Spatial and temporal variations of tintinnids (Ciliata: Protozoa) in the Bay of Mersin, Northeastern Mediterranean Sea

Seasonal variations in species composition and abundance of tintinnids were investigated in the eutrophic coastal and offshore waters of Mersin Bay. Twelve sampling cruises were performed from September 2008 to February 2011. A total of 85 tintinnid taxa were identified. Among the recorded genera, agglutinated Tintinnopsis had the largest number of species (12 species), followed by hyaline loricated Eutintinnius (9 species), and Proplectella (7 species). Stenosemella ventricosa, Tintinnopsis beroidea, T. compressa, Favella azorica, and Helicostemella subulata were the dominant species during the study period. There were clear seasonal variations in species composition and abundance of tintinnids. The highest number of tintinnid species occurred in January 2009 and November 2010 in the entire study area, while the lowest species number occurred in March 2009. Morever, species numbers were higher in offshore stations than coastal stations. Some species were present in the coastal area of the bay, and other species were present offshore. The highest tintinnid abundance values were found in September 2008 (820 ind L-1) and August 2009 (749 ind L-1) at coastal stations. The high abundance values in the coastal stations indicates that an increase of tintinnids is closely related to trophic status of the marine environment. In connection with these results, correlation analysis revealed that chlorophyll-a had an important effect on tintinnid abundance. Tintinnid communities may be used as a potential bio-indicator for assessing the trophic state of the coastal seas and bays.

Simulation of annual plankton productivity cycle in the Black Sea by a one-dimensional physical-biological model

The annual cycle of the plankton dynamics in the central Black Sea is studied by a one-dimensional vertically resolved physical-biological upper ocean model, coupled with the Mellor-Yamada level 2.5 turbulence closure scheme. The biological model involves interactions between the inorganic nitrogen (nitrate, ammonium), phytoplankton and herbivorous zooplankton biomasses, and detritus. Given a knowledge of physical forcing, the model simulates main observed seasonal and vertical characteristic features, in particular, formation of the cold intermediate water mass and yearly evolution of the upper layer stratification, the annual cycle of production with the fall and the spring blooms, and the subsurface phytoplankton maximum layer in summer, as well as realistic patterns of particulate organic carbon and nitrogen. The computed seasonal cycles of the chlorophyll and primary production distributions over the euphotic layer compare reasonably well with the data. Initiation of the spring bloom is shown to be critically dependent on the water column stability. It commences as soon as the convective mixing process weakens and before the seasonal stratification of surface waters begins to develop. It is followed by a weaker phytoplankton production at the time of establishment of the seasonal thermocline in April. While summer nutrient concentrations in the mixed layer are low enough to limit production, the layer between the thermocline and the base of the euphotic zone provides sufficient light and nutrient to support subsurface phytoplankton development. The autumn bloom takes place some time between October and December depending on environmental conditions. In the case of weaker grazing pressure to control the growth rate, the autumn bloom shifts to December-January and emerges as the winter bloom or, in some cases, is connected with the spring bloom to form one unified continuous bloom structure during the January-March period. These bloom structures are similar to the year-to-year variabilities present in the data

Simulation of annual plankton productivity cycle in the Black Sea by a one-dimensional physical-biological model

The annual cycle of the plankton dynamics in the central Black Sea is studied by a one-dimensional vertically resolved physical-biological upper ocean model, coupled with the Mellor-Yamada level 2.5 turbulence closure scheme. The biological model involves interactions between the inorganic nitrogen (nitrate, ammonium), phytoplankton and herbivorous zooplankton biomasses, and detritus. Given a knowledge of physical forcing, the model simulates main observed seasonal and vertical characteristic features, in particular, formation of the cold intermediate water mass and yearly evolution of the upper layer stratification, the annual cycle of production with the fall and the spring blooms, and the subsurface phytoplankton maximum layer in summer, as well as realistic patterns of particulate organic carbon and nitrogen. The computed seasonal cycles of the chlorophyll and primary production distributions over the euphotic layer compare reasonably well with the data. Initiation of the spring bloom is shown to be critically dependent on the water column stability. It commences as soon as the convective mixing process weakens and before the seasonal stratification of surface waters begins to develop. It is followed by a weaker phytoplankton production at the time of establishment of the seasonal thermocline in April. While summer nutrient concentrations in the mixed layer are low enough to limit production, the layer between the thermocline and the base of the euphotic zone provides sufficient light and nutrient to support subsurface phytoplankton development. The autumn bloom takes place some time between October and December depending on environmental conditions. In the case of weaker grazing pressure to control the growth rate, the autumn bloom shifts to December-January and emerges as the winter bloom or, in some cases, is connected with the spring bloom to form one unified continuous bloom structure during the January-March period. These bloom structures are similar to the year-to-year variabilities present in the data

Denizlerdeki Mikrobiyal Reaksiyonların Yeni Yaklaşımlar Kullanılarak Araştırılması: Genetik, Biyojeokimya ve Modelleme

TÜBİTAK ÇAYDAG15.10.2018ODTÜ Deniz Bilimleri Enstitüsü tarafından Mersin Körfezi?nde 1997 yılından bu yanasürdürülen Erdemli Zaman Serisi (ETS) programı dahilinde ölçülen degiskenlere ek olarak, buproje kapsamında toplam su kolonu derinligi 200 metre olan istasyonda altı farklı derinliktenbir yıl boyunca aylık periyotlarda deniz suyu örneklemesi yapılmıstır. Bu örneklerde yeni nesildizileme yönteminin kullanıldıgı amplikon dizilemesi (metagenomik) analizleri yapılarakbiyojeokimyasal döngülerde önemli roller oynayan bakteri türleri tayin edilmis, topluluk yapılarıve bolluklarının zamansal degisimi belirlenmistir. Taksalar arasında Pelagibacteriacea?ya aitolan SAR11 kladının tüm derinlikler ve aylarda baskınlıgı gözlenmistir. Bu kladın üyelerifonksiyonel olarak organik maddeyi oksitleyerek karbondioksit üreten heterotrofik bakterilerdirve dolayısıyla biyojeokimyasal döngülerin remineralizasyon ayagında rol almaktadırlar.SAR11 kladının bollugu yıl boyunca %22 ve %64 arasında degisim göstermistir. SAR11kladının ekotipleri olan Clade Ia ve Clade Ib ise derinlige baglı yayılım göstermektedirler.Clade Ia yüzey sularında baskınlık gösterirken Clade Ib?nin derin sularda komüniteye katkısıdaha fazla olmaktadır. Bunun yanı sıra komünite yapısını belirleyen en önemli çevreselfaktörler sıcaklık, nitrat, görünür oksijen kullanımı, sezon ve ısıklı tabaka derinligi olarakbelirlenmistir. Sezonlar arasındaki filogenetik çesitlilik, belirgin olarak farklı bulunmustur.Bunun yanı sıra bakterilerin aktif metabolizmalarını tayin etmek için sezonluk olarak mRNAörneklemesi yapılmıs ve örnekler metatranskriptom yöntemi ile analiz edilmistir. Bu yöntemaracılıgı ile bakteriler tarafından gerçeklestirilen biyokimyasal reaksiyonların aktif ve inaktifoldukları dönemler saptanmıstır. Nitrifikasyonun ilk basamagı olan amonyak oksitilenmesiKasım ayında oldukça yüksek bulunmustur. Ancak nitrifikasyonun ikinci basamagı olan nitritinnitrata oksitlenme sürecine ait olan belirteç genlere herhangi bir örnekde rastlanmamıstır.Sisteme yeni azot girdisi saglayan azot fiksasyonuna mRNA ifadelerinde rastlanmamıstır.Metatranskriptom yöntemine elde edilen bulgulara ek olarak nitrifikasyon ve azot fiksasyonsüreçleri izotop yöntemi ile de her ay dört farklı derinlikten yapılan örneklemeler ilearastırılmıstır. Nitrifikasyonun sadece afotik bölgede gerçeklesmedigi görülmüstür. Azotfiksasyonu belirteç genlerine rastlanmadıgı halde izotop yöntemi ile yapılan çalısmada azotfiksasyonu tüm yıl boyunca ve tüm derinliklerde çok düsük de olsa tespit edilmistir. Azotdöngüsüne ek olarak, metatranskriptom çalısması ile kısıtlı inorganik fosfat varlıgında aktiveolan alkalin fosfataz?ın sezonluk degisimi de göstermistir. Buna göre, ortamda düsük fosfatkonsantrasyonları gözlemlendiginde bakterilerin diger fosfor kaynaklarına yöneldigigözlemlenmistir.Bunlara ek olarak denizdeki biyokimyasal döngüleri sayısal olarak temsil eden ve tahminleridirekt olarak ölçümlerle karsılastırılabilecek bir modelleme sistemi bölgeye uyarlanmıstır. Bumodelleme sistemi bir parametre tahmin algoritması ve proje kapsamında yapılan ölçümverileri ile birlestirilerek modelde reaksiyon hızlarını kontrol eden parametrelerin tahminiyapılmıstır. Bu tahmin sonucunda ortaya çıkan nitrifikasyon hızları izotop yöntemi ile yapılannitrifikasyon hızları ile karsılastırılmıstır. Bu karsılastırma reaksiyon hızları tahmini içinmodelleme sistemi ve parametre tahmini kullanımının zor olan izotop yöntemine alternatif biryöntem olma potansiyelini göstermistir.Yapılan bir yıllık gözlemler, kullanılan izotop yöntemleri ve modelleme yaklasımı bölgedekibilimsel bilgiye önemli katkılar saglamıstır. Bakteri topluluk yapıları Türkiye kıyılarında ilk defakültür bagımsız yöntemlerle ortaya konmustur. Bunun yanı sıra izotop yöntemleri ve yapılanmetatranscriptom çalısması bölgede azot fiksasyonunun baskın bir süreç olmadıgını ortayakoymustur. Biyojeokimyasal bir modelleme sistemi basarıyla bölgeye uyarlanmıstır.In addition to the measured variables within the Erdemli Time Series (ETS) monitoring programcarried out in Mersin Bay since 1997 by the METU-Institute of Marine Sciences, sea watersampling was performed where the total water column depth is 200 meters and from sixdifferent depths monthly for one year. These samples were analyzed by next generationsequencing using amplicon sequencing (metagenomic) approach and the bacterial speciesthat play important roles in biogeochemical cycles and the temporal changes of communitystructures and abundances were determined. SAR11 clade belonging to Pelagibacteriaceawas the most dominant taxa in all depths and months. SAR11 is ubiquitous in the seas andreplicate under the most limiting nutrient conditions. The abundance of the SAR11 cladethroughout the year ranged between 22% and 64%. Clade Ia and Clade Ib, the ecotypes ofthe SAR11 clade, showed depth-dependent distribution. Clade Ia dominated the surfacewaters, while Clade Ib contributes the most to the community in deeper waters. The mostimportant environmental factors that determine the community composition were determinedto be; temperature, nitrate, apparent oxygen utilization, season and euphotic zone depth.Phylogenetic diversity between seasons was found to be significantly different.Furthermore, to determine the active metabolism of bacteria mRNA samples were collectedseasonally and analyzed by metatranscriptomics approach. By using this approach, active andinactive periods of biochemical reactions mediated by bacteria was discovered. Ammoniaoxidation, the first step of nitrification, was found to be high in November. However, markergenes that are belong to nitrite oxidation to nitrate which is the second step of nitrification, havenot been detected in any samples. Indicator genes of nitrogen fixation which provides newnitrogen to the system was not found in mRNA expressions. In addition to the findings obtainedfrom the metatranscriptomics study, nitrification and nitrogen fixation processes wereinvestigated using isotope measurements from four different depths each month. It wasobserved that the nitrification did not occur only in the aphotic zone. Nitrogen fixation was notdetected in the indicator genes, but in the study conducted with isotope method, even with lowlevels, nitrogen fixation was determined throughout the year and depths. Additionally, to thenitrogen cycle, the seasonal change of alkaline phosphatase activity which is active especiallyduring inorganic phosphate limitation was also identified by the metatranscriptomics study.Accordingly, when low phosphate concentrations were observed in the environment, it wasobserved that bacteria adapt to use other phosphorus sources.Furthermore, a modeling system that represents the marine biochemical cycles numericallyand whose estimates can be compared directly with the measurements was adapted to theregion. This modeling system was combined with a parameter estimation scheme and measurements obtained in the project, and the parameters controlling the reaction rates in themodel were estimated. Nitrification rates according to the estimations were cpmpared with theresults of nitrification rates obtained by isotopic measurements. This comparison showed thepotential of using modeling system and parameter estimation as an alternative approach to thehard isotope measurements for estimating reaction rates.One-year long observations, isotope methods used and modeling approach have madesignificant contributions to scientific knowledge in the region. Bacterial community structurehave been revealed by culture-independent method for the first time in the coasts of Turkey.In addition, isotope methods and metatranscriptom study showed that nitrogen fixation is nota dominant process in the region. And a biogeochemical modeling system has beensuccessfully adapted to the region

Doğu Akdeniz deki Atmosferik Parçacıkların, Kuru ve Yaş Çökellerin Kimyasal Karakterinin Belirlenmesi ve Türleştirilmesi: Menşe, Kaynak Bölgeler, Biyo-kullanılabilirlik ve Atmosferik Girdilerin Denizsel Üretime Etkisi

TÜBİTAK ÇAYDAG15.03.2016Ocak 2014 ve Nisan 2015 tarihleri arasında yoğun bir şekilde aerosol (iri, ince ve bulk) ve kuru ve yaş-çökel (yağmur) örneklemeleri yapılmıştır. Atmosferik parçacıkların kütle derişimleri, suda-çözünebilir majör türler, suda-çözünebilir organik azot, üre ve aminoasit konsantrasyonları belirlenmiştir. Son on yılda partikül madde kompozisyonun belirgin bir şekilde değiştiği gözlenirken özellikle ikincil aerosoller sülfat, amonyum ve nitrat derişimlerinin % 50’lere varan düşüşler sergiledikleri belirlenmiştir. Suda-çözünebilir organik azot’un hem atmosferik parçacık (% 37) hem de yağmur (% 29) fazında toplam azota, sudaçözünebilir inorganik azotlar kadar katkı yapabileceği bulgulanmıştır. Tespit edilen üre derişimlerinin aerosol ve yağmurda organik azota sırasıyla % 17 ve % 6 katkı yaptığı bulunurken aminoasit azot katkılarının pek önemli olmadığı gözlenmiştir. Polifosfatların suda-çözünebilir fosfatlara % 20’ler seviyesinde katkı yapabileceği anlaşılırken göz ardı edilemeyecekleri ortaya konmuştur. Suda-çözünebilir organik azotun büyük bir kısmının tarımsal aktivitelerden kaynaklandığı ne var ki, ürenin hem mineral toz hem de tarımsal kökene sahip olduğu bulgulanmıştır. Fosforun; mineral toz (% 34) ve tarımsal (% 33) olmak üzere başlıca iki ana kaynağı olduğu anlaşılmıştır. Alüminyum iz metalinin büyük bir kısmı anyonik forumda gözlenirken demirin anyonik formunun katyonik formuna kıyasla 1,2 kat daha yüksek olduğu görülmüştür. Hem Kıyı hem de Açık istasyonlardan elde edilen yüzey sularına iki değişik içeriğe sahip toz eklenmiştir. Deneyler süresince klorofil miktarının artış sergilediği gözlenirken fosforun ortamdan çekilerek 0,3 nM seviyelerine düşürüldüğü tespit edilmiştir. Denizsel alan çalışmaları, 10 Nisan ve 29-30 Nisan 2015 tarihlerinde yüzey sularında tespit edilen Chl-a artışının, yağan yağmurlarla ilişkili olabileceği göstermiştir.Intensive samplings of both aerosol (fine/coarse and bulk) and rainwater were carried out between January 2014 and April 2015. Determination of mass composition, water soluble major species, water soluble organic nitrogen, urea and amino acid concentrations in atmospheric particles was carried out. Significant changes have been observed in the composition of particulate matter in the last ten years, especially the concentrations of secondary aerosols such as sulfate, amonnium and nitrate were determined to have decreased down to 50% of previous levels. It was found out that contribution of water soluble organic nitrogen is comparable to those of water soluble inorganic nitrogen in both aerosols (37%) and rainwater (29%). While it was observed that urea comprised 17% and 7% of total organic nitrogen in aerosol and rainwater, respectively, contribution of amino acids was found to be insignificant. It has been established that contribution of polyphosphates to water soluble phospates can reach up to a non-negligible 20%. Majority of water soluble organic nitrogen was found to originate from agricultural activities, while urea, was found to be of mixed origin, with comparable contributions from mineral dust and agricultural activities. The two main sources of phosphorus was determined to be mineral dust and agriculture, accounting for 34 and 33 % of total concentration, respectively. It has been observed that major fraction of soluble Al is found in anionic form, while the concentration of anionic soluble Fe is 1.2 times greater than of cationic Fe. Surface waters which were obtained from both coastal and open waters were treated with atmospheric dust of two different compositions. In the course of experiments, chlorophyll was recorded to increase in all treatments while phosphorus was assimilated from the medium down to 0,3 nM. The possible relationship between rain event and Chl-a increase in the surface waters observed in the cruises of April 10 and 29-30 2015 has been documented

Doğu Akdeniz'de mevcut farklı ekosistemlerin - upwelling bölgeleri, açık deniz ve kıta sahanlığı suları - dinamikleri, bakteriyel ve birincil üretim potansiyelleri, üst trofik seviyelere yansımaları

TÜBİTAK ÇAYDAG15.10.2014Türkiye denizleri, su bütçesi, atmosferik ve karasal girdiler, taban topoğrafyası, iklimsel evrim gibi temel etkenlerin belirlediği fiziksel, kimyasal, biyolojik özellikler bakımından büyük farklılıklar içeren zengin ve değişken deniz ekosistemlerini barındırmaktadır. Birincil üretim potansiyelleri açısından Karadeniz’in özellikle kuzeybatı kıta sahanlığı ötrofik, Marmara Denizi ve körfezleri ileri derecede ötrofik, Ege Denizi ve Doğu Akdeniz oligotrofik yapı sergilemektedir. Özgün bir dinamiği olan Doğu Akdeniz, genelde bir uç oligotrofik sistem olarak tanımlansa da, kendi içinde önemli bölgesel farklılıklar göstermektedir. Özellikle karasal tatlı su ve besin girdilerinden etkilenen kuzeydoğu kıta sahanlığı (Mersin ve İskenderun Körfezleri) ve ‘upwelling’ dinamiğinden etkilenen Rodos döngüsünde önemli düzeylerde birincil üretim potansiyeline sahiptirler ve daha yoksul olan açık denizden farklıdırlar. Aktif dinamik yapıya ve zengin biyolojik çeşitliliğe sahip kıyısal denizlerimizin sürekli gözlem, analiz ve model öngörüleri aracılığıyla araştırılmasının sürdürülmesi, büyük stratejik önemi haizdir. Çalışma O.D.T.Ü. Deniz Bilimleri Enstitüsü Araştırma Gemisi Bilim-2 ile anılan sahalarda ve istasyonlarda mevsimsel bazda gerçekleştirilmiştir. Bu çalışma ile fonksiyonel olarak üç farklı ekosistemi teşkil eden alanlarda bakteriden balıklara uzanan besin zincirinde olası yapısal farklılıklar, üretim potansiyelleri, dinamikleri karşılaştırılmış, toplanan diğer çevre faktörleri ile etkileşimleri irdelenmiştir.Turkish seas accommodate rich and varied marine ecosystems which are diverse in their physical, chemical, biological characteristics as a result of differences in basic driving factors such as the water budget, atmospheric and land-based inputs, bottom topography, climatic evolution. In terms of primary production potential, the Black Sea especially the northwestern continental shelf exhibits eutrophic characteristics, while Marmara Sea and its bays are highly eutrophic, and Aegean and Eastern Mediterranean Seas display oligotrophic structure. Although the Eastern Mediterranean with its rather unique characteristics is often defined as an ultra-oligotrophic system, there are significant regional differences within the system. The northeastern continental shelf (Mersin and İskenderun Bays) influenced by land-based fresh water and nutrient sources and the Rhodes Gyre influenced by ‘upwelling’ dynamics have potential for high primary production, while the open sea is relatively poor. Continued research through continuous observations, analyses and model predictions have immense strategic importance for the well being of our coastal seas possessing energetic dynamics and rich biological diversity. It is proposed that the physical-biochemical variability of the diverse northern Levantine Sea ecosystems be investigated through systematic observations during oceanographic cruises, as well as model-based predictions. Study has been conducted seasonally aboard Research Vessel Bilim-2 of the Institute of Marine Sciences of Middle East Technical University in the referred areas and stations. Throughout the study, in areas that represent the three different functional ecosystems, possible structural differences, productivity potential, and dynamics were compared in the food chain spanning bacteria to fish, and their interactions with the other environmental factors were investigated

Comparison of TOC concentrations by persulphate UV and high temperature catalytic oxidation techniques in the Marmara and Black Seas

Total organic carbon (TOC) concentrations were determined in the Marmara Sea and both oxic and anoxic waters of the Black Sea, using the Shimadzu high-temperature catalytic oxidation technique and the Technicon persulphate-UV oxidation method. The TOC values in the deep waters of the Marmara Sea ranged between 60 and 73 μ MC by the Shimadzu technique and from 40 to 50 μMC by the Technicon method. The TOC values obtained by both methods in the deep anoxic waters of the Black Sea varied between 105 and 130 μM. These values differ significantly from those in the literature, indicating that available TOC data are not accurate enough for reliable estimation of the carbon budget of the Black Sea. Storage of the anoxic water samples accompanied by freezing, acidifying or poisoning with HgCl2 did not increase TOC recovery