The aim of this study is to determine the phytoplankton species found on the shores of Burgaz Island and the basic ecological variables that affect their seasonal distribution between May 2013 and February 2014. Water samples were collected from four stations at six different depths and plankton samples were gathered horizontally and vertically. The analysis of phytoplankton community composition revealed 101 phytoplankton taxa belonging to five classes. As a result of the study, two taxa belonging to the Dinophyceae (Corythodinium frenguellii and Gonyaulax scrippsae) were new records for Turkish coastal waters. Additionally, a taxon belonging to Dinophyceae (Pronoctiluca pelagica) and a taxon belonging to Bacillariophyceae (Nitzschia reversa) were new records for the Sea of Marmara. Prorocentrum micans, was the dominant species throughout all sampling periods. During the study, the highest phytoplankton abundance was observed at 0.5 m depth in May 2013 (138,500 cells l−1) and February 2014 (52,620 cells l−1). Primary ecological variables, such as temperature (9.0–21.5 °C), salinity (15.23–37.22‰) and dissolved oxygen (4.89–15.84 mg l−1), were recorded on each sampling occasion. In addition, nitrite + nitrate–N (NO2 + NO3–N) (0.01–7.37 μg-at N l−1), phosphate (PO4–P) (0.05–51.95 μg-at P l−1) and silicate (SiO4–Si) (0.01–0.20 μg-at Si l−1) concentrations were measured. Chlorophyll a and suspended material values ranged between 0.01–3.17 μg l−1 and 10.0–61.5 mg l−1, respectively. Spearman's rank correlation was used to determine the relationship between phytoplankton species and ecological variables, and Bray–Curtis analysis and Euclidean distance were applied to bring out the similarity between stations.

Changes in phytoplankton composition of the Golden Horn Estuary were investigated following remediation, through seawater transfer from the Strait of Istanbul to the estuary. Average values of Secchi depth, salinity and dissolved oxygen increased during this study when compared with a previous study. The average number of species (S) and species diversity (H′) increased and they correlated positively with Secchi depth, salinity and dissolved oxygen. There was a similar phytoplankton group composition between this and a previous study, however, the species composition differed. A total of 127 taxa consisting of diatoms (66 taxa), dinoflagellates (49 taxa) and others (12 taxa) were identified. Abundance of dinoflagellates and phytoflagellates and their relative contribution to the total phytoplankton abundance increased during this study, however, the abundance of diatoms and their relative contribution decreased notably, as compared with the previous study. There was a significant positive correlation between salinity and dinoflagellates and phytoflagellates (P < 0.01), and also between Secchi depth and dinoflagellates (P < 0.01) in the upper estuary. Additionally, salinity and Secchi depth correlated positively with species diversity (H′) and number of species (S) (P < 0.01). The increase in water transparency probably contributed to the increase in abundance of dinoflagellates and phytoflagellates. The results revealed that water transparency was one of the most important factors affecting phytoplankton composition in the study area. Changes in some environmental conditions following seawater transfer appear to have changed phytoplankton composition. As a result, phytoplankton species were confirmed as a very good indicator of changed environmental conditions.

The abundance pattern and species diversity of phytoplankton in the surface waters of the Golden Horn Estuary were investigated between August 2011 and July 2012 in relation to environmental factors. Seventy-eight phytoplankton taxa (38 diatoms, 30 dinoflagellates and 10 phytoflagellates) belonging to eight taxonomic classes were identified in bottle and net samples. Phytoplankton abundance increased in spring and summer (from March to August) and reached its highest (10,429 × 103 cells L−1) during the bloom of Heterosigma akashiwo (Raphidophyceae) in the middle and upper estuary in late May. In general, phytoplankton abundance was higher in the middle estuary indicating more suitable conditions for phytoplankton growth, while species richness and diversity was higher in the lower estuary. The most abundant species were Skeletonema marinoi and Thalassiosira sp. among diatoms; Scrippsiella trochoidea among dinoflagellates; Plagioselmis prolonga and Heterosigma akashiwo among phytoflagellates. Diatoms were more abundant in the lower and middle estuary, while dinoflagellates and phytoflagellates in the upper estuary. The main factors causing the spatio-temporal variation of phytoplankton in the study area were temperature, salinity, water transparency and nutrients. Water transparency in the upper estuary is mostly influenced by organic and inorganic matter carried by two streams. As a result, this area should be considered a potential risk area for future algal blooms.

The sedimentary sequence discovered at archaeological excavations in ancient Theodosius Harbour at İstanbul contains the records of sea level, environmental changes and the cultural history of the region. The cobbles at the base of the sequence include archaeological remnants of Neolithic culture that settled in the area between 8.4 and 7.3 14C ka BP, and are located at 6 m below the present sea level. The sediments representing a coastal environment indicate that the area was used as a harbour from AD 4th to at least the 11th century and were filled by the sediments derived from Lykos Stream after 11th century.

An extensive rescue excavation has been conducted in the ancient harbor of İstanbul (Yenikapı) by the Sea of Marmara, revealing a depositional sequence displaying clear evidence of transgression and coastal progradation during the Holocene. The basal layer of this sequence lies at 6 m below the present sea level and contains remains of a Neolithic settlement known to have been present in the area, indicating that the sea level at ~ 8–9 cal ka BP was lower than 6 m below present. Sea level advanced to its maximum at ~ 6.8–7 cal ka BP, drowning Lykos Stream and forming an inlet at its mouth. After ~ 3 cal ka BP, coastal progradation became evident. Subsequent construction of the Byzantine Harbor (Theodosius; 4th century AD) created a restricted small basin and accumulation of fine-grained sediments. The sedimentation rate was increased due to coastal progradation and anthropogenic factors during the deposition of coarse-grained sediments at the upper parts of the sequence (7th–9th centuries AD). The harbor was probably abandoned after the 11th century AD by filling up with Lykos Stream detritus and continued seaward migration of the coastline.

Spatial and temporal variability and bloom formation of the potentially toxic diatom Pseudo-nitzschia spp. was investigated weekly to monthly from October 2009 to October 2010 in a eutrophic estuary, the Golden Horn. Pseudo-nitzschia spp. were detected in 195 of 512 samples (38%) collected throughout the year. Two species, P. calliantha and P. pungens, were identified based on the SEM examination. Blooms of Pseudo-nitzschia occurred in the lower and middle estuary in January and May. The bloom in January mainly comprised P. calliantha. In the bloom in early May, P. calliantha made up 72% of the Pseudo-nitzschia cells and P. pungens 28%. However, the contribution of P. pungens increased to 83% in late May. The Pseudo-nitzschia blooms occurred at low temperature (9–15°C) and moderate salinity (17–18), and for P. calliantha a significant negative correlation was found with temperature and a significant positive correlation with salinity. The percentage of Pseudo-nitzschia cells decreased gradually from lower to upper estuary (59–14%), correlating with a decrease in Secchi depth (5.5–0.5 m). Principal components analyses (PCA) were used to explore the spatial and temporal variability of environmental factors in relation to Pseudo-nitzschia abundances, and showed that NH4, pH, Secchi depth and DO values were the most important factors reflecting spatial differences, while temperature, salinity, Chl-a and Si:N were more important factors showing temporal differences. High abundances of P. pungens correlated mainly with pH, Secchi depth and DO values, whereas P. calliantha also correlated with NO3 + NO2. Low light availability due to high concentrations of suspended material and very variable environmental conditions (e.g. pH, DO and NH4) may have limited growth of Pseudo-nitzschia in the upper estuary. Regular monitoring of Pseudo-nitzschia is important for improving the understanding of the influence of environmental parameters on bloom dynamics in the study area.

The occurrence of Cavernularia pusilla is reported for the first time from the Sea of Marmara, extending the range of the species in the eastern Mediterranean and providing the first report of the species from Turkish waters.

The oldest records on the sharks of the Sea of Marmara are limited to a few notes on two great white sharks, Carcharodon carcharias, which were caught in the southern part of the Bosphorus Strait by the bluefin tuna (Thunnus thynnus) handliners in February and November of 1881 (Fergusson, 1996: Appendix 3, 345). A review of the shark-specific or general ichthyology studies of the Sea of Marmara, as well as of the daily newspapers published since the beginning of 1900s, providing information on the capture of sharks in Marmaric waters, revealed the historical and contemporary occurrence of 21 shark species in the Sea of Marmara. The contemporary occurrence of 13 of the 21 species in the Sea of Marmara has been confirmed by recent studies and fishery records. Recent studies showed that the fish fauna of the Sea of Marmara comprises 235 species, 13 of which are shark species, with the confirmed contemporary occurrences of sharks representing 5.53% of the total ichthyofauna.

Our current knowledge on the carcharhinid sharks occurring in Turkey's seas comprises rudimentary data. Recently discovered photographic evidence suggests that Carcharhinus spp. have been present in the Sea of Marmara since the 1950s. This evidence also extends the known historical distributional range of Carcharhinus spp. into Marmaric waters, a northern extension of the Mediterranean basin. The results of previous and recent ichthyological inventories of the Sea of Marmara suggest that, currently, no species of the Carcharhinidae family occur in Marmaric waters. Further studies could provide an answer to the question: do any species of the Carcharhinidae family inhabit the Sea of Marmara?

Aggregates of the Polychaeta Phyllochaetopterus socialis were recorded for the first time off Gemlik Bay in the Sea of Marmara, in August 2008. These were found at about 53 m depth, on the soft sediments around the sub-sea part of the North Anatoly Earthquake Fault. Samples were landed by beam trawl. Total wet weight of the mats was 58 kg. Forty-three species belonging to 10 phyla associated with P. socialis were recorded from the whole landing materials. Echinodermata and Gastropoda were the most abundant (12 and 8 species, respectively). Shannon–Wiener diversity and Margalef species richness indices were applied to analyse the structure of benthic communities. Presence and abundance lognormal distribution of the species and communities in mat habitat are shown. The hydrographic environment of the water mass is also discussed.

We report on the recent captures of the bramble shark, Echinorhinus brucus, from the Sea of Marmara, Turkey. A short description is given. Based on available data, current status of the species in the Sea of Marmara is discussed.

Following the ‘Volgoneft-248’ oil spill, phytoplankton distribution within the affected area was investigated for two years. Simultaneously measured physical variables such as salinity, temperature, Secchi disc, current speed and direction, and total petroleum hydrocarbons (TPH) were evaluated together with phytoplankton data. At the time of the accident, the TPH concentration in surface water was measured as 2.17 mg l−1 and decreased to 88.5 µg l−1 after five days. In the first sampling period, no diatoms were detected in surface water, while dinoflagellates were dominant in the phytoplankton community. The species composition of phytoplankton changed rapidly in two months and the diatoms increased in terms of abundance and diversity. This indicated that the diatoms might be more sensitive to oil pollution than the dinoflagellates. In comparison with the historical datasets, the low phytoplankton abundance following the oil spill should be considered as the small effect of oil on the phytoplankton rather than natural variability of the ecosystem. High oil concentration in the water column caused stress on the phytoplankton and influenced the species composition negatively depending on the sensitivity of groups and the natural variability of the ecosystem.

Cirratulus dollfusi Fauvel, 1928 is re-described from the material from the Sea of Marmara. The specimens collected from the Sea of Marmara were compared to the holotype of the species. The species is a multitentaculate and multibranchiate cirratulid; it differs from all other known cirratulid genera in its type of chaetae and the way the multiple branchial filaments arise from the notopodia. Chaetae are of two types: numerous long, fine capillaries in both rami throughout, also 2–4 shorter, wider, finely tapering spines in noto- and neuropodia. There are no slightly flattened sigmoid spines, typical of most Cirratulus species. Very short, slender grooved tentacles arise in a small circular group on either side of chaetiger 1. Branchial filaments are multiple; they arise as 1–2 filaments from each of 4–8 raised notopodial lobes on parapodia of anterior and middle segments, with lobes fading out and fewer (holotype) or no branchiae posteriorly (our material). No other cirratulid genera appear to have straight, tapering spines plus so many fine capillaries. We propose Fauvelicirratulus gen. nov. for this species. The species seems most closely related to Cirratulus hedgpethi Hartman, 1951, from the northern Gulf of Mexico, still only known from the incomplete original description. Features of some cirratulid genera are compared and the use of multiple branchiae as a generic character is discussed.

Field surveys and literature review revealed the capture of 50 bluntnose sixgill sharks from the Sea of Marmara. Total lengths of the observed specimens ranged from 1.2–6 m, and weighed between 10 and 1000 kg. Nine specimens were males, 23 were females and 18 were of unknown sex. Regarding the bathymetric distribution of the captured bluntnose sixgill sharks, majority of the specimens (78%) were recorded in slope and shelf waters of the eastern and northern Sea of Marmara. Fishing presents the only known proximate threat to bluntnose sixgill shark populations in Marmaric waters. Inclusion of Hexanchus griseus in the endangered marine fish list of the Turkish Fisheries Act, would be the first step before subjecting H. griseus to 100% protection.