Christina Pavloudi

@article{keklikoglou_disrupted_2025,

title = {Disrupted darkness: the impact of anthropogenic light at night on melatonin secretion of \textit{Hermodice carunculata (Polychaeta, Annelida)}},

author = {Kleoniki Keklikoglou and Manolis Mandalakis and Eleftheria Fanouraki and Thekla I Anastasiou and Eirini Kagiampaki and Katerina Vasileiadou and Christina Pavloudi and Christos Arvanitidis and Michail Pavlidis},

url = {https://link.springer.com/10.1007/s43630-025-00744-5

/wp-content/uploads/2025/06/2025-Keklikoglou-PP-Sci-31.pdf},

doi = {10.1007/s43630-025-00744-5},

issn = {1474-905X, 1474-9092},

year  = {2025},

date = {2025-06-20},

urldate = {2025-06-20},

journal = {Photochemical & Photobiological Sciences},

volume = {24},

number = {6},

pages = {1031--1040},

abstract = {Abstract 

 

 Anthropogenic light at night (ALAN) can have serious impacts on marine environments. Several studies have demonstrated that ALAN disrupts melatonin production, a hormone critical for regulating circadian rhythm. In this study, the effects of ALAN on melatonin and two of its related indolamines were investigated in the annelid 

 Hermodice carunculata 

 . Specifically, melatonin, serotonin and tryptamine levels were measured every three hours over a 24 h period in the heads of the annelids maintained under constant light and a 12 h light/12 h dark photoperiod, representing control conditions. Melatonin concentration was quantified using an enzyme immunoassay, while serotonin and tryptamine were analyzed by liquid chromatography–tandem mass spectrometry. Melatonin levels in annelid heads remained relatively constant with a pronounced peak at 11:00. A similar pattern was observed under constant light, but the melatonin peak shifted to 14:00. However, serotonin and tryptamine did not exhibit any significant diurnal variations due to constant light exposure. These findings suggest that melatonin secretion in 

 H. carunculata 

 is sensitive to ALAN, whereas its related indolamines are potentially not. The disruption of 

 H. carunculata' 

 s melatonin secretion pattern may affect its night-time behavior and reproduction, highlighting the need for further studies to assess the ecological effects of ALAN on various marine invertebrates. 

 

 

 Graphical abstract},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{daraghmeh_longterm_2025,

title = {A Long-Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS-MBON 2018–2020},

author = {Nauras Daraghmeh and Katrina Exter and Justine Pagnier and Piotr Balazy and Ibon Cancio and Giorgos Chatzigeorgiou and Eva Chatzinikolaou and Maciej Chelchowski and Nathan Alexis Mitchell Chrismas and Thierry Comtet and Thanos Dailianis and Klaas Deneudt and Oihane Diaz De Cerio and Markos Digenis and Vasilis Gerovasileiou and José González and Laura Kauppi and Jon Bent Kristoffersen and Piotr Kukliński and Rafał Lasota and Liraz Levy and Magdalena Małachowicz and Borut Mavrič and Jonas Mortelmans and Estefania Paredes and Anita Poćwierz‐Kotus and Henning Reiss and Ioulia Santi and Georgia Sarafidou and Grigorios Skouradakis and Jostein Solbakken and Peter A U Staehr and Javier Tajadura and Jakob Thyrring and Jesus S Troncoso and Emmanouela Vernadou and Frederique Viard and Haris Zafeiropoulos and Małgorzata Zbawicka and Christina Pavloudi and Matthias Obst},

url = {https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.14073

/wp-content/uploads/2025/02/2025-Daraghmeh-MolEcoRes-6.pdf},

doi = {10.1111/1755-0998.14073},

issn = {1755-098X, 1755-0998},

year  = {2025},

date = {2025-02-05},

urldate = {2025-02-05},

journal = {Molecular Ecology Resources},

pages = {e14073},

abstract = {ABSTRACT 

 

 Molecular methods such as DNA/eDNA metabarcoding have emerged as useful tools to document the biodiversity of complex communities over large spatio‐temporal scales. We established an international Marine Biodiversity Observation Network (ARMS‐MBON) combining standardised sampling using autonomous reef monitoring structures (ARMS) with metabarcoding for genetic monitoring of marine hard‐bottom benthic communities. Here, we present the data of our first sampling campaign comprising 56 ARMS units deployed in 2018–2019 and retrieved in 2018–2020 across 15 observatories along the coasts of Europe and adjacent regions. We describe the open‐access data set (image, genetic and metadata) and explore the genetic data to show its potential for marine biodiversity monitoring and ecological research. Our analysis shows that ARMS recovered more than 60 eukaryotic phyla capturing diversity of up to textasciitilde5500 amplicon sequence variants and textasciitilde1800 operational taxonomic units, and up to textasciitilde250 and textasciitilde50 species per observatory using the cytochrome 

 c 

 oxidase subunit I (COI) and 18S rRNA marker genes, respectively. Further, ARMS detected threatened, vulnerable and non‐indigenous species often targeted in biological monitoring. We show that while deployment duration does not drive diversity estimates, sampling effort and sequencing depth across observatories do. We recommend that ARMS should be deployed for at least 3–6 months during the main growth season to use resources as efficiently as possible and that post‐sequencing curation is applied to enable statistical comparison of spatio‐temporal entities. We suggest that ARMS should be used in biological monitoring programs and long‐term ecological research and encourage the adoption of our ARMS‐MBON protocols.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pavloudi_first_2025,

title = {First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples},

author = {Christina Pavloudi and Ioulia Santi and Iñigo Azua and Zuriñe Baña and Mauro Bastianini and Caroline Belser and Jone Bilbao and Julie Bitz-Thorsen and Caroline Broudin and Mathieu Camusat and Ibon Cancio and Louis Caray-Counil and Raffaella Casotti and Jade Castel and Thierry Comtet and Cymon Cox and Claire Daguin and Oihane Díaz De Cerio and Katrina Exter and Cécile Fauvelot and Miguel Frada and Pierre Galand and Laurence Garczarek and Jose González Fernández and Laure Guillou and Pascal Hablützel and Hanneloor Heynderickx and Céline Houbin and Anne Kervella and Apostolos Krystallas and Rune Lagaisse and Arnaud Laroquette and Lyvia Lescure and Eva Lopes and Melina Loulakaki and Bruno Louro and Catarina Magalhaes and Maria Maidanou and Francesca Margiotta and Marina Montresor and Fabrice Not and Estefanía Paredes and Isabella Percopo and Erwan Péru and Julie Poulain and Kim Præbel and Fabienne Rigaut-Jalabert and Sarah Romac and Melanthia Stavroulaki and Jesús Souza Troncoso and Eric Thiébaut and Wilfried Thomas and Andrzej Tkacz and Anna Chiara Trano and Patrick Wincker and Nicolas Pade},

url = {https://bdj.pensoft.net/article/143585/

/wp-content/uploads/2025/04/2025-Pavloudi-BDJ-17.pdf},

doi = {10.3897/BDJ.13.e143585},

issn = {1314-2828, 1314-2836},

year  = {2025},

date = {2025-01-01},

urldate = {2025-04-03},

journal = {Biodiversity Data Journal},

volume = {13},

pages = {e143585},

abstract = {The European Marine Omics Biodiversity Observation Network (EMO BON) is an initiative of the European Marine Biological Resource Centre (EMBRC) to establish a persistent genomic observatory amongst designated European coastal marine sites, sharing the same protocols for sampling and data curation. Environmental samples are collected from the water column and, at some sites, soft sediments and hard substrates (Autonomous Reef Monitoring Structures - ARMS), together with a set of mandatory and discretionary metadata (including Essential Ocean Variables - EOVs). Samples are collected following standardised protocols at regular and specified intervals and sequenced in large six-monthly batches at a centralised sequencing facility. The use of standard operating procedures (SOPs) during data collection, library preparation and sequencing aims to provide uniformity amongst the data collected from the sites. Coupled with strict adherence to open and FAIR (Findable, Accessible, Interoperable, Reusable) data principles, this ensures maximum comparability amongst samples and enhances reusability and interoperability of the data with other data sources. The observatory network was launched in June 2021, when the first sampling campaign took place.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{skliros_unveiling_2024,

title = {Unveiling Emerging Opportunistic Fish Pathogens in Aquaculture: A Comprehensive Seasonal Study of Microbial Composition in Mediterranean Fish Hatcheries},

author = {Dimitrios Skliros and Maria Kostakou and Constantina Kokkari and Maria Ioanna Tsertou and Christina Pavloudi and Haris Zafeiropoulos and Pantelis Katharios and Emmanouil Flemetakis},

url = {https://www.mdpi.com/2076-2607/12/11/2281

https://imbbc.hcmr.gr/wp-content/uploads/2024/11/2024-Skliros-microorganisms-45.pdf},

doi = {10.3390/microorganisms12112281},

issn = {2076-2607},

year  = {2024},

date = {2024-11-12},

urldate = {2024-11-12},

journal = {Microorganisms},

volume = {12},

number = {11},

pages = {2281},

abstract = {The importance of microbial communities in fish hatcheries for fish health and welfare has been recognized, with several studies mapping these communities during healthy rearing conditions and disease outbreaks. In this study, we analyzed the bacteriome of the live feeds, such as microalgae, rotifers, and Artemia, used in fish hatcheries that produce Mediterranean species. Our goal was to provide baseline information about their structure, emphasizing in environmental putative fish pathogenic bacteria. We conducted 16S rRNA amplicon Novaseq sequencing for our analysis, and we inferred 46,745 taxonomically annotated ASVs. Results showed that incoming environmental water plays a significant role in the presence of important taxa that constitute presumptive pathogens. Bio-statistical analyses revealed a relatively stable bacteriome among seasonal samplings for every hatchery but a diverse bacteriome between sampling stations and a distinct core bacteriome for each hatchery. Analysis of putative opportunistic fish pathogenic genera revealed some co-occurrence correlation events and a high average relative abundance of Vibrio, Tenacibaculum, and Photobacterium genera in live feeds, reaching a grand mean average of up to 7.3% for the hatchery of the Hellenic Center of Marine Research (HCMR), 12% for Hatchery A, and 11.5% for Hatchery B. Mapping the bacteriome in live feeds is pivotal for understanding the marine environment and distinct aquaculture practices and can guide improvements in hatchery management, enhancing fish health and sustainability in the Mediterranean region.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{skaraki_microbial_2024,

title = {Microbial diversity in four Mediterranean irciniid sponges},

author = {Katerina Skaraki and Christina Pavloudi and Thanos Dailianis and Jacques Lagnel and Adriani Pantazidou and Antonios Magoulas and Georgios Kotoulas},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/02/2024-Skaraki-BioDDJ-6.pdf

https://bdj.pensoft.net/article/114809/},

doi = {10.3897/BDJ.12.e114809},

issn = {1314-2828, 1314-2836},

year  = {2024},

date = {2024-02-01},

urldate = {2024-02-05},

journal = {Biodiversity Data Journal},

volume = {12},

pages = {e114809},

abstract = {This paper describes a dataset of microbial communities from four different sponge species: 

 Ircinia oros 

 (Schmidt, 1864), 

 Ircinia variabilis 

 (Schmidt, 1862), 

 Sarcotragus spinosulus 

 Schmidt, 1862 and 

 Sarcotragus fasciculatus 

 (Pallas, 1766). The examined sponges all belong to Demospongiae (Class); Keratosa (Subclass); Dictyoceratida (Order); Irciniidae (Family). Samples were collected by scuba diving at depths between 6-14 m from two sampling sites of rocky formations at the northern coast of Crete (Cretan Sea, eastern Mediterranean) and were subjected to metabarcoding for the V5-V6 region of the 16S rRNA gene.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{vasileiadou_editorial_2024,

title = {Editorial: Marine biodiversity hotspots – challenges and resilience},

author = {Katerina Vasileiadou and Eva Chatzinikolaou and Stefania Klayn and Christina Pavloudi and Sofia Reizopoulou},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/01/2024-Vasileiadou-fmars-3.pdf

https://www.frontiersin.org/articles/10.3389/fmars.2024.1338242/full},

doi = {10.3389/fmars.2024.1338242},

issn = {2296-7745},

year  = {2024},

date = {2024-01-17},

urldate = {2024-01-22},

journal = {Frontiers in Marine Science},

volume = {11},

pages = {1338242},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{sarafidou_insights_2023,

title = {Insights on \textit{Pinna nobilis} population genetic structure in the Aegean and Ionian Sea},

author = {Georgia Sarafidou and Dimitris Tsaparis and Yiannis Issaris and Giorgos Chatzigeorgiou and Panos Grigoriou and Eva Chatzinikolaou and Christina Pavloudi},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/12/2023-Sarafidou-peerj-61.pdf

https://peerj.com/articles/16491},

doi = {10.7717/peerj.16491},

issn = {2167-8359},

year  = {2023},

date = {2023-12-01},

urldate = {2023-12-01},

journal = {PeerJ},

volume = {11},

pages = {e16491},

abstract = {The fan mussel 

 Pinna nobilis 

 Linnaeus, 1758 is an endemic species of the Mediterranean Sea, protected by international agreements. It is one of the largest bivalves in the world, playing an important role in the benthic communities; yet it has been recently characterized as Critically Endangered by the IUCN, due to mass mortality events. In this context, the assessment of the genetic variation of the remaining 

 P. nobilis 

 populations and the evaluation of connectivity among them are crucial elements for the conservation of the species. For this purpose, samples were collected from six regions of the Eastern Mediterranean Sea; the Islands of Karpathos, Lesvos and Crete; the Chalkidiki and Attica Peninsulas; and the Amvrakikos Gulf. Sampling was performed either by collecting tissue from the individuals or by using a non-invasive method, 

 i.e. 

 , by scraping the inside of their shells aiming to collect their mucus and thus avoid stress induction to them. Conventional molecular techniques with the use of the COI and 16S rRNA mitochondrial markers were selected for the depiction of the intra-population genetic variability. The analyses included 104 samples from the present study and publicly available sequences of individuals across the whole Mediterranean Sea. The results of this work (a) suggest the use of eDNA as an efficient sampling method for protected bivalves and (b) shed light to the genetic structure of 

 P. nobilis 

 population in the Eastern Mediterranean; this latter knowledge might prove to be fundamental for the species conservation and hence the ecosystem resilience. The haplotype analyses reinforced the evidence that there is a certain degree of connectivity among the distinct regions of the Mediterranean; yet there is evidence of population distinction within the basin, namely between the Western and the Eastern basins. The combination of both genetic markers in the same analysis along with the inclusion of a large number of individuals produced more robust results, revealing a group of haplotypes being present only in the Eastern Mediterranean and providing insights for the species’ most suitable conservation management.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{zafeiropoulos_metagoflow_2022,

title = {metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data},

author = {Haris Zafeiropoulos and Martin Beracochea and Stelios Ninidakis and Katrina Exter and Antonis Potirakis and Gianluca De Moro and Lorna Richardson and Erwan Corre and João Machado and Evangelos Pafilis and Georgios Kotoulas and Ioulia Santi and Robert D Finn and Cymon J Cox and Christina Pavloudi},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/10/2023-Zafeiropoulos-GiGa-57.pdf

https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giad078/7321054},

doi = {10.1093/gigascience/giad078},

issn = {2047-217X},

year  = {2023},

date = {2023-10-19},

urldate = {2023-10-23},

journal = {GigaScience},

volume = {12},

pages = {giad078},

abstract = {Abstract 

 

 Background 

 Genomic Observatories (GOs) are sites of long-term scientific study that undertake regular assessments of the genomic biodiversity. The European Marine Omics Biodiversity Observation Network (EMO BON) is a network of GOs that conduct regular biological community samplings to generate environmental and metagenomic data of microbial communities from designated marine stations around Europe. The development of an effective workflow is essential for the analysis of the EMO BON metagenomic data in a timely and reproducible manner. 

 

 

 Findings 

 Based on the established MGnify resource, we developed metaGOflow. metaGOflow supports the fast inference of taxonomic profiles from GO-derived data based on ribosomal RNA genes and their functional annotation using the raw reads. Thanks to the Research Object Crate packaging, relevant metadata about the sample under study, and the details of the bioinformatics analysis it has been subjected to, are inherited to the data product while its modular implementation allows running the workflow partially. The analysis of 2 EMO BON samples and 1 Tara Oceans sample was performed as a use case. 

 

 

 Conclusions 

 metaGOflow is an efficient and robust workflow that scales to the needs of projects producing big metagenomic data such as EMO BON. It highlights how containerization technologies along with modern workflow languages and metadata package approaches can support the needs of researchers when dealing with ever-increasing volumes of biological data. Despite being initially oriented to address the needs of EMO BON, metaGOflow is a flexible and easy-to-use workflow that can be broadly used for one-sample-at-a-time analysis of shotgun metagenomics data.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bilbao_phytoplankton_2023,

title = {Phytoplankton community composition in relation to environmental variability in the Urdaibai estuary (SE Bay of Biscay): Microscopy and eDNA metabarcoding},

author = {Jone Bilbao and Christina Pavloudi and Esther Blanco-Rayón and Javier Franco and Iosu Madariaga and Sergio Seoane},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/10/2023-Bilbao-MERes-53.pdf

https://linkinghub.elsevier.com/retrieve/pii/S0141113623003033},

doi = {10.1016/j.marenvres.2023.106175},

issn = {01411136},

year  = {2023},

date = {2023-10-06},

urldate = {2023-10-13},

journal = {Marine Environmental Research},

volume = {191},

pages = {106175},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{santi_european_2023,

title = {European marine omics biodiversity observation network: a strategic outline for the implementation of omics approaches in ocean observation},

author = {Ioulia Santi and Odette Beluche and Mélanie Beraud and Pier Luigi Buttigieg and Raffaella Casotti and Cymon J Cox and Michael Cunliffe and Neil Davies and Oihane Diaz De Cerio and Katrina Exter and Anne Emmanuelle Kervella and Georgios Kotoulas and Rune Lagaisse and Arnaud Laroquette and Bruno Louro and Fabrice Not and Matthias Obst and Christina Pavloudi and Julie Poulain and Kim Præbel and Jan Vanaverbeke and Nicolas Pade},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/06/2023-Santi-Frontiers-MarSci-24.pdf

https://www.frontiersin.org/articles/10.3389/fmars.2023.1118120/full},

doi = {10.3389/fmars.2023.1118120},

issn = {2296-7745},

year  = {2023},

date = {2023-05-29},

urldate = {2023-06-06},

journal = {Frontiers in Marine Science},

volume = {10},

pages = {1118120},

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.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pavloudi_investigation_2023,

title = {Investigation of systemic granulomatosis in cultured meagre, Argyrosomus regius, using clinical metagenomics},

author = {Christina Pavloudi and Maria Ioanna Tsertou and Efthimia Antonopoulou and Pantelis Katharios},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/01/2023-Pavloudi-AQUA-pre-print-8.pdf

https://linkinghub.elsevier.com/retrieve/pii/S0044848623000224},

doi = {10.1016/j.aquaculture.2023.739249},

issn = {00448486},

year  = {2023},

date = {2023-01-25},

urldate = {2023-01-25},

journal = {Aquaculture},

volume = {567},

pages = {739249},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pavloudi_deciphering_2022,

title = {Deciphering the community structure and the functional potential of a hypersaline marsh microbial mat community},

author = {Christina Pavloudi and Haris Zafeiropoulos},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/12/2022-Pavloudi-Zafeiropoulos-FEMS-preprint.pdf

https://academic.oup.com/femsec/article/doi/10.1093/femsec/fiac141/6843573},

doi = {10.1093/femsec/fiac141},

issn = {1574-6941},

year  = {2022},

date = {2022-12-12},

urldate = {2022-12-13},

journal = {FEMS Microbiology Ecology},

volume = {98},

number = {12},

pages = {fiac141},

abstract = {Abstract 

 Microbial mats are vertically stratified communities of microorganisms characterized by pronounced physiochemical gradients allowing for high species diversity and a wide range of metabolic capabilities. High Throughput Sequencing has the potential to reveal the biodiversity and function of such ecosystems in the cycling of elements. The present study combines 16S rRNA amplicon sequencing and shotgun metagenomics on a hypersaline marsh in Tristomo bay (Karpathos, Greece). Samples were collected in July 2018 and November 2019 from microbial mats, deeper sediment, aggregates observed in the water overlying the sediment, as well as sediment samples with no apparent layering. Metagenomic samples’ coassembly and binning revealed 250 bacterial and 39 archaeal metagenome-assembled genomes, with completeness estimates higher than 70% and contamination less than 5%. All MAGs had KEGG Orthology terms related to osmoadaptation, with the ‘salt in’ strategy ones being prominent. Halobacteria and Bacteroidetes were the most abundant taxa in the mats. Photosynthesis was most likely performed by purple sulphur and nonsulphur bacteria. All samples had the capacity for sulphate reduction, dissimilatory arsenic reduction, and conversion of pyruvate to oxaloacetate. Overall, both sequencing methodologies resulted in similar taxonomic compositions and revealed that the formation of the microbial mat in this marsh exhibits seasonal variation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{grau_wide-geographic_2022,

title = {Wide-Geographic and Long-Term Analysis of the Role of Pathogens in the Decline of Pinna nobilis to Critically Endangered Species},

author = {Amalia Grau and Antonio Villalba and José I Navas and Beatriz Hansjosten and José M Valencia and José R García-March and Patricia Prado and Guillermo Follana-Berná and Titouan Morage and Maite Vázquez-Luis and Elvira Álvarez and Pantelis Katharios and Christina Pavloudi and Elisabet Nebot-Colomer and José Tena-Medialdea and Monserrat Lopez-Sanmartín and Claire Peyran and Hrvoje Čižmek and Georgia Sarafidou and Yiannis Issaris and Inci Tüney-Kizilkaya and Salud Deudero and Serge Planes and Gaetano Catanese},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Grau-FMSci-21.pdf

https://www.frontiersin.org/articles/10.3389/fmars.2022.666640/full},

doi = {10.3389/fmars.2022.666640},

issn = {2296-7745},

year  = {2022},

date = {2022-03-01},

urldate = {2022-05-09},

journal = {Frontiers in Marine Science},

volume = {9},

pages = {666640},

abstract = {A mass mortality event (MME) affecting the fan mussel 

 Pinna nobilis 

 was first detected in Spain in autumn 2016 and spread north- and eastward through the Mediterranean Sea. Various pathogens have been blamed for contributing to the MME, with emphasis in 

 Haplosporidium pinnae 

 , 

 Mycobacterium 

 sp. and 

 Vibrio 

 spp. In this study, samples from 762 fan mussels (necropsies from 263 individuals, mantle biopsies from 499) of various health conditions, with wide geographic and age range, taken before and during the MME spread from various environments along Mediterranean Sea, were used to assess the role of pathogens in the MME. The number of samples processed by both histological and molecular methods was 83. The most important factor playing a main role on the onset of the mass mortality of 

 P. nobilis 

 throughout the Mediterranean Sea was the infection by 

 H. pinnae 

 . It was the only non-detected pathogen before the MME while, during MME spreading, its prevalence was higher in sick and dead individuals than in asymptomatic ones, in MME-affected areas than in non-affected sites, and it was not associated with host size, infecting both juveniles and adults. Conversely, infection with mycobacteria was independent from the period (before or during MME), from the affection of the area by MME and from the host health condition, and it was associated with host size. Gram (-) bacteria neither appeared associated with MME.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{paragkamian_automating_2022,

title = {Automating the Curation Process of Historical Literature on Marine Biodiversity Using Text Mining: The DECO Workflow},

author = {Savvas Paragkamian and Georgia Sarafidou and Dimitra Mavraki and Christina Pavloudi and Joana Beja and Menashè Eliezer and Marina Lipizer and Laura Boicenco and Leen Vandepitte and Ruben Perez-Perez and Haris Zafeiropoulos and Christos Arvanitidis and Evangelos Pafilis and Vasilis Gerovasileiou},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Paragkaminan-fmars-53.pdf

},

doi = {10.3389/fmars.2022.940844},

issn = {2296-7745},

year  = {2022},

date = {2022-01-01},

urldate = {2022-07-29},

journal = {Frontiers in Marine Science},

volume = {9},

pages = {940844},

abstract = {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 a multidisciplinary effort involving four tasks: (a) Document digitisation (b) Transcription, which involves text recognition and correction, and (c) Information Extraction, which is performed using text mining tools and involves the entity identification, their normalisation and their co-mentions in text. Finally, the extracted data go through (d) Publication to a data repository in a standardised format. Each of these tasks requires a dedicated multistep methodology with standards and procedures. During the past 8 years, Information Extraction (IE) tools have undergone remarkable advances, which created a landscape of various tools with distinct capabilities specific to biodiversity data. These tools recognise entities in text such as taxon names, localities, phenotypic traits and thus automate, accelerate and facilitate the curation process. Furthermore, they assist the normalisation and mapping of entities to specific identifiers. This work focuses on the IE step (c) from the marine historical biodiversity data perspective. It orchestrates IE tools and provides the curators with a unified view of the methodology; as a result the documentation of the strengths, limitations and dependencies of several tools was drafted. Additionally, the classification of tools into Graphical User Interface (web and standalone) applications and Command Line Interface ones enables the data curators to select the most suitable tool for their needs, according to their specific features. In addition, the high volume of already digitised marine documents that await curation is amassed and a demonstration of the methodology, with a new scalable, extendable and containerised tool, “DECO” (bioDivErsity data Curation programming wOrkflow) is presented. DECO’s usage will provide a solid basis for future curation initiatives and an augmented degree of reliability towards high value data products that allow for the connection between the past and the present, in marine biodiversity research.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{keklikoglou_micro-ct_2021,

title = {Micro-CT for Biological and Biomedical Studies: A Comparison of Imaging Techniques},

author = {Kleoniki Keklikoglou and Christos Arvanitidis and Georgios Chatzigeorgiou and Eva Chatzinikolaou and Efstratios Karagiannidis and Triantafyllia Koletsa and Antonios Magoulas and Konstantinos Makris and George Mavrothalassitis and Eleni-Dimitra Papanagnou and Andreas S Papazoglou and Christina Pavloudi and Ioannis P Trougakos and Katerina Vasileiadou and Angeliki Vogiatzi},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/09/2021-Keklikoglou-jimaging-66-1.pdf

https://www.mdpi.com/2313-433X/7/9/172},

doi = {10.3390/jimaging7090172},

issn = {2313-433X},

year  = {2021},

date = {2021-09-01},

urldate = {2021-09-22},

volume = {7},

number = {9},

pages = {172},

abstract = {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 digitisation 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 techniques applied in biological and biomedical fields, such as optical microscopy, confocal laser scanning microscopy, and scanning electron microscopy, are presented and compared with the micro-CT technique through five use cases. Finally, the ability of micro-CT to create non-destructively 3D anatomical and morphological data in sub-micron resolution and the necessity to develop complementary methods with other imaging techniques, in order to overcome limitations caused by each technique, is emphasised.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nikolopoulou_benthic_2021,

title = {Benthic habitat mapping of Plazh Gradina – Zlatna ribka (Black Sea) and Karpathos and Saria Islands (Mediterranean Sea)},

author = {Stamatina Nikolopoulou and Dimitar Berov and Stefania Klayn and Lyubomir Dimitrov and Kiril Velkovsky and Eva Chatzinikolaou and Giorgos Chatzigeorgiou and Ventzislav Karamfilov and Christina Pavloudi},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/09/2021-Nikolopoulou-BDJ-64.pdf

https://bdj.pensoft.net/article/71972/},

doi = {10.3897/BDJ.9.e71972},

issn = {1314-2828, 1314-2836},

year  = {2021},

date = {2021-08-23},

urldate = {2021-09-16},

volume = {9},

pages = {e71972},

abstract = {Habitat mapping is nеcessary for the efficient conservation and protection of marine ecosystems. In addition, it is a requirement for EU Member States as stated in the European Union (EU) Habitats Directive (92/43/EEC), as well as necessary for the achievement and maintenance of 'good environmental status (GES)' of benthic marine habitats in the framework of the EU Marine Strategy Framework Directive (2008/56/EC). 

 

 This study provides baseline information on the marine benthic habitats of Sozopol Bay (Black Sea) and Karpathos and Saria Islands (Mediterranean Sea). These two Natura 2000 sites were selected as study sites of the RECONNECT project, which aimed at creating a transnational cooperative network to confront the environmental threats of ecosystems with a high natural and cultural interest, by the establishment of common practices and a joint regional strategy. The specific objective was to map the marine habitats using a defined 

 a priori 

 classification (EUNIS), with the ultimate purpose of supporting government marine spatial planning, management and decision-making processes through the development of a Decision Support System.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chatzinikolaou_benthic_2021,

title = {Benthic communities in three Mediterranean touristic ports: MAPMED project},

author = {Eva Chatzinikolaou and Panagiotis Damianidis and Christina Pavloudi and Aikaterini Vasileiadou and Sarah Faulwetter and Kleoniki Keklikoglou and Wanda Plaitis and Dimitra Mavraki and Stamatina Nikolopoulou and Christos Arvanitidis},

url = {https://bdj.pensoft.net/article/66420/

https://imbbc.hcmr.gr/wp-content/uploads/2021/05/2021-Chatzinikolaou-DioDiv-Data-J-32.pdf},

doi = {10.3897/BDJ.9.e66420},

issn = {1314-2828},

year  = {2021},

date = {2021-04-01},

urldate = {2021-04-27},

journal = {Biodiversity Data Journal},

volume = {9},

pages = {e66420},

abstract = {Mediterranean ports are sources of significant economic activity and at the same time they act as recipients of considerable anthropogenic disturbance and pollution. Macrobenthic communities are an important component of the port biota and have been used as environmental quality indicators.Macrobenthic assemblages were recorded in three Mediterranean touristic ports under the framework of the ENPI CBC MED project MAPMED. Samples were collected from Cagliari (Sardinia, Italy), Heraklion (Crete, Greece) and El Kantaoui (Tunisia) ports during February, May and September 2012. The sampling stations were selected according to the different sectors within each port (i.e. leisure, fishing, passenger/cargo vessels, shipyard). A total number of 277 taxa belonging to 12 phyla were found, of which the 96 taxa were found in all three ports. El Kantaoui port hosted the highest number of macrobenthic taxa. Mollusca were the most abundant group (34%) in all ports. The highest percentage of opportunistic taxa per station was found before the touristic period in the shipyard of Heraklion port (89.3%).},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{zafeiropoulos_0s_2021,

title = {0s and 1s in marine molecular research: a regional HPC perspective},

author = {Haris Zafeiropoulos and Anastasia Gioti and Stelios Ninidakis and Antonis Potirakis and Savvas Paragkamian and Nelina Angelova and Aglaia Antoniou and Theodoros Danis and Eliza Kaitetzidou and Panagiotis Kasapidis and Jon Bent Kristoffersen and Vasileios Papadogiannis and Christina Pavloudi and Quoc Viet Ha and Jacques Lagnel and Nikos Pattakos and Giorgos Perantinos and Dimitris Sidirokastritis and Panagiotis Vavilis and Georgios Kotoulas and Tereza Manousaki and Elena Sarropoulou and Costas S Tsigenopoulos and Christos Arvanitidis and Antonios Magoulas and Evangelos Pafilis},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/08/2021-Zafeiropoulos-GiGa-63.pdf

https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giab053/6353916},

doi = {10.1093/gigascience/giab053},

issn = {2047-217X},

year  = {2021},

date = {2021-01-01},

urldate = {2021-08-23},

journal = {GigaScience},

volume = {10},

number = {8},

pages = {giab053},

abstract = {Abstract 

 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 challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade’s experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility’s future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{samuel_toward_2021,

title = {Toward a Global Public Repository of Community Protocols to Encourage Best Practices in Biomolecular Ocean Observing and Research},

author = {Robyn M Samuel and Raissa Meyer and Pier Luigi Buttigieg and Neil Davies and Nicholas W Jeffery and Christopher Meyer and Christina Pavloudi and Kathleen Johnson Pitz and Maxime Sweetlove and Susanna Theroux and Jodie van de Kamp and Alison Watts},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/12/2021-Samuel-FMS-79.pdf

https://www.frontiersin.org/article/10.3389/fmars.2021.758694},

doi = {10.3389/fmars.2021.758694},

issn = {2296-7745},

year  = {2021},

date = {2021-01-01},

urldate = {2021-12-01},

journal = {Frontiers in Marine Science},

volume = {8},

pages = {1488},

abstract = {Biomolecular ocean observing and research is a rapidly evolving field that uses omics approaches to describe biodiversity at its foundational level, giving insight into the structure and function of marine ecosystems over time and space. It is an especially effective approach for investigating the marine microbiome. To mature marine microbiome research and operations within a global ocean biomolecular observing network (OBON) for the UN Decade of Ocean Science for Sustainable Development and beyond, research groups will need a system to effectively share, discover, and compare “omic” practices and protocols. While numerous informatic tools and standards exist, there is currently no global, publicly-supported platform specifically designed for sharing marine omics [or any omics] protocols across the entire value-chain from initiating a study to the publication and use of its results. Toward that goal, we propose the development of the Minimum Information for an Omic Protocol (MIOP), a community-developed guide of curated, standardized metadata tags and categories that will orient protocols in the value-chain for the facilitated, structured, and user-driven discovery of suitable protocol suites on the Ocean Best Practices System. Users can annotate their protocols with these tags, or use them as search criteria to find appropriate protocols. Implementing such a curated repository is an essential step toward establishing best practices. Sharing protocols and encouraging comparisons through this repository will be the first steps toward designing a decision tree to guide users to community endorsed best practices.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{zafeiropoulos_dark_2021,

title = {The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data},

author = {Haris Zafeiropoulos and Laura Gargan and Sanni Hintikka and Christina Pavloudi and Jens Carlsson},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/12/2021-Zafeiropoulos-ΜΒΜΓ-81.pdf

https://mbmg.pensoft.net/article/69657/},

doi = {10.3897/mbmg.5.69657},

issn = {2534-9708},

year  = {2021},

date = {2021-01-01},

urldate = {2021-12-01},

journal = {Metabarcoding and Metagenomics},

volume = {5},

pages = {e69657},

abstract = {The mitochondrial cytochrome C oxidase subunit I gene (COI) is commonly used in environmental DNA (eDNA) metabarcoding studies, especially for assessing metazoan diversity. Yet, a great number of COI operational taxonomic units (OTUs) or/and amplicon sequence variants (ASVs) retrieved from such studies do not get a taxonomic assignment with a reference sequence. To assess and investigate such sequences, we have developed the Dark mAtteR iNvestigator (DARN) software tool. For this purpose, a reference COI-oriented phylogenetic tree was built from 1,593 consensus sequences covering all the three domains of life. With respect to eukaryotes, consensus sequences at the family level were constructed from 183,330 sequences retrieved from the Midori reference 2 database, which represented 70% of the initial number of reference sequences. Similarly, sequences from 431 bacterial and 15 archaeal taxa at the family level (29% and 1% of the initial number of reference sequences respectively) were retrieved from the BOLD and the PFam databases. DARN makes use of this phylogenetic tree to investigate COI pre-processed sequences of amplicon samples to provide both a tabular and a graphical overview of their phylogenetic assignments. To evaluate DARN, both environmental and bulk metabarcoding samples from different aquatic environments using various primer sets were analysed. We demonstrate that a large proportion of non-target prokaryotic organisms, such as bacteria and archaea, are also amplified in eDNA samples and we suggest prokaryotic COI sequences to be included in the reference databases used for the taxonomy assignment to allow for further analyses of dark matter. DARN source code is available on GitHub at https://github.com/hariszaf/darn and as a Docker image at https://hub.docker.com/r/hariszaf/darn.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{obst_marine_2020,

title = {A Marine Biodiversity Observation Network for Genetic Monitoring of Hard-Bottom Communities (ARMS-MBON)},

author = {Matthias Obst and Katrina Exter and Louise A Allcock and Christos Arvanitidis and Alizz Axberg and Maria Bustamante and Ibon Cancio and Diego Carreira-Flores and Eva Chatzinikolaou and Giorgos Chatzigeorgiou and Nathan Chrismas and Melody S Clark and Thierry Comtet and Thanos Dailianis and Neil Davies and Klaas Deneudt and Oihane Diaz de Cerio and Ana Fortič and Vasilis Gerovasileiou and Pascal I Hablützel and Kleoniki Keklikoglou and Georgios Kotoulas and Rafal Lasota and Barbara R Leite and Stéphane Loisel and Laurent Lévêque and Liraz Levy and Magdalena Malachowicz and Borut Mavrič and Christopher Meyer and Jonas Mortelmans and Joanna Norkko and Nicolas Pade and Anne Marie Power and Andreja Ramšak and Henning Reiss and Jostein Solbakken and Peter A Staehr and Per Sundberg and Jakob Thyrring and Jesus S Troncoso and Frédérique Viard and Roman Wenne and Eleni Ioanna Yperifanou and Malgorzata Zbawicka and Christina Pavloudi},

url = {https://www.frontiersin.org/articles/10.3389/fmars.2020.572680/full},

doi = {10.3389/fmars.2020.572680},

issn = {2296-7745},

year  = {2020},

date = {2020-11-01},

urldate = {2020-12-08},

journal = {Frontiers in Marine Science},

volume = {7},

pages = {572680},

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 

 ).},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{tsiola_viral_2020,

title = {Viral Metagenomic Content Reflects Seawater Ecological Quality in the Coastal Zone},

author = {Anastasia Tsiola and Grégoire Michoud and Stilianos Fodelianakis and Ioannis Karakassis and Georgios Kotoulas and Alexandra Pavlidou and Christina Pavloudi and Paraskevi Pitta and Nomiki Simboura and Daniele Daffonchio and Manolis Tsapakis},

url = {https://www.mdpi.com/1999-4915/12/8/806},

doi = {10.3390/v12080806},

year  = {2020},

date = {2020-08-01},

urldate = {2020-08-06},

journal = {Viruses},

volume = {12},

number = {8},

pages = {806},

abstract = {Viruses interfere with their host’s metabolism through the expression of auxiliary metabolic genes (AMGs) that, until now, are mostly studied under large physicochemical gradients. Here, we focus on coastal marine ecosystems and we sequence the viral metagenome (virome) of samples with discrete levels of human-driven disturbances. We aim to describe the relevance of viromics with respect to ecological quality status, defined by the classic seawater trophic index (TRIX). Neither viral (family level) nor bacterial (family level, based on 16S rRNA sequencing) community structure correlated with TRIX. AMGs involved in the Calvin and tricarboxylic acid cycles were found at stations with poor ecological quality, supporting viral lysis by modifying the host’s energy supply. AMGs involved in “non-traditional” energy-production pathways (3HP, sulfur oxidation) were found irrespective of ecological quality, highlighting the importance of recognizing the prevalent metabolic paths and their intermediate byproducts. Various AMGs explained the variability between stations with poor vs. good ecological quality. Our study confirms the pivotal role of the virome content in ecosystem functioning, acting as a “pool” of available functions that may be transferred to the hosts. Further, it suggests that AMGs could be used as an ultra-sensitive metric of energy-production pathways with relevance in the vulnerable coastal zone and its ecological quality.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bariche_new_2020,

title = {New Alien Mediterranean Biodiversity Records 2020},

author = {Michel Bariche and Sara A A Al-Mabruk and Maria Ayca Ateş and Adnan Büyük and Fabio Crocetta and Michail Dritsas and Diala Edde and Ana Fortič and Elissavet Gavriil and Vasilis Gerovasileiou and Mehmet Gökoğlu and Fatih M Huseyinoglu and Paraskevi K Karachle and Periklis Kleitou and Tuba Terbiyik Kurt and Joachim Langeneck and Claudio Lardicci and Lovrenc Lipej and Christina Pavloudi and Maurizio Pinna and Jamila Rizgalla and Mehmet Rüştü Özen and Francisco Sedano and Ergun Taşkin and Gamze Yildiz and Francesco Zangaro},

url = {https://ejournals.epublishing.ekt.gr/index.php/hcmr-med-mar-sc/article/view/21987},

doi = {10.12681/mms.21987},

issn = {1791-6763, 1108-393X},

year  = {2020},

date = {2020-04-01},

urldate = {2020-08-06},

journal = {Mediterranean Marine Science},

volume = {21},

number = {1},

pages = {129},

abstract = {The current article presents 18 new records from seven Mediterranean countries. These records include one rhodophyte, fournudibranchs, two crustaceans, one stingray and 10 bony fishes. They are grouped by country as follows: Lebanon - first record ofthe Striped bass Morone saxatilis, the stingray Himantura leoparda, the Areolate grouper Epinephelus areolatus and the Spot-finporcupinefish Diodon hystrix from various parts of the country; Turkey - first record of the invasive red alga Grateloupia turuturufrom the sea of Marmara (region of Bandırma), the sea slug Goniobranchus obsoletus and the crab Arcania brevifrons from theGulf of Antalya and the cladoceran Pleopis schmackeri from several locations along the Aegean Sea; Cyprus - first record of thealien sea slug Berthellina citrina from the region of Cape Greco and an observation of a butterflyfish Heniochus sp. from the northeasternside of the island; Greece - first record of the alien sea slug Anteaeolidiella lurana from the region of Heraklion in Creteand the record of the Atlantic spadefish Chaetodipterus faber and the Black surgeonfish Acanthurus cfr gahhm from SalaminaIsland; Slovenia - first record of the alien sea slug Thecacera pennigera from Izola; Italy - first record of the hybrid Striped bass(Morone saxatilis × Morone chrysops) from the northern Tyrrhenian Sea and a first record of the goldfish Carassius auratus fromthe region of Apulia; Libya - first record of the Red Sea goatfish Parupeneus forsskali and the African surgeonfish Acanthurusmonroviae, respectively from the eastern (Al-Tamimi area) and the western shore (Al-Khums area).},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{zafeiropoulos_pema_2020,

title = {PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes},

author = {Haris Zafeiropoulos and Ha Quoc Viet and Katerina Vasileiadou and Antonis Potirakis and Christos Arvanitidis and Pantelis Topalis and Christina Pavloudi and Evangelos Pafilis},

url = {https://doi.org/10.1093/gigascience/giaa022},

doi = {10.1093/gigascience/giaa022},

issn = {2047-217X},

year  = {2020},

date = {2020-01-01},

journal = {GigaScience},

volume = {9},

number = {3},

abstract = {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 experiment's idiosyncrasy. Adding to this complexity, the computation capacity of high-performance computing systems is frequently required for such analyses. To address the difficulties, bioinformatic pipelines need to combine state-of-the art technologies and algorithms with an easy to get-set-use framework, allowing researchers to tune each study. Software containerization technologies ease the sharing and running of software packages across operating systems; thus, they strongly facilitate pipeline development and usage. Likewise programming languages specialized for big data pipelines incorporate features like roll-back checkpoints and on-demand partial pipeline execution.PEMA is a containerized assembly of key metabarcoding analysis tools that requires low effort in setting up, running, and customizing to researchers’ needs. Based on third-party tools, PEMA performs read pre-processing, (molecular) operational taxonomic unit clustering, amplicon sequence variant inference, and taxonomy assignment for 16S and 18S ribosomal RNA, as well as ITS and COI marker gene data. Owing to its simplified parameterization and checkpoint support, PEMA allows users to explore alternative algorithms for specific steps of the pipeline without the need of a complete re-execution. PEMA was evaluated against both mock communities and previously published datasets and achieved results of comparable quality.A high-performance computing–based approach was used to develop PEMA; however, it can be used in personal computers as well. PEMA's time-efficient performance and good results will allow it to be used for accurate environmental DNA metabarcoding analysis, thus enhancing the applicability of next-generation biodiversity assessment studies.},

note = {_eprint: https://academic.oup.com/gigascience/article-pdf/9/3/giaa022/32894405/giaa022.pdf},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{vasileiadou_genetic_2018,

title = {Genetic diversity of Nephtys hombergii (Phyllodocida, Polychaeta) associated with environmental factors in a highly fluctuating ecosystem},

author = {K Vasileiadou and C Pavloudi and F Camisa and I Tsikopoulou and N Fragopoulou and G Kotoulas and C Arvanitidis},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85009786126&doi=10.1017%2fS0025315416001910&partnerID=40&md5=8e7cb2651bd57afe644615018866185a},

doi = {10.1017/S0025315416001910},

issn = {00253154},

year  = {2018},

date = {2018-01-01},

journal = {Journal of the Marine Biological Association of the United Kingdom},

volume = {98},

number = {4},

pages = {777--789},

abstract = {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 population establishment. For the study, seasonal samples were collected from four lagoons in the lagoonal complex of Amvrakikos Gulf (W Greece). The mitochondrial DNA (COI gene) was analysed from polychaetes of Nephtys hombergii, as it is considered an important component of these assemblages and shows great dispersal ability. The results of the genetic analysis showed intraspecific variability in all the lagoons, with genetic structuring tending to follow a seasonal pattern rather than a spatial one. The results of BIOENV analysis indicated correlation of the observed pattern with the water pH levels, the redox potential and the concentration of phosphate in the sediment. The complexity of the network suggested the enhancement of the local population with more recently established haplotypes. The findings of the study support the necessity of designing management strategies by taking into account genetic diversity and population demography approaches in addition to those based on species and habitats. © Copyright Marine Biological Association of the United Kingdom 2017.},

note = {Publisher: Cambridge University Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pavloudi_sediment_2017,

title = {Sediment microbial taxonomic and functional diversity in a natural salinity gradient challenge Remane's 'species minimum' concept},

author = {C Pavloudi and J B Kristoffersen and A Oulas and M De Troch and C Arvanitidis},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85031101355&doi=10.7717%2fpeerj.3687&partnerID=40&md5=6860a76d415733f23eeb5d4df199a4d5},

doi = {10.7717/peerj.3687},

issn = {21678359},

year  = {2017},

date = {2017-01-01},

journal = {PeerJ},

volume = {2017},

number = {10},

abstract = {Several models have been developed for the description of diversity in estuaries and other brackish habitats, with the most recognized being Remane's Artenminimum ("species minimum") concept. It was developed for the Baltic Sea, one of the world's largest semi-enclosed brackish water body with a unique permanent salinity gradient, and it argues that taxonomic diversity of macrobenthic organisms is lowest within the horohalinicum (5 to 8 psu). The aim of the present study was to investigate the relationship between salinity and sediment microbial diversity at a freshwater-marine transect in Amvrakikos Gulf (Ionian Sea, Western Greece) and assess whether species composition and community function follow a generalized concept such as Remane's. DNA was extracted from sediment samples from six stations along the aforementioned transect and sequenced for the 16S rRNA gene using high-throughput sequencing. The metabolic functions of the OTUs were predicted and the most abundant metabolic pathways were extracted. Key abiotic variables, i.e., salinity, temperature, chlorophyll-a and oxygen concentration etc., were measured and their relation with diversity and functional patterns was explored. Microbial communities were found to differ in the three habitats examined (river, lagoon and sea) with certain taxonomic groups being more abundant in the freshwater and less in the marine environment, and vice versa. Salinity was the environmental factor with the highest correlation to the microbial community pattern, while oxygen concentration was highly correlated to the metabolic functional pattern. The total number of OTUs showed a negative relationship with increasing salinity, thus the sediment microbial OTUs in this study area do not follow Remane's concept. © 2017 Pavloudi et al.},

note = {Publisher: PeerJ Inc.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pavloudi_diversity_2017,

title = {Diversity and abundance of sulfate-reducing microorganisms in a Mediterranean lagoonal complex (Amvrakikos Gulf, Ionian Sea) derived from dsrB gene},

author = {C Pavloudi and A Oulas and K Vasileiadou and G Kotoulas and M De Troch and M W Friedrich and C Arvanitidis},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85021092263&doi=10.3354%2fame01829&partnerID=40&md5=8be345d2d8f932cc9b640cf2072c2bb0},

doi = {10.3354/ame01829},

issn = {09483055},

year  = {2017},

date = {2017-01-01},

journal = {Aquatic Microbial Ecology},

volume = {79},

number = {3},

pages = {209--219},

abstract = {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 aim of the present study was to explore the biodiversity patterns of SRMs and to examine the extent to which these patterns are associated with biogeographic and environmental factors. Sediment samples were collected from 5 lagoons in the Amvrakikos Gulf (Ionian Sea, western Greece). DNA was extracted from the sediment and was further processed through pyrosequencing of a region of the dissimilatory sulfite reductase β-subunit (dsrB). The results of this exploratory study show that the majority of the observed operational taxonomic units (OTUs) belong to the Deltaproteobacteria supercluster and more specifically, to the Desulfobacteraceae family. Salinity and ammonium ions are the environmental factors that best correlated with the SRM community pattern. Furthermore, the SRM community of the brackish lagoons is differentiated from that of the brackish-marine lagoons and the studied lagoons have distinct SRM communities. © Inter-Research 2017.},

note = {Publisher: Inter-Research},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{hummel_geographic_2017,

title = {Geographic patterns of biodiversity in European coastal marine benthos},

author = {H Hummel and P Van Avesaath and S Wijnhoven and L Kleine-Schaars and S Degraer and F Kerckhof and N Bojanic and S Skejic and O Vidjak and M Rousou and H Orav-Kotta and J Kotta and J Jourde and M L Pedrotti and J -C Leclerc and N Simon and F Rigaut-Jalabert and G Bachelet and N Lavesque and C Arvanitidis and C Pavloudi and S Faulwetter and T Crowe and J Coughlan and L Benedetti-Cecchi and M Dal Bello and P Magni and S Como and S Coppa and A Ikauniece and T Ruginis and E Jankowska and J M Weslawski and J Warzocha and S Gromisz and B Witalis and T Silva and P Ribeiro and V K Fernandes De Matos and I Sousa-Pinto and P Veiga and J Troncoso and X Guinda and J A Juanes De La Pena and A Puente and F Espinosa and A Pérez-Ruzafa and M Frost and C L McNeill and O Peleg and G Rilov},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84987600709&doi=10.1017%2fS0025315416001119&partnerID=40&md5=8af26b11dedcb6c3ee86e02f6517eb15},

doi = {10.1017/S0025315416001119},

issn = {00253154},

year  = {2017},

date = {2017-01-01},

journal = {Journal of the Marine Biological Association of the United Kingdom},

volume = {97},

number = {3},

pages = {507--523},

abstract = {Within the COST action EMBOS (European Marine Biodiversity Observatory System) the degree and variation of the diversity and densities of soft-bottom communities from the lower intertidal or the shallow subtidal was measured at 28 marine sites along the European coastline (Baltic, Atlantic, Mediterranean) using jointly agreed and harmonized protocols, tools and indicators. The hypothesis tested was that the diversity for all taxonomic groups would decrease with increasing latitude. The EMBOS system delivered accurate and comparable data on the diversity and densities of the soft sediment macrozoobenthic community over a large-scale gradient along the European coastline. In contrast to general biogeographic theory, species diversity showed no linear relationship with latitude, yet a bell-shaped relation was found. The diversity and densities of benthos were mostly positively correlated with environmental factors such as temperature, salinity, mud and organic matter content in sediment, or wave height, and related with location characteristics such as system type (lagoons, estuaries, open coast) or stratum (intertidal, subtidal). For some relationships, a maximum (e.g. Temperature from 15-20°C; mud content of sediment around 40%) or bimodal curve (e.g. salinity) was found. In lagoons the densities were twice higher than in other locations, and at open coasts the diversity was much lower than in other locations. We conclude that latitudinal trends and regional differences in diversity and densities are strongly influenced by, i.e. merely the result of, particular sets and ranges of environmental factors and location characteristics specific to certain areas, such as the Baltic, with typical salinity clines (favouring insects) and the Mediterranean, with higher temperatures (favouring crustaceans). Therefore, eventual trends with latitude are primarily indirect and so can be overcome by local variation of environmental factors. Copyright © Marine Biological Association of the United Kingdom 2016.},

note = {Publisher: Cambridge University Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{dal_bello_consistent_2017,

title = {Consistent patterns of spatial variability between NE Atlantic and Mediterranean rocky shores},

author = {M Dal Bello and J -C Leclerc and L Benedetti-Cecchi and G Andrea De Lucia and C Arvanitidis and P Van Avesaath and G Bachelet and N Bojanic and S Como and S Coppa and J Coughlan and T Crowe and S Degraer and F Espinosa and S Faulwetter and M Frost and X Guinda and E Jankowska and J Jourde and J A Juanes De La Pena and F Kerckhof and J Kotta and N Lavesque and P Magni and V De Matos and H Orav-Kotta and C Pavloudi and M L Pedrotti and O Peleg and A Pérez-Ruzafa and A Puente and P Ribeiro and F Rigaut-Jalabert and G Rilov and M Rousou and M Rubal and T Ruginis and T Silva and N Simon and I Sousa-Pinto and J Troncoso and J Warzocha and J M Weslawski and H Hummel},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84995532117&doi=10.1017%2fS0025315416001491&partnerID=40&md5=2960e83afbd9938d643b92f5bb8d29af},

doi = {10.1017/S0025315416001491},

issn = {00253154},

year  = {2017},

date = {2017-01-01},

journal = {Journal of the Marine Biological Association of the United Kingdom},

volume = {97},

number = {3},

pages = {539--547},

abstract = {Examining how variability in population abundance and distribution is allotted among different spatial scales can inform of processes that are likely to generate that variability. Results of studies dealing with scale issues in marine benthic communities suggest that variability is concentrated at small spatial scales (from tens of centimetres to few metres) and that spatial patterns of variation are consistent across ecosystems characterized by contrasting physical and biotic conditions, but this has not been formally tested. Here we quantified the variability in the distribution of intertidal rocky shore communities at a range of spatial scales, from tens of centimetres to thousands of kilometres, both in the NE Atlantic and the Mediterranean, and tested whether the observed patterns differed between the two basins. We focused on canopy-forming macroalgae and associated understorey assemblages in the low intertidal, and on the distribution of Patella limpets at mid intertidal levels. Our results highlight that patterns of spatial variation, at each scale investigated, were consistent between the Atlantic and the Mediterranean, suggesting that similar ecological processes operate in these regions. In contrast with former studies, variability in canopy cover, species richness and limpet abundance was equally distributed among spatial scales, possibly reflecting the fingerprint of multiple processes. Variability in community structure of low intertidal assemblages, instead, peaked at the largest scale, suggesting that oceanographic processes and climatic gradients may be important. We conclude that formal comparisons of variability across scales nested in contrasting systems are needed, before any generalization on patterns and processes can be made. Copyright © Marine Biological Association of the United Kingdom 2016.},

note = {Publisher: Cambridge University Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kotta_essence_2017,

title = {Essence of the patterns of cover and richness of intertidal hard bottom communities: A pan-European study},

author = {J Kotta and H Orav-Kotta and H Jänes and H Hummel and C Arvanitidis and P Van Avesaath and G Bachelet and L Benedetti-Cecchi and N Bojanić and S Como and S Coppa and J Coughlan and T Crowe and M Dal Bello and S Degraer and J A J De La Pena and V K Fernandes De Matos and F Espinosa and S Faulwetter and M Frost and X Guinda and E Jankowska and J Jourde and F Kerckhof and N Lavesque and J -C Leclerc and P Magni and C Pavloudi and M L Pedrotti and O Peleg and A Pérez-Ruzafa and A Puente and P Ribeiro and G Rilov and M Rousou and T Ruginis and T Silva and N Simon and I Sousa-Pinto and J Troncoso and J Warzocha and J M Weslawski},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84990183671&doi=10.1017%2fS0025315416001351&partnerID=40&md5=99f1c2fafcfd35575a76d4e7b1a7befb},

doi = {10.1017/S0025315416001351},

issn = {00253154},

year  = {2017},

date = {2017-01-01},

journal = {Journal of the Marine Biological Association of the United Kingdom},

volume = {97},

number = {3},

pages = {525--538},

abstract = {Coastal ecosystems are highly complex and driven by multiple environmental factors. To date we lack scientific evidence for the relative contribution of natural and anthropogenic drivers for the majority of marine habitats in order to adequately assess the role of different stressors across the European seas. Such relationship can be investigated by analysing the correlation between environmental variables and biotic patterns in multivariate space and taking into account non-linearities. Within the framework of the EMBOS (European Marine Biodiversity Observatory System) programme, hard bottom intertidal communities were sampled in a standardized way across European seas. Links between key natural and anthropogenic drivers and hard bottom communities were analysed using Boosted Regression Trees modelling. The study identified strong interregional variability and showed that patterns of hard bottom macroalgal and invertebrate communities were primarily a function of tidal regime, nutrient loading and water temperature (anomalies). The strength and shape of functional form relationships varied widely however among types of organisms (understorey algae composing mostly filamentous species, canopy-forming algae or sessile invertebrates) and aggregated community variables (cover or richness). Tidal regime significantly modulated the effect of nutrient load on the cover and richness of understorey algae and sessile invertebrates. In contrast, hydroclimate was more important for canopy algae and temperature anomalies and hydroclimate separately or interactively contributed to the observed patterns. The analyses also suggested that climate-induced shifts in weather patterns may result in the loss of algal richness and thereby in the loss of functional diversity in European hard bottom intertidal areas. Copyright © Marine Biological Association of the United Kingdom 2016.},

note = {Publisher: Cambridge University Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{puente_role_2017,

title = {The role of physical variables in biodiversity patterns of intertidal macroalgae along European coasts},

author = {A Puente and X Guinda and J A Juanes and E Ramos and B Echavarri-Erasun and C F De La Hoz and S Degraer and F Kerckhof and N Bojanić and M Rousou and H Orav-Kotta and J Kotta and J Jourde and M L Pedrotti and J -C Leclerc and N Simon and G Bachelet and N Lavesque and C Arvanitidis and C Pavloudi and S Faulwetter and T P Crowe and J Coughlan and L B Cecchi and M Dal Bello and P Magni and S Como and S Coppa and G A De Lucia and T Rugins and E Jankowska and J M Weslawski and J Warzocha and T Silva and P Ribeiro and V De Matos and I Sousa-Pinto and J Troncoso and O Peleg and G Rilov and F Espinosa and A P Ruzafa and M Frost and H Hummel and P Van Avesaath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85006276987&doi=10.1017%2fS0025315416001673&partnerID=40&md5=db3f3559d7c51f85e9d9f64a427a569e},

doi = {10.1017/S0025315416001673},

issn = {00253154},

year  = {2017},

date = {2017-01-01},

journal = {Journal of the Marine Biological Association of the United Kingdom},

volume = {97},

number = {3},

pages = {549--560},

abstract = {In the frame of the COST ACTION 'EMBOS' (Development and implementation of a pan-European Marine Biodiversity Observatory System), coverage of intertidal macroalgae was estimated at a range of marine stations along the European coastline (Subarctic, Baltic, Atlantic, Mediterranean). Based on these data, we tested whether patterns in macroalgal diversity and distribution along European intertidal rocky shores could be explained by a set of meteo-oceanographic variables. The variables considered were salinity, sea surface temperature, photosynthetically active radiation, significant wave height and tidal range and were compiled from three different sources: remote sensing, reanalysis technique and in situ measurement. These variables were parameterized to represent average conditions (mean values), variability (standard deviation) and extreme events (minimum and maximum values). The results obtained in this study contribute to reinforce the EMBOS network approach and highlight the necessity of considering meteo-oceanographic variables in long-term assessments. The broad spatial distribution of pilot sites has allowed identification of latitudinal and longitudinal gradients manifested through species composition, diversity and dominance structure of intertidal macroalgae. These patterns follow a latitudinal gradient mainly explained by sea surface temperature, but also by photosynthetically active radiation, salinity and tidal range. Additionally, a longitudinal gradient was also detected and could be linked to wave height. Copyright © Marine Biological Association of the United Kingdom 2016.},

note = {Publisher: Cambridge University Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pavloudi_macrofaunal_2016,

title = {Macrofaunal assemblages associated with the sponge Sarcotragus foetidus Schmidt, 1862 (Porifera: Demospongiae) at the coasts of Cyprus and Greece},

author = {Christina Pavloudi and Magdalini Christodoulou and Michalis Mavidis},

url = {http://bdj.pensoft.net/articles.php?id=8210},

doi = {10.3897/BDJ.4.e8210},

year  = {2016},

date = {2016-11-01},

journal = {Biodiversity Data Journal},

volume = {4},

pages = {e8210},

abstract = {Background This paper describes a dataset of macrofaunal organisms associated with the sponge Sarcotragus foetidus Schmidt, 1862, collected by scuba diving from two sampling sites: one in Greece (North Aegean Sea) and one in Cyprus (Levantine Sea). New information This dataset includes macrofaunal taxa inhabiting the demosponge Sarcotragus foetidus and contributes to the ongoing efforts of the Ocean Biogeographic Information System (OBIS) which aims at filling the gaps in our current knowledge of the world's oceans. This is the first paper, to our knowledge, where the macrofauna associated with S. foetidus from the Levantine Basin is being recorded. In total, 90 taxa were recorded, from which 83 were identified to the species level. Eight of these species are new records for the Levantine Basin. The dataset contains 213 occurrence records, fully annotated with all required metadata. It is accessible at http://lifewww-00.her.hcmr.gr:8080/medobis/resource.do?r=organismic_assemblages_sarcotragus_foetidus_cyprus_greece},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{vasileiadou_environmental_2016,

title = {Environmental variability and heavy metal concentrations from five lagoons in the Ionian Sea (Amvrakikos Gulf, W Greece)},

author = {K Vasileiadou and C Pavloudi and I Kalantzi and E T Apostolaki and G Chatzigeorgiou and E Chatzinikolaou and E Pafilis and N Papageorgiou and L Fanini and S Konstas and N Fragopoulou and C Arvanitidis},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018621471&doi=10.3897%2fBDJ.4.e8233&partnerID=40&md5=91104fbd24f94063ee946df8c2486376},

doi = {10.3897/BDJ.4.e8233},

issn = {13142828},

year  = {2016},

date = {2016-01-01},

journal = {Biodiversity Data Journal},

volume = {4},

number = {1},

abstract = {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 status of these lagoons is crucial for the well-being of the biodiversity and the economic prosperity of the local communities. Thus, monitoring of the area is necessary to detect possible sources of disturbance and restore stability. New information The environmental variables and heavy metals concentrations, from five lagoons of Amvrakikos Gulf were measured from seasonal samplings and compared to the findings of previous studies in the area, in order to check for possible sources of disturbance. The analysis, showed that i) the values of the abiotic parameters vary with time (season), space (lagoon) and with space over time; ii) the variability of the environmental factors and enrichment in certain elements is naturally induced and no source of contamination is detected in the lagoons. © Vasileiadou K et al.},

note = {Publisher: Pensoft Publishers},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pavloudi_salinity_2016,

title = {Salinity is the major factor influencing the sediment bacterial communities in a Mediterranean lagoonal complex (Amvrakikos Gulf, Ionian Sea)},

author = {C Pavloudi and A Oulas and K Vasileiadou and E Sarropoulou and G Kotoulas and C Arvanitidis},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84955611416&doi=10.1016%2fj.margen.2016.01.005&partnerID=40&md5=a226c6872c0a3044831db4a1b5f65ca3},

doi = {10.1016/j.margen.2016.01.005},

issn = {18747787},

year  = {2016},

date = {2016-01-01},

journal = {Marine Genomics},

volume = {28},

pages = {71--81},

abstract = {Lagoons are naturally enriched habitats, with unstable environmental conditions caused by their confinement, shallow depth and state of saprobity. The frequent fluctuations of the abiotic variables cause severe changes in the abundance and distribution of biota. This relationship has been studied extensively for the macrofaunal communities, but not sufficiently so for the bacterial ones. The aim of the present study was to explore the biodiversity patterns of bacterial assemblages and to examine whether these patterns are associated with biogeographic and environmental factors. For this purpose, sediment samples were collected from five lagoons located in the Amvrakikos Gulf (Ionian Sea, Western Greece). DNA was extracted from the sediment and was further processed through 16S rRNA pyrosequencing. The results of this exploratory study imply that salinity is the environmental factor best correlated with the bacterial community pattern, which has also been suggested in similar studies but for macrofaunal community patterns. In addition, the bacterial community of the brackish lagoons is differentiated from that of the brackish-marine lagoons. The findings of this study indicate that the studied lagoons have distinct bacterial communities. © 2016 Elsevier B.V.},

note = {Publisher: Elsevier B.V.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{vasileiadou_unique_2016,

title = {Unique COI haplotypes in hediste diversicolor populations in lagoons adjoining the Ionian Sea},

author = {K Vasileiadou and C Pavloudi and E Sarropoulou and N Fragopoulou and G Kotoulas and C Arvanitidis},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84971596901&doi=10.3354%2fab00654&partnerID=40&md5=4039a8b37d89de3fef4adb17862554df},

doi = {10.3354/ab00654},

issn = {18647782},

year  = {2016},

date = {2016-01-01},

journal = {Aquatic Biology},

volume = {25},

pages = {7--15},

abstract = {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 purpose, the intraspecific diversity of H. diversicolor and the similarities among its populations in the brackish water habitats of the Eastern Mediterranean were investigated. Samples were collected from the lagoonal complex of Am - vrakikos Gulf in 2010 and 2011. Analysis showed that populations in the Amvrakikos Gulf share unique haplotypes which are distinct from the haplotypes hitherto reported, suggesting that these populations are highly isolated. This evidence partially supports Cognetti’s hypothesis. The results indicate that the genetic differentiation in the studied populations was probably caused by the complete isolation of the gulf and periodic hypoxic conditions during its formation history. The occurrence of unique haplotypes in the gulf underlines the importance of considering genetic diversity in the design of long-term biodiversity management and conservation plans. © The authors 2016.},

note = {Publisher: Inter-Research},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{varsos_optimized_2016,

title = {Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab)},

author = {C Varsos and T Patkos and A Oulas and C Pavloudi and A Gougousis and U Z Ijaz and I Filiopoulou and N Pattakos and E V Berghe and A Fernández-Guerra and S Faulwetter and E Chatzinikolaou and E Pafilis and C Bekiari and M Doerr and C Arvanitidis},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018640003&doi=10.3897%2fBDJ.4.e8357&partnerID=40&md5=6003e9caf6582fdde7f4bffec91e154f},

doi = {10.3897/BDJ.4.e8357},

issn = {13142828},

year  = {2016},

date = {2016-01-01},

journal = {Biodiversity Data Journal},

volume = {4},

number = {1},

abstract = {Background Parallel data manipulation using R has previously been addressed by members of the R community, however most of these studies produce ad hoc solutions that are not readily available to the average R user. Our targeted users, ranging from the expert ecologist/ microbiologists to computational biologists, often experience difficulties in finding optimal ways to exploit the full capacity of their computational resources. In addition, improving performance of commonly used R scripts becomes increasingly difficult especially with large datasets. Furthermore, the implementations described here can be of significant interest to expert bioinformaticians or R developers. Therefore, our goals can be summarized as: (i) description of a complete methodology for the analysis of large datasets by combining capabilities of diverse R packages, (ii) presentation of their application through a virtual R laboratory (RvLab) that makes execution of complex functions and visualization of results easy and readily available to the end-user. New information In this paper, the novelty stems from implementations of parallel methodologies which rely on the processing of data on different levels of abstraction and the availability of these processes through an integrated portal. Parallel implementation R packages, such as the pbdMPI (Programming with Big Data - Interface to MPI) package, are used to implement Single Program Multiple Data (SPMD) parallelization on primitive mathematical operations, allowing for interplay with functions of the vegan package. The dplyr and RPostgreSQL R packages are further integrated offering connections to dataframe like objects (databases) as secondary storage solutions whenever memory demands exceed available RAM resources. The RvLab is running on a PC cluster, using version 3.1.2 (2014-10-31) on a x86_64-pclinux- gnu (64-bit) platform, and offers an intuitive virtual environmet interface enabling users to perform analysis of ecological and microbial communities based on optimized vegan functions. A beta version of the RvLab is available after registration at: https:// portal.lifewatchgreece.eu/.},

note = {Publisher: Pensoft Publishers},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{sinclair_seqenv_2016,

title = {Seqenv: Linking sequences to environments through text mining},

author = {L Sinclair and U Z Ijaz and L J Jensen and M J L Coolen and C Gubry-Rangin and A Chroňáková and A Oulas and C Pavloudi and J Schnetzer and A Weimann and A Ijaz and A Eiler and C Quince and E Pafilis},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85007364069&doi=10.7717%2fpeerj.2690&partnerID=40&md5=d6fb9302c27b05c3c656dcf2f8aa9512},

doi = {10.7717/peerj.2690},

issn = {21678359},

year  = {2016},

date = {2016-01-01},

journal = {PeerJ},

volume = {2016},

number = {12},

abstract = {Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this biogeographical topic. However, these studies are often focused on specific environment types or processes leading to the production of individual, unconnected datasets. The large amounts of legacy sequence data with associated metadata that exist can be harnessed to better place the genetic information found in these surveys into a wider environmental context. Here we introduce a software program, seqenv, to carry out precisely such a task. It automatically performs similarity searches of short sequences against the “nt” nucleotide database provided by NCBI and, out of every hit, extracts-if it is available-the textual metadata field. After collecting all the isolation sources from all the search results, we run a text mining algorithm to identify and parse words that are associated with the Environmental Ontology (EnvO) controlled vocabulary. This, in turn, enables us to determine both in which environments individual sequences or taxa have previously been observed and, by weighted summation of those results, to summarize complete samples. We present two demonstrative applications of seqenv to a survey of ammonia oxidizing archaea as well as to a plankton paleome dataset from the Black Sea. These demonstrate the ability of the tool to reveal novel patterns in HTS and its utility in the fields of environmental source tracking, paleontology, and studies of microbial biogeography. To install seqenv, go to: https://github.com/xapple/seqenv. © 2016 Sinclair et al.},

note = {Publisher: PeerJ Inc.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pafilis_environments_2015,

title = {ENVIRONMENTS and EOL: Identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life},

author = {E Pafilis and S P Frankild and J Schnetzer and L Fanini and S Faulwetter and C Pavloudi and K Vasileiadou and P Leary and J Hammock and K Schulz and C S Parr and C Arvanitidis and L J Jensen},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84941662911&doi=10.1093%2fbioinformatics%2fbtv045&partnerID=40&md5=521c1035d81d477752f37d09c638a7c0},

doi = {10.1093/bioinformatics/btv045},

issn = {13674803},

year  = {2015},

date = {2015-01-01},

journal = {Bioinformatics},

volume = {31},

number = {11},

pages = {1872--1874},

abstract = {Summary: 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 developed ENVIRONMENTS, a fast dictionary- based tagger capable of identifying Environment Ontology (ENVO) terms in text. We evaluate the accuracy of the tagger on a new manually curated corpus of 600 Encyclopedia of Life (EOL) species pages. We use the tagger to associate taxa with environments by tagging EOL text content monthly, and integrate the results into the EOL to disseminate them to a broad audience of users. Availability and implementation: The software and the corpus are available under the open-source BSD and the CC-BY-NC-SA 3.0 licenses, respectively, at http://environments.hcmr.gr. © The Author 2015. Published by Oxford University Press. All rights reserved.},

note = {Publisher: Oxford University Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{faulwetter_resistance_2015,

title = {Resistance of polychaete species and trait patterns to simulated species loss in coastal lagoons},

author = {S Faulwetter and N Papageorgiou and P Koulouri and L Fanini and E Chatzinikolaou and V Markantonatou and C Pavloudi and G Chatzigeorgiou and K Keklikoglou and K Vasileiadou and A Basset and M Pinna and I Rosati and S Reizopoulou and A Nicolaidou and C Arvanitidis},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84930278022&doi=10.1016%2fj.seares.2014.09.003&partnerID=40&md5=4f1ebcb9d504ea078f66a78cf0199509},

doi = {10.1016/j.seares.2014.09.003},

issn = {13851101},

year  = {2015},

date = {2015-01-01},

journal = {Journal of Sea Research},

volume = {98},

pages = {73--82},

abstract = {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 trait patterns in six Mediterranean coastal lagoons change under computationally simulated scenarios of random species loss. Species were progressively removed from the full polychaete assemblage and the similarity between the full assemblage and the reduced matrices of both species and trait patterns was calculated. The results indicate the magnitude of changes that might follow species loss in the real world, and allow consideration of the resistance of the system's functional capacity to loss of species, expressed through the species' biological traits as an approximation to functioning. Comparisons were made between the changes in the distribution of species and of traits, as well as between the six different lagoons. While the change of species and trait patterns was strongly correlated within most lagoons, different lagoons showed distinctly different patterns. In disturbed lagoons, the dominance of one or few species was the major driver for the observed patterns and the loss of these species caused extreme changes. Less disturbed lagoons were less susceptible to extreme changes and had a greater resistance towards species loss. Species richness appears to be less important for the ability of the lagoons to buffer changes, instead the initial composition of the assemblage and the identity of the lost species determine the response of the system and our ability to predict changes of the assemblage's functional potential. © 2014 Elsevier B.V.},

note = {Publisher: Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{oulas_metagenomics_2015,

title = {Metagenomics: Tools and insights for analyzing next-generation sequencing data derived from biodiversity studies},

author = {A Oulas and C Pavloudi and P Polymenakou and G A Pavlopoulos and N Papanikolaou and G Kotoulas and C Arvanitidis and I Iliopoulos},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84981483022&doi=10.4137%2fBBI.S12462&partnerID=40&md5=c1dbc4e466d691d4a86eecd6ba7d7a08},

doi = {10.4137/BBI.S12462},

issn = {11779322},

year  = {2015},

date = {2015-01-01},

journal = {Bioinformatics and Biology Insights},

volume = {9},

pages = {75--88},

abstract = {Advances in next-generation sequencing (NGS) have allowed significant breakthroughs in microbial ecology studies. This has led to the rapid expansion of research in the field and the establishment of "metagenomics", often defined as the analysis of DNA from microbial communities in environmental samples without prior need for culturing. Many metagenomics statistical/computational tools and databases have been developed in order to allow the exploitation of the huge influx of data. In this review article, we provide an overview of the sequencing technologies and how they are uniquely suited to various types of metagenomic studies. We focus on the currently available bioinformatics techniques, tools, and methodologies for performing each individual step of a typical metagenomic dataset analysis. We also provide future trends in the field with respect to tools and technologies currently under development. Moreover, we discuss data management, distribution, and integration tools that are capable of performing comparative metagenomic analyses of multiple datasets using well-established databases, as well as commonly used annotation standards. © the authors.},

note = {Publisher: Libertas Academica Ltd.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{hummel_comparison_2015,

title = {A comparison of the degree of implementation of marine biodiversity indicators by European countries in relation to the Marine Strategy Framework Directive (MSFD)},

author = {H Hummel and M Frost and J A Juanes and J Kochmann and C F C P Bolde and F Aneiros and F Vandenbosch and J N Franco and B Echavarri and X Guinda and A Puente and C Fernández and C Galván and M Merino and E Ramos and P Fernández and V Pitacco and M Alberte and D Wojcik and M Grabowska and M Jahnke and F Crocetta and L Carugati and S Scorrano and S Fraschetti and P P García and J A Sanabria Fernández and A Poromov and A Iurchenko and A Isachenko and A Chava and C Pavloudi and F Bordeyne and S F Andersen and E G T Eronat and T Cakmak and P Louizidou and J Rico and S Ruci and D Corta Diego and S Mendez and M Rousou and L De Clippele and A Eriksson and W Van Zanten and A Diamant and V K F De Matos},

doi = {10.1017/S0025315415000235},

issn = {14697769 00253154},

year  = {2015},

date = {2015-01-01},

journal = {Journal of the Marine Biological Association of the United Kingdom},

volume = {95},

number = {8},

pages = {1519--1531},

abstract = {The degree of development and operability of the indicators for the Marine Strategy Framework Directive (MSFD) using Descriptor 1 (D1) Biological Diversity was assessed. To this end, an overview of the relevance and degree of operability of the underlying parameters across 20 European countries was compiled by analysing national directives, legislation, regulations, and publicly available reports. Marked differences were found between countries in the degree of ecological relevance as well as in the degree of implementation and operability of the parameters chosen to indicate biological diversity. The best scoring EU countries were France, Germany, Greece and Spain, while the worst scoring countries were Italy and Slovenia. No country achieved maximum scores for the implementation of MSFD D1. The non-EU countries Norway and Turkey score as highly as the top-scoring EU countries. On the positive side, the chosen parameters for D1 indicators were generally identified as being an ecologically relevant reflection of Biological Diversity. On the negative side however, less than half of the chosen parameters are currently operational. It appears that at a pan-European level, no consistent and harmonized approach currently exists for the description and assessment of marine biological diversity. The implementation of the MSFD Descriptor 1 for Europe as a whole can therefore at best be marked as moderately successful.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{faulwetter_polytraits_2014,

title = {Polytraits: A database on biological traits of marine polychaetes},

author = {S Faulwetter and V Markantonatou and C Pavloudi and N Papageorgiou and K Keklikoglou and E Chatzinikolaou and E Pafilis and G Chatzigeorgiou and K Vasileiadou and T Dailianis and L Fanini and P Koulouri and C Arvanitidis},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018193846&doi=10.3897%2fBDJ.2.e1024&partnerID=40&md5=621b076567d09921bf9b5146a7f8844e},

doi = {10.3897/BDJ.2.e1024},

issn = {13142828},

year  = {2014},

date = {2014-01-01},

journal = {Biodiversity Data Journal},

volume = {2},

number = {1},

abstract = {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 the literature is however a laborious and time-consuming process, and gaps of knowledge and restricted availability of literature are a common problem. Trait data are not yet readily being shared by research communities, and even if they are, a lack of trait data repositories and standards for data formats leads to the publication of trait information in forms which cannot be processed by computers. This paper describes Polytraits (http:// polytraits.lifewatchgreece.eu), a database on biological traits of marine polychaetes (bristle worms, Polychaeta: Annelida). At present, the database contains almost 20,000 records on morphological, behavioural and reproductive characteristics of more than 1,000 marine polychaete species, all referenced by literature sources. All data can be freely accessed through the project website in different ways and formats, both human-readable and machine-readable, and have been submitted to the Encyclopedia of Life for archival and integration with trait information from other sources. © Faulwetter S et al.},

note = {Publisher: Pensoft Publishers},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pafilis_species_2013,

title = {The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text},

author = {E Pafilis and S P Frankild and L Fanini and S Faulwetter and C Pavloudi and A Vasileiadou and C Arvanitidis and L J Jensen},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84879162734&doi=10.1371%2fjournal.pone.0065390&partnerID=40&md5=fee446181731231a273637d3d09c5002},

doi = {10.1371/journal.pone.0065390},

issn = {19326203},

year  = {2013},

date = {2013-01-01},

journal = {PLoS ONE},

volume = {8},

number = {6},

abstract = {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 here use to identify names of species and other taxa in text. The tool, SPECIES, is more than an order of magnitude faster and as accurate as existing tools. The precision and recall was assessed both on an existing gold-standard corpus and on a new corpus of 800 abstracts, which were manually annotated after the development of the tool. The corpus comprises abstracts from journals selected to represent many taxonomic groups, which gives insights into which types of organism names are hard to detect and which are easy. Finally, we have tagged organism names in the entire Medline database and developed a web resource, ORGANISMS, that makes the results accessible to the broad community of biologists. The SPECIES software is open source and can be downloaded from http://species.jensenlab.org along with dictionary files and the manually annotated gold-standard corpus. The ORGANISMS web resource can be found at http://organisms.jensenlab.org. © 2013 Pafilis et al.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{arvanitidis_engaging_2011,

title = {Engaging the broader community in biodiversity research: The concept of the COMBER pilot project for divers in vibrant},

author = {C Arvanitidis and S Faulwetter and G Chatzigeorgiou and L Penev and O Bánki and T Dailianis and E Pafilis and M Kouratoras and E Chatzinikolaou and L Fanini and A Vasileiadou and C Pavloudi and P Vavilis and P Koulouri and C Dounas},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84856457337&doi=10.3897%2fzookeys.150.2149&partnerID=40&md5=48d27ff65c2def3588c3e0f3a8b72a92},

doi = {10.3897/zookeys.150.2149},

issn = {13132989},

year  = {2011},

date = {2011-01-01},

journal = {ZooKeys},

volume = {150},

pages = {211--229},

abstract = {This paper discusses the design and implementation of a citizen science pilot project, COMBER (Citizens' Network for the Observation of Marine Biodiv ERsity, http://www.comber.hcmr.gr, which has been initiated under the Vi BRANT EU e-infrastructure. It is designed and implemented for divers and snorkelers who are interested in participating in marine biodiversity citizen science projects. It shows the necessity of engaging the broader community in the marine biodiversity monitoring and research projects, networks and initiatives. It analyses the stakeholders, the industry and the relevant markets involved in diving activities and their potential to sustain these activities. The principles, including data policy and rewards for the participating divers through their own data, upon which this project is based are thoroughly discussed. The results of the users analysis and lessons learned so far are presented. Future plans include promotion, links with citizen science web developments, data publishing tools, and development of new scientific hypotheses to be tested by the data collected so far.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}