Call number:
AWI Bio-24-95742
Description / Table of Contents:
The arctic is warming 2 – 4 times faster than the global average, resulting in a strong feedback on northern ecosystems such as boreal forests, which cover a vast area of the high northern latitudes. With ongoing global warming, the treeline subsequently migrates northwards into tundra areas. The consequences of turning ecosystems are complex: on the one hand, boreal forests are storing large amounts of global terrestrial carbon and act as a carbon sink, dragging carbon dioxide out of the global carbon cycle, suggesting an enhanced carbon uptake with increased tree cover. On the other hand, with the establishment of trees, the albedo effect of tundra decreases, leading to enhanced soil warming. Meanwhile, permafrost thaws, releasing large amounts of previously stored carbon into the atmosphere. So far, mainly vegetation dynamics have been assessed when studying the impact of warming onto ecosystems. Most land plants are living in close symbiosis with bacterial and fungal communities, sustaining their growth in nutrient poor habitats. However, the impact of climate change on these subsoil communities alongside changing vegetation cover remains poorly understood. Therefore, a better understanding of soil community dynamics on multi millennial timescales is inevitable when addressing the development of entire ecosystems. Unravelling long-term cross-kingdom dependencies between plant, fungi, and bacteria is not only a milestone for the assessment of warming on boreal ecosystems. On top, it also is the basis for agriculture strategies to sustain society with sufficient food in a future warming world.
The first objective of this thesis was to assess ancient DNA as a proxy for reconstructing the soil microbiome (Manuscripts I, II, III, IV). Research findings across these projects enable a comprehensive new insight into the relationships of soil microorganisms to the surrounding vegetation. First, this was achieved by establishing (Manuscript I) and applying (Manuscript II) a primer pair for the selective amplification of ancient fungal DNA from lake sediment samples with the metabarcoding approach. To assess fungal and plant co-variation, the selected primer combination (ITS67, 5.8S) amplifying the ITS1 region was applied on samples from five boreal and
arctic lakes. The obtained data showed that the establishment of fungal communities is impacted by warming as the functional ecological groups are shifting. Yeast and saprotroph dominance during the Late Glacial declined with warming, while the abundance of mycorrhizae and parasites increased with warming. The overall species richness was also alternating. The results were compared to shotgun sequencing data reconstructing fungi and bacteria (Manuscripts III, IV), yielding overall comparable results to the metabarcoding approach. Nonetheless, the comparison also pointed out a bias in the metabarcoding, potentially due to varying ITS lengths or copy numbers per genome.
The second objective was to trace fungus-plant interaction changes over time (Manuscripts II, III). To address this, metabarcoding targeting the ITS1 region for fungi and the chloroplast P6 loop for plants for the selective DNA amplification was applied (Manuscript II). Further, shotgun sequencing data was compared to the metabarcoding results (Manuscript III). Overall, the results between the metabarcoding and the shotgun approaches were comparable, though a bias in the metabarcoding was assumed. We demonstrated that fungal shifts were coinciding with changes in the vegetation. Yeast and lichen were mainly dominant during the Late Glacial with tundra vegetation, while warming in the Holocene lead to the expansion of boreal forests with increasing mycorrhizae and parasite abundance. Aside, we highlighted that Pinaceae establishment is dependent on mycorrhizal fungi such as Suillineae, Inocybaceae, or Hyaloscypha species also on long-term scales.
The third objective of the thesis was to assess soil community development on a temporal gradient (Manuscripts III, IV). Shotgun sequencing was applied on sediment samples from the northern Siberian lake Lama and the soil microbial community dynamics compared to ecosystem turnover. Alongside, podzolization processes from basaltic bedrock were recovered (Manuscript III). Additionally, the recovered soil microbiome was compared to shotgun data from granite and sandstone catchments (Manuscript IV, Appendix). We assessed if the establishment of the soil microbiome is dependent on the plant taxon and as such comparable between multiple geographic locations or if the community establishment is driven by abiotic soil properties and as such the bedrock area. We showed that the development of soil communities is to a great extent driven by the vegetation changes and temperature variation, while time only plays a minor role.
The analyses showed general ecological similarities especially between the granite and basalt locations, while the microbiome on species-level was rather site-specific. A greater number of correlated soil taxa was detected for deep-rooting boreal taxa in comparison to grasses with shallower roots. Additionally, differences between herbaceous taxa of the late Glacial compared to taxa of the Holocene were revealed.
With this thesis, I demonstrate the necessity to investigate subsoil community dynamics on millennial time scales as it enables further understanding of long-term ecosystem as well as soil development processes and such plant establishment. Further, I trace long-term processes leading to podzolization which supports the development of applied carbon capture strategies under future global warming.
Type of Medium:
Dissertations
Pages:
xii, 198 Seiten
,
Illustrationen, Diagramme
URL:
https://doi.org/10.25932/publishup-63600
URN:
urn:nbn:de:kobv:517-opus4-636009
DOI:
10.25932/publishup-63600
Language:
English
Note:
Dissertation, Universität Potsdam, 2024
,
Table of Contents
Summary
Deutsche Zusammenfassung
1 Introduction
1.1 Arctic ecosystems under global warming
1.2 The plant-associated microbiome
1.3 Drivers of soil development
1.4 Ancient DNA to unravel past ecosystems
1.4.1 Lake sediments as archives of past community changes
1.4.2 Metabarcoding for targeting specific communities
1.4.3 Shotgun sequencing for broader overview
1.5 Thesis objective
1.6 Thesis outline and author contributions
2 Manuscript I
2.1 Abstract
2.2 Introduction
2.3 Materials and Methods
2.3.1 Primer design and evaluation
In silico analyses
Evaluation of lake sediment core DNA for analyses of fungal paleoecology
2.4 Results
Primer design and evaluation
Evaluation of lake sediment core DNA for fungal paleoecology
2.4.1 Taxonomic resolution across the cores
2.4.2 Comprehensiveness: Rarefaction and accumulation curves
2.4.3 Amplicon length and GC content to assess bias through degradation
2.4.4 General taxonomic composition of fungi in Siberian lake sediment cores
Diversity of fungal paleocommunities from lake CH12
2.5 Discussion
2.5.1 Preservation biases and potential contamination
2.5.2 Characteristics of the optimized sedaDNA ITS1 metabarcoding assay
2.5.3 Potential of lake sediment fungal DNA for paleoecology
2.6 Author contributions
2.7 Acknowledgements
2.8 Conflict of interest
2.9 References
3 Manuscript II
3.1 Abstract
3.2 Introduction
3.3 Geographic setting and study sites
3.4 Materials and Methods
3.4.1 Sampling
3.4.2 DNA extraction and amplification
3.4.3 Bioinformatic analysis
3.4.4 Assessment of negative controls and contamination
3.4.5 Statistical analysis and visualization
3.5 Results
3.5.1 Fungi: sedaDNA sequencing results and overall patterns of alpha diversity and taxonomic composition
3.5.2 Vegetation: sedaDNA sequencing results and overall patterns of alpha diversity and taxonomic composition
3.5.3 Site-specific plant-fungus covariation
3.5.3.1 Fungus and plant covariation in arctic Siberia from MIS3 to the Holocene
3.5.3.2 Quantitative relationships between fungi and plant richness and composition
3.6 Discussion
3.6.1 Fungus and plant diversity along a spatiotemporal gradient in Siberia
3.6.2 Changes in ecosystem functioning over a spatiotemporal gradient
3.6.3 Implications of our results for ecosystem functioning and future research avenues
3.7 Conclusions
Funding
Availability of data and material
Author contribution
Declaration of competing interest
Acknowledgements
3.8 References
4 Manuscript III
4.1 Abstract
4.2 Introduction
4.3 Results and Discussion
4.3.1 Compositional changes of plants, fungi, and bacteria in ancient metagenomic datasets
4.3.2 Long-term soil development: a trajectory or environmentally driven processes?
4.3.3 Bioweathering supported by lichens and mycorrhiza
4.3.4 Turnover in carbon, nitrogen, and sulphur cycling
4.3.5 Tracing podzolization
4.4 Implications and conclusions
4.5 Material and methods
4.5.1 Geographical setting and study site
4.5.2 X-ray fluorescence scanning of the sediment core
4.5.3 Core sub-sampling
4.5.4 DNA extraction
4.5.5 Single stranded DNA library build
4.5.6 Bioinformatic pipeline for the analysis of the sequencing results
4.5.7 Data analysis
4.5.8 Analysis of the ancient patterns
4.5.9 Statistical analysis of the dataset
Acknowledgements
4.6 References
Declarations
5 Discussion and synthesis
5.1 Long-term rhizosphere establishment in tundra and taiga areas
5.1.1 SedaDNA as a proxy for soil microbiome
5.1.1.1 Fungal DNA metabarcoding
5.1.1.2 Targeting soil communities with shotgun sequencing
5.1.1.3 Comparison between metabarcoding and shotgun sequencing for the soil microbiome
5.1.2 Fungi-vegetation interaction changes over time
5.1.3 Soil development on a temporal gradient
5.2 Conclusion and future perspectives
6 References
7 Appendix
7.1 Appendix to manuscript I
7.2 Appendix to manuscript II
7.3 Appendix to manuscript III
7.4 Manuscript IV
7.4.1 Abstract
7.4.2 Introduction
7.4.3 Geographical setting and study sites
7.4.4 Material & Methods
7.4.4.1 Sub-sampling of the sediment cores
7.4.4.2 DNA extraction
7.4.4.3 Single stranded DNA library built
7.4.4.4 Bioinformatic pipeline for the analysis of the sequencing data
7.4.4.5 Data analysis
7.4.4.6 Statistical analysis of the datasets
7.4.5 Results
7.4.5.1 Compositional changes of representative plant taxa alongside dynamics in fungal ecologies and bacterial element cycling in ancient metagenomic datasets
7.4.5.2 Impact of abiotic and biotic drivers on soil establishment across geographical locations
7.4.5.3 Relative positive correlations of functional soil taxa with plants across the locations
7.4.5.4 Assessment of the plant taxon-specific microbiome across the locations
7.4.6 Discussion
7.4.6.1 Site-specific soil development
7.4.6.2 Differences in the bedrock
7.4.6.3 Correlation between the lake biota
7.4.6.3.1 General Trends in positively correlated rhizosphere taxa
7.4.6.3.2 Plant taxa specific microbiome
7.4.7 Implications and future directions
7.4.8 References
7.4.9 Supplement to manuscript IV
Acknowledgements
Eidesstattliche Erklärung
Damage pattern analysis – Auflagen Doktorarbeit
Summary
Main
References
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AWI Reading room
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