Golden Horn Estuary: Description of the ecosystem and an attempt to assess its ecological quality status using various classification metrics

In this paper, we describe the pelagic and benthic ecosystem of the Golden Horn  estuary opening into the Marmara Sea. To improve the water quality of the estuary, which had long been subject to severe anthropogenic pollution (industrial, chemical, shipping),  industrial facilities were moved from the estuary in the 1980s, followed by a rehabilitation plan in the 1990s. Our results, based on chemical parameters and phytoplankton showed some signs of improvement of water conditions in the upper layer. However, macrozoobenthic findings of this study did not reflect such a recovery in bottom life.An approach to the Ecological Quality Status (EQS) assessment was performed by applying the biotic indices BENTIX, AMBI, BOPA, BO2A. Our final assessment was based on 'expert-judgements' and revealed a very disturbed overall ecosystem with 'bad' EQS for the station at the head of the estuary,  'poor' in the rest of the estuary and 'moderate' EQS only in the middle station

The response of benthic foraminifer, ostracod and mollusc assemblages to environmental conditions: a case study from the Camalti Saltpan (Izmir-Western Turkey)

The subject of this report is benthic foraminifer populations preserved in the saltpan of Camalti in the Province of Izmir. High salinity in certain habitats of Ammonia tepida Cushman may be the primary cause of the high rate of twins and triplets as well as other morphological abnormalities recorded within this species (50 % as compared to an anomaly rate of 1 % in normal marine waters). Thicker cyst membrane developing in extremely saline environments may encourage twins and other morphological deformities by denying free movement of the offspring. Ecological factors such as heavy metal contamination of ambient waters as well as contamination by other wastes are also not ruled out as leading to such developmental anomalies. Of the 27 collected samples, Number 5 (that is closest to the sea) includes the typical marine foraminifers. Nonion depressulum (Walker & Jacob), Ammonia tepida Cushman and Porosononion subgronosum(Egger) are the dominant species in other samples. A total of 63 abnormal individuals (8 triplets, 24 twins, and 31 morphological anomalies) was found within seven of the 27 samples collected. Ten samples contained freshwater ostracods: Darwinula stevensoni(Brady and Robertson), Leptocythere lacertosa Hirschmann, Cyprideis torasa (Jones), Cyprideis (C.) anatolica Bassiouni, and Loxochoncha elliptica Brady. Among these samples (some of which contained only a few species of ostracods - and those limited in number of offspring), one had an unusually high ratio of healthy foraminifers vs those with anomalies. Worthy of note in another sample was a high abundance of molluscs. Among pelecypods, were found Ostrea edulis Linné, Lucinella divaricata (Linné), Pseudocama gryphina Lamarck,Cerastoderma edule (Linné), and Scrobicularia plana da Costa; and among gastropods were identified Hydrobi (Hydrobia) acuta(Draparnaud), Rissoa labiosa (Montagu), R. parva (da Costa), R. violacea Desmarest, Pirenella conica (Blainville), Bittium desayesi(Cerulli and Irelli), B. lacteum Philippi and B. reticulatum Philippi

Phytoplankton composition related to the environmental conditions in the coastal waters of the Gulf of Erdek

1545-1559Seasonal changes of phytoplankton communities in the coastal waters of the Gulf of Erdek from November 2006 to August 2008 were examined in relation to some environmental variables and 95 species from 6 different algae groups were identified. In addition, two species were recorded for the first time in the Turkish coastal waters and one species for the Sea of Marmara. The maximum total phytoplankton abundance (1.99 × 105 cells L-1) were observed in May 2008, with Pseudo-nitzschia sp. being the most dominant species of that month (1.52 × 105 cells L-1). Both the Bray-Curtis diversity index and the Euclidean distance indicated that the upper and lower water layers were separated from each other at the stations, and the Spearman’s rank-correlation and CCA analyses also showed that environmental variables affected the abundance of species. Furthermore, according to the CCA diagram, especially the temperature and dissolved oxygen had a bigger impact on the distribution of species. The Shannon-Wiener diversity index (Hʹ) values were low when Pseudo-nitzschia sp., Prorocentrum micans, Gymnodinium sp. and Prorocentrum scutellum were dominant over other species in the sampling period

A rapid and sensitive system for recovery of nucleic acids from Mycobacteria sp. on archived glass slides

The field of diagnostics continues to advance rapidly with a variety of novel approaches, mainly dependent upon high technology platforms. Nonetheless much diagnosis, particularly in developing countries, still relies upon traditional methods such as microscopy. Biological material, particularly nucleic acids, on archived glass slides is a potential source of useful information both for diagnostic and epidemiological purposes. There are significant challenges faced when examining archived samples in order that an adequate amount of amplifiable DNA can be obtained. Herein, we describe a model system to detect low numbers of bacterial cells isolated from glass slides using (laser capture microscopy) LCM coupled with PCR amplification of a suitable target. Mycobacterium smegmatis was used as a model organism to provide a proof of principle for a method to recover bacteria from a stained sample on a glass slide using a laser capture system. Ziehl-Neelsen (ZN) stained cells were excised and catapulted into tubes. Recovered cells were subjected to DNA extraction and pre-amplified with multiple displacement amplification (MDA). This system allowed a minimum of 30 catapulted cells to be detected following a nested real-time PCR assay, using rpoB specific primers. The combination of MDA and nested real-time PCR resulted in a 30-fold increase in sensitivity for the detection of low numbers of cells isolated using LCM. This study highlights the potential of LCM coupled with MDA as a tool to improve the recovery of amplifiable nucleic acids from archived glass slides. The inclusion of the MDA step was essential to enable downstream amplification. This platform should be broadly applicable to a variety of diagnostic applications and we have used it as a proof of principle with a Mycobacterium sp. model system

A check-list of tintinnids (protozoa: Ciliophora) in the Coastal Zone of Turkey

In the last ten years, it was more clearly understood that in marine ecosystems members of Protozoa play a significant role in the flow of energy and biochemical cycles of carbon. It is known that tintinnids, also known as lorica-bearing ciliates, are the most important assistants of the cycle. In Turkey, which has coastlines of notable length in the Black Sea, Aegean Sea and Levantine Sea as well as harbors the Marmara Sea within the Straits Complex, tintinnids have been studied according to mainly their lorica shapes. In this study we used a lorica based classification and organized 109 tintinnid morpho-species from previously published works and we aimed to provide for the first time a reliable check-list of the region following the International Code of Zoological Nomenclature rules. Copyright 2014 Zoological Society of Pakistan