| dc.contributor.advisor | Daniel, Rolf Prof. Dr. | |
| dc.contributor.author | von Hoyningen-Huene, Avril Jean Elisabeth | |
| dc.date.accessioned | 2021-11-25T14:52:40Z | |
| dc.date.available | 2021-12-02T00:50:05Z | |
| dc.date.issued | 2021-11-25 | |
| dc.identifier.uri | http://hdl.handle.net/21.11130/00-1735-0000-0008-59A6-9 | |
| dc.identifier.uri | http://dx.doi.org/10.53846/goediss-8975 | |
| dc.language.iso | eng | de |
| dc.relation.uri | http://creativecommons.org/licenses/by-nc-nd/4.0/ | |
| dc.subject.ddc | 570 | de |
| dc.title | Characterization of microbial communities in carbonate sediments | de |
| dc.type | doctoralThesis | de |
| dc.contributor.referee | Hoppert, Michael PD Dr. | |
| dc.date.examination | 2021-09-28 | |
| dc.description.abstracteng | Microbial 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 cycling. | de |
| dc.contributor.coReferee | Arp, Gernot Prof. Dr. | |
| dc.contributor.thirdReferee | Pöggeler, Stefanie Prof. Dr. | |
| dc.contributor.thirdReferee | Heimel, Kai Prof. Dr. | |
| dc.contributor.thirdReferee | de Vries, Jan Jun.-Prof. Dr. | |
| dc.subject.eng | microbial communities | de |
| dc.subject.eng | carbonate sediments | de |
| dc.subject.eng | Aldabra Atoll | de |
| dc.subject.eng | 16S rRNA | de |
| dc.subject.eng | metagenomes | de |
| dc.subject.eng | genomes | de |
| dc.subject.eng | isolation of bacteria | de |
| dc.identifier.urn | urn:nbn:de:gbv:7-21.11130/00-1735-0000-0008-59A6-9-7 | |
| dc.affiliation.institute | Göttinger Graduiertenschule für Neurowissenschaften, Biophysik und molekulare Biowissenschaften (GGNB) | de |
| dc.subject.gokfull | Biologie (PPN619462639) | de |
| dc.description.embargoed | 2021-12-02 | |
| dc.identifier.ppn | 1779152744 | |