scholarly journals Rapid establishment of the non-indigenous ascidian Styela plicata and its associated bacteria in marinas and fishing harbors along the Mediterranean coast of Israel

2017 ◽  
Vol 18 (2) ◽  
pp. 324 ◽  
Author(s):  
L. NOVAK ◽  
S. LÓPEZ-LEGENTIL ◽  
E. SIERADZKI ◽  
N. SHENKAR
Keyword(s):  
Horizontal Transmission ◽  
Mediterranean Coast ◽  
Rrna Gene ◽  
Associated Bacteria ◽  
Bacterial Phyla ◽  
Styela Plicata ◽  
Solitary Ascidian ◽  
Successful Establishment ◽  
The Mediterranean ◽  
Surrounding Seawater

Styela plicata (Lesueur, 1823) (Tunicata; Stolidobranchia; Styelidae) is a solitary ascidian with a global distribution. Until recently it had not been observed along the Mediterranean coast of Israel, but is now to be found in many harbors attached to suspended ropes and other artificial structures. In order to monitor the populations of S. plicata, we surveyed eight harbors along the Israeli Mediterranean coast. Our results show that the condition and maintenance of each harbor significantly affected the presence of S. plicata. We also characterized the microbial communities in the tunic of three individuals using 16S rRNA gene tag pyrosequencing and compared them to those in the surrounding seawater, in order to determine whether the symbiotic bacteria may contribute to the successful establishment of this ascidian species. We found 15 bacterial phyla in total, of which 14 were present in the animal hosts: 6 were present in all of the individuals and 4 in two of the individuals. Three of the 15 phyla observed were absent in the surrounding seawater. The high variability among the three hosts suggests a mechanism of horizontal transmission and may play a role in the process of invading new and less tolerant niches.

scholarly journals Identification of plastic-associated species in the Mediterranean Sea using DNA metabarcoding with Nanopore MinION

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Keren Davidov ◽  
Evgenia Iankelevich-Kounio ◽  
Iryna Yakovenko ◽  
Yuri Koucherov ◽  
Maxim Rubin-Blum ◽  
...  
Keyword(s):  
Flow Cell ◽  
Taxonomic Composition ◽  
Mediterranean Coast ◽  
Rrna Gene ◽  
Free Living ◽  
Oxford Nanopore ◽  
Dna Metabarcoding ◽  
The Mediterranean ◽  
Associated Species

Abstract Plastic debris in the ocean form a new ecosystem, termed ‘plastisphere’, which hosts a variety of marine organisms. Recent studies implemented DNA metabarcoding to characterize the taxonomic composition of the plastisphere in different areas of the world. In this study, we used a modified metabarcoding approach which was based on longer barcode sequences for the characterization of the plastisphere biota. We compared the microbiome of polyethylene food bags after 1 month at sea to the free-living biome in two proximal but environmentally different locations on the Mediterranean coast of Israel. We targeted the full 1.5 kb-long 16S rRNA gene for bacteria and 0.4–0.8 kb-long regions within the 18S rRNA, ITS, tufA and COI loci for eukaryotes. The taxonomic barcodes were sequenced using Oxford Nanopore Technology with multiplexing on a single MinION flow cell. We identified between 1249 and 2141 species in each of the plastic samples, of which 61 species (34 bacteria and 27 eukaryotes) were categorized as plastic-specific, including species that belong to known hydrocarbon-degrading genera. In addition to a large prokaryotes repertoire, our results, supported by scanning electron microscopy, depict a surprisingly high biodiversity of eukaryotes within the plastisphere with a dominant presence of diatoms as well as other protists, algae and fungi.

scholarly journals Host species determine symbiotic community composition in Antarctic sponges (Porifera: Demospongiae)

2020 ◽  
Author(s):  
Oriol Sacristán-Soriano ◽  
Natalia Pérez Criado ◽  
Conxita Avila
Keyword(s):  
Community Composition ◽  
High Throughput Sequencing ◽  
South Shetland Islands ◽  
Ecological Niches ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Strict Core ◽  
The Antarctic ◽  
Surrounding Seawater ◽  
Antarctic Sponges

AbstractThe microbiota of four Antarctic sponges, Dendrilla antarctica, Sphaerotylus antarcticus, Mycale acerata, and Hemigellius pilosus, collected at two South Shetland Islands and at two locations in the Antarctic Peninsula separated by ca. 670 km, were analyzed together with surrounding seawater. We used high throughput sequencing of the V4 region of the 16S rRNA gene common to Bacteria and Archaea to investigate the microbial diversity and community composition. Our study reveals that sponge-associated prokaryote communities are consistently detected within a particular sponge species regardless of the collection site. Their community structure and composition are typical of low microbial abundance (LMA) sponges. We conclude that prokaryote communities from Antarctic sponges are less diverse and differ in their composition compared to those in the water column. Microbiome analysis indicates that Antarctic sponges harbor a strict core consisting of seven OTUs, and a small variable community comprising several tens of OTUs. Two abundant prokaryotes from the variable microbiota that are affiliated to the archaeal and bacterial phyla Thaumarchaeota and Nitrospirae may be involved in the sponge nitrification process and might be relevant components of the nitrogen cycling in Antarctica. The likely generalist nature of dominant microbes and the host-specific structure of symbiont communities suggest that these Antarctic sponges represent different ecological niches for particular microbial enrichments.

Genetic Diversity and Structure of the Nile Soft-Shelled Turtle (Trionyx triunguis) Along the Mediterranean coast of Turkey

2020 ◽  
Vol 27 (6) ◽  
pp. 307-315
Author(s):  
Özgür Güçlü ◽  
Bülent Bozdoğan
Keyword(s):  
Microsatellite Loci ◽  
Geographic Distance ◽  
Iucn Red List ◽  
Genetic Variations ◽  
Mediterranean Coast ◽  
Critically Endangered ◽  
Mediterranean Populations ◽  
Genetic Diversity And Structure ◽  
Polymorphic Microsatellite ◽  
The Mediterranean

The Nile soft-shelled turtle (Trionyx triunguis) is distributed between Dalyan and Samandağ throughout the Mediterranean coast in Turkey. The Mediterranean subpopulation of the Nile soft-shelled turtle is listed as critically endangered in the IUCN Red List Categories. This investigation aimed to determinate levels of genetic variations and patterns of genetic structures among Mediterranean populations in Turkey by using T. triunguis-specific microsatellite primers. A total of 13 polymorphic microsatellite loci were studied among samples of 121 individuals collected from five populations in Turkey. Of 13 polymorphic microsatellite loci used, 3 new were identified in this study. The genetic differentiation among the 5 studied populations of T. triunguis was significant (p 0.001). The analysis of molecular variance (AMOVA) indicated that genetic variations occurred mainly within populations (89.7%) rather than among populations (10.3%). Structure analysis showed presence of two main groups among the Mediterranean T. triunguis populations. However genetic variations among populations were not correlated with geographic distance between the locations. Analysis of data showed that one of the populations (Dalyan) had undergone a bottleneck effect. Migration analysis indicates that T. triunguis migrates between five Mediterranean populations in Turkey. We concluded that based on our results the status of ‘critically endangered’ of T. triunguis should be maintained. Long term population genetic survey studies should be undertaken and changes in habitats of T. triunguis populations, as well as their population size and structure should be monitored for each population to be able to establish a clear strategy for protection of T. triunguis.

The formation of the Egyptian Arabic dialect area

2018 ◽  
Author(s):  
Peter Behnstedt ◽  
Manfred Woidich
Keyword(s):  
Mediterranean Coast ◽  
External Factors ◽  
Internal Factors ◽  
Dialect Contact ◽  
Historical Information ◽  
Egyptian Arabic ◽  
Transitional Area ◽  
The Mediterranean

This chapter deals with the sedentary dialects of Egypt, excluding the bedouin dialects of Sinai and the Libyan bedouin dialects on the Mediterranean coast. It attempts to combine historical information on the settlement of Arabic tribes in Egypt with accounts of present-day Egyptian dialects and those of the regions from which those tribes came, initially Yemen and the Levant, later Hejaz, and then the Maghreb. The diversity of the Egyptian Arabic dialect area is partly explained by external factors, namely different layers of arabization over centuries. It is also explained by internal factors, namely dialect contact, which implies phenomena such as hyperdialectisms. Egypt is seen as a dialect area in its own right, but one that shows phenomena of a transitional area between the Arab East and West. A case study of Alexandria deals with dialect death. The role of substrata is discussed, but is considered negligible.

Floristic patterns and ecological drivers of sand dune ecosystem along the Mediterranean coast of Egypt

2019 ◽  
Vol 33 (4) ◽  
pp. 388-411 ◽  
Author(s):  
Mohamed Abdelaal ◽  
Dalia Ahmed ◽  
Mauro Fois ◽  
Giuseppe Fenu ◽  
Gianluigi Bacchetta
Keyword(s):  
Sand Dune ◽  
Mediterranean Coast ◽  
Floristic Patterns ◽  
The Mediterranean

scholarly journals Gut Microbiome in a Russian Cohort of Pre- and Post-Cholecystectomy Female Patients

2021 ◽  
Vol 11 (4) ◽  
pp. 294
Author(s):  
Irina Grigor’eva ◽  
Tatiana Romanova ◽  
Natalia Naumova ◽  
Tatiana Alikina ◽  
Alexey Kuznetsov ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
Gallstone Disease ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Female Patients ◽  
Composition And Structure ◽  
Before And After

The last decade saw extensive studies of the human gut microbiome and its relationship to specific diseases, including gallstone disease (GSD). The information about the gut microbiome in GSD-afflicted Russian patients is scarce, despite the increasing GSD incidence worldwide. Although the gut microbiota was described in some GSD cohorts, little is known regarding the gut microbiome before and after cholecystectomy (CCE). By using Illumina MiSeq sequencing of 16S rRNA gene amplicons, we inventoried the fecal bacteriobiome composition and structure in GSD-afflicted females, seeking to reveal associations with age, BMI and some blood biochemistry. Overall, 11 bacterial phyla were identified, containing 916 operational taxonomic units (OTUs). The fecal bacteriobiome was dominated by Firmicutes (66% relative abundance), followed by Bacteroidetes (19%), Actinobacteria (8%) and Proteobacteria (4%) phyla. Most (97%) of the OTUs were minor or rare species with ≤1% relative abundance. Prevotella and Enterocossus were linked to blood bilirubin. Some taxa had differential pre- and post-CCE abundance, despite the very short time (1–3 days) elapsed after CCE. The detailed description of the bacteriobiome in pre-CCE female patients suggests bacterial foci for further research to elucidate the gut microbiota and GSD relationship and has potentially important biological and medical implications regarding gut bacteria involvement in the increased GSD incidence rate in females.

scholarly journals Characterization of symbiotic and associated bacteria from entomopathogenic nematode Heterorhabditis sp. (nematode: Heterorhabditidae) isolated from India

2020 ◽  
Vol 30 (1) ◽  
Author(s):  
Rashid Pervez ◽  
Showkat Ahmad Lone ◽  
Sasmita Pattnaik
Keyword(s):  
Insect Pests ◽  
Entomopathogenic Nematode ◽  
Alcaligenes Faecalis ◽  
Symbiotic Bacteria ◽  
Rrna Gene ◽  
Main Body ◽  
Associated Bacteria ◽  
Molecular Approaches

Abstract Background Entomopathogenic nematodes (EPNs) harboring symbiotic bacteria are one of the safest alternatives to the chemical insecticides for the control of various insect pests. Infective juveniles of EPNs locate a target insect, enter through the openings, and reach the hemocoel, where they release the symbiotic bacteria and the target gets killed by the virulence factors of the bacteria. Photorhabdus with Heterorhabditis spp. are well documented; little is known about the associated bacteria. Main body In this study, we explored the presence of symbiotic and associated bacteria from Heterorhabditis sp. (IISR-EPN 09) and characterized by phenotypic, biochemical, and molecular approaches. Six bacterial isolates, belonging to four different genera, were recovered and identified as follows: Photorhabdus luminescens, one each strain of Providencia vermicola, Pseudomonas entomophila, Alcaligenes aquatilis, and two strains of Alcaligenes faecalis based on the phenotypic, biochemical criteria and the sequencing of 16S rRNA gene. Conclusion P. luminescens is symbiotically associated with Heterorhabditis sp. (IISR-EPN 09), whereas P. vermicola, P. entomophila, A. aquatilis, and A. faecalis are the associated bacteria. Further studies are needed to determine the exact role of the bacterial associates with the Heterorhabditis sp.

scholarly journals An experimental intraradicular biofilm model in the pig for evaluating irrigation techniques

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Toshinori Tanaka ◽  
Yoshio Yahata ◽  
Keisuke Handa ◽  
Suresh V. Venkataiah ◽  
Mary M. Njuguna ◽  
...  
Keyword(s):  
16S Rrna ◽  
Root Canal ◽  
Apical Periodontitis ◽  
Exposure Model ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
Bacterial Phyla ◽  
Biofilm Model ◽  
Biofilm Removal

Abstract Background We established an in vivo intraradicular biofilm model of apical periodontitis in pigs in which we compared the efficacy of different irrigant activation techniques for biofilm removal. Methods Twenty roots from the deciduous mandibular second premolar of 5 male pigs were used. After pulpectomy, canals were left open for 2 weeks and then sealed for 4 weeks to enable the development of an intracanal biofilm. The intraradicular biofilms was evaluated using SEM and bacterial 16S rRNA gene-sequencing. To investigate the efficacy of biofilm removal, root canal irrigations were performed using conventional needle, passive ultrasonic, subsonic, or laser-activated irrigation. Real-time PCR was conducted to quantitate the remaining biofilm components. Statistical analysis was performed using ANOVA followed by a Tukey kramer post-hoc test with α = 0.05. Results The pulp exposure model was effective in inducing apical periodontitis and SEM analysis revealed a multi-layer biofilm formation inside the root canal. 16S rRNA sequence analysis identified Firmicutes, Bacteroidetes, and Fusobacteria as the predominant bacterial phyla components, which is similar to the microbiome profile seen in humans. None of the tested irrigation techniques completely eradicated the biofilm components from the root canal, but the subsonic and laser-activated irrigation methods produced the lowest bacterial counts (p < 0.05). Conclusions An experimental intraradicular biofilm model has been successfully established in pigs. Within the limitations of the study, subsonic or laser-activated irrigation demonstrated the best biofilm removal results in the pig system.

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