Melanthia (Melina) Stavroulaki

@article{pagnier_long-term_2025,

title = {A long-term ecological research dataset from the marine genetic monitoring programme ARMS-MBON 2020-2021},

author = {Justine Pagnier and Louise Allcock and Ibon Cancio and Eva Chatzinikolaou and Giorgos Chatzigeorgiou and Nathan Chrismas and Federica Costantini and Thanos Dailianis and Klaas Deneudt and Oihane Díaz De Cerio and Markos Digenis and Katrina Exter and Vasilis Gerovasileiou and Jose González Fernández and Laura Kauppi and Kleoniki Keklikoglou and Jon Bent Kristoffersen and Rune Lagaisse and Borut Mavrič and Jonas Mortelmans and Estefania Paredes and Christina Pavloudi and Alessandro Piazza and Anne Marie Power and Andreja Ramšak and Ioulia Santi and Jostein Solbakken and Melanthia Stavroulaki and Peter Stæhr and Javier Tajadura and Jesus Souza Troncoso and Katerina Vasileiadou and Emmanouela Vernadou and Matthias Obst},

url = {https://bdj.pensoft.net/article/148981/

/wp-content/uploads/2025/12/2025-Pagnier-BDJ-74.pdf},

doi = {10.3897/BDJ.13.e148981},

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

year  = {2025},

date = {2025-12-08},

urldate = {2025-11-01},

journal = {Biodiversity Data Journal},

volume = {13},

pages = {e148981},

abstract = {Continuing the international efforts of the ARMS Marine Biodiversity Observation Network (ARMS-MBON), we present data from the second sampling campaign, coming from 56 Autonomous Reef Monitoring Structures (ARMS) deployed in 2020 and 2021 along European coasts under the European Marine Omics Biodiversity Observation Network (EMO BON). The dataset includes information on sampling locations and conditions, sample archiving and quality reports of collected samples. Data and metadata are openly accessible and can be downloaded from the associated GitHub repository. Sequence data can be accessed via the European Nucleotide Archive (ENA) through the corresponding accession numbers. Images of ARMS plates are stored on PlutoF and can be downloaded through links provided in this paper. Sequence data were processed and explored with the PEMA pipeline, resulting in 17,194, 7,235 and 5,261 unique ASVs/OTUs for COI, 18S and ITS, respectively. In this dataset, ARMS revealed the presence of over 61 eukaryotic phyla, aligning with our previous sampling campaign. Amongst these phyla, 35 had sequences identified to the species level. With this dataset and its associated paper, we provide a standardised resource for marine biodiversity monitoring and scientific analyses of benthic biodiversity. The presented data product supports future studies on the status and changes in species composition, distribution and genetic diversity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{holm_first_2025,

title = {First island-wide, single-day soil collection study on Crete reveals environmental drivers of microbial diversity},

author = {Johanna B Holm and Savvas Paragkamian and Mike Humphreys and Apaala Chatterjee and Stephanie Yarwood and Josh Gaimaro and Melanthia Stavroulaki and Dimitris Tsaparis and Manolis Plaitis and Panagiotis Kasapidis and Stelios Darivianakis and Georgios Kotoulas and Antonios Magoulas and Anastasis Oulas and Zacharias Kyrpiotakis and Pavlos Pavlidis and Petra Ten Hoopen and Guy Cochrane and Wiebe H C F Kooistra and Jason R Schriml and Bronwen E Schriml and Ilias Lagkouvardos and Panos Gkorezis and Neil Davies and Christine Laney and Lee Stanish and Granger Sutton and Scott Tighe and Ilene Karsch Mizrachi and Donovan Parks and Pelin Yilmaz and Chelsea Carey and Pier Buttigieg and Philip Goldstein and Evangelos Pafilis and Lynn M Schriml},

url = {https://environmentalmicrobiome.biomedcentral.com/articles/10.1186/s40793-025-00752-z

/wp-content/uploads/2025/09/2025-Holm-Paragkamian-EnvMicro-46.pdf},

doi = {10.1186/s40793-025-00752-z},

issn = {2524-6372},

year  = {2025},

date = {2025-09-04},

urldate = {2025-09-08},

journal = {Environmental Microbiome},

volume = {20},

number = {1},

pages = {94},

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{bravakos_genomic_2021,

title = {Genomic adaptation of Pseudomonas strains to acidity and antibiotics in hydrothermal vents at Kolumbo submarine volcano, Greece},

author = {Panos Bravakos and Manolis Mandalakis and Paraskevi Nomikou and Thekla I Anastasiou and Jon Bent Kristoffersen and Melanthia Stavroulaki and Stephanos Kilias and Georgios Kotoulas and Antonios Magoulas and Paraskevi N Polymenakou},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/02/2021-Bravakos-SciReport-4.pdf

http://www.nature.com/articles/s41598-020-79359-y},

doi = {10.1038/s41598-020-79359-y},

issn = {2045-2322},

year  = {2021},

date = {2021-01-01},

urldate = {2021-02-02},

journal = {Sci Rep},

volume = {11},

number = {1},

pages = {1336},

abstract = {Abstract 

 

 Although the rise of antibiotic and multidrug resistant bacteria is one of the biggest current threats to human health, our understanding of the mechanisms involved in antibiotic resistance selection remains scarce. We performed whole genome sequencing of 21 

 Pseudomonas 

 strains, previously isolated from an active submarine volcano of Greece, the Kolumbo volcano. Our goal was to identify the genetic basis of the enhanced co-tolerance to antibiotics and acidity of these 

 Pseudomonas 

 strains. Pangenome analysis identified 10,908 Gene Clusters (GCs). It revealed that the numbers of phage-related GCs and sigma factors, which both provide the mechanisms of adaptation to environmental stressors, were much higher in the high tolerant 

 Pseudomonas 

 strains compared to the rest ones. All identified GCs of these strains were associated with antimicrobial and multidrug resistance. The present study provides strong evidence that the CO 

 2 

 -rich seawater of the volcano associated with low pH might be a reservoir of microorganisms carrying multidrug efflux-mediated systems and pumps. We, therefore, suggest further studies of other extreme environments (or ecosystems) and their associated physicochemical parameters (or factors) in the rise of antibiotic resistance.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{polymenakou_high_2020,

title = {High genetic diversity and variability of microbial communities in near-surface atmosphere of Crete island, Greece},

author = {Paraskevi N Polymenakou and Manolis Mandalakis and Michalis Macheras and Anastasis Oulas and Jon Bent Kristoffersen and Christos A Christakis and Vasso Terzoglou and Melanthia Stavroulaki},

url = {http://link.springer.com/10.1007/s10453-020-09636-w},

doi = {10.1007/s10453-020-09636-w},

issn = {0393-5965, 1573-3025},

year  = {2020},

date = {2020-09-01},

urldate = {2020-08-31},

journal = {Aerobiologia},

volume = {36},

number = {3},

pages = {341--353},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{tsakogiannis_importance_2020,

title = {The Importance of Genomics for Deciphering the Invasion Success of the Seagrass Halophila stipulacea in the Changing Mediterranean Sea},

author = {Alexandros Tsakogiannis and Tereza Manousaki and Vasileia Anagnostopoulou and Melanthia Stavroulaki and Eugenia T Apostolaki},

url = {https://www.mdpi.com/1424-2818/12/7/263},

doi = {10.3390/d12070263},

issn = {1424-2818},

year  = {2020},

date = {2020-01-01},

journal = {Diversity},

volume = {12},

number = {7},

abstract = {The Mediterranean Sea is subject to pressures from biological invasion due to coastal anthropic activities and global warming, which potentially modify its biogeography. The Red Sea tropical seagrass Halophila stipulacea entered the Eastern Mediterranean over a century ago, and its occurrence is expanding towards the northwest. Here, we highlight the importance of genomics for deciphering the evolutionary and ecological procedures taking place during the invasion process of H. stipulacea and review the relatively sparse genetic information available for the species to date. We report the first draft whole-genome sequencing of a H. stipulacea individual from Greece, based on Illumina Sequencing technology. A comparison of the Internal Transcribed Spacer (ITS) regions revealed a high divergence of the herein sequenced individual compared to Mediterranean populations sequenced two decades ago, rendering further questions on the evolutionary processes taking place during H. stipulacea adaptation in the invaded Mediterranean Sea. Our work sets the baseline for a future analysis of the invasion genomic of the focal species.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}