Environmental Risk Assessment (MERA) procedure....
Article
Estimating the potential environmental risks of worldwide coastal recreational navigation on water quality is an important step towards designing a sustainable global market. This study proposes the creation of a global atlas of the environmental risk of marinas on water quality by applying the Marina Environmental Risk Assessment (MERA) procedure....
Article
1. Despite the Mediterranean being both a hotspot for recreational boating and for non-indigenous species (NIS), no data currently exists on the recreational boating sector's contribution to the spread of NIS in this Sea. 2. To improve the basis for management decisions, a wide-scale sampling study on the biofouling communities of recreational vess...
Article
Full-text available
European natural history collections are a critical infrastructure for meeting the most important challenge humans face over the next 30 years – creating a sustainable future for ourselves and the natural systems on which we depend – and for answering fundamental scientific questions about ecological, evolutionary, and geological processes. Since 2...
Article
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The present study aimed to evaluate the impact of polycyclic aromatic hydrocarbons (PAHs) produced by multiple emission sources on prokaryotic communities in sediments chronically affected by anthropogenic pressures. In this context, surface sediments were investigated in three Mediterranean touristic ports over three sampling periods and in differ...
Article
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The collaboration between LifeWatch ERIC and DiSSCo (Distributed System of Scientific Collections), both pan-European research infrastructures focusing on biodiversity, can be achieved in a number of ways. The direct initiation of this collaboration can be carried out through their joint support to GBIF (Global Biodiversity Information Facility). T...
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...
Article
• Factors shaping non-indigenous species (NIS) richness are tested in the Mediterranean. • There is a higher trend of NIS richness going from east to west in the Mediterranean. • NIS richness in marinas is mainly influenced by proximity to other major vectors. • NIS similarities between marinas are more influenced by environmental factors. • The Su...
Conference Paper
Full-text available
Marine caves constitute unique biodiversity reservoirs of high conservation value. Nevertheless, marine caves of the Aegean Sea have been studied less intensively than those in other Mediterranean regions. In this study, benthic biodiversity and physicochemical parameters were investigated for the first time in the Elephant Cave of Crete (Greece),...
Article
Full-text available
Research Infrastructures (RIs) are facilities, resources and services used by scientists to perform research and support innovation. A number of EU research infrastructures [e.g. e-Science and Technology European Infrastructure for Biodiversity and Ecosystem Research (LifeWatch) European Research Iinfrastructures Consortium (ERIC); The European lif...
Article
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Imagine you are a scientist, working on collections. You have your pet taxon and you need information which is distributed in a number of books and publications but also in the specimens deposited in Museums or Herbaria. Instead of paying visits to these establishments, around the world, you wish there was a means to transform all the information y...
Article
Full-text available
Micro-computed tomography (micro-CT or microtomography) is a non-destructive imaging technique using X-rays which allows the digitisation of an object in three dimensions. The ability of micro-CT imaging to visualise both internal and external features of an object, without destroying the specimen, makes the technique ideal for the digitisation of...
Conference Paper
Full-text available
Two decades ago, a unique marine cave was discovered in Crete (Greece, Eastern Mediterranean). The so-called Elephant Cave was very soon meant to become one of the most iconic diving destinations in the island. It stands out for its aesthetic value with a variety of speleoforms and the remaining fossil bones of deers and a dwarf elephant which are...
Poster
Sponges are organisms with simple body plan, without true tissue differentiation. Moreover, they are notorious for hosting rich, regulated symbiotic bacterial communities, thus creating the sponge holobiont. These traits, combined with the expansive and diverse nature of the poriferan phylum and the fact that only two sponge species have been seque...
Article
Ports are open systems with direct connection to the sea, therefore any potential impact on port waters may have implications for the health of adjacent marine ecosystems. European WFD addressed ports in the category of Heavily Modified Water Bodies (HMWBs) and promoted implementation of protocols to monitor and improve their ecological status. TRI...
Article
Full-text available
The NaGISA project (Natural Geography Ιn Shore Areas) is a global initiative within the framework of the Census of Marine Life. The Mediterranean Sea has joined with 4 stations, 2 in Italy and 2 on the island of Crete, Greece. Two different sites were sampled during two consecutive years (2007 and 2008) by means of SCUBA diving. On the basis of the...
Article
Subtidal hard bottoms are of particular scientific and economic value as they are highly productive systems. They are less well studied compared with soft bottoms, as they often require manual sample collection via scuba diving. Although a multitude of sampling devices is available for soft bottoms, only a few are suitable for hard substrates, and...
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...
Article
Full-text available
Habitat-forming species sustain biodiversity and ecosystem functioning in harsh environments through the amelioration of physical stress. Nonetheless, their role in shaping patterns of species distribution under future climate scenarios is generally overlooked. Focusing on coastal systems, we assess how habitat-forming species can influence the abi...
Article
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We review and compare four broad categories of spatially-explicit modelling approaches currently used to understand and project changes in the distribution and productivity of living marine resources including: 1) statistical species distribution models, 2) physiology-based, biophysical models of single life stages or the whole life cycle of specie...
Article
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Background: The last annotated checklist of marine polychaetes in Greece was published in 2001. Since then, global taxonomic progress, combined with many new species records for Greece, required a thorough review of the taxonomic, nomenclatural and biogeographic status of the national species list. This checklist revises the status of all extant p...
Article
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The Mediterranean Sea is one of the busiest areas worldwide in terms of maritime activity, facing considerable anthropogenic disturbance, such as pollution by hydrocarbons and heavy metals. The present study has evaluated the environmental and benthic biodiversity characteristics of three touristic ports, Cagliari (Sardinia, Italy), Heraklion (Cret...
Article
Full-text available
Invasive ecosystem engineers (IEE) are potentially one of the most influential types of biological invaders. They are expected to have extensive ecological impacts by altering the physical-chemical structure of ecosystems, thereby changing the rules of existence for a broad range of resident biota. To test the generality of this expectation, we use...
Article
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The concept of essential biodiversity variables (EBVs) was proposed in 2013 to improve harmonization of biodiversity data into meaningful metrics. EBVs were conceived as a small set of variables which collectively capture biodiversity change at multiple spatial scales and within time intervals that are of scientific and management interest. Despite...