First basin-wide experimental results on N2-fixation in the open Mediterranean Sea.

Mediterranean Sea presents several biogeochemical anomalies compared to the global ocean. Unbalanced N budget, high nitrate/phosphate ratios in subsurface waters and light isotopic signals in particulate and dissolved nitrogen have suggested a relevant occurrence of N2-fixation. This study presents, for the first time, N2-fixation rate measurements in the open Mediterranean Sea on a basin scale during early summer, compared to one site in the North Atlantic. Very low rates (0.052?0.031 nmols N l-1d-1) were observed in all sub-regions of the Mediterranean, unlike the higher values measured in the North Atlantic surface waters (0.300?0.115 nmols N l-1d-1). No evidence of phosphate limitation emerges from this study. Low N2-fixation rates associated to light isotopic composition of PON (from -2.10 to 4.11?) suggest that other light N sources, different from atmospheric N2, fuel the Mediterranean ecosystem

Nitrogen fixation in the Mediterranean Sea

The Mediterranean Sea is an oligotrophic basin characterized by low nutrient levels and unusually high NO3/PO4 molar ratios in the deeper layers, that reach the maximum (N/P = 28) in the Eastern Mediterranean. An external nitrogen source needs to be claimed in order to explain the nitrogen excess. Pantoja et al. (2002) found that the 15N/14N natural abundance in particulate and in dissolved inorganic nitrogen display low values, suggesting an important role of a "light" nitrogen source. Two hypotheses can be invoked: (i) nitrogen compounds from atmospheric deposition and/or(ii)atmospheric molecular nitrogen throughout nitrogen fixation . During TRANSMED oceanographic cruise carried out in the framework of Italian project VECTOR(June 2007), N2 fixation experiments have been carried out all over the Mediterranean Sea and outside the Gibraltar Strait. Surprisingly, very low rates (< 0.10 nmol N2*l-1*d-1) have been observed in different areas of the basin, while higher values have been observed in Atlantic Ocean according with literature data. These preliminary results suggest a major role for nitrogen atmospheric deposition in shaping the NO3/PO4 anomaly of the basin. Pantoja, S., D. J. Repeta, J. P. Sachs, and D. M. Sigman (2002). Stable isotope constraints on the nitrogen cycle of the Mediterranean Sea water column, Deep Sea Res., Part I, 4, 1609- 1621

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

Ocean acidification research in the Mediterranean Sea : status, trends and next steps

Ocean acidification (OA) is a serious consequence of climate change with complex organism-to-ecosystem effects that have been observed through field observations but are mainly derived from experimental studies. Although OA trends and the resulting biological impacts are likely exacerbated in the semi-enclosed and highly populated Mediterranean Sea, some fundamental knowledge gaps still exist. These gaps are at tributed to both the uneven capacity for OA research that exists between Mediterranean countries, as well as to the subtle and long-term biological, physical and chemical interactions that define OA impacts. In this paper, we systematically analyzed the different aspects of OA research in the Mediterranean region based on two sources: the United Nation’s International Atomic Energy Agency’s (IAEA) Ocean Acidification International Coordination Center (OA-ICC) database, and an extensive survey. Our analysis shows that 1) there is an uneven geographic capacity in OA research, and illustrates that both the Algero-Provencal and Ionian sub-basins are currently the least studied Mediterranean areas, 2) the carbonate system is still poorly quantified in coastal zones, and long-term time-series are still sparse across the Mediterranean Sea, which is a challenge for studying its variability and assessing coastal OA trends, 3) the most studied groups of organisms are autotrophs (algae, phanerogams, phytoplankton), mollusks, and corals, while microbes, small mollusks (mainly pteropods), and sponges are among the least studied, 4) there is an overall paucity in socio-economic, paleontological, and modeling studies in the Mediterranean Sea, and 5) in spite of general resource availability and the agreement for improved and coordinated OA governance, there is a lack of consistent OA policies in the Mediterranean Sea. In addition to highlighting the current status, trends and gaps of OA research, this work also provides recommendations, based on both our literature assessment and a survey that targeted the Mediterranean OA scientific community. In light of the ongoing 2021-2030 United Nations Decade of Ocean Science for Sustainable Development, this work might provide a guideline to close gaps of knowledge in the Mediterranean OA research.peer-reviewe

New hints on nutrients dynamics and their impact on carbon sequestration in the Mediterranean Sea

In the World Ocean nitrogen and phosphorus cycles are deeply linked to the carbon cycle. As nitrate and phosphate play an important role in controlling biological production, the intensity of atmospheric carbon sequestration is strongly influenced by nutrient bioavailability. This thesis aims to contribute to the understanding of the ability of the Mediterranean Sea in absorbing C and N from the atmosphere. The Mediterranean Sea presents several biogeochemical anomalies compared to the global ocean. The high nitrate/phosphate ratios in subsurface waters and the low 15N/14N ratios in particulate and dissolved nitrogen have suggested a significant occurrence of nitrogen fixation (N2 fixation) or an important impact of nitrogen atmospheric deposition. This study presents, for the first time, a basin-wide overview of direct measurements of N2 fixation, with values in the North Atlantic for comparison. Very low N2 fixation rates (0.0520.031 nmols N l-1d-1) were observed in all sub-regions of the Mediterranean, in contrast to the higher values measured in the North Atlantic (0.3000.115 nmols N l-1d-1). Higher phosphorus (inorganic or organic) concentrations were not associated with higher N2 fixation rates. An isotopic evaluation of the nitrogen sources based on isotopic signature of deep nitrate, N atmospheric deposition and Atlantic inflow nitrate, provides a rough estimate of the amount of N atmospheric deposition. The range varies between 22 and 60% of the total nitrate entering the Mediterranean Sea. Large amount of N deposition from the atmosphere can explain both P-limitation and anomalous N/P ratio in deep layers. The external inputs of N, determining the excess of N in the marine system could ultimately fuel new production and enhance Mediterranean’s ability in carbon sequestration

Discovering the diversity and functionality of diazotrophs in the East Mediterranean Sea (DIAZOGENE)

Biological nitrogen fixation (NF) is the process transferring nitrogen (N) from atmosphere to ocean interior. Primary production in the sea, often limited by the scarcity of N, benefits by the activity of marine diazotrophs, able to convert N2 gas into organic form. N2 can be fixed following two main pathways: i) autotrophic process, in the euphotic layer and ii) heterotrophic process all over the water column. Although, occurrence of marine autotrophic NF is largely documented, a proper understanding of its ecological role, limiting and triggering factors is still missing. On the other side, heterotrophic NF in surface and deep ocean, has just been recently reported. Investigating gene diversity and gene expression can provide important information about role and functioning of these organisms.In the current study, we aim to analyze the diversity, functionality and abundance of both autotrophic and heterotrophic N2-fixing community in the East Mediterranean Sea. Metatranscriptomic analysis, revealing gene expression of the bacterial community will be carried out, in the surface and deep layers. Sampling will continue for one year, in four seasons at Erdemli Time Series site (ETS).Metatranscriptomic data will be coupled to a large dataset of parameters (metagenomic, NF rates, biogeochemical and physical measures) collected during a parallel project focusing on marine microbial community (TUBITAK, 116Y629), which will also provide logistics support for the field activities