Abstract
The role of chemolithoautotrophic microorganisms has been considered to be of minor importance in coastal marine sediments and the impact of seasonal hypoxic/anoxic conditions on microbial chemolithoautotrophy in coastal marine sediments has not been investigated. Therefore, in this thesis the temporal and spatial changes of the diversity, abundance and activity
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of specific groups of chemolithoautotrophic microorganisms involved in the nitrogen and sulfur cycling, as well as the total microbial community, has been determined in coastal sediments by using DNA/RNA- and lipid-based biomarker approaches, i.e. the analysis and quantification of 16S rRNA and functional genes involved in carbon fixation and reoxidation pathways, intact polar and core lipids of Archaea, i.e. glycerol dibiphytanyl glycerol tetraethers (GDGTs), and ladderane lipids specific for anammox bacteria, as well as bacterial phospholipid-derived fatty acids (PLFAs). We focused on coastal marine sediments; (1) the Oyster Grounds in the central North Sea, exposed to decreasing bottom water oxygen concentrations (0−12 cm sediment depth), (2) different sediment types (sand, clay, and mud) of the Iceland Shelf (0−10 cm sediment depth), and (3) seasonally hypoxic and sulfidic sediments of saline Lake Grevelingen (The Netherlands) (0−5 cm sediment depth). Results show the presence and potential importance of chemolithoautotrophs in the biogeochemical cycling of carbon, nitrogen and sulfur. The research presented in this thesis has provided new insights on the temporal and spatial distribution of the diversity, abundance and activity of chemolithoautotrophic microorganisms such as ammonia oxidizing archaea (AOA, i.e. Thaumarchaeota) and ammonia oxidizing bacteria (AOB), anammox and denitrifying bacteria, as well as sulfate reducing and sulfur oxidizing microorganisms, including sulfide-dependent denitrifiers, and chemolithoautotrophic microorganisms involved in the Calvin-Benson-Bassham (CBB) and the reductive tricarboxylic acid (rTCA) cycle, in coastal marine sediments. Hypoxia and increasing sulfide concentration have proven to be key factors restricting the presence and activity of these groups. In addition, the interactions with other microbial groups and bioturbation seem to favor the presence of specific chemolithoautotrophs in unexpected sediment depths, for example the presence of Thaumarchaeota in depths where the oxygen concentration was expected to be undetectable, or the presence of anammox bacteria in bioturbated sediments where nitrate reducers could thrive and provide nitrite to fuel the anammox process.
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