scholarly journals Comparative analysis of morphological and molecular approaches integrated into the study of the dinoflagellate biodiversity within the recently deposited Black Sea sediments – benefits and drawbacks

2020 ◽  
Vol 8 ◽  
Author(s):  
Nina Dzhembekova ◽  
Fernando Rubino ◽  
Satoshi Nagai ◽  
Ivelina Zlateva ◽  
Nataliya Slabakova ◽  
...  
Keyword(s):  
Black Sea ◽  
Dna Sequences ◽  
Aquatic Ecosystems ◽  
Integrated Approach ◽  
The Black Sea ◽  
Morphological Identification ◽  
Toxic Dinoflagellate ◽  
Phytoplankton Diversity ◽  
Morphological Taxonomy ◽  
Molecular Approaches

One of the assets, assigned to the phytoplankton resting stages, is that of serving as the “memory” of the aquatic ecosystems and preserved biodiversity in the course of time. However, an accurate cyst identification proves to be a more difficult and extremely challenging process, even today. In order to gain a better taxonomic coverage of cyst assemblages in the Black Sea, an integrated approach of the classical morphological identification with metabarcoding methods (MySeq sequencing of V7-V9 regions of the 18S rDNA) was applied on thirteen surface sediment samples collected from different sites. A total number of 112 dinoflagellate taxa was detected at the species level and ascribed to 51 genera. In general, it is the molecular analysis that yields a higher number of taxa as compared to those obtained through the morphological taxonomy (66 taxa based on the DNA sequences versus 56 morphologically-identified taxa). Besides, it should be pointed out that the integrated dataset includes 14 potentially toxic dinoflagellate species. Discerned, subsequently, was a good dataset consistency for ten species, followed by some discrepancies as to a number of taxa, identified with one of the methods only, due to specific methodological biases. On the whole, it could be concluded that the combination of morphological and molecular methods is likely to increase the potential for a more reliable taxonomic assessment of phytoplankton diversity in marine sediments which, in turn, proves conclusively the utmost importance of the integrated approach.

scholarly journals Wild Pacific oyster Magallana gigas (Thunberg, 1793) populations in Romanian Black Sea waters – friend or foe?

2019 ◽  
Vol 62 (2) ◽  
pp. 175-183
Author(s):  
Ana-Maria Krapal ◽  
Marin Ioniță ◽  
Mihaela Caplan ◽  
Elena Buhaciuc-Ioniță
Keyword(s):  
Dna Barcoding ◽  
Black Sea ◽  
Pacific Oyster ◽  
Small Population ◽  
The Black Sea ◽  
Morphological Identification ◽  
Oyster Population

A relatively small population of Magallana gigas was discovered near the Agigea harbor (Constanța, Romania) in 2017. The DNA barcoding method was used to confirm the morphological identification of the species. We consider this colony to be the first instance of a possibly stable Pacific oyster population in the Black Sea, outside of farming activities. The possible impact on native ecosystems is briefly discussed.

The genus Cystoseira s.l. (Ochrophyta, Fucales, Sargassaceae) in the Black Sea: morphological variability and molecular taxonomy of Gongolaria barbata and endemic Ericaria crinita f. bosphorica comb. nov.

Phytotaxa ◽  
2021 ◽  
Vol 480 (1) ◽  
pp. 1-21
Author(s):  
SOFIA S. SADOGURSKA ◽  
JOÃO NEIVA ◽  
ANNALISA FALACE ◽  
ESTER A. SERRÃO ◽  
ÁLVARO ISRAEL
Keyword(s):  
Mediterranean Sea ◽  
Black Sea ◽  
Molecular Taxonomy ◽  
Morphological Variability ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Morphological Data ◽  
The Black Sea ◽  
Morphological Identification ◽  
Additional Tool

Brown algae of the genus Cystoseira sensu lato form the most diverse and productive marine ecosystems throughout the Mediterranean Sea and have equal roles also in the Black Sea where they have been decreasing in the recent years. The taxonomy of Cystoseira s.l. taxa from the Black Sea is still not well understood, and questions arise when related taxa have to be delimited. In addition to morphological descriptions, this study provides for the first time molecular data of the Black Sea Cystoseira s.l. distinct morphologies as an additional tool to clarify their identities and phylogenetic affinities. The analysis of two mitochondrial markers (cytochrome oxidase subunit 1—COI, and 23S-tRNAVal intergenic spacer—mt-spacer) showed that Cystoseira s.l. specimens from the Black Sea belong to two recently resurrected genera, namely Gongolaria and Ericaria. Molecular data confirm the morphological identification of G. barbata, which is characterized by high morphological plasticity in the Black Sea. The morphological data presented in this study support the transition of G. barbata to the genus Gongolaria, which was previously proposed based solely on genetic data. For the Black Sea endemic taxon C. bosphorica, sequence divergence suggests conspecificity with Mediterranean Sea species E. crinita and E. barbatula. However, considering original morphological characteristics of the taxon, its geographical isolation, and endemism, the new combination Ericaria crinita f. bosphorica comb. nov. is proposed.

DNA barcoding of five common stored-product pest species of genus Cryptolestes (Coleoptera: Laemophloeidae)

2014 ◽  
Vol 104 (4) ◽  
pp. 486-493 ◽  
Author(s):  
Y.J. Wang ◽  
Z.H. Li ◽  
S.F. Zhang ◽  
Z. Varadínová ◽  
F. Jiang ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Dna Sequences ◽  
Morphological Identification ◽  
Pest Species ◽  
Dna Barcodes ◽  
Molecular Approaches ◽  
Worldwide Distribution ◽  
Haplotype Networks ◽  
Stored Product Pest ◽  
The Usa

AbstractSeveral species of the genus Cryptolestes Ganglbauer, 1899 (Coleoptera: Laemophloeidae) are commonly found in stored products. In this study, five species of Cryptolestes, with almost worldwide distribution, were obtained from laboratories in China, Czech Republic and the USA: Cryptolestes ferrugineus (Stephens, 1831), Cryptolestes pusillus (Schönherr, 1817), Cryptolestes turcicus (Grouvelle, 1876), Cryptolestes pusilloides (Steel & Howe, 1952) and Cryptolestes capensis (Waltl, 1834). Molecular identification based on a 658 bp fragment from the mitochondrial DNA cytochrome c oxidase subunit I (COI) was adopted to overcome some problems of morphological identification of Cryptolestes species. The utility of COI sequences as DNA barcodes in discriminating the five Cryptolestes species was evaluated on adults and larvae by analysing Kimura 2-parameter distances, phylogenetic tree and haplotype networks. The results showed that molecular approaches based on DNA barcodes were able to accurately identify these species. This is the first study using DNA barcoding to identify Cryptolestes species and the gathered DNA sequences will complement the biological barcode database.

Ecological niche modeling of toxic dinoflagellate prorocentrum cordatum in the black sea

2021 ◽  
Author(s):  
Igor Goncharenko ◽  
Maxim Krakhmalnyi ◽  
Violeta Velikova ◽  
Enrique Ascencio ◽  
Aleksandr Krakhmalnyi
Keyword(s):  
Black Sea ◽  
Ecological Niche ◽  
Ecological Niche Modeling ◽  
Niche Modeling ◽  
The Black Sea ◽  
Toxic Dinoflagellate

scholarly journals Subfossil 16S rRNA Gene Sequences of Green Sulfur Bacteria in the Black Sea and Their Implications for Past Photic Zone Anoxia

2007 ◽  
Vol 74 (3) ◽  
pp. 624-632 ◽  
Author(s):  
Ann K. Manske ◽  
Uta Henßge ◽  
Jens Glaeser ◽  
Jörg Overmann
Keyword(s):  
16S Rrna ◽  
Black Sea ◽  
Dna Sequences ◽  
Green Sulfur Bacteria ◽  
The Black Sea ◽  
Rrna Gene ◽  
Photic Zone ◽  
Low Light ◽  
Sulfur Bacteria ◽  
Green Sulfur

ABSTRACT The Black Sea is the largest extant anoxic water body on Earth. Its oxic-anoxic boundary is located at a depth of 100 m and is populated by a single phylotype of marine green sulfur bacteria. This organism, Chlorobium sp. strain BS-1, is extraordinarily low light adapted and can therefore serve as an indicator of deep photic zone anoxia (A. K. Manske, J. Glaeser, M. M. M. Kuypers, and J. Overmann, Appl. Environ. Microbiol. 71:8049-8060, 2005). In the present study, two sediment cores were retrieved from the bottom of the Black Sea at depths of 2,006 and 2,162 m and were analyzed for the presence of subfossil DNA sequences of BS-1 using ancient-DNA methodology. Using optimized cultivation media, viable cells of the BS-1 phylotype were detected only at the sediment surface and not in deeper layers. In contrast, green sulfur bacterial 16S rRNA gene fragments were amplified from all the sediment layers investigated, including turbidites. After separation by denaturing gradient gel electrophoresis and sequencing, 14 different sequence types were distinguished. The sequence of BS-1 represented only a minor fraction of the amplification products and was found in 6 of 22 and 4 of 26 samples from the 2,006- and 2,162-m stations, respectively. Besides the sequences of BS-1, three additional phylotypes of the marine clade of green sulfur bacteria were detected. However, the majority of sequences clustered with groups from freshwater habitats. Our results suggest that a considerable fraction of green sulfur bacterial chemofossils did not originate in a low-light marine chemocline environment and therefore were likely to have an allochthonous origin. Thus, analysis of subfossil DNA sequences permits a more differentiated interpretation and reconstruction of past environmental conditions if specific chemofossils of stenoec species, like Chlorobium sp. strain BS-1, are employed.

scholarly journals Seasonal dynamics and spatial distribution of structural indicators of the bacterioplankton community of the Sevastopol Bay (the Black Sea)

2021 ◽  
Vol 6 (1) ◽  
pp. 82-101
Author(s):  
O. A. Rylkova ◽  
I. G. Polikarpov
Keyword(s):  
Black Sea ◽  
Aquatic Ecosystems ◽  
World Ocean ◽  
Morphological Structure ◽  
The State ◽  
The Black Sea ◽  
Bacterioplankton Community ◽  
Biological Variables ◽  
Sevastopol Bay ◽  
Structural Indicators

Bacterioplankton community determines formation of a significant part of the secondary production and mineralization of organic matter in aquatic ecosystems, as well as responds quickly to any changes in the environment. Data on the state of the microbial community are required for understanding the processes of substance and energy flow transfer in aquatic ecosystems; this is especially important for coastal waters, where significant negative transformations have occurred in recent decades. The aim of this study was to investigate and analyze changes in structural indicators of the bacterioplankton community in different areas of the Sevastopol Bay (the Black Sea) during 1992–2005. Bacterial abundance was determined by direct microscopy, using adsorption (erythrosine) or fluorescent (acridine orange) stains; biomass was calculated using a conversion factor (2·10−14 g C·cell−1) or by direct cell measurements. Cell morphotypes were determined by scanning electron microscopy. The total abundance of microorganisms varied 0.2·106 to 10·106 cells·mL−1; biomass – 2 to 201 mg C·m−3. In the morphological structure of bacterioplankton community, cocci (0.36–0.86 μm in diameter) with a volume of 0.02–0.27 μm³ and rod-shaped cells (0.6–1.2 μm length; 0.2–0.4 μm width) with a volume of 0.50–0.65 μm³ prevailed. Maximum values of the bacterioplankton abundance, biomass, and cell size in the Sevastopol Bay were registered in summer and autumn (June to October), while minimum values were recorded in winter and spring. The observed values of bacterioplankton quantitative indicators were comparable with the values for various coastal water areas of the World Ocean, inter alia the Black Sea. The dynamics of bacterioplankton structural indicators of the Sevastopol Bay during the annual cycle was determined by abiotic and biotic environmental factors. High correlation (86 %, p < 0.01) between the hydrological, hydrochemical, and biological variables confirms the non-random nature of the relationship between them. The discriminant analysis revealed significant differences in the structure of bacterioplankton communities for the bay areas with different intensity of water exchange, degree of general pollution, and distance from the open sea. Significantly smaller bacterial cell volume in 2004 [(0.16 ± 0.05) μm³] compared with that of 2005 [(0.20 ± 0.03) μm³] (paired t-test, p < 0.05) was probably related to intense microorganisms’ grazing by phagotrophic protozoa. The obtained data on the structure of the bacterioplankton community can be used for forecasting the state of the Sevastopol Bay ecosystem, as well as for developing and verifying mathematical models of coastal ecosystems functioning.

The taxonomy of the Caloplaca citrina group (Teloschistaceae) in the Black Sea region; with contributions to the cryptic species concept in lichenology

2009 ◽  
Vol 41 (6) ◽  
pp. 571-604 ◽  
Author(s):  
Jan VONDRÁK ◽  
Pavel ŘÍHA ◽  
Ulf ARUP ◽  
Ulrik SØCHTING
Keyword(s):  
Cryptic Species ◽  
Black Sea ◽  
Atlantic Coast ◽  
Morphological Characters ◽  
Molecular Data ◽  
The Black Sea ◽  
Morphological Identification ◽  
Secondary Chemistry ◽  
Black Sea Region ◽  
Taxonomic Importance

AbstractA new taxonomy of the Caloplaca citrina group in the Black Sea region is presented. It is based on the nrDNA ITS molecular data, chemistry (anthraquinone contents) and 20 morphological characters. Six species previously known in the region are accepted: Caloplaca arcis, C. calcitrapa, C. dichroa, C. flavocitrina, C. geleverjae, C. limonia. Five new species are described: Caloplaca arcisproxima, C. austrocitrina, C. communis, C. confusa and C. nigromarina. Seven further species, Caloplaca britannica, C. citrina, C. marina, C. maritima, C. microthallina, C. ora and C. phlogina are also treated briefly. Some maritime species known from the Atlantic coast of Europe are absent from the region, and, surprisingly, Caloplaca citrina s. str. could not be confirmed from the study area. A key to the species present in the region is provided, although morphological characters are of very limited value in this group. The variability and taxonomic importance of particular features are discussed. No significant differences in secondary chemistry were observed among the species.Many examples of convergence and some semi-cryptic species were revealed by molecular data. The term ‘semi-cryptic species’ is introduced here into lichenology for those species which cannot be clearly diagnosed by their morphology, but which are determined by other characters, mainly by their ecology and distribution. We propose to describe formally such species, in spite of difficulties with subsequent morphological identification.

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