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Investigations on the nitrogen cycle in the coastal North Sea
Fan, H. (2016). Investigations on the nitrogen cycle in the coastal North Sea. PhD Thesis. UvA: Amsterdam. ISBN 978-94-91407-32-1. 156 pp. hdl.handle.net/11245/1.522126

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Documenttype: Doctoraat/Thesis/Eindwerk

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Abstract
    This thesis focuses on the nitrogen cycle in Dutch coastal waters and sediments. Themain hypothesis of this study was that the different steps of the nitrogen cycle occurspatially and temporally separated from each other rather than that the cycle is closedin the same place and time. To verify this hypothesis, multiple experimentalapproaches were applied to investigate N2 fixation, denitrification, anammox andnitrification in the some selected ecosystems of the Dutch coast.Chapters 2, 3 and 4 investigate N2 fixation, denitrification, anammox and nitrificationin an intertidal microbial mat. Microbial mats are benthic communities of verticallystratified functional groups of microorganisms. The oxygenic phototrophiccyanobacteria are conspicuously present, and by fixing carbon dioxide and dinitrogen,they form the basis of the microbial food web in this small-scale ecosystem. Microbialmats develop on nitrogen-depleted intertidal sandy beaches and therefore nitrogenfixation plays an important role in supplying the mats with bound nitrogen. Thisaspect has received considerable attention but not much is known about the fate of thefixed nitrogen, the responsible microorganisms, and the factors that control thenitrogen cycle in microbial mats.The GeoChip is a DNA microchip that contains probes for virtually all known genesinvolved in the major biogeochemical processes. The study of the microbial mats ofthe Dutch barrier island Schiermonnikoog using this GeoChip revealed that theoverall functionality of these mats is similar and seemed to be independent on the mattype or the season. The nitrogen cycle was prominently present as indicated by thepresence of a variety of functional genes involved in this cycle. Especially, the genesinvolved in denitrification were abundant, following those involved in nitrogenfixation and nitrification (Chapter 4).N2 production was measured in microbial mats that develop along a tidal and salinitygradient from the supra littoral to the low water mark (Chapter 2). Denitrification isthe main sink for nitrogen in these mats. The seasonality of denitrification is notconsistent in different types of mats. Station 2 (marine station) and Station 3(intermediate station) revealed much lower rates of denitrification, which showed alsoless seasonality when compared to Station 1. The denitrifying community at Station 1was more diverse than that at Station 2 and Station 3. The denitrifying communities ofthese stations were more similar than either of these stations with Station 1. Therefore,the seasonality of denitrification may be mainly attributed to the denitrifyingcommunity composition. The spatial organization of the denitrifying community inthe microbial mats was likely the result of changing environmental conditions. Furtherinvestigation on the potential rate of nitrification and the diversity and abundance of130amoA gene of AOB and AOA in these mats showed that AOB are responsible formost of the aerobic ammonium oxidation in the mats (Chapter 3). Salinity has beenproposed as the major driver of the microbial community composition for thesemicrobial mats. This also applies to the denitrifier and aerobic ammonia-oxidizercommunity. In conclusion, nitrogen fixation and denitrification occur predominantlyin summer in these microbial mats. Denitrification may benefit from the supply oforganic matter that is produced by the photoautotrophs. Nitrification was highest inautumn and lowest in summer and therefore it occurred temporally separated fromnitrogen fixation and denitrification.Chapter 5 and Chapter 6 report on studies on N2 fixation, denitrification, andanammox in the surface of the water column (only N2 fixation), and the bottomsediments of the southern North Sea. In contrast to microbial mats, N2 fixation wasthought to be uncommon in the southern North Sea waters due to the high nitrogenavailability in these regions. It was shown that N2 fixation occurred in the watercolumn and in the surface sediment and was mainly attributed to the anaerobic sulfatereducing bacteria. Compared to anammox, denitrification was responsible for themain nitrogen loss from the system. The contribution of denitrification to N2production varied among stations and between seasons. The functional generepresenting denitrification, nirS, could not be assigned to a specific group ofmicroorganisms. In the sediment, N2 fixation and denitrification were temporally andspatial separated. The former was highest in August in the offshore DB station, asandy area with low organic content, while the latter was high in May in the OGstation, a muddy depression in the North Sea with high organic content. The rates ofboth processes coincided with the expression of the functional genes nifH and nirS.The spatial and temporal separation of denitrification and nitrogen fixation is alsoprojected on the composition of chemotrophic diazotrophic and denitrifyingcommunities. The diazotrophic community composition at the three stations appearedto correlate with geographic location (coastal and offshore) while the denitrifyingcommunity composition was determined by sediment type. Chapter 6 studiedanammox and anammox bacteria during four seasons. It was shown that higherabundance and activity of the anammox bacteria were associated with higher organiccarbon and elevated temperature.In conclusion, N2 fixation, denitrification anammox and nitrification and theresponsible microorganisms occur on different spatial and temporal scales inecosystems of the Dutch coast. A number of factors may drive the observed changesin the main processes in the nitrogen cycle. These may include composition andnature of the diazotrophic community and physicochemical factors includingtemperature, salinity, oxygen, and availability of substrates. Future studies arerecommended in order to provide knowledge on the effects of environmental131conditions on the nitrogen cycle in coastal environments, using quantitativeexperiments in mesocosms and laboratory experiments with the key microorganisms.

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