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Meziti A, Smeti E, Daniilides D, Spatharis S, Tsirtsis G, Kormas KA. Increased contribution of parasites in microbial eukaryotic communities of different Aegean Sea coastal systems. PeerJ 2023; 11:e16655. [PMID: 38144191 PMCID: PMC10740597 DOI: 10.7717/peerj.16655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/21/2023] [Indexed: 12/26/2023] Open
Abstract
Background-Aim Protistan communities have a major contribution to biochemical processes and food webs in coastal ecosystems. However, related studies are scarce and usually limited in specific groups and/or sites. The present study examined the spatial structure of the entire protistan community in seven different gulfs and three different depths in a regional Mediterranean Sea, aiming to define taxa that are important for differences detected in the marine microbial network across the different gulfs studied as well as their trophic interactions. Methods Protistan community structure analysis was based on the diversity of the V2-V3 hypervariable region of the 18S rRNA gene. Operational taxonomic units (OTUs) were identified using a 97% sequence identity threshold and were characterized based on their taxonomy, trophic role, abundance and niche specialization level. The differentially abundant, between gulfs, OTUs were considered for all depths and interactions amongst them were calculated, with statistic and network analysis. Results It was shown that Dinophyceae, Bacillariophyta and Syndiniales were the most abundant groups, prevalent in all sites and depths. Gulfs separation was more striking at surface corroborating with changes in environmental factors, while it was less pronounced in higher depths. The study of differentially abundant, between gulfs, OTUs revealed that the strongest biotic interactions in all depths occurred between parasite species (mainly Syndiniales) and other trophic groups. Most of these species were generalists but not abundant highlighting the importance of rare species in protistan community assemblage. Conclusion Overall this study revealed the emergence of parasites as important contributors in protistan network regulation regardless of depth.
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Affiliation(s)
- Alexandra Meziti
- Department of Marine Sciences, University of the Aegean, Mytilene, Greece
| | - Evangelia Smeti
- Department of Marine Sciences, University of the Aegean, Mytilene, Greece
- Institute of Marine Biological Resources & Inland Waters, Hellenic Centre for Marine Research, Anavissos, Greece
| | - Daniil Daniilides
- Faculty of Biology, Department of Ecology and Systematics, University of Athens, Athens, Greece
| | - Sofie Spatharis
- School of Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - George Tsirtsis
- Department of Marine Sciences, University of the Aegean, Mytilene, Greece
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Katsoulis-Dimitriou S, Lefkaditis M, Barmpagiannakos S, Kormas KA, Kyparissis A. Comparison of iCOR and Rayleigh atmospheric correction methods on Sentinel-3 OLCI images for a shallow eutrophic reservoir. PeerJ 2022; 10:e14311. [PMID: 36353601 PMCID: PMC9639424 DOI: 10.7717/peerj.14311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
Remote sensing of inland waters is challenging, but also important, due to the need to monitor the ever-increasing harmful algal blooms (HABs), which have serious effects on water quality. The Ocean and Land Color Instrument (OLCI) of the Sentinel-3 satellites program is capable of providing images for the monitoring of such waters. Atmospheric correction is a necessary process in order to retrieve the desired surface-leaving radiance signal and several atmospheric correction methods have been developed through the years. However, many of these correction methods require programming language skills, or function as commercial software plugins, limiting their possibility of use by end users. Accordingly, in this study, the free SNAP software provided by the European Space Agency (ESA) was used to evaluate the possible differences between a partial atmospheric correction method accounting for Rayleigh scattering and a full atmospheric correction method (iCOR), applied on Sentinel-3 OLCI images of a shallow, highly eutrophic water reservoir. For the complete evaluation of the two methods, in addition to the comparison of the band reflectance values, chlorophyll (CHL) and cyanobacteria (CI) indices were also calculated and their values were intercompared. The results showed, that although the absolute values between the two correction methods did not coincide, there was a very good correlation between the two methods for both bands' reflectance (r > 0.73) and the CHL and CI indices values (r > 0.95). Therefore, since iCOR correction image processing time is 25 times longer than Rayleigh correction, it is proposed that the Rayleigh partial correction method may be alternatively used for seasonal water monitoring, especially in cases of long time-series, enhancing time and resources use efficiency. Further comparisons of the two methods in other inland water bodies and evaluation with in situ chlorophyll and cyanobacteria measurements will enhance the applicability of the methodology.
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Affiliation(s)
| | - Marios Lefkaditis
- Department of Agriculture Ichthyology & Aquatic Environment, University of Thessaly, Volos, Magnesia, Greece
| | - Sotirios Barmpagiannakos
- Department of Agriculture Ichthyology & Aquatic Environment, University of Thessaly, Volos, Magnesia, Greece
| | - Konstantinos A. Kormas
- Department of Agriculture Ichthyology & Aquatic Environment, University of Thessaly, Volos, Magnesia, Greece
| | - Aris Kyparissis
- Department of Agriculture Crop Production and Rural Environment, University of Thessaly, Volos, Magnesia, Greece
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3
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Tsoumalakou E, Papadimitriou T, Berillis P, Kormas KA, Levizou E. Spray irrigation with microcystins-rich water affects plant performance from the microscopic to the functional level and food safety of spinach (Spinacia oleracea L.). Sci Total Environ 2021; 789:147948. [PMID: 34051502 DOI: 10.1016/j.scitotenv.2021.147948] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 06/12/2023]
Abstract
Irrigation water coming from freshwater bodies that suffer toxic cyanobacterial blooms causes adverse effects on crop productivity and quality and raises concerns regarding food contamination and human exposure to toxins. The common agricultural practice of spray irrigation is an important exposure route to cyanotoxins, yet its impact on crops has received little attention. In the present study we attempted an integrated approach at the macro- and microscopic level to investigate whether spray or drip irrigation with microcystins (MCs)-rich water differently affect spinach performance. Growth and functional features, structural characteristics of stomata, and toxin bioaccumulation were determined. Additionally, the impact of irrigation method and water type on the abundance of leaf-attached microorganisms was assessed. Drip irrigation with MCs-rich water had detrimental effects on growth and photosynthetic characteristics of spinach, while spray irrigation ameliorated to various extents the observed impairments. The stomatal characteristics were differently affected by the irrigation method. Drip-irrigated spinach leaves showed significantly lower stomatal density in the abaxial epidermis and smaller stomatal size in the adaxial side compared to spray-irrigation treatment. Nevertheless, the latter deteriorated traits related to fresh produce quality and safety for human consumption; both the abundance of leaf-attached microorganisms and the MCs bioaccumulation in edible tissues well exceeded the corresponding values of drip-irrigated spinach with MC-rich water. The results highlight the significance of both the use of MCs-contaminated water in vegetable production and the irrigation method in shaping plant responses as well as health risk due to human and livestock exposure to MCs.
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Affiliation(s)
- E Tsoumalakou
- University of Thessaly, Department of Agriculture Crop Production and Rural Environment, Fytokou, 38446 Nea Ionia, Volos, Greece
| | - T Papadimitriou
- University of Thessaly, Department of Agriculture Ichthyology & Aquatic Environment, Fytokou, 38446 Nea Ionia, Volos, Greece
| | - P Berillis
- University of Thessaly, Department of Agriculture Ichthyology & Aquatic Environment, Fytokou, 38446 Nea Ionia, Volos, Greece
| | - K A Kormas
- University of Thessaly, Department of Agriculture Ichthyology & Aquatic Environment, Fytokou, 38446 Nea Ionia, Volos, Greece
| | - E Levizou
- University of Thessaly, Department of Agriculture Crop Production and Rural Environment, Fytokou, 38446 Nea Ionia, Volos, Greece.
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Stathopoulou P, Berillis P, Vlahos N, Nikouli E, Kormas KA, Levizou E, Katsoulas N, Mente E. Freshwater-adapted sea bass Dicentrarchus labrax feeding frequency impact in a lettuce Lactuca sativa aquaponics system. PeerJ 2021; 9:e11522. [PMID: 34141483 PMCID: PMC8180194 DOI: 10.7717/peerj.11522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/05/2021] [Indexed: 12/14/2022] Open
Abstract
The aim of this study is to investigate the effect of three daily fish feeding frequencies, two, four and eight times per day (FF2, FF4, and FF8, respectively) on growth performance of sea bass (Dicentrarchus labrax)and lettuce plants (Lactuca sativa) reared in aquaponics. 171 juvenile sea bass with an average body weight of 6.80 ± 0.095 g were used, together with 24 lettuce plants with an average initial height of 11.78 ± 0.074 cm over a 45-day trial period. FF2 fish group showed a significantly lower final weight, weight gain and specific growth rate than the FF4 and FF8 groups. Voluntary feed intake was similar for all the three feeding frequencies treatmens (p > 0.05). No plant mortality was observed during the 45-day study period. All three aquaponic systems resulted in a similar leaf fresh weight and fresh and dry aerial biomass. The results of the present study showed that the FF4 or FF8 feeding frequency contributes to the more efficient utilization of nutrients for better growth of sea bass adapted to fresh water while successfully supporting plant growth to a marketable biomass.
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Affiliation(s)
- Paraskevi Stathopoulou
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Panagiotis Berillis
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Nikolaos Vlahos
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece.,Department of Animal Production, Fisheries and Aquaculture, School of Agricultural Sciences, University of Patras, Mesolonghi, Greece
| | - Eleni Nikouli
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Konstantinos A Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Efi Levizou
- Department of Agriculture Crop Production and Rural Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Nikolaos Katsoulas
- Department of Agriculture Crop Production and Rural Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Eleni Mente
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
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5
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Meziti A, Nikouli E, Hatt JK, Konstantinidis KT, Kormas KA. Time series metagenomic sampling of the Thermopyles, Greece, geothermal springs reveals stable microbial communities dominated by novel sulfur-oxidizing chemoautotrophs. Environ Microbiol 2021; 23:3710-3726. [PMID: 33350070 DOI: 10.1111/1462-2920.15373] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/19/2020] [Indexed: 11/29/2022]
Abstract
Geothermal springs are essentially unaffected by environmental conditions aboveground as they are continuously supplied with subsurface water with little variability in chemistry. Therefore, changes in their microbial community composition and function, especially over a long period, are expected to be limited but this assumption has not yet been rigorously tested. Toward closing this knowledge gap, we applied whole metagenome sequencing to 17 water samples collected between 2010 and 2016 from the Thermopyles sulfur-rich geothermal springs in central Greece. As revealed by 16S rRNA gene fragments recovered in the metagenomes, Epsilonproteobacteria-related operational taxonomic units (OTUs) dominated most samples and grouping of samples based on OTU abundances exhibited no apparent seasonal pattern. Similarities between samples regarding functional gene content were high, with all samples sharing >70% similarity in functional pathways. These community-wide patterns were further confirmed by analysis of metagenome-assembled genomes (MAGs), which showed that novel species and genera of the chemoautotrophic Campylobacterales order dominated the springs. These MAGs carried different pathways for thiosulfate or sulfide oxidation coupled to carbon fixation pathways. Overall, our study showed that even in the long term, functions of microbial communities in a moderately hot terrestrial spring remain stable, presumably driving the corresponding stability in community structure.
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Affiliation(s)
- A Meziti
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, 38446, Greece.,School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | - E Nikouli
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, 38446, Greece.,School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | - J K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | - K T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA.,School of Biological Sciences, Georgia Institute of Technology, Ford Environmental Sciences and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | - K A Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, 38446, Greece
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6
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Panteli N, Mastoraki M, Nikouli E, Lazarina M, Antonopoulou E, Kormas KA. Imprinting statistically sound conclusions for gut microbiota in comparative animal studies: A case study with diet and teleost fishes. Comp Biochem Physiol Part D Genomics Proteomics 2020; 36:100738. [PMID: 32896688 DOI: 10.1016/j.cbd.2020.100738] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022]
Abstract
Despite the technical progress in high-throughput sequencing technologies, defining the sample size which is capable of yielding representative inferences in metabarcoding analysis still remains debatable. The present study addresses the influence of individual variability in assessing dietary effects on fish gut microbiota parameters and estimates the biological sample size that is sufficient to imprint a statistically secure outcome. European sea bass (Dicentrarchus labrax) and gilthead sea bream (Sparus aurata) were fed three alternative animal protein diets and a fishmeal control diet. Gut microbiota data from 12 individuals per diet, derived from Illumina sequencing of the V3-V4 region of the 16S rRNA gene, were randomized in all possible combinations of n-1 individuals. Results in this study showcased that increasing the sample size can limit the prevalence of individuals with high microbial load on the outcome and can ensure the statistical confidence required for an accurate validation of dietary-induced microbe shifts. Inter-individual variability was evident in the four dietary treatments where consequently misleading inferences arose from insufficient biological replication. These findings have critical implications for the design of future metabarcoding studies and highlight the urgency in selecting an adequate sample size able to safely elucidate the dietary effects on fish gut microbial communities.
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Affiliation(s)
- Nikolas Panteli
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Maria Mastoraki
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Eleni Nikouli
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece
| | - Maria Lazarina
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Efthimia Antonopoulou
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece.
| | - Konstantinos A Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece
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7
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Beam JP, Becraft ED, Brown JM, Schulz F, Jarett JK, Bezuidt O, Poulton NJ, Clark K, Dunfield PF, Ravin NV, Spear JR, Hedlund BP, Kormas KA, Sievert SM, Elshahed MS, Barton HA, Stott MB, Eisen JA, Moser DP, Onstott TC, Woyke T, Stepanauskas R. Ancestral Absence of Electron Transport Chains in Patescibacteria and DPANN. Front Microbiol 2020; 11:1848. [PMID: 33013724 PMCID: PMC7507113 DOI: 10.3389/fmicb.2020.01848] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/15/2020] [Indexed: 12/21/2022] Open
Abstract
Recent discoveries suggest that the candidate superphyla Patescibacteria and DPANN constitute a large fraction of the phylogenetic diversity of Bacteria and Archaea. Their small genomes and limited coding potential have been hypothesized to be ancestral adaptations to obligate symbiotic lifestyles. To test this hypothesis, we performed cell-cell association, genomic, and phylogenetic analyses on 4,829 individual cells of Bacteria and Archaea from 46 globally distributed surface and subsurface field samples. This confirmed the ubiquity and abundance of Patescibacteria and DPANN in subsurface environments, the small size of their genomes and cells, and the divergence of their gene content from other Bacteria and Archaea. Our analyses suggest that most Patescibacteria and DPANN in the studied subsurface environments do not form specific physical associations with other microorganisms. These data also suggest that their unusual genomic features and prevalent auxotrophies may be a result of ancestral, minimal cellular energy transduction mechanisms that lack respiration, thus relying solely on fermentation for energy conservation.
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Affiliation(s)
- Jacob P Beam
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Eric D Becraft
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Frederik Schulz
- Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Jessica K Jarett
- Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Oliver Bezuidt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Nicole J Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Kayla Clark
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - John R Spear
- Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
| | - Brian P Hedlund
- School of Life Sciences - Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Konstantinos A Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Hazel A Barton
- Department of Biology, University of Akron, Akron, OH, United States
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Jonathan A Eisen
- Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, Genome Center, University of California, Davis, Davis, CA, United States
| | - Duane P Moser
- Desert Research Institute, Las Vegas, NV, United States
| | - Tullis C Onstott
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Berkeley, CA, United States
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Moustaka-Gouni M, Sommer U, Economou-Amilli A, Arhonditsis GB, Katsiapi M, Papastergiadou E, Kormas KA, Vardaka E, Karayanni H, Papadimitriou T. Implementation of the Water Framework Directive: Lessons Learned and Future Perspectives for an Ecologically Meaningful Classification Based on Phytoplankton of the Status of Greek Lakes, Mediterranean Region. Environ Manage 2019; 64:675-688. [PMID: 31748947 DOI: 10.1007/s00267-019-01226-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
Abstract
The enactment of the Water Framework Directive (WFD) initiated scientific efforts to develop reliable methods for comparing prevailing lake conditions against reference (or nonimpaired) states, using the state of a set biological elements. Drawing a distinction between impaired and natural conditions can be a challenging exercise. Another important aspect is to ensure that water quality assessment is comparable among the different Member States. In this context, the present paper offers a constructive critique of the practices followed during the WFD implementation in Greece by pinpointing methodological weaknesses and knowledge gaps that undermine our ability to classify the ecological quality of Greek lakes. One of the pillars of WDF is a valid lake typology that sets ecological standards transcending geographic regions and national boundaries. The national typology of Greek lakes has failed to take into account essential components. WFD compliance assessments based on the descriptions of phytoplankton communities are oversimplified and as such should be revisited. Exclusion of most chroococcal species from the analysis of cyanobacteria biovolume in Greek lakes/reservoirs and most reservoirs in Spain, Portugal, and Cyprus is not consistent with the distribution of those taxa in lakes. Similarly, the total biovolume reference values and the indices used in classification schemes reflect misunderstandings of WFD core principles. This hampers the comparability of ecological status across Europe and leads to quality standards that are too relaxed to provide an efficient target for the protection of Greek/transboundary lakes such as the ancient Lake Megali Prespa.
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Affiliation(s)
- Maria Moustaka-Gouni
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 541 24, Thessaloniki, Greece.
| | - Ulrich Sommer
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany, Düsternbrooker Weg 20, 24105, Kiel, Germany.
| | - Athena Economou-Amilli
- National & Kapodistrian University of Athens, Faculty of Biology, Department of Ecology & Systematics, Panepistimiopolis, 15784, Athens, Greece
| | - George B Arhonditsis
- Department of Physical & Environmental Sciences, University of Toronto, 1065 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Matina Katsiapi
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 541 24, Thessaloniki, Greece
| | - Eva Papastergiadou
- Department of Biology, University of Patras, University Campus, 26504, Rio, Greece
| | - Konstantinos A Kormas
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46, Volos, Greece
| | - Elisabeth Vardaka
- Department of Nutrition and Dietetics, Alexander Technological Educational Institute of Thessaloniki, 574 00, Thessaloniki, Greece
| | - Hera Karayanni
- Department of Biological Applications and Technology, University of Ioannina, 45110, Ioannina, Greece
| | - Theodoti Papadimitriou
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46, Volos, Greece
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Spatharis S, Lamprinou V, Meziti A, Kormas KA, Danielidis DD, Smeti E, Roelke DL, Mancy R, Tsirtsis G. Everything is not everywhere: can marine compartments shape phytoplankton assemblages? Proc Biol Sci 2019; 286:20191890. [PMID: 31662088 DOI: 10.1098/rspb.2019.1890] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The idea that 'everything is everywhere, but the environment selects' has been seminal in microbial biogeography, and marine phytoplankton is one of the prototypical groups used to illustrate this. The typical argument has been that phytoplankton is ubiquitous, but that distinct assemblages form under environmental selection. It is well established that phytoplankton assemblages vary considerably between coastal ecosystems. However, the relative roles of compartmentalization of regional seas and site-specific environmental conditions in shaping assemblage structures have not been specifically examined. We collected data from coastal embayments that fall within two different water compartments within the same regional sea and are characterized by highly localized environmental pressures. We used principal coordinates of neighbour matrices (PCNM) and asymmetric eigenvector maps (AEM) models to partition the effects that spatial structures, environmental conditions and their overlap had on the variation in assemblage composition. Our models explained a high percentage of variation in assemblage composition (59-65%) and showed that spatial structure consistent with marine compartmentalization played a more important role than local environmental conditions. At least during the study period, surface currents connecting sites within the two compartments failed to generate sufficient dispersal to offset the impact of differences due to compartmentalization. In other words, our findings suggest that, even for a prototypical cosmopolitan group, everything is not everywhere.
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Affiliation(s)
- Sofie Spatharis
- School of Life Sciences, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK.,Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Vasiliki Lamprinou
- Faculty of Biology, Department of Ecology and Systematics, University of Athens, Panepistimiopolis, Athens 15784, Greece
| | - Alexandra Meziti
- Department of Ichthyology and Aquatic Environment, University of Thessaly, 3844 46 Volos, Greece
| | - Konstantinos A Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, 3844 46 Volos, Greece
| | - Daniel D Danielidis
- Faculty of Biology, Department of Ecology and Systematics, University of Athens, Panepistimiopolis, Athens 15784, Greece
| | - Evangelia Smeti
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, 46.7 km Athens-Souniou Avenue, 19013 Anavissos, Attica, Greece
| | - Daniel L Roelke
- Department of Marine Biology, Texas A&M University at Galveston, 200 Seawolf Parkway, Galveston, TX 77554, USA
| | - Rebecca Mancy
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - George Tsirtsis
- Department of Marine Sciences, University of the Aegean, University Hill, 81100 Mytilene, Greece
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10
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Meziti A, Tsementzi D, Rodriguez-R LM, Hatt JK, Karayanni H, Kormas KA, Konstantinidis KT. Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient. ISME J 2018; 13:767-779. [PMID: 30397261 DOI: 10.1038/s41396-018-0307-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 09/26/2018] [Accepted: 10/02/2018] [Indexed: 12/31/2022]
Abstract
Recent diversity studies have revealed that microbial communities of natural environments are dominated by species-like, sequence-discrete populations. However, how stable the sequence and gene-content diversity are within these populations and especially in highly dynamic lotic habitats remain unclear. Here we quantified the dynamics of intra-population diversity in samples spanning two years and five sites in the Kalamas River (Northwest Greece). A significant positive correlation was observed between higher intra-population sequence diversity and longer persistence over time, revealing that more diverse populations tended to represent more autochthonous (vs. allochthonous) community members. Assessment of intra-population gene-content changes caused by strain replacement or gene loss over time revealed different profiles with the majority of populations exhibiting gene-content changes close to 10% of the total genes, while one population exhibited ~21% change. The variable genes were enriched in hypothetical proteins and mobile elements, and thus, were probably functionally neutral or attributable to phage predation. A few notable exceptions to this pattern were also noted such as phototrophy-related proteins in summer vs. winter populations. Taken together, these results revealed that some freshwater genomes are remarkably dynamic, even across short time and spatial scales, and have implications for the bacterial species concept and microbial source tracking.
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Affiliation(s)
- Alexandra Meziti
- Department of Biological Applications and Technology, University of Ioannina, 45110, Ioannina, Greece.,School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science & Technology Building, 311 Ferst Drive, 30332, Atlanta, GA, Georgia
| | - Despina Tsementzi
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science & Technology Building, 311 Ferst Drive, 30332, Atlanta, GA, Georgia
| | - Luis M Rodriguez-R
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science & Technology Building, 311 Ferst Drive, 30332, Atlanta, GA, Georgia
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science & Technology Building, 311 Ferst Drive, 30332, Atlanta, GA, Georgia
| | - Hera Karayanni
- Department of Biological Applications and Technology, University of Ioannina, 45110, Ioannina, Greece
| | - Konstantinos A Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, 38446, Volos, Greece
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science & Technology Building, 311 Ferst Drive, 30332, Atlanta, GA, Georgia. .,School of Biological Sciences, Georgia Institute of Technology, Ford Environmental Sciences & Technology Building, 311 Ferst Drive, 30332, Atlanta, GA, Georgia.
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Nikouli E, Meziti A, Antonopoulou E, Mente E, Kormas KA. Gut Bacterial Communities in Geographically Distant Populations of Farmed Sea Bream ( Sparus aurata) and Sea Bass ( Dicentrarchus labrax). Microorganisms 2018; 6:microorganisms6030092. [PMID: 30200504 PMCID: PMC6164763 DOI: 10.3390/microorganisms6030092] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 08/28/2018] [Accepted: 08/31/2018] [Indexed: 01/21/2023] Open
Abstract
This study investigated the profile of the autochthonous gut bacterial communities in adult individuals of Sparus aurata and Dicentrarchus labrax reared in sea cages in five distantly located aquaculture farms in Greece and determine the impact of geographic location on them in order to detect the core gut microbiota of these commercially important fish species. Data analyses resulted in no significant geographic impact in the gut microbial communities within the two host species, while strong similarities between them were also present. Our survey revealed the existence of a core gut microbiota within and between the two host species independent of diet and geographic location consisting of the Delftia, Pseudomonas, Pelomonas, Propionibacterium, and Atopostipes genera.
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Affiliation(s)
- Eleni Nikouli
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos 384 46, Greece.
| | - Alexandra Meziti
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos 384 46, Greece.
| | - Efthimia Antonopoulou
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki 541 24, Greece.
| | - Eleni Mente
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos 384 46, Greece.
| | - Konstantinos A Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos 384 46, Greece.
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Mente E, Nikouli E, Antonopoulou E, Martin SAM, Kormas KA. Core versus diet-associated and postprandial bacterial communities of the rainbow trout ( Oncorhynchus mykiss) midgut and faeces. Biol Open 2018; 7:bio.034397. [PMID: 29776922 PMCID: PMC6031335 DOI: 10.1242/bio.034397] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
This study investigated the impact of different dietary ingredients, with different protein/lipid sources, on midgut and faeces bacteria community structures just before feeding and 3 h after feeding a single meal to individual rainbow trout (Oncorhynchus mykiss). Fish were kept in experimental rearing facilities and fed ad libitum twice daily for 5 weeks. Fish were fed three different commercial diets, which contained variations of high or low marine fishmeal/fish oil content. DNA was extracted from midgut and faeces samples for analysis of their bacterial 16S rRNA gene diversity by targeting the V3-V4 region with 454 pyrosequencing. A total of 332 unique bacterial operational taxonomic units (OTUs) were revealed in all samples. However, each sample was dominated (>80% relative abundance) by 2–14 OTUs, with the single most dominant OTU having >30% dominance, indicating that only a few bacteria were fundamental in terms of relative abundance in each treatment. Fifteen OTUs occurred in all samples (core microbiota). The majority of these OTUs belonged to the Proteobacteria, Firmicutes or Tenericutes, and were associated with other animal gut environments. The faecal material and the midgut samples had few overlaps in their shared OTUs. A postprandial response in the gut bacterial community structure 3 h after feeding highlights how dietary stimulation induces structural changes in the microbiota profiles in the established gut bacteria. This study showed that feeding O. mykiss different diets and even single meals lead to perturbations in the established gut bacteria of O. mykiss. Summary: The gut bacterial microbiome of rainbow trout contains a few core bacterial taxa and has little overlap with its faeces. Bacterial communities can change even 3 h after feeding.
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Affiliation(s)
- Eleni Mente
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece.,School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Eleni Nikouli
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece
| | - Efthimia Antonopoulou
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Samuel A M Martin
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Konstantinos A Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece
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Karayanni H, Meziti A, Spatharis S, Genitsaris S, Courties C, Kormas KA. Changes in Microbial (Bacteria and Archaea) Plankton Community Structure after Artificial Dispersal in Grazer-Free Microcosms. Microorganisms 2017; 5:microorganisms5020031. [PMID: 28587211 PMCID: PMC5488102 DOI: 10.3390/microorganisms5020031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 05/16/2017] [Accepted: 05/30/2017] [Indexed: 11/16/2022] Open
Abstract
Microbes are considered to have a global distribution due to their high dispersal capabilities. However, our knowledge of the way geographically distant microbial communities assemble after dispersal in a new environment is limited. In this study, we examined whether communities would converge because similar taxa would be selected under the same environmental conditions, or would diverge because of initial community composition, after artificial dispersal. To this aim, a microcosm experiment was performed, in which the temporal changes in the composition and diversity of different prokaryoplankton assemblages from three distant geographic coastal areas (Banyuls-sur-Mer in northwest Mediterranean Sea, Pagasitikos Gulf in northeast Mediterranean and Woods Hole, MA, USA in the northwest Atlantic), were studied. Diversity was investigated using amplicon pyrosequencing of the V1–V3 hypervariable regions of the 16S rRNA. The three assemblages were grown separately in particle free and autoclaved Banyuls-sur-mer seawater at 18 °C in the dark. We found that the variability of prokaryoplankton community diversity (expressed as richness, evenness and dominance) as well as the composition were driven by patterns observed in Bacteria. Regarding community composition, similarities were found between treatments at family level. However, at the OTU level microbial communities from the three different original locations diverge rather than converge during incubation. It is suggested that slight differences in the composition of the initial prokaryoplankton communities, resulted in separate clusters the following days even when growth took place under identical abiotic conditions.
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Affiliation(s)
- Hera Karayanni
- Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Greece.
| | - Alexandra Meziti
- Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Greece.
| | - Sofie Spatharis
- University of Glasgow, BAHCM Institute and School of Life Sciences, Glasgow G12 8QQ, Scotland, UK.
| | - Savvas Genitsaris
- Laboratoire d'Océanologie et Géosciences (LOG), UMR CNRS 8187, Université du Littoral Côte d'Opale (ULCO), 32 av. Foch, 62930 Wimereux, France.
| | - Claude Courties
- Sorbonne Universités, UPMC Univ Paris 06, UMS2348, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, 66650 Banyuls-sur-mer, France.
| | - Konstantinos A Kormas
- Department of Ichthyology & Aquatic Environment, University of Thessaly, 383 46 Volos, Greece.
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Berillis P, Mente E, Kormas KA. The Use of Copper Alloy in Aquaculture Fish Net Pens: Mechanical, Economic and Environmental Advantages. ACTA ACUST UNITED AC 2017. [DOI: 10.21767/1307-234x.1000134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Moustaka-Gouni M, Kormas KA, Scotti M, Vardaka E, Sommer U. Warming and Acidification Effects on Planktonic Heterotrophic Pico- and Nanoflagellates in a Mesocosm Experiment. Protist 2016; 167:389-410. [DOI: 10.1016/j.protis.2016.06.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 06/27/2016] [Accepted: 06/29/2016] [Indexed: 01/16/2023]
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Edgcomb VP, Pachiadaki MG, Mara P, Kormas KA, Leadbetter ER, Bernhard JM. Gene expression profiling of microbial activities and interactions in sediments under haloclines of E. Mediterranean deep hypersaline anoxic basins. ISME J 2016; 10:2643-2657. [PMID: 27093045 DOI: 10.1038/ismej.2016.58] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 02/11/2016] [Accepted: 03/03/2016] [Indexed: 11/09/2022]
Abstract
Deep-sea hypersaline anoxic basins (DHABs) in the Eastern Mediterranean Sea are considered some of the most polyextreme habitats on Earth. In comparison to microbial activities occurring within the haloclines and brines of these unusual water column habitats near the Mediterranean seafloor, relatively little is known about microbial metabolic activities in the underlying sediments. In addition, it is not known whether activities are shaped by the unique chemistries of the different DHAB brines and whether evidence exists for active microbial eukaryotes in those sediments. Metatranscriptome analysis was applied to sediment samples collected using ROV Jason from underneath the haloclines of Urania, Discovery and L'Atalante DHABs and a control site. We report on expression of genes associated with sulfur and nitrogen cycling, putative osmolyte biosynthetic pathways and ion transporters, trace metal detoxification, selected eukaryotic activities (particularly of fungi), microbe-microbe interactions, and motility in sediments underlying the haloclines of three DHABs. Relative to our control sediment sample collected outside of Urania Basin, microbial communities (including eukaryotes) in the Urania and Discovery DHAB sediments showed upregulation of expressed genes associated with nitrogen transformations, osmolyte biosynthesis, heavy metals resistance and metabolism, eukaryotic organelle functions, and cell-cell interactions. Sediments underlying DHAB haloclines that have cumulative physico-chemical stressors within the limits of tolerance for microoorganisms can therefore be hotspots of activity in the deep Mediterranean Sea.
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Affiliation(s)
- Virginia P Edgcomb
- Department of Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Maria G Pachiadaki
- Department of Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Paraskevi Mara
- Department of Chemistry, University of Crete, Heraklion, Greece
| | - Konstantinos A Kormas
- Department of Ichthyology & Aquatic Environment, University of Thessaly, Volos, Greece
| | - Edward R Leadbetter
- Department of Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Joan M Bernhard
- Department of Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
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Vardaka E, Kormas KA, Katsiapi M, Genitsaris S, Moustaka-Gouni M. Molecular diversity of bacteria in commercially available "Spirulina" food supplements. PeerJ 2016; 4:e1610. [PMID: 26819852 PMCID: PMC4727962 DOI: 10.7717/peerj.1610] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 12/29/2015] [Indexed: 12/02/2022] Open
Abstract
The cyanobacterium Arthrospira is among the most well-known food supplements worldwide known as “Spirulina.” While it is a widely recognized health-promoting natural product, there are no reports on the molecular diversity of commercially available brands of “Spirulina” supplements and the occurrence of other cyanobacterial and heterotrophic bacterial microorganisms in these products. In this study, 454-pyrosequencing analysis of the total bacterial occurrence in 31 brands of “Spirulina” dietary supplements from the Greek market was applied for the first time. In all samples, operational taxonomic units (OTUs) of Arthrospira platensis were the predominant cyanobacteria. Some products contained additional cyanobacterial OTUs including a few known potentially toxic taxa. Moreover, 469 OTUs were detected in all 31 products collectively, with most of them being related to the Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Verrucomicrobia. All samples included heterotrophic bacterial OTUs, ranging from 9–157 per product. Among the most common OTUs were ones closely related to taxa known for causing health issues (i.e., Pseudomonas, Flavobacterium, Vibrio, Aeromonas, Clostridium, Bacillus, Fusobacterium, Enterococcus). The observed high cyanobacterial and heterotrophic bacterial OTUs richness in the final product is a point for further research on the growth and processing of Arthrospira biomass for commercial purposes.
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Affiliation(s)
- Elisabeth Vardaka
- Department of Nutrition and Dietetics, Alexander Technological Educational Institute of Thessaloniki , Thessaloniki , Greece
| | - Konstantinos A Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly , Volos , Greece
| | - Matina Katsiapi
- Department of Nutrition and Dietetics, Alexander Technological Educational Institute of Thessaloniki, Thessaloniki, Greece; School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Savvas Genitsaris
- School of Biology, Aristotle University of Thessaloniki , Thessaloniki , Greece
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Kormas KA, Pachiadaki MG, Karayanni H, Leadbetter ER, Bernhard JM, Edgcomb VP. Inter-comparison of the potentially active prokaryotic communities in the halocline sediments of Mediterranean deep-sea hypersaline basins. Extremophiles 2015; 19:949-60. [DOI: 10.1007/s00792-015-0770-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 06/28/2015] [Indexed: 11/29/2022]
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Meziti A, Kormas KA, Moustaka-Gouni M, Karayanni H. Spatially uniform but temporally variable bacterioplankton in a semi-enclosed coastal area. Syst Appl Microbiol 2015; 38:358-67. [PMID: 25976032 DOI: 10.1016/j.syapm.2015.04.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 04/10/2015] [Accepted: 04/13/2015] [Indexed: 10/23/2022]
Abstract
Studies focusing on the temporal and spatial dynamics of bacterioplankton communities within littoral areas undergoing direct influences from the coast are quite limited. In addition, they are more complicated to resolve compared to communities in the open ocean. In order to elucidate the effects of spatial vs. temporal variability on bacterial communities in a highly land-influenced semi-enclosed gulf, surface bacterioplankton communities from five coastal sites in Igoumenitsa Gulf (Ionian Sea, Greece) were analyzed over a nine-month period using 16S rDNA 454-pyrosequencing. Temporal differences were more pronounced than spatial ones, with lower diversity indices observed during the summer months. During winter and early spring, bacterial communities were dominated by SAR11 representatives, while this pattern changed in May when they were abruptly replaced by members of Flavobacteriales, Pseudomonadales, and Alteromonadales. Additionally, correlation analysis showed high negative correlations between the presence of SAR11 OTUs in relation to temperature and sunlight that might have driven, directly or indirectly, the disappearance of these OTUs in the summer months. The dominance of SAR11 during the winter months further supported the global distribution of the clade, not only in the open-sea, but also in coastal systems. This study revealed that specific bacteria exhibited distinct succession patterns in an anthropogenic-impacted coastal system. The major bacterioplankton component was represented by commonly found marine bacteria exhibiting seasonal dynamics, while freshwater and terrestrial-related phylotypes were absent.
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Affiliation(s)
- Alexandra Meziti
- Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Greece
| | - Konstantinos A Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, 38446 Volos, Greece
| | - Maria Moustaka-Gouni
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Hera Karayanni
- Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Greece.
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Kormas KA, Meziti A, Mente E, Frentzos A. Dietary differences are reflected on the gut prokaryotic community structure of wild and commercially reared sea bream (Sparus aurata). Microbiologyopen 2014; 3:718-28. [PMID: 25066034 PMCID: PMC4234263 DOI: 10.1002/mbo3.202] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Revised: 06/29/2014] [Accepted: 07/03/2014] [Indexed: 02/06/2023] Open
Abstract
We compared the gut prokaryotic communities in wild, organically-, and conventionally reared sea bream (Sparus aurata) individuals. Gut microbial communities were identified using tag pyrosequencing of the 16S rRNA genes. There were distinct prokaryotic communities in the three different fish nutritional treatments, with the bacteria dominating over the Archaea. Most of the Bacteria belonged to the Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. The number of bacterial operational taxonomic units (OTUs) was reduced from the wild to the conventionally reared fish, implying a response of the gut microorganisms to the supplied food and possibly alterations in food assimilation. The dominant bacterial OTU in all examined fish was closely related to the genus Diaphorobacter. This is the first time that a member of the β-Proteobacteria, which dominate in freshwaters, are so important in a marine fish gut. In total the majority of the few Archaea OTUs found, were related to methane metabolism. The inferred physiological roles of the dominant prokaryotes are related to the metabolism of carbohydrates and nitrogenous compounds. This study showed the responsive feature of the sea bream gut prokaryotic communities to their diets and also the differences of the conventional in comparison to the organic and wild sea bream gut microbiota.
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Affiliation(s)
- Konstantinos A Kormas
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece
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Christaki U, Kormas KA, Genitsaris S, Georges C, Sime-Ngando T, Viscogliosi E, Monchy S. Winter-summer succession of unicellular eukaryotes in a meso-eutrophic coastal system. Microb Ecol 2014; 67:13-23. [PMID: 24081282 DOI: 10.1007/s00248-013-0290-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 09/03/2013] [Indexed: 06/02/2023]
Abstract
The objective of this study was to explore the succession of planktonic unicellular eukaryotes by means of 18S rRNA gene tag pyrosequencing in the eastern English Channel (EEC) during the winter to summer transition. The 59 most representative (>0.1%, representing altogether 95% of total reads), unique operational taxonomic units (OTUs) from all samples belonged to 18 known high-level taxonomic groups and 1 unaffiliated clade. The five most abundant OTUs (69.2% of total reads) belonged to Dinophyceae, Cercozoa, Haptophyceae, marine alveolate group I, and Fungi. Cluster and network analysis between samples distinguished the winter, the pre-bloom, the Phaeocystis globosa bloom and the post-bloom early summer conditions. The OTUs-based network revealed that P. globosa showed a relatively low number of connections-most of them negative-with all other OTUs. Fungi were linked to all major taxonomic groups, except Dinophyceae. Cercozoa mostly co-occurred with the Fungi, the Bacillariophyceae and several of the miscellaneous OTUs. This study provided a more detailed exploration into the planktonic succession pattern of the EEC due to its increased depth of taxonomic sampling over previous efforts based on classical monitoring observations. Data analysis implied that the food web concept in a coastal system based on predator-prey (e.g. grazer-phytoplankton) relationships is just a part of the ecological picture; and those organisms exploiting a variety of strategies, such as saprotrophy and parasitism, are persistent and abundant members of the community.
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Affiliation(s)
- Urania Christaki
- Laboratoire d'Océanologie et Géosciences (LOG), UMR CNRS 8187, Université du Littoral Côte d'Opale (ULCO), 32 av. Foch, 62930, Wimereux, France,
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Meziti A, Kormas KA. Comparison of the Norway lobster (Nephrops norvegicus) gut bacterial communities using 16S rDNA clone libraries and pyrosequencing. Anaerobe 2013; 23:9-11. [PMID: 23933515 DOI: 10.1016/j.anaerobe.2013.07.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Revised: 07/25/2013] [Accepted: 07/29/2013] [Indexed: 11/26/2022]
Abstract
By comparing 16S rDNA cloning and 454 pyrosequencing in the Nephrops norvegicus midgut, several common bacterial OTUs were detected. However, when only one method is to be selected, it needs to be considered whether the revealing of rare OTUs or their accurate phylogenetic relationships is mostly preferred.
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Affiliation(s)
- Alexandra Meziti
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos 38446, Greece
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Pachiadaki MG, Lykousis V, Stefanou EG, Kormas KA. Prokaryotic community structure and diversity in the sediments of an active submarine mud volcano (Kazan mud volcano, East Mediterranean Sea). FEMS Microbiol Ecol 2010; 72:429-44. [PMID: 20370830 DOI: 10.1111/j.1574-6941.2010.00857.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We investigated 16S rRNA gene diversity at a high sediment depth resolution (every 5 cm, top 30 cm) in an active site of the Kazan mud volcano, East Mediterranean Sea. A total of 242 archaeal and 374 bacterial clones were analysed, which were attributed to 38 and 205 unique phylotypes, respectively (> or = 98% similarity). Most of the archaeal phylotypes were related to ANME-1, -2 and -3 members originating from habitats where anaerobic oxidation of methane (AOM) occurs, although they occurred in sediment layers with no apparent AOM (below the sulphate depletion depth). Proteobacteria were the most abundant and diverse bacterial group, with the Gammaproteobacteria dominating in most sediment layers and these were related to phylotypes involved in methane cycling. The Deltaproteobacteria included several of the sulphate-reducers related to AOM. The rest of the bacterial phylotypes belonged to 15 known phyla and three unaffiliated groups, with representatives from similar habitats. Diversity index H was in the range 0.56-1.73 and 1.47-3.82 for Archaea and Bacteria, respectively, revealing different depth patterns for the two groups. At 15 and 20 cm below the sea floor, the prokaryotic communities were highly similar, hosting AOM-specific Archaea and Bacteria. Our study revealed different dominant phyla in proximate sediment layers.
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Affiliation(s)
- Maria G Pachiadaki
- Environmental Chemical Processes Laboratory, Department of Chemistry, University of Crete, Voutes-Heraklion, Greece
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Kormas KA, Meziti A, Dählmann A, DE Lange GJ, Lykousis V. Characterization of methanogenic and prokaryotic assemblages based on mcrA and 16S rRNA gene diversity in sediments of the Kazan mud volcano (Mediterranean Sea). Geobiology 2008; 6:450-460. [PMID: 19076636 DOI: 10.1111/j.1472-4669.2008.00172.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The diversity of the methyl-coenzyme reductase A (mcrA) and 16S rRNA genes was investigated in gas hydrate containing sediment from the Kazan mud volcano, eastern Mediterranean Sea. mcrA was detected only at 15 and 20 cm below seafloor (cmbsf) from a 40-cm long push core, while based on chemical profiles of methane, sulfate, and sulfide, possible anaerobic oxidation of methane (AOM) depth was inferred at 12-15 cmbsf. The phylogenetic relationships of the obtained mcrA, archaeal and bacterial 16S rRNA genes, showed that all the found sequences were found in both depths and at similar relative abundances. mcrA diversity was low. All sequences were related to the Methanosarcinales, with the most dominant (77.2%) sequences falling in group mcrA-e. The 16S rRNA-based archaeal diversity also revealed low diversity and clear dominance (72.8% of all archaeal phylotypes) of the Methanosarcinales and, in particular, ANME-2c. Bacteria showed higher diversity but 83.2% of the retrieved phylotypes from both sediment layers belonged to the delta-Proteobacteria. These phylotypes fell in the SEEP-SRB1 putative AOM group. In addition, the rest of the less abundant phylotypes were related to yet-uncultivated representatives of the Actinobacteria, Spirochaetales, and candidate divisions OP11 and WS3 from gas hydrate-bearing habitats. These phylotype patterns indicate that AOM is occurring in the 15 and 20 cmbsf sediment layers.
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Affiliation(s)
- K A Kormas
- Department of Ichthyology & Aquatic Environment, University of Thessaly, 38446 Nea Ionia, Greece
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Kormas KA, Tivey MK, Von Damm K, Teske A. Bacterial and archaeal phylotypes associated with distinct mineralogical layers of a white smoker spire from a deep-sea hydrothermal vent site (9 degrees N, East Pacific Rise). Environ Microbiol 2006; 8:909-20. [PMID: 16623747 DOI: 10.1111/j.1462-2920.2005.00978.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A diffusely venting chimney spire from the East Pacific Rise (9 degrees N) was analysed by petrographic thin sectioning and 16S rRNA gene cloning and sequencing in parallel, to correlate microbial community composition with mineralogy and inferred in situ conditions within the chimney mineral matrix. Both approaches indicated a zonation of the chimney spire into distinct microhabitats for different bacteria and archaea. The thermal gradient inferred from the mineral composition and porosity of the chimney was consistent with the distribution of bacterial and archaeal phylotypes in the chimney matrix. A novel phylogenetic lineage of euryarchaeota was found that co-occurred with clones related to cultured hyperthermophilic archaea. A few phylotypes related to mesophilic bacteria were found in the hot core of the chimney, indicating that seawater influx during retrieval and cooling of these highly porous structures can entrain microorganisms into chimney layers that are not their native habitat.
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Affiliation(s)
- Konstantinos A Kormas
- Department of Animal Production and Aquatic Environment, University of Thessaly, 383 34 N, Ionia, Volos, Greece
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