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Characterization of microbial communities in carbonate sediments

dc.contributor.advisorDaniel, Rolf Prof. Dr.
dc.contributor.authorvon Hoyningen-Huene, Avril Jean Elisabeth
dc.titleCharacterization of microbial communities in carbonate sedimentsde
dc.contributor.refereeHoppert, Michael PD Dr.
dc.description.abstractengMicrobial communities in carbonate sediments from the alkaline Lake Neusiedl and the Aldabra Atoll were characterized. The aim was to determine the microbial community composition and function in the context of their contribution to biogeochemical cycles and carbonate precipitation. Total DNA and RNA were extracted from sediment and water samples. 16S ribosomal RNA genes and transcripts were amplified and sequenced to determine the bacterial community composition. Metagenomes were assembled from selected sampling sites to determine the functional potential encoded within the microbial community. Detailed insights into bacterial genomes and metabolism were gained through isolation and characterisation of two novel bacterial species derived from Aldabra. The first sampling campaign represents the proof-of-concept study at Lake Neusiedl (Chapter C.1 & C.2). In this study the sampling procedure for the push-cores and water column was established. Bacterial 16S rRNA genes were amplified from the total DNA, sequenced, and analysed. The results showed that freshwater picoplanktonic Alphaproteobacteria and Actinobacteriota were abundant in the water column (Chapter C.1). Together with Synechococcales sheaths they may provide nucleation sites for carbonate precipitation in the water column. The sediment followed the standard biogeochemical succession and showed signs of diatom dissolution (Chapter C.2). This was linked to high abundance of heterotrophic Gammaproteobacteria and fermenting Chloroflexota, which likely contributed to maintaining the neutral pH and supported the dissolution process. The main sampling campaign to the Aldabra Atoll took place at the end of the dry season in November 2017. Sediment cores and water samples were taken at three sampling sites in the lagoon and one pool at the island rim (Chapter C.3). The bacterial community composition was identified using both 16S rRNA genes and transcripts, covering both present and past members of the community. The sampling sites Cinq Cases and Westpool D were selected for direct metagenome sequencing and analysis, as these were landlocked pools with a history of stromatolites (Chapter C.5). The sand sediment was oxic with low bacterial diversities and dominant Pseudomonas. The surface was covered by a slightly lithified crust, potentially linked to tidally induced carbonate oversaturation and precipitation driven by the activity of Gloeocapsopsis (Chapter C.3). In the mud and silt sediments bioturbation and tidal mixing led to a mixed surface and sulphate reduction zone. These were followed by atypical low bacterial phylogenetic diversity zones with high proportions of Gammaproteobacteria. Their onset was linked to changes in redox conditions, sediment age and available organic material (Chapter C.3). This was supported by results from the analysis of abundant metagenome-assembled genomes (MAGs) of the low-diversity zones at Cinq Cases. The MAGs harboured key genes for aerobic metabolism and denitrification (Chapter C.5). MAGs and 16S rRNA genes from Westpool D suggested that a biofilm comprising Gloeocapsa, Salinivibrio and Francisella is responsible for biologically induced carbonate precipitation of the local stromatolites. The unlithified microbial mat at the bottom of the pond harboured Cyanobium and Arthrospira, indicating that only specific Cyanobacteria support carbonate precipitation (Chapter C.5). To identify novel bacteria and provide information on the vast majority of uncultured taxa, we enriched halophilic members of the bacterial community. Two isolates were selected and characterized both physiologically and genomically (Chapter C.4). Pontibacillus sp. ALD_SL1 was isolated form the mudflat of the South Lagoon and exhibited a high relative abundance (30%) in the active bacterial community of the water column at Cinq Cases. Psychroflexus sp. ALD_RP9 was isolated from the bacterial bloom at Westpool D. Its ability to form extensive EPS to protect itself from salt and solar radiation may result in binding Ca2+-ions. Upon EPS degradation, local increase of Ca2+ and rearrangement of the EPS residues support the nucleation of carbonates. This study encompasses the first characterization of microbial communities from the Aldabra Atoll using amplicon, metagenome, and genome analyses. The study highlights the different modes of carbonate precipitation, which can occur in the lacustrine and lagoonal environments. It also provides a basis for in-depth analysis of individual members of the community and their involvement in sediment biogeochemical
dc.contributor.coRefereeArp, Gernot Prof. Dr.
dc.contributor.thirdRefereePöggeler, Stefanie Prof. Dr.
dc.contributor.thirdRefereeHeimel, Kai Prof. Dr.
dc.contributor.thirdRefereede Vries, Jan Jun.-Prof. Dr.
dc.subject.engmicrobial communitiesde
dc.subject.engcarbonate sedimentsde
dc.subject.engAldabra Atollde
dc.subject.eng16S rRNAde
dc.subject.engisolation of bacteriade
dc.affiliation.instituteGöttinger Graduiertenschule für Neurowissenschaften, Biophysik und molekulare Biowissenschaften (GGNB)de
dc.subject.gokfullBiologie (PPN619462639)de

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