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Polymenakou PN, Nomikou P, Hannington M, Petersen S, Kilias SP, Anastasiou TI, Papadimitriou V, Zaka E, Kristoffersen JB, Lampridou D, Wind S, Heinath V, Lange S, Magoulas A. Taxonomic diversity of microbial communities in sub-seafloor hydrothermal sediments of the active Santorini-Kolumbo volcanic field. Front Microbiol 2023; 14:1188544. [PMID: 37455712 PMCID: PMC10345502 DOI: 10.3389/fmicb.2023.1188544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
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.
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Affiliation(s)
- Paraskevi N. Polymenakou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology, and Aquaculture, Heraklion, Greece
| | - Paraskevi Nomikou
- Faculty of Geology and Geoenvironment, National and Kapodistrian University of Athens, Athens, Greece
| | - Mark Hannington
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Sven Petersen
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Stephanos P. Kilias
- Faculty of Geology and Geoenvironment, National and Kapodistrian University of Athens, Athens, Greece
| | - Thekla I. Anastasiou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology, and Aquaculture, Heraklion, Greece
| | - Vasiliki Papadimitriou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology, and Aquaculture, Heraklion, Greece
| | - Eleutheria Zaka
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology, and Aquaculture, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
| | - Jon Bent Kristoffersen
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology, and Aquaculture, Heraklion, Greece
| | - Danai Lampridou
- Faculty of Geology and Geoenvironment, National and Kapodistrian University of Athens, Athens, Greece
| | - Sandra Wind
- Department of Earth and Environmental Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Verena Heinath
- Institute of Geosciences, University of Kiel (CAU), Kiel, Germany
| | - Sabine Lange
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Antonios Magoulas
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology, and Aquaculture, Heraklion, Greece
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Salvà-Serra F, Pérez-Pantoja D, Donoso RA, Jaén-Luchoro D, Fernández-Juárez V, Engström-Jakobsson H, Moore ERB, Lalucat J, Bennasar-Figueras A. Comparative genomics of Stutzerimonas balearica ( Pseudomonas balearica): diversity, habitats, and biodegradation of aromatic compounds. Front Microbiol 2023; 14:1159176. [PMID: 37275147 PMCID: PMC10234333 DOI: 10.3389/fmicb.2023.1159176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/13/2023] [Indexed: 06/07/2023] Open
Abstract
Stutzerimonas balearica (Pseudomonas balearica) has been found principally in oil-polluted environments. The capability of S. balearica to thrive from the degradation of pollutant compounds makes it a species of interest for potential bioremediation applications. However, little has been reported about the diversity of S. balearica. In this study, genome sequences of S. balearica strains from different origins were analyzed, revealing that it is a diverse species with an open pan-genome that will continue revealing new genes and functionalities as the genomes of more strains are sequenced. The nucleotide signatures and intra- and inter-species variation of the 16S rRNA genes of S. balearica were reevaluated. A strategy of screening 16S rRNA gene sequences in public databases enabled the detection of 158 additional strains, of which only 23% were described as S. balearica. The species was detected from a wide range of environments, although mostly from aquatic and polluted environments, predominantly related to petroleum oil. Genomic and phenotypic analyses confirmed that S. balearica possesses varied inherent capabilities for aromatic compounds degradation. This study increases the knowledge of the biology and diversity of S. balearica and will serve as a basis for future work with the species.
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Affiliation(s)
- Francisco Salvà-Serra
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Raúl A. Donoso
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Víctor Fernández-Juárez
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Hedvig Engström-Jakobsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Edward R. B. Moore
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jorge Lalucat
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Antoni Bennasar-Figueras
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
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Roufou S, Griffin S, Katsini L, Polańska M, Van Impe JF, Valdramidis VP. The (potential) impact of seasonality and climate change on the physicochemical and microbial properties of dairy waste and its management. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.07.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Mandalakis M, Anastasiou TI, Martou N, Keisaris S, Greveniotis V, Katharios P, Lazari D, Krigas N, Antonopoulou E. Antibacterial Effects of Essential Oils of Seven Medicinal-Aromatic Plants Against the Fish Pathogen Aeromonas veronii bv. sobria: To Blend or Not to Blend? Molecules 2021; 26:2731. [PMID: 34066575 PMCID: PMC8125735 DOI: 10.3390/molecules26092731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 11/17/2022] Open
Abstract
Despite progress achieved, there is limited available information about the antibacterial activity of constituents of essential oils (EOs) from different medicinal-aromatic plants (MAPs) against fish pathogens and the complex interactions of blended EOs thereof. The present study aimed to investigate possible synergistic antimicrobial effects of EOs from seven Greek MAPs with strong potential against Aeromonas veronii bv. sobria, a fish pathogen associated with aquaculture disease outbreaks. The main objective was to evaluate whether blending of these EOs can lead to increased antimicrobial activity against the specific microorganism. A total of 127 combinations of EOs were prepared and their effect on A. veronii bv. sobria growth was tested in vitro. We examined both the inhibitory and bactericidal activities of the individual EOs and compared them to those of the blended EOs. The vast majority of the investigated combinations exhibited significant synergistic and additive effects, while antagonistic effects were evident only in a few cases, such as the mixtures containing EOs from rosemary, lemon balm and pennyroyal. The combination of EOs from Greek oregano and wild carrot, as well as the combinations of those two with Spanish oregano or savoury were the most promising ones. Overall, Greek oregano, savoury and Spanish oregano EOs were the most effective ones when applied either in pure form or blended with other EOs.
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Affiliation(s)
- Manolis Mandalakis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, 71500 Heraklion, Greece; (M.M.); (T.I.A.); (P.K.)
| | - Thekla I. Anastasiou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, 71500 Heraklion, Greece; (M.M.); (T.I.A.); (P.K.)
| | - Natalia Martou
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (N.M.); (S.K.)
| | - Sofoklis Keisaris
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (N.M.); (S.K.)
| | - Vasileios Greveniotis
- Institute of Industrial and Forage Crops, Hellenic Agricultural Organization Demeter, 41335 Larisa, Greece;
| | - Pantelis Katharios
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, 71500 Heraklion, Greece; (M.M.); (T.I.A.); (P.K.)
| | - Diamanto Lazari
- Laboratory of Pharmacognosy, School of Pharmacy, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Nikos Krigas
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Demeter, P.O. Box 60458, 57001 Thessaloniki, Greece
| | - Efthimia Antonopoulou
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (N.M.); (S.K.)
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Bravakos P, Mandalakis M, Nomikou P, Anastasiou TI, Kristoffersen JB, Stavroulaki M, Kilias S, Kotoulas G, Magoulas A, Polymenakou PN. Genomic adaptation of Pseudomonas strains to acidity and antibiotics in hydrothermal vents at Kolumbo submarine volcano, Greece. Sci Rep 2021; 11:1336. [PMID: 33446715 PMCID: PMC7809023 DOI: 10.1038/s41598-020-79359-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/04/2020] [Indexed: 12/05/2022] Open
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 CO2-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.
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Affiliation(s)
- Panos Bravakos
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (IMBBC-HCMR), Gournes Pediados, Heraklion Crete, Greece
| | - Manolis Mandalakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (IMBBC-HCMR), Gournes Pediados, Heraklion Crete, Greece
| | - Paraskevi Nomikou
- Department of Geology and Geoenvironment, National and Kapodistrian University of Athens, Athens, Greece
| | - Thekla I Anastasiou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (IMBBC-HCMR), Gournes Pediados, Heraklion Crete, Greece
| | - Jon Bent Kristoffersen
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (IMBBC-HCMR), Gournes Pediados, Heraklion Crete, Greece
| | - Melanthia Stavroulaki
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (IMBBC-HCMR), Gournes Pediados, Heraklion Crete, Greece
| | - Stephanos Kilias
- Department of Geology and Geoenvironment, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios Kotoulas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (IMBBC-HCMR), Gournes Pediados, Heraklion Crete, Greece
| | - Antonios Magoulas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (IMBBC-HCMR), Gournes Pediados, Heraklion Crete, Greece
| | - Paraskevi N Polymenakou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (IMBBC-HCMR), Gournes Pediados, Heraklion Crete, Greece.
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Nelson KS, Baltar F, Lamare MD, Morales SE. Ocean acidification affects microbial community and invertebrate settlement on biofilms. Sci Rep 2020; 10:3274. [PMID: 32094391 PMCID: PMC7039980 DOI: 10.1038/s41598-020-60023-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 02/05/2020] [Indexed: 11/18/2022] Open
Abstract
Increased atmospheric CO2 is driving ocean acidification (OA), and potential changes in marine ecosystems. Research shows that both planktonic and benthic communities are affected, but how these changes are linked remains unresolved. Here we show experimentally that decreasing seawater pH (from pH 8.1 to 7.8 and 7.4) leads to reduced biofilm formation and lower primary producer biomass within biofilms. These changes occurred concurrently with a re-arrangement of the biofilm microbial communities. Changes suggest a potential shift from autotrophic to heterotrophic dominated biofilms in response to reduced pH. In a complimentary experiment, biofilms reared under reduced pH resulted in altered larval settlement for a model species (Galeolaria hystrix). These findings show that there is a potential cascade of impacts arising from OA effects on biofilms that may drive important community shifts through altered settlement patterns of benthic species.
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Affiliation(s)
- Katie S Nelson
- Department of Marine Science, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Federico Baltar
- Department of Marine Science, University of Otago, PO Box 56, Dunedin, 9054, New Zealand.,NIWA/University of Otago Research Centre for Oceanography, PO Box 56, Dunedin, 9054, New Zealand.,Department of Functional and Evolutionary Ecology, University of Vienna, A-1090, Vienna, Austria
| | - Miles D Lamare
- Department of Marine Science, University of Otago, PO Box 56, Dunedin, 9054, New Zealand. .,NIWA/University of Otago Research Centre for Oceanography, PO Box 56, Dunedin, 9054, New Zealand.
| | - Sergio E Morales
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand.
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Anastasiou TI, Mandalakis M, Krigas N, Vézignol T, Lazari D, Katharios P, Dailianis T, Antonopoulou E. Comparative Evaluation of Essential Oils from Medicinal-Aromatic Plants of Greece: Chemical Composition, Antioxidant Capacity and Antimicrobial Activity against Bacterial Fish Pathogens. Molecules 2019; 25:E148. [PMID: 31905915 PMCID: PMC6982863 DOI: 10.3390/molecules25010148] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/23/2019] [Accepted: 12/27/2019] [Indexed: 01/10/2023] Open
Abstract
The administration of antibiotics in aquaculture has raised concern about the impact of their overuse in marine ecosystems, seafood safety and consumers' health. This "green consumerism" has forced researchers to find new alternatives against fish pathogens. The present study focused on 12 Mediterranean medicinal-aromatic plants as potential antimicrobials and antioxidant agents that could be used in fish aquaculture. In vitro assays showed that the essential oils (EOs) from all studied plants had anti-bacterial and antioxidant properties, with their efficacy being dependent on their chemical composition. More specifically, EOs rich in carvacrol, p-cymene and γ-terpinene exhibited not only the strongest inhibitory activity against the growth of bacterial pathogens (inhibitory concentration: 26-88 μg mL-1), but also the greatest total antioxidant capacity (ABTS: 2591-5879 μmole mL-1; CUPRAC: 931-2733 μmole mL-1). These compounds were mainly found in the EOs from Greek oregano (Origanum vulgare subsp. hirtum), Spanish oregano (Thymbra capitata) and savoury (Satureja thymbra) collected from cultivations in Greece. The specific EOs stand out as promising candidates for the treatment of bacterial diseases and oxidative stress in farmed fish. Further in vivo experiments are needed to fully understand the effects of EO dietary supplementation on fish farming processes.
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Affiliation(s)
- Thekla I. Anastasiou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500 Heraklion, Greece; (T.I.A.); (T.V.); (P.K.); (T.D.)
| | - Manolis Mandalakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500 Heraklion, Greece; (T.I.A.); (T.V.); (P.K.); (T.D.)
| | - Nikos Krigas
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Demeter, P.O. Box 60458, 57001 Thessaloniki, Greece;
| | - Thomas Vézignol
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500 Heraklion, Greece; (T.I.A.); (T.V.); (P.K.); (T.D.)
| | - Diamanto Lazari
- Laboratory of Pharmacognosy, School of Pharmacy, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500 Heraklion, Greece; (T.I.A.); (T.V.); (P.K.); (T.D.)
| | - Thanos Dailianis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500 Heraklion, Greece; (T.I.A.); (T.V.); (P.K.); (T.D.)
| | - Efthimia Antonopoulou
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
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