Paraskevi Polymenakou

@article{metcalfe_submarine_2025,

title = {Submarine ash megabed fed by far-traveled, shoreline-crossing pyroclastic currents from a large explosive volcanic eruption},

author = {Abigail Metcalfe and Tim Druitt and Katharina Pank and Steffen Kutterolf and Jonas Preine and Karim Kelfoun and Christian Hübscher and Paraskevi Nomikou and Thomas A Ronge and Shun Chiyonobu and Olga Koukousioura and Adam Woodhouse and Sarah Beethe and Michael Manga and Iona McIntosh and Masako Tominaga and Carole Berthod and Hehe Chen and Acacia Clark and Susan DeBari and Ralf Gertisser and Raymond Johnston and Ally Peccia and Yuzuru Yamamoto and Alexis Bernard and Tatiana Fernandez Perez and Christopher K Jones and Kumar Batuk Joshi and Günther Kletetschka and Molly McCanta and Antony Morris and Paraskevi Polymenakou and Xiaohui Li and Jean-Marie Nedelec and Hao-Yang Lee and Dimitrios Papanikolaou},

url = {https://www.science.org/doi/10.1126/sciadv.ads9642

/wp-content/uploads/2025/09/2025-Metcalfe-Sci-Adv-51.pdf},

doi = {10.1126/sciadv.ads9642},

issn = {2375-2548},

year  = {2025},

date = {2025-09-22},

urldate = {2025-09-22},

journal = {Science Advances},

volume = {11},

number = {33},

pages = {eads9642},

abstract = {Large explosive volcanic eruptions from island volcanoes deliver vast quantities of ash to the marine environment. While many of the transport pathways are understood, those from shoreline-crossing or submarine pyroclastic currents, and their transformation into water-supported gravity flows, remain poorly constrained. We report the discovery by International Ocean Discovery Program (IODP) deep drilling of a 200-meter-thick ash megabed buried in rift basins of the South Aegean Volcanic Arc. The textgreater73–cubic kilometer ash deposit originates from the Kos Plateau Tuff caldera-forming eruption, which occurred 161 thousand years ago, textgreater120 kilometers to the east. The ash forms a chemically uniform, graded megabed lacking bioturbation, interpreted as having been emplaced by a stream of eruption-fed turbidity currents. Bioclastic debris within the ash provides evidence of widespread destruction of marine ecosystems. Large volcanic eruptions can remodel the seafloor landscape, deposit thick ash turbidites, and destroy marine biota on island arc–wide scales in short-lived, catastrophic events. 

 , 

 Volcanic ash from an eruption in Greece poured into the sea, forming a bed 200 m thick in a submarine basin far from the volcano.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{manga_low_2025,

title = {Low Heat Flow in the Anhydros Basin, Aegean Sea, Recorded by Deep Subsurface Temperatures},

author = {Michael Manga and Masako Tominaga and Jonas Preine and Thomas A Ronge and Sarah Beethe and Christian Hübscher and Iona McIntosh and Paraskevi Nomikou and Steffen Kutterolf and Tim Druitt and Alexis Bernard and Carole Berthod and Hehe Chen and Acacia Clark and Susan DeBari and Tatiana I Fernandez‐Perez and Ralf Gertisser and Raymond M Johnston and Christopher K Jones and Batuk K Joshi and Günther Kletetschka and Olga Koukousioura and Molly McCanta and Antony Morris and Katharina Pank and Ally Peccia and Paraskevi N Polymenakou and Adam Woodhouse and Yuzuru Yamamoto},

url = {https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2025GL115919

/wp-content/uploads/2025/07/2025-Manga-GRL-36.pdf},

doi = {10.1029/2025GL115919},

issn = {0094-8276, 1944-8007},

year  = {2025},

date = {2025-07-16},

urldate = {2025-07-16},

journal = {Geophysical Research Letters},

volume = {52},

number = {13},

pages = {e2025GL115919},

abstract = {Abstract 

 

 Subseafloor in situ temperatures in a drilled hole in the Anhydros Basin, Aegean Sea, measured during International Ocean Discovery Program (IODP) Expedition 398, yielded a low heat flow (textless0.023 W/m 

 2 

 ) despite active magmatism and rifting in the region. The coldest and highest temperatures were 13.9°C at 52.5 m below seafloor (mbsf) and 15.5°C for the deepest measurement at 360.4 mbsf, respectively. Comparison of a heat transfer model with measurements suggests that sea bottom temperatures during the last glacial period were up to 10°C cooler than Holocene temperatures. The magnitude of Holocene warming co‐varies with the geothermal heat flow: if the former goes up the latter goes up. Low heat flow may arise from lateral removal of heat through deeper formations by gravity driven advection of fluids. Tectonic separation of the northwestern Anhydros Basin from the Christiana‐Santorini‐Kolumbo volcanic field may lead to minimal magmatic influences on heat flow. 

 

 , 

 Plain Language Summary 

 Temperatures in Earth's crust reveal the processes that create and transport heat. In the rifting Anhydros Basin in the Aegean Sea, north of the active South Aegean Volcanic Arc, International Ocean Discovery Program Expedition 398 measured cold subsurface temperatures in a borehole to depths exceeding 300 m below the seafloor. These temperatures record low heat flow and cold seafloor temperatures from the last glacial period. The low heat flow at shallow depths may be due to deeper fluid circulation that removes heat. Low heat flow further implies that there are no magma bodies within the crust in the northwestern part of the Anhydros Basin. 

 , 

 Key Points 

 

 

 

 Heat flow is low in the Anhydros Basin, Aegean Sea 

 

 

 Ocean bottom temperatures were cold during the last glacial 

 

 

 Subsurface temperature records surface temperature changes and heat flow},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{preine_hazardous_2024,

title = {Hazardous explosive eruptions of a recharging multi-cyclic island arc caldera},

author = {Jonas Preine and Jens Karstens and Christian Hübscher and Tim Druitt and Steffen Kutterolf and Paraskevi Nomikou and Michael Manga and Ralf Gertisser and Katharina Pank and Sarah Beethe and Carole Berthod and Gareth Crutchley and Iona McIntosh and Thomas Ronge and Masako Tominaga and Acacia Clark and Susan DeBari and Raymond Johnston and Zenon Mateo and Ally Peccia and Christopher Jones and Günther Kletetschka and Abigail Metcalfe and Alexis Bernard and Hehe Chen and Shun Chiyonobu and Tatiana Fernandez-Perez and Kumar Batuk Joshi and Olga Koukousioura and Molly McCanta and Antony Morris and Paraskevi Polymenakou and Adam Woodhouse and Yuzuru Yamamoto and Kuo-Lung Wang and Hao-Yang Lee and Xiaohui Li and Dimitrios Papanikolaou},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/04/2024-Preine-Nature-GeoSci-20.pdf

https://www.nature.com/articles/s41561-024-01392-7},

doi = {10.1038/s41561-024-01392-7},

issn = {1752-0894, 1752-0908},

year  = {2024},

date = {2024-04-11},

urldate = {2024-04-11},

journal = {Nature Geoscience},

abstract = {Abstract 

 

 Caldera-forming eruptions of silicic volcanic systems are among the most devastating events on Earth. By contrast, post-collapse volcanic activity initiating new caldera cycles is generally considered less hazardous. Formed after Santorini’s latest caldera-forming eruption of textasciitilde1600  

 bce 

 , the Kameni Volcano in the southern Aegean Sea enables the eruptive evolution of a recharging multi-cyclic caldera to be reconstructed. Kameni’s eruptive record has been documented by onshore products and historical descriptions of mainly effusive eruptions dating back to 197  

 bce 

 . Here we combine high-resolution seismic reflection data with cored lithologies from International Ocean Discovery Program Expedition 398 at four sites to determine the submarine architecture and volcanic history of intra-caldera deposits from Kameni. Our shore-crossing analysis reveals the deposits of a submarine explosive eruption that produced up to 3.1 km 

 3 

 of pumice and ash, which we relate to a historical eruption in 726  

 ce 

 . The estimated volcanic explosivity index of magnitude 5 exceeds previously considered worst-case eruptive scenarios for Santorini. Our finding that the Santorini caldera is capable of producing large explosive eruptions at an early stage in the caldera cycle implies an elevated hazard potential for the eastern Mediterranean region, and potentially for other recharging silicic calderas.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{druitt_giant_2024,

title = {Giant offshore pumice deposit records a shallow submarine explosive eruption of ancestral Santorini},

author = {Tim Druitt and Steffen Kutterolf and Thomas A Ronge and Christian Hübscher and Paraskevi Nomikou and Jonas Preine and Ralf Gertisser and Jens Karstens and Jörg Keller and Olga Koukousioura and Michael Manga and Abigail Metcalfe and Molly McCanta and Iona McIntosh and Katharina Pank and Adam Woodhouse and Sarah Beethe and Carole Berthod and Shun Chiyonobu and Hehe Chen and Acacia Clark and Susan DeBari and Raymond Johnston and Ally Peccia and Yuzuru Yamamoto and Alexis Bernard and Tatiana Fernandez Perez and Christopher Jones and Kumar Batuk Joshi and Günther Kletetschka and Xiaohui Li and Antony Morris and Paraskevi Polymenakou and Masako Tominaga and Dimitrios Papanikolaou and Kuo-Lung Wang and Hao-Yang Lee},

url = {/wp-content/uploads/2024/01/2024-Druitt-Comm-EarthEnvironment-4.pdf

https://www.nature.com/articles/s43247-023-01171-z},

doi = {10.1038/s43247-023-01171-z},

issn = {2662-4435},

year  = {2024},

date = {2024-01-19},

urldate = {2024-01-23},

journal = {Communications Earth & Environment},

volume = {5},

number = {1},

pages = {24},

abstract = {Abstract 

 

 Large explosive volcanic eruptions from island arcs pour pyroclastic currents into marine basins, impacting ecosystems and generating tsunamis that threaten coastal communities and infrastructures. Risk assessments require robust records of such highly hazardous events, which is challenging as most of the products lie buried under the sea. Here we report the discovery by IODP Expedition 398 of a giant rhyolitic pumice deposit emplaced 520 ± 10 ky ago at water depths of 200 to 1000 m during a high-intensity, shallow submarine eruption of ancestral Santorini Volcano. Pyroclastic currents discharged into the sea transformed into turbidity currents and slurries, forming a textgreater89 ± 8 km 

 3 

 volcaniclastic megaturbidite up to 150 m thick in the surrounding marine basins, while breaching of the sea surface by the eruption column laid down veneers of ignimbrite on three islands. The eruption is one of the largest recorded on the South Aegean Volcanic Arc, and highlights the hazards from submarine explosive eruptions.},

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{le_moine_bauer_structure_2023,

title = {Structure and metabolic potential of the prokaryotic communities from the hydrothermal system of Paleochori Bay, Milos, Greece},

author = {Sven Le Moine Bauer and Guang-Sin Lu and Steven Goulaouic and Valentine Puzenat and Anders Schouw and Thibaut Barreyre and Vera Pawlowsky-Glahn and Juan José Egozcue and Jean-Emmanuel Martelat and Javier Escartin and Jan P Amend and Paraskevi Nomikou and Othonas Vlasopoulos and Paraskevi Polymenakou and Steffen Leth Jørgensen},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/01/2023-Le-Moine-Bauer-FinMicro-5.pdf

https://www.frontiersin.org/articles/10.3389/fmicb.2022.1060168/full},

doi = {10.3389/fmicb.2022.1060168},

issn = {1664-302X},

year  = {2023},

date = {2023-01-16},

urldate = {2023-01-16},

journal = {Frontiers in Microbiology},

volume = {13},

pages = {1060168},

abstract = {Introduction 

 Shallow hydrothermal systems share many characteristics with their deep-sea counterparts, but their accessibility facilitates their study. One of the most studied shallow hydrothermal vent fields lies at Paleochori Bay off the coast of Milos in the Aegean Sea (Greece). It has been studied through extensive mapping and its physical and chemical processes have been characterized over the past decades. However, a thorough description of the microbial communities inhabiting the bay is still missing. 

 

 

 Methods 

 We present the first in-depth characterization of the prokaryotic communities of Paleochori Bay by sampling eight different seafloor types that are distributed along the entire gradient of hydrothermal influence. We used deep sequencing of the 16S rRNA marker gene and complemented the analysis with qPCR quantification of the 16S rRNA gene and several functional genes to gain insights into the metabolic potential of the communities. 

 

 

 Results 

 We found that the microbiome of the bay is strongly influenced by the hydrothermal venting, with a succession of various groups dominating the sediments from the coldest to the warmest zones. Prokaryotic diversity and abundance decrease with increasing temperature, and thermophilic archaea overtake the community. 

 

 

 Discussion 

 Relevant geochemical cycles of the Bay are discussed. This study expands our limited understanding of subsurface microbial communities in acidic shallow-sea hydrothermal systems and the contribution of their microbial activity to biogeochemical cycling.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nomikou_santory_2022,

title = {SANTORY: SANTORini’s Seafloor Volcanic ObservatorY},

author = {Paraskevi Nomikou and Paraskevi N Polymenakou and Andrea Luca Rizzo and Sven Petersen and Mark Hannington and Stephanos Pantelis Kilias and Dimitris Papanikolaou and Javier Escartin and Konstantinos Karantzalos and Theodoros J Mertzimekis and Varvara Antoniou and Mel Krokos and Lazaros Grammatikopoulos and Francesco Italiano and Cinzia Giuseppina Caruso and Gianluca Lazzaro and Manfredi Longo and Sergio Sciré Scappuzzo and Walter D’Alessandro and Fausto Grassa and Konstantina Bejelou and Danai Lampridou and Anna Katsigera and Anne Dura},

url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Nomikou-FroMarSci-31.pdf

https://www.frontiersin.org/articles/10.3389/fmars.2022.796376/full},

doi = {10.3389/fmars.2022.796376},

issn = {2296-7745},

year  = {2022},

date = {2022-03-01},

urldate = {2022-05-09},

journal = {Frontiers in Marine Science},

volume = {9},

pages = {796376},

abstract = {Submarine hydrothermal systems along active volcanic ridges and arcs are highly dynamic, responding to both oceanographic (e.g., currents, tides) and deep-seated geological forcing (e.g., magma eruption, seismicity, hydrothermalism, and crustal deformation, etc.). In particular, volcanic and hydrothermal activity may also pose profoundly negative societal impacts (tsunamis, the release of climate-relevant gases and toxic metal(loid)s). These risks are particularly significant in shallow (<1000m) coastal environments, as demonstrated by the January 2022 submarine paroxysmal eruption by the Hunga Tonga-Hunga Ha’apai Volcano that destroyed part of the island, and the October 2011 submarine eruption of El Hierro (Canary Islands) that caused vigorous upwelling, floating lava bombs, and natural seawater acidification. Volcanic hazards may be posed by the Kolumbo submarine volcano, which is part of the subduction-related Hellenic Volcanic Arc at the intersection between the Eurasian and African tectonic plates. There, the Kolumbo submarine volcano, 7 km NE of Santorini and part of Santorini’s volcanic complex, hosts an active hydrothermal vent field (HVF) on its crater floor (textasciitilde500m b.s.l.), which degasses boiling CO 

 2 

 –dominated fluids at high temperatures (textasciitilde265°C) with a clear mantle signature. Kolumbo’s HVF hosts actively forming seafloor massive sulfide deposits with high contents of potentially toxic, volatile metal(loid)s (As, Sb, Pb, Ag, Hg, and Tl). The proximity to highly populated/tourist areas at Santorini poses significant risks. However, we have limited knowledge of the potential impacts of this type of magmatic and hydrothermal activity, including those from magmatic gases and seismicity. To better evaluate such risks the activity of the submarine system must be continuously monitored with multidisciplinary and high resolution instrumentation as part of an 

 in-situ 

 observatory supported by discrete sampling and measurements. This paper is a design study that describes a new long-term seafloor observatory that will be installed within the Kolumbo volcano, including cutting-edge and innovative marine-technology that integrates hyperspectral imaging, temperature sensors, a radiation spectrometer, fluid/gas samplers, and pressure gauges. These instruments will be integrated into a hazard monitoring platform aimed at identifying the precursors of potentially disastrous explosive volcanic eruptions, earthquakes, landslides of the hydrothermally weakened volcanic edifice and the release of potentially toxic elements into the water column.},

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_santorini_2021,

title = {The Santorini Volcanic Complex as a Valuable Source of Enzymes for Bioenergy},

author = {Paraskevi N Polymenakou and Paraskevi Nomikou and Haris Zafeiropoulos and Manolis Mandalakis and Thekla I Anastasiou and Stephanos Kilias and Nikos C Kyrpides and Georgios Kotoulas and Antoniοs Magoulas},

url = {https://www.mdpi.com/1996-1073/14/5/1414

https://imbbc.hcmr.gr/wp-content/uploads/2021/03/2021-Polymenakou-ENERGIES-24.pdf},

doi = {10.3390/en14051414},

issn = {1996-1073},

year  = {2021},

date = {2021-01-01},

urldate = {2021-03-17},

journal = {Energies},

volume = {14},

number = {5},

pages = {1414},

abstract = {Marine microbial communities are an untapped reservoir of genetic and metabolic diversity and a valuable source for the discovery of new natural products of biotechnological interest. The newly discovered hydrothermal vent field of Santorini volcanic complex located in the Aegean Sea is gaining increasing interest for potential biotechnological exploitation. The conditions in these environments, i.e., high temperatures, low pH values and high concentration of heavy metals, often resemble harsh industrial settings. Thus, these environments may serve as pools of enzymes of enhanced catalytic properties that may provide benefits to biotechnology. Here, we screened 11 metagenomic libraries previously constructed from microbial mat samples covering the seafloor and the polymetallic chimneys of Kolumbo volcano as well as mat samples from Santorini caldera, to mine, in silico, genes associated with bioenergy applications. We particularly focused on genes encoding biomass hydrolysis enzymes such as cellulases, hemicellulases and lignin-degrading enzymes. A total of 10,417 genes were found for three specific groups of enzymes—i.e., the endoglucanases, the three different beta-glucosidases BGL, bglX and bglB, and the alpha-galactosidases melA, and rafA. Overall, we concluded that the Santorini–Kolumbo volcanic ecosystems constitute a significant resource of novel genes with potential applications in bioenergy that deserve further investigation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{charalampous_comparison_2021,

title = {Comparison of Hydrocarbon-Degrading Consortia from Surface and Deep Waters of the Eastern Mediterranean Sea: Characterization and Degradation Potential},

author = {Georgia Charalampous and Efsevia Fragkou and Konstantinos A Kormas and Alexandre De B Menezes and Paraskevi N Polymenakou and Nikos Pasadakis and Nicolas Kalogerakis and Eleftheria Antoniou and Evangelia Gontikaki},

url = {https://www.mdpi.com/1996-1073/14/8/2246

https://imbbc.hcmr.gr/wp-content/uploads/2021/05/2021-Charalampous-ENERGIES-30-1.pdf},

doi = {10.3390/en14082246},

year  = {2021},

date = {2021-01-01},

urldate = {2021-04-27},

journal = {Energies},

volume = {14},

number = {8},

pages = {2246},

abstract = {The diversity and degradation capacity of hydrocarbon-degrading consortia from surface and deep waters of the Eastern Mediterranean Sea were studied in time-series experiments. Microcosms were set up in ONR7a medium at in situ temperatures of 25 °C and 14 °C for the Surface and Deep consortia, respectively, and crude oil as the sole source of carbon. The Deep consortium was additionally investigated at 25 °C to allow the direct comparison of the degradation rates to the Surface consortium. In total, textasciitilde50% of the alkanes and textasciitilde15% of the polycyclic aromatic hydrocarbons were degraded in all treatments by Day 24. Approximately textasciitilde95% of the total biodegradation by the Deep consortium took place within 6 days regardless of temperature, whereas comparable levels of degradation were reached on Day 12 by the Surface consortium. Both consortia were dominated by well-known hydrocarbon-degrading taxa. Temperature played a significant role in shaping the Deep consortia communities with Pseudomonas and Pseudoalteromonas dominating at 25 °C and Alcanivorax at 14 °C. Overall, the Deep consortium showed a higher efficiency for hydrocarbon degradation within the first week following contamination, which is critical in the case of oil spills, and thus merits further investigation for its exploitation in bioremediation technologies tailored to the Eastern Mediterranean Sea.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{puzenat_shallow-water_2021,

title = {Shallow-water hydrothermalism at Milos (Greece): Nature, distribution, heat fluxes and impact on ecosystems},

author = {Valentine Puzenat and Javier Escartín and Jean-Emmanuel Martelat and Thibaut Barreyre and Sven Le Moine Bauer and Paraskevi Nomikou and Nuno Gracias and Pascal Allemand and Varvara Antoniou and Omer Coskun and Rafael Garcia and Philippe Grandjean and Steffen Leth Jørgensen and Lluís Magí and Manolis Mandalakis and William Orsi and Paraskevi Polymenakou and Anders Schouw and Guillem Vallicrosa and Othonas Vlasopoulos},

url = {https://linkinghub.elsevier.com/retrieve/pii/S0025322721001031},

doi = {10.1016/j.margeo.2021.106521},

issn = {00253227},

year  = {2021},

date = {2021-01-01},

urldate = {2022-02-22},

journal = {Marine Geology},

volume = {438},

pages = {106521},

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{rizzo_geochemistry_2019,

title = {Geochemistry of CO2-Rich Gases Venting From Submarine Volcanism: The Case of Kolumbo (Hellenic Volcanic Arc, Greece)},

author = {Andrea Luca Rizzo and Antonio Caracausi and Valérie Chavagnac and Paraskevi Nomikou and Paraskevi N Polymenakou and Manolis Mandalakis and Georgios Kotoulas and Antonios Magoulas and Alain Castillo and Danai Lampridou and Nicolas Marusczak and Jeroen E Sonke},

url = {https://www.frontiersin.org/article/10.3389/feart.2019.00060/full},

doi = {10.3389/feart.2019.00060},

issn = {2296-6463},

year  = {2019},

date = {2019-04-01},

urldate = {2022-01-17},

journal = {Frontiers in Earth Science},

volume = {7},

pages = {60},

note = {BIODIV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{vizzini_plant_2019,

title = {Plant and sediment properties in seagrass meadows from two Mediterranean CO2 vents: Implications for carbon storage capacity of acidified oceans},

author = {Salvatrice Vizzini and Eugenia T Apostolaki and Elena Ricevuto and Paraskevi Polymenakou and Antonio Mazzola},

url = {https://linkinghub.elsevier.com/retrieve/pii/S0141113618305543},

doi = {10.1016/j.marenvres.2019.03.001},

issn = {01411136},

year  = {2019},

date = {2019-04-01},

urldate = {2022-01-17},

journal = {Marine Environmental Research},

volume = {146},

pages = {101--108},

note = {BIODIV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{mandalakis_microbial_2019,

title = {Microbial strains isolated from CO2-venting Kolumbo submarine volcano show enhanced co-tolerance to acidity and antibiotics},

author = {M Mandalakis and A Gavriilidou and P N Polymenakou and C A Christakis and P Nomikou and M Medvecký and S P Kilias and M Kentouri and G Kotoulas and A Magoulas},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85059814164&doi=10.1016%2fj.marenvres.2019.01.002&partnerID=40&md5=69e25c6daab89af12b0091a2c75b0d18},

doi = {10.1016/j.marenvres.2019.01.002},

issn = {01411136},

year  = {2019},

date = {2019-01-01},

journal = {Marine Environmental Research},

abstract = {As ocean acidification intensifies, there is growing global concern about the impacts that future pH levels are likely to have on marine life and ecosystems. By analogy, a steep decrease of seawater pH with depth is encountered inside the Kolumbo submarine volcano (northeast Santorini) as a result of natural CO2 venting, making this system ideal for ocean acidification research. Here, we investigated whether the increase of acidity towards deeper layers of Kolumbo crater had any effect on relevant phenotypic traits of bacterial isolates. A total of 31 Pseudomonas strains were isolated from both surface- (SSL) and deep-seawater layers (DSL), with the latter presenting a significantly higher acid tolerance. In particular, the DSL strains were able to cope with H+ levels that were 18 times higher. Similarly, the DSL isolates exhibited a significantly higher tolerance than SSL strains against six commonly used antibiotics and As(III). More importantly, a significant positive correlation was revealed between antibiotics and acid tolerance across the entire set of SSL and DSL isolates. Our findings imply that Pseudomonas species with higher resilience to antibiotics could be favored by the prospect of acidifying oceans. Further studies are required to determine if this feature is universal across marine bacteria and to assess potential ecological impacts. © 2019 Elsevier Ltd},

note = {Publisher: Elsevier Ltd},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{polymenakou_preliminary_2018,

title = {Preliminary assessment of methanogenic microbial communities in marine caves of Zakynthos Island (Ionian Sea, Greece)},

author = {Paraskevi Polymenakou and Manolis Mandalakis and Thanos Dailianis and Charalampos Dimitriadis and Matej Medvecky and Antonios Magoulas and Vasilis Gerovasileiou},

url = {https://ejournals.epublishing.ekt.gr/index.php/hcmr-med-mar-sc/article/view/14374},

doi = {10.12681/mms.14374},

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

year  = {2018},

date = {2018-06-01},

urldate = {2020-08-06},

journal = {Mediterranean Marine Science},

pages = {284},

abstract = {Mediterranean marine caves remain largely unexplored, while particularly limited information is available about the microbial life existing in these unique environments. The present study is a preliminary assessment of the composition of the active anaerobic microbial community colonizing the walls of newly explored systems of underwater caves and small cavities in Zakynthos Island. The interior of these caves is densely coated with egg-shaped, foam-shaped and filamentous biological structures that are characterised by a strong odor of hydrogen sulfide gas. A total of twelve structures scrapped from cave rocks were subjected to anaerobic cultivation for up to 208 days. Strong to moderate methanogenesis was observed in two different types of egg-shaped structures and one foam-like structure. Interestingly, this was observed in experiments that were performed at room temperature (i.e. 25oC) which is substantially lower than those typically considered optimum for methane production (e.g. 35oC). Analysis of the 16S rRNA genes revealed a clear dominance of archaea and bacteria closely related to known methane producers and sulfate reducers, including members of the families Methanomicrobiaceae, Desulfobulbaceae, Desulfobacteraceae, Desulfuromonaceae, Campylobacteraceae, Marinifilaceae, Clostridiaceae, Incertae Sedis – Family I & II. These results show that Mediterranean marine caves can host members of archaea and bacteria with potential biotechnological interest that deserve further investigation.},

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{mandalakis_simple_2018,

title = {A simple cleanup method for the removal of humic substances from soil protein extracts using aluminum coagulation},

author = {M Mandalakis and N S Panikov and P N Polymenakou and M V Sizova and A Stamatakis},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85048049746&doi=10.1007%2fs11356-018-2434-z&partnerID=40&md5=eb9d45b91caf01d89a3baea78220a432},

doi = {10.1007/s11356-018-2434-z},

issn = {09441344},

year  = {2018},

date = {2018-01-01},

journal = {Environmental Science and Pollution Research},

volume = {25},

number = {24},

pages = {23845--23856},

abstract = {Soil proteomics, the large-scale characterization of the entire protein complement in soils, provides a promising approach for deciphering the role of microbial functioning in terrestrial ecosystems. However, the extraction of soil proteins in sufficient quantities and of adequate purity remains a challenging task mainly due to the co-extraction of interfering humic substances. Up to now, the treatment of soil extracts with liquid phenol has been the “gold standard” for reducing humics, while the NoviPure cleanup kit was recently launched as a non-toxic approach. The present study describes an alternative method for delivering high-purity proteins based on humic coagulation with trivalent aluminum ions (Al3+). Various experimental parameters were optimized individually in order to maximize protein yield and diminish co-extracted humics. The optimized method was applied on a set of soil samples with diverse physicochemical characteristics and a comparison with the other two techniques was conducted. The amount of residual humics resulting from Al3+-based method was 26 and 35% higher than that from phenol treatment and NoviPure Kit, respectively, but these differences were of marginal statistical significance. With regard to extracted proteins, the average yields of the three methods were comparable, without showing any statistically significant differences. Overall, humic coagulation with Al3+ offers comparable cleanup performance in terms of protein yield and purity, but it is less toxic and less complex than the phenol-partitioning method, whereas it is far less expensive than the NoviPure Kit. The new technique is expected to facilitate the implementation of proteomic studies in soils. © 2018, Springer-Verlag GmbH Germany, part of Springer Nature.},

note = {Publisher: Springer Verlag},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{moitinho-silva_sponge_2017,

title = {The sponge microbiome project},

author = {Lucas Moitinho-Silva and Shaun Nielsen and Amnon Amir and Antonio Gonzalez and Gail L Ackermann and Carlo Cerrano and Carmen Astudillo-Garcia and Cole Easson and Detmer Sipkema and Fang Liu and Georg Steinert and Giorgos Kotoulas and Grace P McCormack and Guofang Feng and James J Bell and Jan Vicente and Johannes R Björk and Jose M Montoya and Julie B Olson and Julie Reveillaud and Laura Steindler and Mari-Carmen Pineda and Maria V Marra and Micha Ilan and Michael W Taylor and Paraskevi Polymenakou and Patrick M Erwin and Peter J Schupp and Rachel L Simister and Rob Knight and Robert W Thacker and Rodrigo Costa and Russell T Hill and Susanna Lopez-Legentil and Thanos Dailianis and Timothy Ravasi and Ute Hentschel and Zhiyong Li and Nicole S Webster and Torsten Thomas},

url = {https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/gix077/4082886},

doi = {10.1093/gigascience/gix077},

issn = {2047-217X},

year  = {2017},

date = {2017-10-01},

urldate = {2020-08-09},

journal = {GigaScience},

volume = {6},

number = {10},

pages = {gix077},

abstract = {Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 269 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with a) a standard protocol using QIIME closed-reference picking resulting in 39,543 Operational Taxonomic Units (OTU) at 97% sequence identity, b) a de novo protocol using Mothur resulting in 518,246 OTUs, and c) a new high-resolution Deblur protocol resulting in 83,908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host-specificity, convergent evolution, environmental drivers of microbiome structure and the sponge-associated rare biosphere.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{mandalakis_ultrasensitive_2017,

title = {Ultrasensitive and high-throughput analysis of chlorophyll a in marine phytoplankton extracts using a fluorescence microplate reader},

author = {M Mandalakis and A Stravinskaitė and A Lagaria and S Psarra and P Polymenakou},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85019571709&doi=10.1007%2fs00216-017-0392-9&partnerID=40&md5=17de4972e6106b13bb3f85822323f8b2},

doi = {10.1007/s00216-017-0392-9},

issn = {16182642},

year  = {2017},

date = {2017-01-01},

journal = {Analytical and Bioanalytical Chemistry},

volume = {409},

number = {19},

pages = {4539--4549},

abstract = {Chlorophyll a (Chl a) is the predominant pigment in every single photosynthesizing organism including phytoplankton and one of the most commonly measured water quality parameters. Various methods are available for Chl a analysis, but the majority of them are of limited throughput and require considerable effort and time from the operator. The present study describes a high-throughput, microplate-based fluorometric assay for rapid quantification of Chl a in phytoplankton extracts. Microplate sealing combined with ice cooling was proved an effective means for diminishing solvent evaporation during sample loading and minimized the analytical errors involved in Chl a measurements with a fluorescence microplate reader. A set of operating parameters (settling time, detector gain, sample volume) were also optimized to further improve the intensity and reproducibility of Chl a fluorescence signal. A quadratic regression model provided the best fit (r2 = 0.9998) across the entire calibration range (0.05–240 pg μL−1). The method offered excellent intra- and interday precision (% RSD 2.2 to 11.2%) and accuracy (% relative error −3.8 to 13.8%), while it presented particularly low limits of detection (0.044 pg μL−1) and quantification (0.132 pg μL−1). The present assay was successfully applied on marine phytoplankton extracts, and the overall results were consistent (average % relative error −14.8%) with Chl a concentrations (including divinyl Chl a) measured by high-performance liquid chromatography (HPLC). More importantly, the microplate-based method allowed the analysis of 96 samples/standards within a few minutes, instead of hours or days, when using a traditional cuvette-based fluorometer or an HPLC system. [Figure not available: see fulltext.]. © 2017, Springer-Verlag Berlin Heidelberg.},

note = {Publisher: Springer Verlag},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{rizzo_kolumbo_2016,

title = {Kolumbo submarine volcano (Greece): An active window into the Aegean subduction system},

author = {A L Rizzo and A Caracausi and V Chavagnac and P Nomikou and P N Polymenakou and M Mandalakis and G Kotoulas and A Magoulas and A Castillo and D Lampridou},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84975454736&doi=10.1038%2fsrep28013&partnerID=40&md5=e24dc2fa03414abaf410e586529f758d},

doi = {10.1038/srep28013},

issn = {20452322},

year  = {2016},

date = {2016-01-01},

journal = {Scientific Reports},

volume = {6},

abstract = {Submarine volcanism represents ∼80% of the volcanic activity on Earth and is an important source of mantle-derived gases. These gases are of basic importance for the comprehension of mantle characteristics in areas where subaerial volcanism is missing or strongly modified by the presence of crustal/atmospheric components. Though, the study of submarine volcanism remains a challenge due to their hazardousness and sea-depth. Here, we report 3He/4He measurements in CO2-dominated gases discharged at 500 m below sea level from the high-temperature (∼220 °C) hydrothermal system of the Kolumbo submarine volcano (Greece), located 7 km northeast off Santorini Island in the central part of the Hellenic Volcanic Arc (HVA). We highlight that the mantle below Kolumbo and Santorini has a 3He/4He signature of at least 7.0 Ra (being Ra the 3He/4He ratio of atmospheric He equal to 1.39×10-6), 3 Ra units higher than actually known for gases-rocks from Santorini. This ratio is also the highest measured across the HVA and is indicative of the direct degassing of a Mid-Ocean-Ridge-Basalts (MORB)-like mantle through lithospheric faults. We finally highlight that the degassing of high-temperature fluids with a MORB-like 3He/4He ratio corroborates a vigorous outgassing of mantle-derived volatiles with potential hazard at the Kolumbo submarine volcano.},

note = {Publisher: Nature Publishing Group},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{oulas_metagenomic_2016,

title = {Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology.},

author = {Anastasis Oulas and Paraskevi N Polymenakou and Rekha Seshadri and James H Tripp and Manolis Mandalakis and David A Paez-Espino and Amrita Pati and Patrick Chain and Paraskevi Nomikou and Steven Carey and Stephanos Kilias and Christos Christakis and Georgios Kotoulas and Antonios Magoulas and Natalia N Ivanova and Nikos C Kyrpides},

url = {http://www.ncbi.nlm.nih.gov/pubmed/26487573},

doi = {10.1111/1462-2920.13095},

issn = {1462-2920},

year  = {2016},

date = {2016-01-01},

journal = {Environmental Microbiology},

volume = {18},

number = {4},

pages = {1122--1136},

abstract = {Hydrothermal vents represent a deep, hot, aphotic biosphere where chemosynthetic primary producers, fuelled by chemicals from Earth's subsurface, form the basis of life. In this study, we examined microbial mats from two distinct volcanic sites within the Hellenic Volcanic Arc (HVA). The HVA is geologically and ecologically unique, with reported emissions of CO2 -saturated fluids at temperatures up to 220°C and a notable absence of macrofauna. Metagenomic data reveals highly complex prokaryotic communities composed of chemolithoautotrophs, some methanotrophs, and to our surprise, heterotrophs capable of anaerobic degradation of aromatic hydrocarbons. Our data suggest that aromatic hydrocarbons may indeed be a significant source of carbon in these sites, and instigate additional research into the nature and origin of these compounds in the HVA. Novel physiology was assigned to several uncultured prokaryotic lineages; most notably, a SAR406 representative is attributed with a role in anaerobic hydrocarbon degradation. This dataset, the largest to date from submarine volcanic ecosystems, constitutes a significant resource of novel genes and pathways with potential biotechnological applications.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{cheng_biodiversity_2015,

title = {Biodiversity, Anti-Trypanosomal Activity Screening, and Metabolomic Profiling of Actinomycetes Isolated from Mediterranean Sponges},

author = {Cheng Cheng and Lynsey MacIntyre and Usama Ramadan Abdelmohsen and Hannes Horn and Paraskevi N Polymenakou and RuAngelie Edrada-Ebel and Ute Hentschel},

editor = {Luis Angel Maldonado Manjarrez},

url = {https://dx.plos.org/10.1371/journal.pone.0138528},

doi = {10.1371/journal.pone.0138528},

issn = {1932-6203},

year  = {2015},

date = {2015-09-01},

urldate = {2020-08-10},

journal = {PLOS ONE},

volume = {10},

number = {9},

pages = {e0138528},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{polymenakou_pyrosequencing_2015,

title = {Pyrosequencing analysis of microbial communities reveals dominant cosmopolitan phylotypes in deep-sea sediments of the eastern Mediterranean Sea},

author = {Paraskevi N Polymenakou and Christos A Christakis and Manolis Mandalakis and Anastasis Oulas},

url = {http://www.sciencedirect.com/science/article/pii/S0923250815000571},

doi = {http://dx.doi.org/10.1016/j.resmic.2015.03.005},

issn = {0923-2508},

year  = {2015},

date = {2015-06-01},

journal = {Research in Microbiology},

volume = {166},

number = {5},

pages = {448--457},

abstract = {Abstract The deep eastern basin of the Mediterranean Sea is considered to be one of the world's most oligotrophic areas in the world. Here we performed pyrosequenicng analysis of bacterial and archaeal communities in oxic nutrient-poor sediments collected from the eastern Mediterranean at 1025–4393 m depth. Microbial communities were surveyed by targeting the hypervariable V5–V6 regions of the 16S ribosomal RNA gene using bar-coded pyrosequencing. With a total of 13,194 operational taxonomic units (OTUs) or phylotypes at 97% sequence similarities, the phylogenetic affiliation of microbes was assigned to 23 bacterial and 2 archaeal known phyla, 23 candidate divisions at the phylum level and distributed into 186 families. It was further revealed that the microbial consortia inhabiting all sampling sites were highly diverse, but dominated by phylotypes closely related to members of the genus Pseudomonas and Marine Group I archaea. Such pronounced and widespread enrichment probably manifests the cosmopolitan character of these species and raises questions about their metabolic adaptation to the physical stressors and low nutrient availability of the deep eastern Mediterranean Sea.},

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{kopf_ocean_2015,

title = {The ocean sampling day consortium},

author = {A Kopf and M Bicak and R Kottmann and J Schnetzer and I Kostadinov and K Lehmann and A Fernandez-Guerra and C Jeanthon and E Rahav and M Ullrich and A Wichels and G Gerdts and P Polymenakou and G Kotoulas and R Siam and R Z Abdallah and E C Sonnenschein and T Cariou and F O'Gara and S Jackson and S Orlic and M Steinke and J Busch and B Duarte and I Caçador and J Canning-Clode and O Bobrova and V Marteinsson and E Reynisson and C M Loureiro and G M Luna and G M Quero and C R Löscher and A Kremp and M E DeLorenzo and L Øvreås and J Tolman and J LaRoche and A Penna and M Frischer and T Davis and B Katherine and C P Meyer and S Ramos and C Magalhães and F Jude-Lemeilleur and M L Aguirre-Macedo and S Wang and N Poulton and S Jones and R Collin and J A Fuhrman and P Conan and C Alonso and N Stambler and K Goodwin and M M Yakimov and F Baltar and L Bodrossy and J Van De Kamp and D E F Frampton and M Ostrowski and P Van Ruth and P Malthouse and S Claus and K Deneudt and J Mortelmans and S Pitois and D Wallom and I Salter and R Costa and D C Schroeder and M M Kandil and V Amaral and F Biancalana and R Santana and M L Pedrotti and T Yoshida and H Ogata and T Ingleton and K Munnik and N Rodriguez-Ezpeleta and V Berteaux-Lecellier and P Wecker and I Cancio and D Vaulot and C Bienhold and H Ghazal and B Chaouni and S Essayeh and S Ettamimi and E H Zaid and N Boukhatem and A Bouali and R Chahboune and S Barrijal and M Timinouni and F El Otmani and M Bennani and M Mea and N Todorova and V Karamfilov and P Ten Hoopen and G Cochrane and S L'Haridon and K Can Bizsel and A Vezzi and F M Lauro and P Martin and R M Jensen and J Hinks and S Gebbels and R Rosselli and F De Pascale and R Schiavon and A Dos Santos and E Villar and S Pesant and B Cataletto and F Malfatti and R Edirisinghe and J A Herrera Silveira and M Barbier and V Turk and T Tinta and W J Fuller and I Salihoglu and N Serakinci and M C Ergoren and E Bresnan and J Iriberri and P A F Nyhus and E Bente and H E Karlsen and P N Golyshin and J M Gasol and S Moncheva and N Dzhembekova and Z Johnson and C D Sinigalliano and M L Gidley and A Zingone and R Danovaro and G Tsiamis and M S Clark and A C Costa and A El Bour and A M Martins and R Eric Collins and A -L Ducluzeau and J Martinez and M J Costello and L A Amaral-Zettler and J A Gilbert and N Davies and D Field and F O Glöckner},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84939478521&doi=10.1186%2fs13742-015-0066-5&partnerID=40&md5=d32573d75989ec6d70dd25bebc32dff4},

doi = {10.1186/s13742-015-0066-5},

issn = {2047217X},

year  = {2015},

date = {2015-01-01},

journal = {GigaScience},

volume = {4},

number = {1},

abstract = {Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits. © 2015 Kopf et al.},

note = {Publisher: BioMed Central Ltd.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{mandalakis_distribution_2014,

title = {Distribution of aliphatic hydrocarbons, polycyclic aromatic hydrocarbons and organochlorinated pollutants in deep-sea sediments of the southern Cretan margin, eastern Mediterranean Sea: A baseline assessment},

author = {M Mandalakis and P N Polymenakou and A Tselepides and N Lampadariou},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84896546708&doi=10.1016%2fj.chemosphere.2013.12.081&partnerID=40&md5=d9bfaf22c654867d5090f4abfdeee4cd},

doi = {10.1016/j.chemosphere.2013.12.081},

issn = {00456535},

year  = {2014},

date = {2014-01-01},

journal = {Chemosphere},

volume = {106},

pages = {28--35},

abstract = {Deep sediments from the southern Cretan margin were analyzed to establish baseline levels for various types of organic pollutants before the anticipated intensification of anthropogenic activities. The total concentration of aliphatic hydrocarbons (σAH:326-3758ngg-1, dry weight) was similar to those reported for deep sediments of the western Mediterranean Sea, while considerably lower levels were measured for polycyclic aromatic hydrocarbons (σPAH:9-60ngg-1). Source-diagnostic ratios suggested that the aliphatic hydrocarbons in sediments were mainly of terrestrial biogenic origin, while polycyclic aromatic hydrocarbons stemmed from the deposition of long-range transported combustion aerosols. Among the organochlorinated compounds analyzed, β-hexachlorocyclohexane (β-HCH:222-7052pgg-1), 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane (p,p'-DDT:37-2236pgg-1) and polychlorinated biphenyls (σPCB:38-1182pgg-1) showed the highest abundance in sediments. The presence of HCHs and PCBs was attributed to historical inputs that have undergone extensive weathering, whereas an ongoing fresh input was suggested for p,p'-DDT. Multiple linear regression analysis revealed that the levels of the various pollutants in sediments were controlled by different factors, but with organic carbon content playing a prominent role in most cases. © 2014 Elsevier Ltd.},

note = {Publisher: Elsevier Ltd},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{davies_founding_2014,

title = {The founding charter of the Genomic Observatories Network},

author = {N Davies and D Field and L Amaral-Zettler and M S Clark and J Deck and A Drummond and D P Faith and J Geller and J Gilbert and F O Glöckner and P R Hirsch and J -A Leong and C Meyer and M Obst and S Planes and C Scholin and A P Vogler and R D Gates and R Toonen and V Berteaux-Lecellier and M Barbier and K Barker and S Bertilsson and M Bicak and M J Bietz and J Bobe and L Bodrossy and A Borja and J Coddington and J Fuhrman and G Gerdts and R Gillespie and K Goodwin and P C Hanson and J -M Hero and D Hoekman and J Jansson and C Jeanthon and R Kao and A Klindworth and R Knight and R Kottmann and M S Koo and G Kotoulas and A J Lowe and V T Marteinsson and F Meyer and N Morrison and D D Myrold and E Pafilis and S Parker and J J Parnell and P N Polymenakou and S Ratnasingham and G K Roderick and N Rodriguez-Ezpeleta and K Schonrogge and N Simon and N J Valette-Silver and Y P Springer and G N Stone and S Stones-Havas and S -A Sansone and K M Thibault and P Wecker and A Wichels and J C Wooley and T Yahara and A Zingone},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84920397295&doi=10.1186%2f2047-217X-3-2&partnerID=40&md5=a043d700cdaaf754ee7c91c668fc964c},

doi = {10.1186/2047-217X-3-2},

issn = {2047217X},

year  = {2014},

date = {2014-01-01},

journal = {GigaScience},

volume = {3},

number = {1},

abstract = {The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms.An international group of 64 scientists first published the call for a global network of Genomic Observatories in January 2012. The vision for such a network was expanded in a subsequent paper and developed over a series of meetings in Bremen (Germany), Shenzhen (China), Moorea (French Polynesia), Oxford (UK), Pacific Grove (California, USA), Washington (DC, USA), and London (UK). While this community-building process continues, here we express our mutual intent to establish the GOs Network formally, and to describe our shared vision for its future. The views expressed here are ours alone as individual scientists, and do not necessarily represent those of the institutions with which we are affiliated. © 2014 Davies et al.; licensee BioMed Central Ltd.},

note = {Publisher: BioMed Central Ltd.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{sevastou_benthic_2013,

title = {Benthic communities in the deep Mediterranean Sea: exploring microbial and meiofaunal patterns in slope and basin ecosystems},

author = {K Sevastou and N Lampadariou and P N Polymenakou and A Tselepides},

url = {https://bg.copernicus.org/articles/10/4861/2013/},

doi = {10.5194/bg-10-4861-2013},

issn = {1726-4189},

year  = {2013},

date = {2013-07-01},

urldate = {2020-08-10},

journal = {Biogeosciences},

volume = {10},

number = {7},

pages = {4861--4878},

abstract = {Abstract. The long-held perception of the deep sea consisting of monotonous slopes and uniform oceanic basins has over the decades given way to the idea of a complex system with wide habitat heterogeneity. Under the prism of a highly diverse environment, a large dataset was used to describe and compare spatial patterns of the dominant small-size components of deep-sea benthos, metazoan meiofauna and microbes, from Mediterranean basins and slopes. A grid of 73 stations sampled at five geographical areas along the central-eastern Mediterranean Basin (central Mediterranean, northern Aegean Sea, Cretan Sea, Libyan Sea, eastern Levantine) spanning over 4 km in depth revealed a high diversity, irrespective of the benthic group or level of taxonomic analysis. A common decreasing bathymetric trend was detected for meiobenthic abundance, major taxa diversity and nematode genera richness, but no differences were found between the two habitats (basin vs slope). In contrast, microbial richness is significantly higher at the basin ecosystem and tends to increase with depth. Multivariate analyses (β- and δ-diversity and ordination analysis) complemented these results and underlined the high within-habitat variability of benthic communities. Meiofaunal communities in particular were found to change gradually and vary more towards the abyss. On the other hand, microbial communities were highly variable, even among samples of the same area, habitat and bathymetry. A significant proportion of the variation of benthic communities and their descriptors was explained by depth and proxies of food availability (sedimentary pigments and organic content), but the combination of predictor variables and the strength of the relationship varied depending on the data set used (based on type of habitat, benthic component, taxonomic level). This, along with the observed high within-habitat variability suggests that other factors, which tend to vary at local scale (hydrodynamics, substrate structure, geochemistry, food quality, etc.), may also relate to the observed benthic patterns. Overall, the results presented here suggest that differences in small-size benthos between the basin and slope habitats are neither strong nor consistent; it appears that within-habitat variability is high, differences among depth ranges are important and further investigation of possible environmental drivers of benthic patterns is needed.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{wiegert_carbon_2013,

title = {Carbon and chlorine isotope fractionation during microbial degradation of tetra-and trichloroethene},

author = {C Wiegert and M Mandalakis and T Knowles and P N Polymenakou and C Aeppli and J Macháčková and H Holmstrand and R P Evershed and R D Pancost and O Gustafsson},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84879211180&doi=10.1021%2fes305236y&partnerID=40&md5=03f5f7bbfe402bab4b6a88ddd20e0412},

doi = {10.1021/es305236y},

issn = {0013936X},

year  = {2013},

date = {2013-01-01},

journal = {Environmental Science and Technology},

volume = {47},

number = {12},

pages = {6449--6456},

abstract = {Two-dimensional compound-specific isotope analysis (2D-CSIA), combining stable carbon and chlorine isotopes, holds potential for monitoring of natural attenuation of chlorinated ethenes (CEs) in contaminated soil and groundwater. However, interpretation of 2D-CSIA data sets is challenged by a shortage of experimental Cl isotope enrichment factors. Here, isotope enrichments factors for C and Cl (i.e., εC and εCl) were determined for biodegradation of tetrachloroethene (PCE) and trichloroethene (TCE) using microbial enrichment cultures from a heavily CE-contaminated aquifer. The obtained values were εC = -5.6 ± 0.7‰ (95% CI) and εCl = -2.0 ± 0.5‰ for PCE degradation and εC = -8.8 ± 0.2‰ and εCl = -3.5 ± 0.5‰ for TCE degradation. Combining the values for both εC and εCl yielded mechanism-diagnostic εCl/εC ratios of 0.35 ± 0.11 and 0.37 ± 0.11 for the degradation of PCE and TCE, respectively. Application of the obtained εC and εCl values to a previously investigated field site gave similar estimates for the fraction of degraded contaminant as in the previous study, but with a reduced uncertainty in assessment of the natural attenuation. Furthermore, 16S rRNA gene clone library analyses were performed on three samples from the PCE degradation experiments. A species closely related to Desulfitobacterium aromaticivorans UKTL dominated the reductive dechlorination process. This study contributes to the development of 2D-CSIA as a tool for evaluating remediation strategies of CEs at contaminated sites. © 2013 American Chemical Society.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{polymenakou_assessing_2013,

title = {Assessing the short-term variability of bacterial composition in background aerosols of the Eastern Mediterranean during a rapid change of meteorological conditions},

author = {P N Polymenakou and M Mandalakis},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84880310891&doi=10.1007%2fs10453-013-9295-1&partnerID=40&md5=ef667ffa44cfdff0d4e71cddb8e8b969},

doi = {10.1007/s10453-013-9295-1},

issn = {03935965},

year  = {2013},

date = {2013-01-01},

journal = {Aerobiologia},

volume = {29},

number = {3},

pages = {429--441},

abstract = {This study used a PCR-based molecular identification technique to examine bacterial assemblage composition in background aerosols of the eastern Mediterranean Sea during a rapid change of meteorological conditions. 16S rDNA fragments of 166 clones were identified and were affiliated with six bacterial phyla (Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Spirochetes, and Fusobacteria), plant-related sequences, and other uncultivated bacterial groups. The analyzed clones were closely related to sequences previously characterized from diverse sources including soil, plants, marine water and sediment, human skin, activated sludge, house dust, indoor air, gut microbiota, and food. Plant- and human-associated sequences accounted for the largest fraction of the identified clones. Spore-forming Firmicutes showed a considerable increase when air mass origin changed from north to south implying that south winds favored bacterial spores transportation from the inland of Crete or North Africa. However, no conclusive trends were revealed for other groups of microorganisms. The influence of air mass origin was further investigated for marine- and terrestrial-associated sequences. A higher number of marine-associated sequences were identified when south winds crossed the inland of Crete, while the opposite was observed when north winds passed over the Aegean Sea. This discrepancy could be partly explained by the fact that the north winds were blowing at very low speed which constrained the formation of sea-spray aerosols and the ejection of marine microbes from sea surface to the atmosphere. Overall, the interpretation of bacterial assemblage composition in relation to the meteorological conditions was proved to be a complicated task which is in line with previous studies. © 2013 Springer Science+Business Media Dordrecht.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kilias_new_2013,

title = {New insights into hydrothermal vent processes in the unique shallow-submarine arc-volcano, Kolumbo (Santorini), Greece.},

author = {Stephanos P Kilias and Paraskevi Nomikou and Dimitrios Papanikolaou and Paraskevi N Polymenakou and Athanasios Godelitsas and Ariadne Argyraki and Steven Carey and Platon Gamaletsos and Theo J Mertzimekis and Eleni Stathopoulou and Joerg Goettlicher and Ralph Steininger and Konstantina Betzelou and Isidoros Livanos and Christos Christakis and Katherine Croff Bell and Michael Scoullos},

url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3741630&tool=pmcentrez&rendertype=abstract},

doi = {DOI:10.1038/srep02421},

year  = {2013},

date = {2013-01-01},

journal = {Scientific reports},

volume = {3},

pages = {2421},

abstract = {We report on integrated geomorphological, mineralogical, geochemical and biological investigations of the hydrothermal vent field located on the floor of the density-stratified acidic (pH ∼ 5) crater of the Kolumbo shallow-submarine arc-volcano, near Santorini. Kolumbo features rare geodynamic setting at convergent boundaries, where arc-volcanism and seafloor hydrothermal activity are occurring in thinned continental crust. Special focus is given to unique enrichments of polymetallic spires in Sb and Tl (±Hg, As, Au, Ag, Zn) indicating a new hybrid seafloor analogue of epithermal-to-volcanic-hosted-massive-sulphide deposits. Iron microbial-mat analyses reveal dominating ferrihydrite-type phases, and high-proportion of microbial sequences akin to "Nitrosopumilus maritimus", a mesophilic Thaumarchaeota strain capable of chemoautotrophic growth on hydrothermal ammonia and CO2. Our findings highlight that acidic shallow-submarine hydrothermal vents nourish marine ecosystems in which nitrifying Archaea are important and suggest ferrihydrite-type Fe(3+)-(hydrated)-oxyhydroxides in associated low-temperature iron mats are formed by anaerobic Fe(2+)-oxidation, dependent on microbially produced nitrate.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gontikaki_microbial_2012,

title = {Microbial Response to Organic Matter Enrichment in the Oligotrophic Levantine Basin (Eastern Mediterranean)},

author = {E Gontikaki and P N Polymenakou and B Thornton and B E Narayanaswamy and K Black and A Tselepides and U Witte},

url = {http://www.tandfonline.com/doi/abs/10.1080/01490451.2011.605822},

doi = {10.1080/01490451.2011.605822},

issn = {0149-0451, 1521-0529},

year  = {2012},

date = {2012-09-01},

urldate = {2020-08-10},

journal = {Geomicrobiology Journal},

volume = {29},

number = {7},

pages = {648--655},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{croff_bell_continued_2012,

title = {Continued Exploration of the Santorini Volcanic Field and Cretan Basin, Aegean Sea in New Frontiers in Ocean Exploration: The E/V Nautilus and NOAA Ship Okeanos Explorer 2011 Field Season},

author = {K Croff Bell and P Nomikou and S Carey and E Stathopoulou and P N Polymenakou and A Godelitsas and C Roman and M Parks},

year  = {2012},

date = {2012-01-01},

journal = {Oceanography},

volume = {25},

pages = {30--31},

note = {Edition: Supplement},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{polymenakou_atmosphere_2012,

title = {Atmosphere: A source of pathogenic or beneficial microbes?},

author = {P N Polymenakou},

url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84871718076&partnerID=40&md5=c1b5f056ccf45f18b3321aed5fb4d165},

year  = {2012},

date = {2012-01-01},

journal = {Atmosphere},

volume = {3},

pages = {87 -- 102},

abstract = {The atmosphere has been described as one of the last frontiers of biological exploration on Earth. The composition of microbial communities in the atmosphere is still not well-defined, and taxonomic studies of bacterial diversity in the outdoor air have just started to emerge, whereas our knowledge about the functional potential of air microbiota is scant. When in the air, microorganisms can be attached to ambient particles and/or incorporated into water droplets of clouds, fog, and precipitation (i.e., rain, snow, hail). Further, they can be deposited back to earth’s surfaces via dry and wet deposition processes and they can possibly induce an effect on the diversity and function of aquatic and terrestrial ecosystems or impose impacts to human health through microbial pathogens dispersion. In addition to their impact on ecosystem and public health, there are strong indications that air microbes are metabolically active and well adapted to the harsh atmospheric conditions. Furthermore they can affect atmospheric chemistry and physics, with important implications in meteorology and global climate. This review summarizes current knowledge about the ubiquitous presence of microbes in the atmosphere and discusses their ability to survive in the atmospheric environment. The purpose is to evaluate the atmospheric environment as a source of pathogenic or beneficial microbes and to assess the biotechnological opportunities that may offer. © 2012 by the authors.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{mandalakis_free_2011,

title = {Free and combined amino acids in marine background atmospheric aerosols over the Eastern Mediterranean},

author = {M Mandalakis and M Apostolaki and T Tziaras and P Polymenakou and E G Stephanou},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-78650970210&doi=10.1016%2fj.atmosenv.2010.10.046&partnerID=40&md5=2b9f84c32b126f829caf5b42b32eab66},

doi = {10.1016/j.atmosenv.2010.10.046},

issn = {13522310},

year  = {2011},

date = {2011-01-01},

journal = {Atmospheric Environment},

volume = {45},

number = {4},

pages = {1003--1009},

abstract = {During a six-week intensive field campaign at a background marine site of the Eastern Mediterranean, consecutive 24-h air samples were collected and analyzed for combined (CAA) and free amino acids (FAA), as well as for key chemical characteristics of aerosols. The total concentration of CAA (719 ± 326 pmol m-3) was on average four times higher than that of FAA (172 ± 147 pmol m-3), while glycine was the most abundant compound detected in both FAA and CAA. Back-trajectory analysis demonstrated that the geographical origin of the air masses did not have a significant influence on the atmospheric levels of amino acids. Wind speed was found to be the most important meteorological factor and it exhibited a negative correlation with both FAA and CAA. Moreover, FAA and CAA concentrations showed a more pronounced correlation with water-soluble organic carbon (WSOC) than elemental carbon. On average, FAA and CAA accounted for 0.3 ± 0.2% and 1.8 ± 0.8% of WSOC, respectively. The levels of anionic surfactants determined as methylene blue active substances did not show any positive correlation with CAA, while the corresponding correlation with FAA was only of marginal significance. The total protein concentration measured by NanoOrange assay was six times higher compared to that measured through CAA. It is suggested that the results from the application of commercially available protein quantitation kits should always be considered with caution, as these are more prone to matrix-related interferences. © 2010 Elsevier Ltd.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{danovaro_deep-sea_2010,

title = {Deep-Sea Biodiversity in the Mediterranean Sea: The Known, the Unknown, and the Unknowable},

author = {Roberto Danovaro and Joan Batista Company and Cinzia Corinaldesi and Gianfranco D'Onghia and Bella Galil and Cristina Gambi and Andrew J Gooday and Nikolaos Lampadariou and Gian Marco Luna and Caterina Morigi and Karine Olu and Paraskevi Polymenakou and Eva Ramirez-Llodra and Anna Sabbatini and Francesc Sardà and Myriam Sibuet and Anastasios Tselepides},

editor = {Brian Gratwicke},

url = {https://dx.plos.org/10.1371/journal.pone.0011832},

doi = {10.1371/journal.pone.0011832},

issn = {1932-6203},

year  = {2010},

date = {2010-08-01},

urldate = {2020-08-10},

journal = {PLoS ONE},

volume = {5},

number = {8},

pages = {e11832},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kouridaki_phylogenetic_2010,

title = {Phylogenetic diversity of sediment bacteria from the deep Northeastern Pacific Ocean: A comparison with the deep Eastern Mediterranean Sea},

author = {I Kouridaki and P N Polymenakou and A Tselepides and M Mandalakis and K L Smith Jr.},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79251591617&doi=10.2436%2f20.1501.01.119&partnerID=40&md5=2af215d627ad9a23e6fb4253c3cce940},

doi = {10.2436/20.1501.01.119},

issn = {11396709},

year  = {2010},

date = {2010-01-01},

journal = {International Microbiology},

volume = {13},

number = {3},

pages = {143--150},

abstract = {The variability of bacterial community composition and diversity was studied by comparative analysis of five 16S rRNA gene clone libraries from deep-sea sediments (water column depth: 4000 m) of the Northeastern Pacific Ocean and Eastern Mediterranean Sea. This is the first comparison of the bacterial communities living in these deep-sea ecosystems. The estimated chlorophyll a, organic carbon, and C/N ratio provided evidence of significant differences in the trophic state of the sediments between the Northeastern Pacific Ocean and the much warmer Eastern Mediterranean Sea. A diverse range of 16S rRNA gene phylotypes was found in the sediments of both regions. These were represented by 11 different taxonomic groups, with Gammaproteobacteria predominating in the Northeastern Pacific Ocean sediments and Acidobacteria in the Eastern Mediterranean microbial community. In addition, several 16S rRNA gene phylotypes only distantly related to any of the previously identified sequences (non-affiliated rRNA genes) represented a significant fraction of the total sequences. The potential diversity at the two sites differs but remains largely unexplored and remains of continuing scientific interest.},

note = {Publisher: Sociedad Espanola de Microbiologia},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{polymenakou_phylogenetic_2009,

title = {Phylogenetic diversity of sediment bacteria from the southern Cretan margin, Eastern Mediterranean Sea},

author = {P N Polymenakou and N Lampadariou and M Mandalakis and A Tselepides},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-58149484940&doi=10.1016%2fj.syapm.2008.09.006&partnerID=40&md5=17b34fc20d7f492b43bc1cb3ba96588f},

doi = {10.1016/j.syapm.2008.09.006},

issn = {07232020},

year  = {2009},

date = {2009-01-01},

journal = {Systematic and Applied Microbiology},

volume = {32},

number = {1},

pages = {17--26},

abstract = {This study is the first culture-independent report on the regional variability of bacterial diversity in oxic sediments from the unexplored southern Cretan margin (SCM). Three main deep basins (water column depths: 2670-3603 m), located at the mouth of two submarine canyons (Samaria Gorge and Paximades Channel) and an adjacent slope system, as well as two shallow upper-slope stations (water column depths: 215 and 520 m), were sampled. A total of 454 clones were sequenced and the bacterial richness, estimated through five clone libraries using rarefaction analysis, ranged from 71 to 296 unique phylotypes. The average sequence identity of the retrieved Cretan margin sequences compared to the textgreater1,000,000 known rRNA sequences was only 93.5%. A diverse range of prokaryotes was found in the sediments, which were represented by 15 different taxonomic groups at the phylum level. The phylogenetic analysis revealed that these new sequences grouped with the phyla Acidobacteria, Planctomycetes, Actinobacteria, Gamma-, Alpha- and Delta-proteobacteria. Only a few bacterial clones were affiliated with Chloroflexi, Bacteroidetes, Firmicutes, Gemmatimonadetes, Verrucomicrobia, Nitrospirae, Beta-proteobacteria, Lentisphaerae and Dictyoglomi. A large fraction of the retrieved sequences (12%) did not fall into any taxonomic division previously characterized by molecular criteria, whereas four novel division-level lineages, termed candidate division SCMs, were identified. Bacterial community composition demonstrated significant differences in comparison to previous phylogenetic studies. This divergence was mainly triggered by the dominance of Acidobacteria and Actinobacteria and reflected a bacterial community different from that currently known for oxic and pristine marine sediments. © 2008 Elsevier GmbH. All rights reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{borin_sulfur_2009,

title = {Sulfur cycling and methanogenesis primarily drive microbial colonization of the highly sulfidic Urania deep hypersaline basin},

author = {S Borin and L Brusetti and F Mapelli and G D’Auria and T Brusa and M Marzorati and A Rizzi and M Yakimov and D Marty and G J de Lange and P Van Der Wielen and H Bolhuis and T J McGenity and P N Polymenakou and E Malinverno and L Giuliano and C Corselli and D Daffonchio},

url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-67249101298&partnerID=40&md5=0a1da8cf34d5d1b69736bc5aeb7f0f75},

year  = {2009},

date = {2009-01-01},

journal = {Proceedings of the National Academy of Sciences of the United States of America},

volume = {106},

pages = {9151 -- 9156},

abstract = {Urania basin in the deep Mediterranean Sea houses a lake that is textgreater100 m deep, devoid of oxygen, 6 times more saline than seawater, and has very high levels of methane and particularly sulfide (up to 16 mM), making it among the most sulfidic water bodies on Earth. Along the depth profile there are 2 chemoclines, a steep one with the overlying oxic seawater, and another between anoxic brines of different density, where gradients of salinity, electron donors and acceptors occur. To identify and differentiate the microbes and processes contributing to the turnover of organic matter and sulfide along the water column, these chemoclines were sampled at a high resolution. Bacterial cell numbers increased up to a hundredfold in the chemoclines as a consequence of elevated nutrient availability, with higher numbers in the upper interface where redox gradient was steeper. Bacterial and archaeal communities, analyzed by DNA fingerprinting, 16S rRNA gene libraries, activity measurements, and cultivation, were highly stratified and metabolically more active along the chemoclines compared with seawater or the uniformly hypersaline brines. Detailed analysis of 16S rRNA gene sequences revealed that in both chemoclines δ- and ε-Proteobacteria, predominantly sulfate reducers and sulfur oxidizers, respectively, were the dominant bacteria. In the deepest layers of the basin MSBL1, putatively responsible for methanogenesis, dominated among archaea. The data suggest that the complex microbial community is adapted to the basin’s extreme chemistry, and the elevated biomass is driven largely by sulfur cycling and methanogenesis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{polymenakou_exo-enzymatic_2008,

title = {Exo-enzymatic activities and organic matter properties in deep-sea canyon and slope systems off the southern Cretan margin},

author = {Paraskevi N Polymenakou and Nikolaos Lampadariou and Anastasios Tselepides},

url = {https://linkinghub.elsevier.com/retrieve/pii/S0967063708001155},

doi = {10.1016/j.dsr.2008.05.010},

issn = {09670637},

year  = {2008},

date = {2008-10-01},

urldate = {2020-08-10},

journal = {Deep Sea Research Part I: Oceanographic Research Papers},

volume = {55},

number = {10},

pages = {1318--1329},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{polymenakou_particle_2008,

title = {Particle size distribution of airborne microorganisms and pathogens during an intense African dust event in the eastern Mediterranean},

author = {P N Polymenakou and M Mandalakis and E G Stephanou and A Tselepides},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-40849120624&doi=10.1289%2fehp.10684&partnerID=40&md5=60deb0b8f1ff1ce93a2880b8b87b4a54},

doi = {10.1289/ehp.10684},

issn = {00916765},

year  = {2008},

date = {2008-01-01},

journal = {Environmental Health Perspectives},

volume = {116},

number = {3},

pages = {292--296},

abstract = {Background: The distribution of microorganisms, and especially pathogens, over airborne particles of different sizes has been ignored to a large extent, but it could have significant implications regarding the dispersion of these microorganisms across the planet, thus affecting human health. Objectives: We examined the microbial quality of the aerosols over the eastern Mediterranean region during an African storm to determine the size distribution of microorganisms in the air. Methods: We used a five-stage cascade impactor for bioaerosol collection in a coastal city on the eastern Mediterranean Sea during a north African dust storm. Bacterial communities associated with aerosol particles of six different size ranges were characterized following molecular culture-independent methods, regardless of the cell culturability (analysis of 16S rRNA genes). Results: All 16S rDNA clone libraries were diverse, including sequences commonly found in Soil and marine ecosystems. Spore-forming bacteria such as Firmicules dominated large particle sizes (textgreater 3.3 μm), whereas clones affiliated with Actinobacteria (found commonly in soil) and Bacteroidetes (widely distributed in the environment) gradually increased their abundance in aerosol particles of reduced size (textless 33 μm). A large portion of the clones detected at respiratory particle sizes (textless 3.3 μm) were phylogenetic neighbors to human pathogens that have been linked to several diseases. Conclusions: The presence of aerosolized bacteria in small, size particles may have significant implications to human health via intercontinental transportation of pathogens.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{polymenakou_bacterial_2007,

title = {Bacterial and organic matter distribution in the sediments of the Thracian Sea (NE Aegean Sea)},

author = {Paraskevi N Polymenakou and Glykeria Fragkioudaki and Anastasios Tselepides},

url = {https://linkinghub.elsevier.com/retrieve/pii/S0278434307001367},

doi = {10.1016/j.csr.2007.05.003},

issn = {02784343},

year  = {2007},

date = {2007-10-01},

urldate = {2020-08-10},

journal = {Continental Shelf Research},

volume = {27},

number = {17},

pages = {2187--2197},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{polymenakou_organic_2007,

title = {Organic Matter Preservation and Microbial Community Accumulations in Deep-Hypersaline Anoxic Basins},

author = {Paraskevi N Polymenakou and Euripides G Stephanou and Anastasios Tselepides and Stefan Bertilsson},

url = {http://www.tandfonline.com/doi/abs/10.1080/01490450601134283},

doi = {10.1080/01490450601134283},

issn = {0149-0451, 1521-0529},

year  = {2007},

date = {2007-01-01},

urldate = {2020-08-10},

journal = {Geomicrobiology Journal},

volume = {24},

number = {1},

pages = {19--29},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{polymenakou_carbon_2006,

title = {Carbon speciation and composition of natural microbial communities in polluted and pristine sediments of the Eastern Mediterranean Sea},

author = {Paraskevi N Polymenakou and Anastasios Tselepides and Euripides G Stephanou and Stefan Bertilsson},

url = {https://linkinghub.elsevier.com/retrieve/pii/S0025326X06001317},

doi = {10.1016/j.marpolbul.2006.03.021},

issn = {0025326X},

year  = {2006},

date = {2006-11-01},

urldate = {2020-08-10},

journal = {Marine Pollution Bulletin},

volume = {52},

number = {11},

pages = {1396--1405},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{daffonchio_stratified_2006,

title = {Stratified prokaryote network in the oxic-anoxic transition of a deep-sea halocline},

author = {D Daffonchio and S Borin and T Brusa and L Brusetti and P W J J Van Der Wielen and H Bolhuis and M M Yakimov and G D’Auria and L Giuliano and D Marty and C Tamburini and T J McGenity and J E Hallsworth and A M Sass and K N Timmis and A Telepidis and G J de Lange and A Hübner and J Thomson and S P Varnaavs and F Gasparoni and H W Gerber and H W Malinverno and C Corselli and J Garcin and B McKew and P N Golyshin and N Lampadariou and P N Polymenakou and D Calore and S Cenedesse and F Zanon and S Hoog},

url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-33644865958&partnerID=40&md5=45aab482809ee378554f4890a3772cb9},

doi = {https://doi.org/10.1038/nature04418},

year  = {2006},

date = {2006-01-01},

journal = {Nature},

volume = {440},

number = {7081},

pages = {203--207},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pusceddu_effects_2005,

title = {Effects of bottom trawling on the quantity and biochemical composition of organic matter in coastal marine sediments (Thermaikos Gulf, northwestern Aegean Sea)},

author = {A Pusceddu and C Fiordelmondo and P Polymenakou and T Polychronaki and A Tselepides and R Danovaro},

url = {https://linkinghub.elsevier.com/retrieve/pii/S0278434305001421},

doi = {10.1016/j.csr.2005.08.013},

issn = {02784343},

year  = {2005},

date = {2005-12-01},

urldate = {2020-08-10},

journal = {Continental Shelf Research},

volume = {25},

number = {19-20},

pages = {2491--2505},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{polymenakou_benthic_2005,

title = {Benthic microbial abundance and activities in an intensively trawled ecosystem (Thermaikos Gulf, Aegean Sea)},

author = {Paraskevi N Polymenakou and Antonio Pusceddu and Anastasios Tselepides and Thalia Polychronaki and Antonia Giannakourou and Carla Fiordelmondo and Eleni Hatziyanni and Roberto Danovaro},

url = {https://linkinghub.elsevier.com/retrieve/pii/S0278434305001470},

doi = {10.1016/j.csr.2005.08.018},

issn = {02784343},

year  = {2005},

date = {2005-12-01},

urldate = {2020-08-10},

journal = {Continental Shelf Research},

volume = {25},

number = {19-20},

pages = {2570--2584},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{polymenakou_effect_2005,

title = {Effect of temperature and additional carbon sources on phenol degradation by an indigenous soil Pseudomonad},

author = {Paraskevi N Polymenakou and Euripides G Stephanou},

url = {http://link.springer.com/10.1007/s10532-004-3333-1},

doi = {10.1007/s10532-004-3333-1},

issn = {0923-9820, 1572-9729},

year  = {2005},

date = {2005-10-01},

urldate = {2020-08-10},

journal = {Biodegradation},

volume = {16},

number = {5},

pages = {403--413},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{polymenakou_bacterial_2005,

title = {Bacterial Community Composition in Different Sediments from the Eastern Mediterranean Sea: a Comparison of Four 16S Ribosomal DNA Clone Libraries},

author = {Paraskevi N Polymenakou and Stefan Bertilsson and Anastasios Tselepides and Euripides G Stephanou},

url = {http://link.springer.com/10.1007/s00248-005-0005-6},

doi = {10.1007/s00248-005-0005-6},

issn = {0095-3628, 1432-184X},

year  = {2005},

date = {2005-10-01},

urldate = {2020-08-10},

journal = {Microbial Ecology},

volume = {50},

number = {3},

pages = {447--462},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{polymenakou_links_2005,

title = {Links between Geographic Location, Environmental Factors, and Microbial Community Composition in Sediments of the Eastern Mediterranean Sea},

author = {P N Polymenakou and S Bertilsson and A Tselepides and E G Stephanou},

url = {http://link.springer.com/10.1007/s00248-004-0274-5},

doi = {10.1007/s00248-004-0274-5},

issn = {0095-3628, 1432-184X},

year  = {2005},

date = {2005-04-01},

urldate = {2020-08-10},

journal = {Microbial Ecology},

volume = {49},

number = {3},

pages = {367--378},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{polymenakou_study_2005,

title = {Study of the mineralization effect on the distribution of lipids in sediments from the Cretan Sea: Evidence for hydrocarbon degradation and starvation stress},

author = {P N Polymenakou and A Tselepides and E G Stephanou},

url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-27744476221&partnerID=40&md5=d20fdba5930d83604c3f1010a58783da},

year  = {2005},

date = {2005-01-01},

journal = {Continental Shelf Research},

volume = {25},

pages = {2196--2212},

abstract = {Sedimentary diagenetic processes alter the composition and distribution of different lipid compounds. In the present study alterations mediated by microbial communities were investigated along a bathymetric gradient (100 m at 35°23'N-25°09'E, 617 m at 35°33'N- 25°08'E, 1494 m at 35°44'N-25°08'E) over the continental margin of northern Crete (Greece, Eastern Mediterranean Sea). Bacterial abundances and distribution were studied using phospholipid linked fatty acids (PLFA), in the range of C8-C22, released from intact phospholipids. Lipid components (aliphatic hydrocarbons, free fatty acids, glycerides and glycolipids) were studied over a 2-month incubation period. Carbon mineralization rates at all stations indicated an uneven distribution of active aerobic bacteria with values decreasing towards the deeper stations. PLFA homologue profiles denoted that aerobic gram negative and sulfur oxidizing bacteria dominated microbial communities while the anaerobic, gram positive and sulfate reducing bacteria occurred only in traces. The n-alkane (NA) composition revealed a strong predominance of homologues with odd carbon numbers suggesting an important terrestrial contribution to the sediments. The estimated descriptive ratios of NA, the sum of short chain NA (C15-C20) and long chain NA (C21-C 36) to 17α(H),21β(H)-C30-hopane, before and after a two-month incubation period, indicated the occurrence of hydrocarbon degradation processes. Increased ratios of saturated to unsaturated fatty acids were also recorded after the incubation indicating the starvation of bacterial communities by the end of the experiments. © 2005 Elsevier Ltd. All rights reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}