Jon Bent Kristoffersen

@article{di_costanzo_high-quality_2025,

title = {High-quality genome assembly and annotation of Thalassiosira rotula (synonym of Thalassiosira gravida)},

author = {F Di Costanzo and M Di Marsico and I Orefice and J B Kristoffersen and P Kasapidis and T Chaumier and L Ambrosino and M Miralto and R Aiese Cigliano and F Verret and L Tirichine and M Trindade and L Van Zyl and V Di Dato and G Romano},

url = {https://www.nature.com/articles/s41597-025-04634-4

/wp-content/uploads/2025/03/2025-Costanzo-SciData-12.pdf},

doi = {10.1038/s41597-025-04634-4},

issn = {2052-4463},

year  = {2025},

date = {2025-03-14},

urldate = {2025-03-14},

journal = {Scientific Data},

volume = {12},

number = {1},

pages = {310},

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{kitsoulis_near-chromosome_2023,

title = {Near-chromosome level genome assembly of devil firefish, Pterois miles},

author = {Christos V Kitsoulis and Vasileios Papadogiannis and Jon B Kristoffersen and Elisavet Kaitetzidou and Aspasia Sterioti and Costas S Tsigenopoulos and Tereza Manousaki},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/08/2023-Kitsoulis-PeerCJ-43.pdf

https://peercommunityjournal.org/articles/10.24072/pcjournal.295/},

doi = {10.24072/pcjournal.295},

issn = {2804-3871},

year  = {2023},

date = {2023-08-29},

urldate = {2023-08-31},

journal = {Peer Community Journal},

volume = {3},

pages = {e64},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{polymenakou_taxonomic_2023,

title = {Taxonomic diversity of microbial communities in sub-seafloor hydrothermal sediments of the active Santorini-Kolumbo volcanic field},

author = {Paraskevi N Polymenakou and Paraskevi Nomikou and Mark Hannington and Sven Petersen and Stephanos P Kilias and Thekla I Anastasiou and Vasiliki Papadimitriou and Eleutheria Zaka and Jon Bent Kristoffersen and Danai Lampridou and Sandra Wind and Verena Heinath and Sabine Lange and Antonios Magoulas},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/07/2023-Polymenakou-FrontMicro-35.pdf

https://www.frontiersin.org/articles/10.3389/fmicb.2023.1188544/full},

doi = {10.3389/fmicb.2023.1188544},

issn = {1664-302X},

year  = {2023},

date = {2023-07-06},

urldate = {2023-07-06},

journal = {Frontiers in Microbiology},

volume = {14},

pages = {1188544},

abstract = {Introduction 

 Active hydrothermal vents of volcanic origin provide a remarkable manifestation of life on Earth under extreme conditions, which may have consequences for our understanding of habitability on other terrestrial bodies as well. 

 

 

 Methods 

 Here, we performed for the first time Illumina sequencing of bacterial and archaeal communities on sub-seafloor samples collected from the Santorini-Kolumbo volcanic field. A total of 19 (3-m long) gravity corers were collected and processed for microbial community analysis. 

 

 

 Results 

 

 From a total of 6,46,671 produced V4 sequences for all samples, a total of 10,496 different Operational Taxonomic Units (OTUs) were identified that were assigned to 40 bacterial and 9 archaeal phyla and 14 candidate divisions. On average, the most abundant phyla in all samples were Chloroflexi (Chloroflexota) (24.62%), followed by Proteobacteria (Pseudomonadota) (11.29%), Firmicutes (Bacillota) (10.73%), Crenarchaeota (Thermoproteota) (8.55%), and Acidobacteria (Acidobacteriota) (8.07%). At the genus level, a total of 286 known genera and candidate genera were mostly dominated by members of 

 Bacillus, Thermoflexus, Desulfatiglans, Pseudoalteromonas 

 , and 

 Pseudomonas 

 . 

 

 

 

 Discussion 

 In most of the stations, the Chao1 values at the deeper layers were comparable to the surface sediment samples denoting the high diversity in the subsurface of these ecosystems. Heatmap analysis based on the 100 most abundant OTUs, grouped the sampling stations according to their geographical location, placing together the two hottest stations (up to 99°C). This result indicates that this specific area within the active Kolumbo crater create a distinct niche, where microorganisms with adaptation strategies to withstand heat stresses can thrive, such as the endospore-forming Firmicutes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{papadogiannis_chromosome_2023b,

title = {Chromosome genome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution},

author = {Vasileios Papadogiannis and Tereza Manousaki and Orestis Nousias and Alexandros Tsakogiannis and Jon B Kristoffersen and Constantinos C Mylonas and Costas Batargias and Dimitrios Chatziplis and Costas S Tsigenopoulos},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/07/2023-Papadogiannis-FrontGen-34.pdf

https://www.frontiersin.org/articles/10.3389/fgene.2022.1081760/full},

doi = {10.3389/fgene.2022.1081760},

issn = {1664-8021},

year  = {2023},

date = {2023-07-03},

urldate = {2023-07-03},

journal = {Frontiers in Genetics},

volume = {13},

pages = {1081760},

abstract = {The meagre, 

 Argyrosomus regius 

 , has recently become a species of increasing economic interest for the Mediterranean aquaculture and there is ongoing work to boost production efficiency through selective breeding. Access to the complete genomic sequence will provide an essential resource for studying quantitative trait-associated loci and exploring the genetic diversity of different wild populations and aquaculture stocks in more detail. Here, we present the first complete genome for 

 A. regius , produced through a combination of long and short read technologies and an efficient in-house developed pipeline for assembly and polishing. Scaffolding using previous linkage map data allowed us to reconstruct a chromosome level assembly with high completeness, complemented with gene annotation and repeat masking. The 696 Mb long assembly has an N50 = 27.87 Mb and an L50 = 12, with 92.85% of its length placed in 24 chromosomes. We use this new resource to study the evolution of the meagre genome and other Sciaenids, 

 via 

 a comparative analysis of 25 high-quality teleost genomes. Combining a rigorous investigation of gene duplications with base-wise conservation analysis, we identify candidate loci related to immune, fat metabolism and growth adaptations in the meagre. Following phylogenomic reconstruction, we show highly conserved synteny within Sciaenidae. In contrast, we report rapidly evolving syntenic rearrangements and gene copy changes in the sex-related 

 dmrt1 

 neighbourhood in meagre and other members of the family. These novel genomic datasets and findings will add important new tools for aquaculture studies and greatly facilitate husbandry and breeding work in the species.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{papadogiannis_chromosome_2023,

title = {Chromosome genome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution},

author = {Vasileios Papadogiannis and Tereza Manousaki and Orestis Nousias and Alexandros Tsakogiannis and Jon B Kristoffersen and Constantinos C Mylonas and Costas Batargias and Dimitrios Chatziplis and Costas S Tsigenopoulos},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/01/2023-Papadogiannis-FinGenetics-4.pdf

https://www.frontiersin.org/articles/10.3389/fgene.2022.1081760/full},

doi = {10.3389/fgene.2022.1081760},

issn = {1664-8021},

year  = {2023},

date = {2023-01-10},

urldate = {2023-01-11},

journal = {Frontiers in Genetics},

volume = {13},

pages = {1081760},

abstract = {The meagre, 

 Argyrosomus regius 

 , has recently become a species of increasing economic interest for the Mediterranean aquaculture and there is ongoing work to boost production efficiency through selective breeding. Access to the complete genomic sequence will provide an essential resource for studying quantitative trait-associated loci and exploring the genetic diversity of different wild populations and aquaculture stocks in more detail. Here, we present the first complete genome for 

 A. regius , produced through a combination of long and short read technologies and an efficient in-house developed pipeline for assembly and polishing. Scaffolding using previous linkage map data allowed us to reconstruct a chromosome level assembly with high completeness, complemented with gene annotation and repeat masking. The 696 Mb long assembly has an N50 = 27.87 Mb and an L50 = 12, with 92.85% of its length placed in 24 chromosomes. We use this new resource to study the evolution of the meagre genome and other Sciaenids, 

 via 

 a comparative analysis of 25 high-quality teleost genomes. Combining a rigorous investigation of gene duplications with base-wise conservation analysis, we identify candidate loci related to immune, fat metabolism and growth adaptations in the meagre. Following phylogenomic reconstruction, we show highly conserved synteny within Sciaenidae. In contrast, we report rapidly evolving syntenic rearrangements and gene copy changes in the sex-related 

 dmrt1 

 neighbourhood in meagre and other members of the family. These novel genomic datasets and findings will add important new tools for aquaculture studies and greatly facilitate husbandry and breeding work in the species.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gabed_what_2022,

title = {What Was Old Is New Again: The Pennate Diatom Haslea ostrearia (Gaillon) Simonsen in the Multi-Omic Age},

author = {Noujoud Gabed and Frédéric Verret and Aurélie Peticca and Igor Kryvoruchko and Romain Gastineau and Orlane Bosson and Julie Séveno and Olga Davidovich and Nikolai Davidovich and Andrzej Witkowski and Jon Bent Kristoffersen and Amel Benali and Efstathia Ioannou and Aikaterini Koutsaviti and Vassilios Roussis and Hélène Gâteau and Suliya Phimmaha and Vincent Leignel and Myriam Badawi and Feriel Khiar and Nellie Francezon and Mostefa Fodil and Pamela Pasetto and Jean-Luc Mouget},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Gabed-N-Mar-Drugs-33.pdf

https://www.mdpi.com/1660-3397/20/4/234},

doi = {10.3390/md20040234},

issn = {1660-3397},

year  = {2022},

date = {2022-01-01},

urldate = {2022-05-09},

journal = {Marine Drugs},

volume = {20},

number = {4},

pages = {234},

abstract = {The marine pennate diatom Haslea ostrearia has long been known for its characteristic blue pigment marennine, which is responsible for the greening of invertebrate gills, a natural phenomenon of great importance for the oyster industry. For two centuries, this taxon was considered unique; however, the recent description of a new blue Haslea species revealed unsuspected biodiversity. Marennine-like pigments are natural blue dyes that display various biological activities—e.g., antibacterial, antioxidant and antiproliferative—with a great potential for applications in the food, feed, cosmetic and health industries. Regarding fundamental prospects, researchers use model organisms as standards to study cellular and physiological processes in other organisms, and there is a growing and crucial need for more, new and unconventional model organisms to better correspond to the diversity of the tree of life. The present work, thus, advocates for establishing H. ostrearia as a new model organism by presenting its pros and cons—i.e., the interesting aspects of this peculiar diatom (representative of benthic-epiphytic phytoplankton, with original behavior and chemodiversity, controlled sexual reproduction, fundamental and applied-oriented importance, reference genome, and transcriptome will soon be available); it will also present the difficulties encountered before this becomes a reality as it is for other diatom models (the genetics of the species in its infancy, the transformation feasibility to be explored, the routine methods needed to cryopreserve strains of interest).},

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{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{danis_genome_2021,

title = {Genome Analysis of Lagocephalus sceleratus: Unraveling the Genomic Landscape of a Successful Invader},

author = {Theodoros Danis and Vasileios Papadogiannis and Alexandros Tsakogiannis and Jon B Kristoffersen and Daniel Golani and Dimitris Tsaparis and Aspasia Sterioti and Panagiotis Kasapidis and Georgios Kotoulas and Antonios Magoulas and Costas S Tsigenopoulos and Tereza Manousaki},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/01/2021-Danis-FrontGen-84.pdf

https://www.frontiersin.org/article/10.3389/fgene.2021.790850},

doi = {10.3389/fgene.2021.790850},

issn = {1664-8021},

year  = {2021},

date = {2021-01-01},

urldate = {2022-01-12},

journal = {Frontiers in Genetics},

volume = {12},

pages = {2481},

abstract = {The Tetraodontidae family encompasses several species which attract scientific interest in terms of their ecology and evolution. The silver-cheeked toadfish (Lagocephalus sceleratus) is a well-known “invasive sprinter” that has invaded and spread, in less than a decade, throughout the Eastern and part of the Western Mediterranean Sea from the Red Sea through the Suez Canal. In this study, we built and analysed the first near-chromosome level genome assembly of L. sceleratus and explored its evolutionary landscape. Through a phylogenomic analysis, we positioned L. sceleratus closer to T. nigroviridis, compared to other members of the family, while gene family evolution analysis revealed that genes associated with the immune response have experienced rapid expansion, providing a genetic basis for studying how L. sceleratus is able to achieve highly successful colonisation. Moreover, we found that voltage-gated sodium channel (NaV 1.4) mutations previously connected to tetrodotoxin resistance in other pufferfishes are not found in L. sceleratus, highlighting the complex evolution of this trait. The high-quality genome assembly built here is expected to set the ground for future studies on the species biology.},

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{christakis_microbial_2018,

title = {Microbial community differentiation between active and inactive sulfide chimneys of the Kolumbo submarine volcano, Hellenic Volcanic Arc},

author = {C A Christakis and P N Polymenakou and M Mandalakis and P Nomikou and J B Kristoffersen and D Lampridou and G Kotoulas and A Magoulas},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85032008505&doi=10.1007%2fs00792-017-0971-x&partnerID=40&md5=2258d2985b658c3f415f37d92d684597},

doi = {10.1007/s00792-017-0971-x},

issn = {14310651},

year  = {2018},

date = {2018-01-01},

journal = {Extremophiles},

volume = {22},

number = {1},

pages = {13--27},

abstract = {Over the last decades, there has been growing interest about the ecological role of hydrothermal sulfide chimneys, their microbial diversity and associated biotechnological potential. Here, we performed dual-index Illumina sequencing of bacterial and archaeal communities on active and inactive sulfide chimneys collected from the Kolumbo hydrothermal field, situated on a geodynamic convergent setting. A total of 15,701 OTUs (operational taxonomic units) were assigned to 56 bacterial and 3 archaeal phyla, 133 bacterial and 16 archaeal classes. Active chimney communities were dominated by OTUs related to thermophilic members of Epsilonproteobacteria, Aquificae and Deltaproteobacteria. Inactive chimney communities were dominated by an OTU closely related to the archaeon Nitrosopumilus sp., and by members of Gammaproteobacteria, Deltaproteobacteria, Planctomycetes and Bacteroidetes. These lineages are closely related to phylotypes typically involved in iron, sulfur, nitrogen, hydrogen and methane cycling. Overall, the inactive sulfide chimneys presented highly diverse and uniform microbial communities, in contrast to the active chimney communities, which were dominated by chemolithoautotrophic and thermophilic lineages. This study represents one of the most comprehensive investigations of microbial diversity in submarine chimneys and elucidates how the dissipation of hydrothermal activity affects the structure of microbial consortia in these extreme ecological niches. © 2017, Springer Japan KK.},

note = {Publisher: Springer Tokyo},

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{remmas_dominance_2017,

title = {Dominance of candidate Saccharibacteria in a membrane bioreactor treating medium age landfill leachate: Effects of organic load on microbial communities, hydrolytic potential and extracellular polymeric substances},

author = {N Remmas and P Melidis and I Zerva and J B Kristoffersen and S Nikolaki and G Tsiamis and S Ntougias},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85017698743&doi=10.1016%2Fj.biortech.2017.04.019&partnerID=40&md5=0b208ee873eee62193ad01e8a854a12f},

doi = {10.1016/j.biortech.2017.04.019},

issn = {09608524},

year  = {2017},

date = {2017-01-01},

journal = {Bioresource Technology},

volume = {238},

pages = {48--56},

abstract = {A membrane bioreactor (MBR), accomplishing high nitrogen removal efficiencies, was evaluated under various landfill leachate concentrations (50, 75 and 100% v/v). Proteinous and carbohydrate extracellular polymeric substances (EPS) and soluble microbial product (SMP) were strongly correlated (p textbackslashtextless 0.01) with organic load, salinity and NH4+-N. Exceptionally high β-glucosidase activities (6700–10,100 U g−1) were determined during MBR operation with 50% v/v leachate, as a result of the low organic carbon availability that extendedly induced β-glucosidases to breakdown the least biodegradable organic fraction. Illumina sequencing revealed that candidate Saccharibacteria were dominant, independently of the leachate concentration applied, whereas other microbiota (21.2% of total reads) disappeared when undiluted leachate was used. Fungal taxa shifted from a Saccharomyces- to a newly-described Cryptomycota-based community with increasing leachate concentration. Indeed, this is the first report on the dominance of candidate Saccharibacteria and on the examination of their metabolic behavior in a bioreactor treating real wastewater. © 2017 Elsevier Ltd},

note = {Publisher: Elsevier Ltd},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bobrova_metagenomic_2016,

title = {Metagenomic 16s rRNA investigation of microbial communities in the Black Sea estuaries in South-West of Ukraine},

author = {O Bobrova and J B Kristoffersen and A Oulas and V Ivanytsia},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84976871399&doi=10.18388%2Fabp.2015_1145&partnerID=40&md5=ede0e6981e07f9f419640e4b2c605d1e},

doi = {10.18388/abp.2015_1145},

issn = {0001527X},

year  = {2016},

date = {2016-01-01},

journal = {Acta Biochimica Polonica},

volume = {63},

number = {2},

pages = {315--319},

abstract = {The Black Sea estuaries represent interfaces of the sea and river environments. Microorganisms that inhabit estuarine water play an integral role in all biochemical processes that occur there and form unique ecosystems. There are many estuaries located in the Southern-Western part of Ukraine and some of them are already separated from the sea. The aim of this research was to determine the composition of microbial communities in the Khadzhibey, Dniester and Sukhyi estuaries by metagenomic 16S rDNA analysis. This study is the first complex analysis of estuarine microbiota based on isolation of total DNA from a biome that was further subjected to sequencing. DNA was extracted from water samples and sequenced on the Illumina Miseq platform using primers to the V4 variable region of the 16S rRNA gene. Computer analysis of the obtained raw sequences was done with QIIME (Quantitative Insights Into Microbial Ecology) software. As the outcome, 57970 nucleotide sequences were retrieved. Bioinformatic analysis of bacterial community in the studied samples demonstrated a high taxonomic diversity of Prokaryotes at above genus level. It was shown that majority of 16S rDNA bacterial sequences detected in the estuarine samples belonged to phyla Cyanobacteria, Proteobacteria, Bacteroidetes, Actinobacteria, Verrucomicrobia, Planctomycetes. The Khadhzibey estuary was dominated by the Proteobacteria phylum, while Dniester and Sukhyi estuaries were characterized by dominance of Cyanobacteria. The differences in bacterial populations between the Khadzhibey, Dniester and Sukhyi estuaries were demonstrated through the Beta-diversity analysis. It showed that the Khadzhibey estuary's microbial community significantly varies from the Sukhyi and Dniester estuaries. The majority of identified bacterial species is known as typical inhabitants of marine environments, however, for 2.5% of microbial population members in the studied estuaries no relatives were determined.},

note = {Publisher: Polskie Towarzystwo Biochemiczne},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{tsagkarakou_population_2012,

title = {Population genetic structure and secondary endosymbionts of Q Bemisia tabaci (Hemiptera: Aleyrodidae) from Greece},

author = {A Tsagkarakou and L Mouton and J B Kristoffersen and E Dokianakis and M Grispou and K Bourtzis},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84861087020&doi=10.1017%2FS0007485311000757&partnerID=40&md5=6713cf44e68560a7cea1758c051c0ec0},

doi = {10.1017/S0007485311000757},

issn = {00074853},

year  = {2012},

date = {2012-01-01},

journal = {Bulletin of Entomological Research},

volume = {102},

number = {3},

pages = {353--365},

abstract = {We investigated the molecular diversity of the major agricultural pest Bemisia tabaci and of its associated secondary endosymbionts in Greece. Analyzing mitochondrial DNA, we found that the Q1 (=Q west) is predominant. We used eight microsatellite polymorphic markers to study the genetic structure of 37 populations from mainland and insular Greece, collected on different host species from outdoor and protected crops as well as from non-cultivated plants. In some cases, gene flow was found to be low even between populations separated by just a few kilometres. Bayesian analysis identified two main genetic groups, the first encompassing populations from south Crete and the second composed of populations from north Crete, two other Aegean islands and mainland Greece. Genetic differentiation was not correlated with different host plant species or habitat, or greenhouse versus open environment populations. Gene flow significantly decreased with geographic distance, but no isolation by distance existed when only the samples from mainland Greece or only the samples from Crete were considered. The secondary symbionts Wolbachia and Hamiltonella were present at high frequencies while Arsenophonus, Cardinium and Rickettsia were absent from Greek populations. Multilocus sequence typing of Wolbachia identified two Wolbachia strains. These two strains were found together in most of the populations studied but never in the same host individual. Their role on the observed population structure is discussed. © 2012 Cambridge University Press.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kristoffersen_distribution_2009,

title = {Distribution, growth, and population genetics of the glacier lanternfish (Benthosema glaciale) in Norwegian waters: Contrasting patterns in fjords and the ocean},

author = {J B Kristoffersen and A G V Salvanes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77649174678&doi=10.1080%2F17451000903042479&partnerID=40&md5=0c0a66144f69e6e7266640309ee5ff07},

doi = {10.1080/17451000903042479},

issn = {17451000},

year  = {2009},

date = {2009-01-01},

journal = {Marine Biology Research},

volume = {5},

number = {6},

pages = {596--604},

abstract = {The mesopelagic fish Benthosema glaciale was found to be widely distributed in the Norwegian Sea and several west Norwegian fjords, but mostly absent above the continental shelf. Areas with bottom depths of less than 300 m were almost totally devoid of B. glaciale. There were significant differences in allozyme frequencies and growth between fjords and the Norwegian Sea, with a slower growth towards a larger asymptotic length in the oceanic population. Allozyme and growth differences among fjords were smaller yet significant after pooling samples within each fjord, which suggests there is only limited connectivity among these fjords. The physical barrier to gene flow represented by the continental shelf probably serves as an isolating mechanism between the fjordic and oceanic populations, while shallow sills at the mouths of fjords may restrict gene flow, and in particular limit exchange of adults among fjords. The catch per unit effort of B. glaciale was generally higher in fjords, and in some cases as much as one to two orders of magnitude higher than in the Norwegian Sea. We discuss physical characteristics of fjords that may make them a beneficial habitat for B. glaciale and other mesopelagic fish compared to the Norwegian Sea. © 2009 Taylor & Francis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{roditakis_current_2009,

title = {Current status of insecticide resistance in Q biotype Bemisia tabaci populations from Crete},

author = {E Roditakis and M Grispou and E Morou and J B Kristoffersen and N Roditakis and R Nauen and J Vontas and A Tsagkarakou},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-62549166712&doi=10.1002%2Fps.1690&partnerID=40&md5=51467d5e7b0e19580694fcfc93788d40},

doi = {10.1002/ps.1690},

issn = {1526498X},

year  = {2009},

date = {2009-01-01},

journal = {Pest Management Science},

volume = {65},

number = {3},

pages = {313--322},

abstract = {BACKGROUND: A major problem of crop protection in Crete, Greece, is the control of Bemisia tabaci (Gennadius) (Homoptera: Aleyrodidae) with chemical insecticides owing to the rapid development of resistance. The aim of this study was to investigate the establishment of resistance and the underlying mechanisms to major insecticide classes with classical bioassays and known biochemical resistance markers. RESULTS: During a 2005-2007 survey, 53 Q biotype populations were collected. Application history records showed extensive use of neonicotinoids, organophosphates, carbamates and pyrethroids. High resistance levels were identified in the majority of populations (textbackslashtextgreater80%) for imidacloprid (RF: 38-1958x) and α-cypermethrin (RF: 30-600x). Low resistance levels (RF textbackslashtextless 12) were observed for pirimiphos-methyl. A strong correlation between resistance to imidacloprid and the number of applications with neonicotinoids was observed. Significant correlations were observed between COE and P450-dependent monoxygenase activity with resistance to α-cypermethrin and imidacloprid respectively. A propoxur-based AChE diagnostic test indicated that iAChE was widespread in most populations. Resistance levels for α-cypermethrin were increased when compared with a previous survey (2002-2003). Differentiation of LC50 values between localities was observed for imidacloprid only. CONCLUSION: Bemisia tabaci resistance evolved differently in each of the three insecticides studied. Imidacloprid resistance seems less established and less persistent than α-cypermethrin resistance. The low resistance levels for pirimiphos-methyl suggest absence of cross-resistance with other organophosphates or carbamates used. © 2008 Society of Chemical Industry.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kristoffersen_fluctuating_2009,

title = {Fluctuating asymmetry and fitness correlations in two Engraulis encrasicolus populations},

author = {J B Kristoffersen and A Magoulas},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-75149159614&doi=10.1111%2Fj.1095-8649.2009.02473.x&partnerID=40&md5=e2390cc6c9f4ad9fc16c1101907979a6},

doi = {10.1111/j.1095-8649.2009.02473.x},

issn = {00221112},

year  = {2009},

date = {2009-01-01},

journal = {Journal of Fish Biology},

volume = {75},

number = {10},

pages = {2723--2736},

abstract = {Correlations among several measures of fluctuating asymmetry (FA) and fitness-related variables were assessed in two populations of the European anchovy Engraulis encrasicolus with fast growth (Aegean Sea) and slow growth (Ionian Sea), respectively. FA levels were borderline significantly higher in the Ionian than in the Aegean for some variables. Variation in otolith shape (deviation from population norm) was lower in the Ionian than the Aegean, contrary to expectation. Within the Aegean, there was no relation between any of the FA indexes and fitness estimators, while in the Ionian a composite otolith FA index was significantly negatively correlated to standard length at age only in 2 year-old individuals. This difference between the Aegean and Ionian may have been related to the lower growth rate in the Ionian, as FA-fitness relations may be more apparent in less-beneficial environments. The absence of significant correlations in the Aegean and the low correlation in one age group in the Ionian suggests that FA is not a sensitive indicator of individual fitness in adult E. encrasicolus. © 2009 The Fisheries Society of the British Isles.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kristoffersen_population_2008,

title = {Population structure of anchovy Engraulis encrasicolus L. in the Mediterranean Sea inferred from multiple methods},

author = {J B Kristoffersen and A Magoulas},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-43049181335&doi=10.1016%2Fj.fishres.2007.11.024&partnerID=40&md5=087aa04263c4eaca6aacfe6bc2fb92ae},

doi = {10.1016/j.fishres.2007.11.024},

issn = {01657836},

year  = {2008},

date = {2008-01-01},

journal = {Fisheries Research},

volume = {91},

number = {2-3},

pages = {187--195},

abstract = {Population structure of anchovy, Engraulis encrasicolus L., in the northern Mediterranean was investigated using multiple methods. Variation in body shape, otolith shape and growth was investigated in samples from the central Aegean and Ionian Seas. Intron length polymorphism from nuclear DNA, and mitochondrial DNA variation was investigated for samples from these basins, as well as northern Adriatic (ADR) and Gulf of Lions (LION). Two lineages (clades) of mtDNA that co-occur in the populations of anchovy throughout the region were compared with respect to growth, body shape, otolith shape, and intron variation, to check for any reproductive isolation within areas between the clades. The two clades were not different in any of the investigated parameters and appear to be completely crossbreeding. There were significant differences among areas with regard to mtDNA clade proportions, nuclear allele frequencies, body shape and otolith shape, indicating that several reproductively isolated populations of anchovy exists in the northern Mediterranean. There was an overall fair to good agreement between population structures inferred from the different classes of markers. The mitotype variation indicated a larger population differentiation than the two nuclear DNA loci, which may be related to the uniparental transmission and the lack of recombination of mtDNA. © 2007 Elsevier B.V. All rights reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{tsagkarakou_biotype_2008,

title = {Biotype monitoring and genetic relationships of Bemisia tabaci in Greece: Mitochondrial DNA and microsatellite polymorphism},

author = {A Tsagkarakou and C S Tsigenopoulos and K Gorman and JB Kristoffersen and J Lagnel and D Bedford},

url = {<Go to ISI>://000253056900096},

year  = {2008},

date = {2008-01-01},

journal = {Journal of Insect Science},

volume = {8},

pages = {48--48},

note = {ISBN: 1536-2442},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kristoffersen_growth_2007,

title = {Growth rate and relative otolith size in populations of adult Müller's pearlside Maurolicus muelleri},

author = {J B Kristoffersen},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-35448986194&doi=10.1111%2Fj.1095-8649.2007.01593.x&partnerID=40&md5=1e8d0ba6fad21179930bb8582907daf0},

doi = {10.1111/j.1095-8649.2007.01593.x},

issn = {00221112},

year  = {2007},

date = {2007-01-01},

journal = {Journal of Fish Biology},

volume = {71},

number = {5},

pages = {1317--1330},

abstract = {Within populations of adult Müller's pearlside Maurolicus muelleri the otolith radius tended to increase with age at a given fish length, which indicated the presence of a growth-rate effect. Among populations the relative otolith size was negatively correlated to growth-rate estimates, which again indicated a growth-rate effect. There were only minor differences in temperature conditions among the locations, and birth-date differences did not appear to account for variation in otolith radius relative to fish length in older age groups. The presence of a growth-rate effect may be useful, as the relative otolith size may be used for evaluation of age and growth estimates, although there are several limitations to its usefulness. © 2007 The Author.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kristoffersen_sexual_2001,

title = {Sexual size dimorphism and sex ratio in Müller's pearlside (Maurolicus muelleri)},

author = {J B Kristoffersen and A G V Salvanes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0034933210&doi=10.1007%2Fs002270000529&partnerID=40&md5=231a7d359b6ca8692eeba623e13d94a0},

doi = {10.1007/s002270000529},

issn = {00253162},

year  = {2001},

date = {2001-01-01},

journal = {Marine Biology},

volume = {138},

number = {6},

pages = {1087--1092},

abstract = {From a series of samples from the Norwegian Sea and fjords, we demonstrate sexual size dimorphism in Maurolicus muelleri, and geographical variation in the degree of dimorphism. The dimorphism was smaller in the Norwegian Sea than in the fjord populations. In fjords, males had a lower maximum size and higher mortality than females. One-year-old females weighed on average about 50% more than males in fjords, but this weight difference was reduced to about 10% among 3-year-old fish. Possible causes of this decreasing sexual size dimorphism are discussed.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{asplin_nonlocal_1999,

title = {Nonlocal wind-driven fjord-coast advection and its potential effect on plankton and fish recruitment},

author = {Lars Asplin and Anne Gro Vea Salvanes and Jon Bent Kristoffersen},

url = {http://doi.wiley.com/10.1046/j.1365-2419.1999.00109.x},

doi = {10.1046/j.1365-2419.1999.00109.x},

issn = {1054-6006, 1365-2419},

year  = {1999},

date = {1999-12-01},

urldate = {2020-08-18},

journal = {Fisheries Oceanography},

volume = {8},

number = {4},

pages = {255--263},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kristoffersen_effects_1998,

title = {Effects of formaldehyde and ethanol preservation on body and otoliths of Maurolicus muelleri and Benthosema glaciale},

author = {Jon Bent Kristoffersen and Anne Gro Vea Salvanes},

url = {http://www.tandfonline.com/doi/full/10.1080/00364827.1998.10413675},

doi = {10.1080/00364827.1998.10413675},

issn = {0036-4827},

year  = {1998},

date = {1998-06-01},

urldate = {2020-08-18},

journal = {Sarsia},

volume = {83},

number = {2},

pages = {95--102},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kristoffersen_life_1998,

title = {Life history of Maurolicus muelleri in fjordic and oceanic environments},

author = {J B Kristoffersen and A G V Salvanes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032432626&doi=10.1006%2Fjfbi.1998.0799&partnerID=40&md5=a54c3a94e98cf1400b83d5c425bf3141},

doi = {10.1006/jfbi.1998.0799},

issn = {00221112},

year  = {1998},

date = {1998-01-01},

journal = {Journal of Fish Biology},

volume = {53},

number = {6},

pages = {1324--1341},

abstract = {Life history parameters are compared for populations of Maurolicus muelleri from Norwegian fjords and the Norwegian Sea in 1995 and 1996. The mortality rate was higher in the oceanic population (2.55 for males, 2.00 for females) than in the fjords (1.15 for males, 0.97 for females). Fish from the Norwegian Sea population occupied a depth with higher light levels, which may have contributed to the higher mortality through increased visibility to predators. Differences in growth, condition and gonad weight indicated different resource levels caused by different population densities. Recruitment was weak in many fjords in 1994, but not in the Norwegian Sea. It is suggested that wind-generated advection may affect recruitment in fjords on the western coast of Norway.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kristoffersen_marin_1994,

title = {Marin bløtbunn - verdens største habitat. Historikk og nyere viten},

author = {JB Kristoffersen and L Buhl-Mortensen and K Miskov-Larsen},

year  = {1994},

date = {1994-01-01},

journal = {Naturen},

volume = {5},

pages = {206--215},

keywords = {},

pubstate = {published},

tppubtype = {article}

}