Changes in microbial (Bacteria and Archaea) plankton community structure after artificial dispersal in grazer-free microcosms

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

Everything is not everywhere: can marine compartments shape phytoplankton assemblages?

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

Increased contribution of parasites in microbial eukaryotic communities of different Aegean Sea coastal systems

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

Molecular diversity of bacterial communities from the digestive tract of Norway lobster (nephrops norvegicus) individuals in natural and reared populations

2. The Norway lobster Nephrops norvegicus, also known as Dublin bay prawn is a Decapod Crustacean of the Family Nephropidae that is widely distributed in silty areas, of the continental shelf and the upper continental slope, of the Northeast Atlantic and the Mediterranean Sea. The Norway lobster is a highly commercial species in the areas where it is found. Efforts for the commercial rearing of the species have not succeeded yet due to lack of knowledge on the nutritional habits of the species on rearing conditions and on its exact nutritional demands. 3. This thesis studied for the first time the gut bacterial diversity of Nephrops norvegicus. Studies were performed in natural and reared populations, where different food sources were provided. The project targeted in finding the factors that shape gut bacterial diversity and in detecting symbiotic, non toxic and non pathogenic bacterial species that can influence the digestive functions of N. norvegicus and could potentially be used as probiotics in future rearing efforts. 4. For the study of the natural populations N. norvegicus individuals were collected from Pagasitikos gulf during different months in 2007. The digestive tract was extracted and evacuated, followed by DNA extraction. DNA was analyzed with the use of molecular tools studying 16S rRNA and the Intergenic Transcribed Spacer (ITS). The 16S rRNA diversity was studied with the use of clone libraries and Fluorescence in Situ Hybridization (FISH) while the ITS diversity was studied with the use of clone libraries and Automated Ribosomal Intergenic Spacer Analysis (ARISA). The study of the ITS diversity with the use of ARISA showed that gut bacterial microdiversity was influenced by sampling season while other factors that were checked such as sex or weight had no influence. Seasonal differences in Pagasitikos gulf, and mostly in the areas where N. norvegicus is found, are based in changes in food availability and quality and not in physicochemical factors. In this area temperature and salinity are almost stable all over the year, while changes are observed in the quantity and the quality of the organic matter from upper layers that finally influences the trophic webs in the bottom. 5. Further analysis of selected samples from all collection months with 16S-ITS clone libraries showed the dominance of specific phylotypes (>58%) in each one of them. The dominant phylotypes in the samples of February/March, May, July, August and October clustered in the genera of Pseudoalteromonas, Psychrobacter and Photobacterium while the ones in the samples of September and December clustered in an uncultured Mollicutes group and in the candidate division CK-1C4-19 respectively. The presence of γ-Proteobacteria in August samples and of uncultured Mollicutes in September samples was further verified with the FISH results. For the detection of cells belonging to γ-Proteobacteria, probe GAM42a was used while for the cells belonging to the dominant Mollicute phylotype a specific probe was designed. 6. The combination of ARISA results with the ITS lengths of the dominant phylotypes from the clone libraries further confirmed the presence of Photobacterium sp. and Psychrobacter sp. representatives in most of the samples studied. However the presence of the Mollicutes and CK-1C4-19 phylotypes was underestimated in the ARISA as a result of mismatches of their sequences with the primers used. 7. Rearing experiments were performed in order to confirm the effect of feeding in gut bacterial diversity. N. norvegicus individuals were divided in three groups and were kept for six months in rearing tanks where three different kinds of food were checked (S: starvation, M: mussels, P: pellets). Mussels and pellets were provided in the respective groups three times per week. In order to study the gut bacterial diversity, N. norvegicus samplings were performed at the beginning of the experiment (t0) and after three (t1) and six months (t2). At the same time water samples from the rearing tanks and samples from the food provided were analyzed. 8. All the samples were analyzed using 16S rRNA clone libraries. Samples from the initial time point (t0) had similar results with the natural populations showing low bacterial diversities and dominant phylotypes with closest relatives belonging to the genera Psychrobacter and Photobacterium. All samples after six month rearing with pellets and mussels showed higher bacterial diversity than wild samples. However all of them had dominant phylotypes, with frequencies ranging from 22% to 73.5%, clustering in the species Photobacterium leiognathi and showing high percentages of similarity (>98%) with the respective Photobacterium like phylotypes of the wild populations. Previous microbiological and genomic studies have shown the presence of lipolytic, proteinolytic and chitinolytic enzymes in P. leiognathi enhancing the hypothesis of its assistance in N. norvegicus digestive activity. 9. Starvation samples as well as the three months mussel reared sample showed higher bacterial diversity than all other samples. As it was proved after statistical analysis their bacterial diversity was mostly influenced by the tanks’ water bacterial diversity. Statistical analysis for all samples showed the existence of two groups depending mostly on whether food was provided or not regardless of its kind. The basic discriminative characteristic between these two groups was the presence of phylotypes clustering in P. leiognathi. 10. For the first time, it was proved that food provision is an important factor for the shaping of gut bacterial communities of N. norvegicus. The factors that shape gut bacterial diversity, as well as abundant and potentially symbiotic microorganisms were detected. Bacterial phylotypes clustering in P. leiognathi with potential chitinolytic, proteinolytic and lipolytic activities were found abundant in the gut of wild and reared populations of N. norvegicus suggesting their use as probiotics in future rearing efforts.Η καραβίδα Nephrops norvegicus ή Νορβηγικός αστακός αποτελεί ένα μέλος της οικογένειας Nephropidae των καρκινοειδών και είναι ένα είδος ευρέως κατανεμημένο σε ιλυώδεις περιοχές της ηπειρωτικής κρηπίδας και της ανώτερης ηπειρωτικής κατωφέρειας του Βορειοανατολικού Ατλαντικού και της Μεσογείου. Το N. norvegicus αποτελεί ένα ιδιαίτερα εμπορικό είδος στις περιοχές όπου εντοπίζεται. Για αυτό το λόγο πραγματοποιούνται προσπάθειες για την εμπορική καλλιέργειά του οι οποίες δεν έχουν επιτευχθεί ακόμα εξαιτίας της ελλιπούς γνώσης σχετικά με τις διατροφικές συνήθειές του σε συνθήκες εργαστηρίου αλλά και σχετικά με τις ακριβείς διατροφικές του απαιτήσεις. Στην παρούσα εργασία μελετήθηκε για πρώτη φορά η βακτηριακή ποικιλότητα και αφθονία του πεπτικού συστήματος του N. norvegicus σε φυσικούς και εκτρεφόμενους πληθυσμούς υπό την παροχή διαφορετικών σιτηρεσίων. Σκοπός ήταν η μελέτη της βακτηριακής ποικιλότητας του μεσέντερου, η εύρεση των παραγόντων που την επηρεάζουν, η ανίχνευση των επικρατών φυλότυπων σε φυσικούς και εκτρεφόμενους πληθυσμούς, καθώς και ο εντοπισμός συμβιωτικών, μη τοξικών και μη παθογόνων βακτηριακών ειδών με πιθανή προσφορά στις πεπτικές λειτουργίες, που θα μπορούσαν στο μέλλον να χρησιμοποιηθούν ως προβιοτικά σε προσπάθειες εμπορικής εκτροφής. Για τη μελέτη των φυσικών πληθυσμών συλλέχθηκαν 49 άτομα από τον Παγασητικό Κόλπο σε σχεδόν μηνιαία βάση κατά τη διάρκεια του 2007. Απομονώθηκε DNA από τον πεπτικό σωλήνα των δειγμάτων, το οποίο αναλύθηκε με τη χρήση μοριακών τεχνικών μελέτης του 16S rRNA και του διαγονιδιακού ριβοσωμικού χώρου (Intergenic Transcribed Spacer, ITS). Η μελέτη του ITS με την τεχνική της αυτοματοποιημένης ανάλυσης του διαγονιδιακού ριβοσωμικού χώρου (Automated Ribosomal Intergenic Spacer Analysis, ARISA) έδειξε ότι η εποχή συλλογής των δειγμάτων επηρέαζε τη βακτηριακή ποικιλότητα του πεπτικού σωλήνα σε αντίθεση με άλλους παράγοντες, όπως το φύλο ή το βάρος που δεν είχαν καμία επίδραση. Στον Παγασητικό κόλπο και στα σημεία που ζει το N. norvegicus οι εποχικές αλλαγές εντοπίζονται κυρίως σε αλλαγές στη διαθεσιμότητα της τροφής και όχι στις φυσικοχημικές συνθήκες, δείχνοντας ότι οι εποχικές αλλαγές της βακτηριακής ποικιλότητας του μεσέντερου πιθανότατα οφείλονταν σε αλλαγές στην κατανάλωση τροφής. Η περαιτέρω ανάλυση επιλεγμένων δειγμάτων από κάθε μήνα συλλογής με 16S-ITS βιβλιοθήκες έδειξε την ύπαρξη επικρατών φυλότυπων (>58%) σε κάθε μία από αυτές. Στα δείγματα του Φεβρουαρίου/Μαρτίου, Μαΐου, Ιουλίου, Αυγούστου και Οκτωβρίου εντοπίστηκαν φυλότυποι με κοντινότερους συγγενείς από τα γένη Pseudoalteromonas, Psychrobacter και Photobacterium ενώ στα δείγματα του Σεπτεμβρίου και του Δεκεμβρίου εντοπίστηκαν φυλότυποι από μία ακαλλιέργητη ομάδα των Mollicutes και από το ακαλλιέργητο υποψήφιο φύλο CK-1C4-19, αντίστοιχα. Η παρουσία των ακαλλιέργητων Mollicutes στα δείγματα του Σεπτεμβρίου και των γ-Proteobacteria στα δείγματα του Αυγούστου επιβεβαιώθηκε και με την τεχνική του επιτόπιου φθορίζοντος υβριδισμού (Fluorescence in Situ Hybridization, FISH). Ο συνδυασμός των αποτελεσμάτων της ARISA με τις αλληλουχίες των ITS από τις βιβλιοθήκες έδειξε για άλλη μία φορά την έντονη παρουσία αντιπροσώπων των γενών Photobacterium και Psychrobacter στα περισσότερα από τα δείγματα που μελετήθηκαν. Για την εξακρίβωση της επίδρασης της τροφής στη βακτηριακή ποικιλότητα του εντέρου πραγματοποιήθηκαν πειράματα εκτροφής στο εργαστήριο. Συνολικά οχτώ άτομα N. norvegicus χωρίστηκαν σε τρεις ομάδες και παρέμειναν για έξι μήνες σε ειδικές ατομικές δεξαμενές, όπου ελέγχθηκαν τρία είδη διατροφής (S: ασιτία, M: μύδια και Ρ: σύμπηκτα), με ελεγχόμενη παροχή τροφής τρεις φορές την εβδομάδα. Για τη μελέτη της βακτηριακής ποικιλότητας του μεσέντερου πραγματοποιήθηκαν δειγματοληψίες στην αρχή του πειράματος (t0), στους τρεις μήνες (t1) και στους έξι μήνες (t2). Παράλληλα αναλύθηκαν και δείγματα νερού από τα ενυδρεία, αλλά και από τις τροφές που παρασχέθηκαν. Τα δείγματα αυτά αναλύθηκαν με 16S rRNA βιβλιοθήκες. Τα αρχικά δείγματα (t0) παρουσίασαν αντίστοιχα αποτελέσματα με τους φυσικούς πληθυσμούς, με χαμηλή βακτηριακή ποικιλότητα και με επικρατείς φυλότυπους με πλησιέστερους συγγενείς από τα γένη Psychrobacter και Photobacterium. Τα δείγματα από τις εκτροφές με σύμπηκτα και μύδια, για χρονική περίοδο έξι μηνών, παρουσίασαν υψηλότερη ποικιλότητα από τα δείγματα των φυσικών πληθυσμών αλλά σε όλα εντοπίστηκαν σε υψηλές αφθονίες (22%-73,5%) αντιπρόσωποι του είδους Photobacterium leiognathi παρόμοιοι (> 98%) με τους φυλότυπους των φυσικών πληθυσμών. Μικροβιολογικές και γονιδιωματικές μελέτες από προηγούμενες έρευνες έχουν ανιχνεύσει τις λιπολυτικές, χιτινολυτικές και πρωτεϊνολυτικές ιδιότητες του P. leiognathi, δείχνοντας τις πιθανές ευεργετικές δράσεις αυτού του είδους στην πεπτική λειτουργία του N. norvegicus. Τα δείγματα της ασιτίας, καθώς και αυτό από την τρίμηνη εκτροφή με μύδια, παρουσίασαν υψηλότερη ποικιλότητα από όλα τα υπόλοιπα και η ποικιλότητά τους, όπως αποδείχθηκε από τη στατιστική ανάλυση των αποτελεσμάτων, φάνηκε να επηρεάζεται κυρίως από τη βακτηριακή ποικιλότητα του νερού των δεξαμενών. Η βακτηριακή ποικιλότητα των τροφών δε φάνηκε να επηρεάζει τη βακτηριακή ποικιλότητα του μεσέντερου. Η στατιστική ανάλυση των αποτελεσμάτων για όλα τα δείγματα έδειξε την ύπαρξη δύο ομάδων, εξαρτώμενων κυριώς από το αν είχε καταναλωθεί τροφή ανεξαρτήτως του είδους της. Βασικό διακριτικό χαρακτηριστικό των δύο ομάδων αποδείχθηκε η παρουσία αντιπροσώπων του είδους P. leiognathi. Συνεπώς φάνηκε ότι η παροχή τροφής αποτελεί έναν καθοριστικό παράγοντα για τη διαμόρφωση της βακτηριακής ποικιλότητας του πεπτικού συστήματος του N. norvegicus. Για πρώτη φόρα βρέθηκε ότι συγκεκριμένα βακτηριακά είδη όπως το P. leiognathi, με πιθανές λιπολυτικές, πρωτεϊνολυτικές και χιτινολυτικές ιδιότητες, έχουν έντονη παρουσία στο πεπτικό σύστημα της καραβίδας και θα μπορούσαν στο μέλλον να χρησιμοποιηθούν ως προβιοτικά σε προσπάθειες εκτροφής του N. norvegicus. Συνολικά αυτή η μελέτη έδωσε σημαντικά στοιχεία για τη βακτηριακή ποικιλότητα του εντέρου του N. norvegicus και για τους παράγοντες που την καθορίζουν και έθεσε τις βάσεις για τις μελλοντικές προσπάθειες στη χρήση προβιοτικών για την εκτροφή του είδους

Comparison of the Norway lobster (Nephrops norvegicus) gut bacterial communities using 16S rDNA clone libraries and pyrosequencing

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. (c) 2013 Elsevier Ltd. All rights reserved

Microbiological Confinement of Two Adjacent Water Wells in Lake Karla Basin, Greece

We analyzed the bacterial and archaeal community structure of two adjacent irrigation well waters of the Lake Karla Basin, Central Greece, in order to elucidate their connectivity or confinement by using 454 tag pyrosequencing of the 16S rRNA genes. Although considerable overlap was found at the phylum/high taxonomic level, and also at the operational taxonomic units (OTU) level, the dominant, and most likely active, prokaryotes represented by these OTUs were very different between the two wells. As expected, we found higher bacterial species richness compared to that of archaeal, and this renders Bacteria better for the study of connectivity or confinement of water wells. Some of the taxonomic groups found are amongst those found typically in the terrestrial subsurface and also those that have been recently described, enhancing the importance of the subsurface for expanding our knowledge on microbial diversity. The majority of the archaeal and several of the bacterial OTUs, including the most dominant ones in each well, were related to marine or saline environments, indicating the previously suggested persistence of fertilizer residuals in the basin’s soils

Host-Associated Bacterial Succession during the Early Embryonic Stages and First Feeding in Farmed Gilthead Sea Bream (Sparus aurata)

One of the most widely reared fish in the Mediterranean Sea is Sparus aurata. The succession of S. aurata whole-body microbiota in fertilized eggs, five, 15, 21 and 71 days post hatch (dph) larvae and the contribution of the rearing water and the provided feed (rotifers, Artemia sp. and commercial diet) to the host’s microbiota was investigated by 454 pyrosequencing of the 16S rRNA gene diversity. In total, 1917 bacterial operational taxonomic units (OTUs) were found in all samples. On average, between 93 ± 2.1 and 366 ± 9.2 bacterial OTUs per sample were found, with most of them belonging to Proteobacteria and Bacteroidetes. Ten OTUs were shared between all S. aurata stages and were also detected in the rearing water or diet. The highest OTU richness occurred at the egg stage and the lowest at the yolk sac stage (5 dph). The rearing water and diet microbial communities contributed in S. aurata microbiota without overlaps in their microbial composition and structure. The commercial diet showed higher contribution to the S. aurata microbiota than the rearing water. After stage D71 the observed microbiota showed similarities with that of adult S. aurata as indicated by the increased number of OTUs associated with γ-Proteobacteria and Firmicutes

Gut Bacterial Communities in Geographically Distant Populations of Farmed Sea Bream (Sparus aurata) and Sea Bass (Dicentrarchus labrax)

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

First record of a Trichodesmium erythraeum bloom in the Mediterranean Sea

Trichodesmium erythraeum is a species of marine cyanobacteria that forms extensive blooms in tropical and subtropical areas, predominantly in the Indian and Pacific oceans. An extensive bloom of this species, identified by microscopic and molecular analysis, is recorded for the first time at latitude greater than 30°N in Lesvos Island, Aegean Sea, eastern Mediterranean. Analysis of climatological trends revealed that the September 2010 bloom followed an extended period of the highest sea surface temperature and lowest wind speed observed since 1955, leading to a shallow thermocline formation. These conditions are considered among the main prerequisites for T. erythraeum bloom development. Analysis of abiotic parameters showed that other important factors for Trichodesmium proliferations, such as iron availability, oligotrophic conditions, and salinity levels, typical for the eastern Mediterranean, were also favourable. These findings seem directly linked to climate change already reported for the Mediterranean Sea and provide further evidence of the “tropicalization” of the area. Expansion of Trichodesmium blooms to greater latitudes may have important regional and global implications potentially affecting the global nitrogen cycle, the biological carbon pump, productivity levels, and harmful algal bloom frequency