This study was implemented to determine the environmental factors and causative organisms of the recent mucilage formation in the Marmara Sea. Samples were taken during the study from 7 different depths (0.5–30 m) of one sampling point of the Büyükada Island shore between January and June 2008. As a result, 62 phytoplankton species belonging to 5 different groups were identified. Dinoflagellates were dominant in terms of species number, and diatoms in terms of cell number. In January and February, mucilage formation was very dense, where 5 phytoplankton species (Clindrotheca closterium, Pseudo-nitzschiasp.,Skeletonema costatum, Thalassiosira rotula(Bacillariophyceae) andGonyaulax fragilis(Dinophyceae)) were reported as dominant organisms. Among them,Gonyaulax fragilishas never been reported in the Marmara Sea previously, thus that organism appeared firstly with the formation of dense mucilage and then when the mucilage decayed in May and June 2008,G. fragilisdisappeared. Autofluorescent single-celled organisms were classified in three groups depending on their cell sizes (>20 μm, >2 μm, >0.2 μm) by membrane filtration and total count of bacteria were determined by epifluorescence microscope after dying with DAPI. The highest total bacteria was recorded in April at 25 m depth (6655 ± 44.4 cells ml−1) while the lowest count was in June at 0.5 m depth (1077 ± 26.1 cells ml−1). The seawater temperature ranged between 7.0 and 21.5°C, salinity between 20.9 and 37.4 ppt and dissolved oxygen amount between 2.75 and 12.75 mg l−1. The chlorophyll-aamount ranged between 0.10 and 6.35 μg l−1, the higher values were recorded in January at 15 m depth (6.35 μg l−1) and in April at 10 m depth (4.89 μg l−1). Among the nutrients, the amounts of nitrite + nitrate-N varied between 0.02 and 7.67 μg-at N l−1, phosphate-P between 0.11 and 0.96 μg-at P l−1and silicate-Si between 0.37 and 8.93 μg-at Si l−1. The highest values were determined at a deeper layer where nutrients are accumulated. On the other hand, the N:P ratio interval was found as 0.1–11.3, Si:P ratio as 2.92–52.33 and N:Si ratio as 0.01–1.10 during the sampling period. Nitrogen was the limiting nutrient and the silica amount was enough to enable the development of diatoms.

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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.

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This study was carried out to explore the effectiveness of different biotic indexes in the Marmara Sea. The assessment of ecological quality status (EQS) was performed by applying the biotic indexes BENTIX, AMBI, BOPA, BO2A and Shannon-Wiener diversity, in combination with the estimation of total organic carbon (TOC) content of sediments. BOPA and BO2A indexes tended to overestimate the EQS of the stations. BENTIX was the most efficient index as it demonstrated conceivable EQS results with respect to TOC load and successfuly determined "acceptable" or "not acceptable" status of the stations. TOC content of sediment, which significantly correlated with several benthic measures (S, N, AMBI, BENTIX), proved to be a valuable proxy measure in evaluating the likelihood of benthic impairment. When overall EQS of northern Marmara Sea was discussed, the region was designated as ecologically disturbed with only 25.7% of the stations in acceptable status.