| 1. |
- Centler, Florian, et al.
(författare)
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Keystone Species and Modularity in Microbial Hydrocarbon Degradation Uncovered by Network Analysis and Association Rule Mining
- 2020
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Ingår i: Microorganisms. - : MDPI AG. - 2076-2607. ; 8:2
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Tidskriftsartikel (refereegranskat)abstract
- Natural microbial communities in soils are highly diverse, allowing for rich networks of microbial interactions to unfold. Identifying key players in these networks is difficult as the distribution of microbial diversity at the local scale is typically non-uniform, and is the outcome of both abiotic environmental factors and microbial interactions. Here, using spatially resolved microbial presence-absence data along an aquifer transect contaminated with hydrocarbons, we combined co-occurrence analysis with association rule mining to identify potential keystone species along the hydrocarbon degradation process. Derived co-occurrence networks were found to be of a modular structure, with modules being associated with specific spatial locations and metabolic activity along the contamination plume. Association rules identify species that never occur without another, hence identifying potential one-sided cross-feeding relationships. We find that hub nodes in the rule network appearing in many rules as targets qualify as potential keystone species that catalyze critical transformation steps and are able to interact with varying partners. By contrasting analysis based on data derived from bulk samples and individual soil particles, we highlight the importance of spatial sample resolution. While individual inferred interactions are hypothetical in nature, requiring experimental verification, the observed global network patterns provide a unique first glimpse at the complex interaction networks at work in the microbial world.
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| 2. |
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| 3. |
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| 4. |
- Hubalek, Valerie, 1981-, et al.
(författare)
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Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions
- 2017
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Ingår i: mSystems. - 2379-5077. ; 2:5
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Tidskriftsartikel (refereegranskat)abstract
- Syntrophy among Archaea and Bacteria facilitates the anaerobic degra- dation of organic compounds to CH4 and CO2 . Particularly during aliphatic and aro- matic hydrocarbon mineralization, as in the case of crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutu- alistic microbial partners are of central importance. Using micromanipulation com- bined with shotgun metagenomic approaches, we describe the genomes of complex consortia within short-chain alkane-degrading cultures operating under methano- genic conditions. Metabolic reconstruction revealed that only a small fraction of genes in the metagenome-assembled genomes encode the capacity for fermenta- tion of alkanes facilitated by energy conservation linked to H2 metabolism. Instead, the presence of inferred lifestyles based on scavenging anabolic products and inter- mediate fermentation products derived from detrital biomass was a common fea- ture. Additionally, inferred auxotrophy for vitamins and amino acids suggests that the hydrocarbon-degrading microbial assemblages are structured and maintained by multiple interactions beyond the canonical H2 -producing and syntrophic alkane degrader-methanogen partnership. Compared to previous work, our report points to a higher order of complexity in microbial consortia engaged in anaerobic hydrocar- bon transformation. IMPORTANCE
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| 5. |
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| 6. |
- Jeske, Jan Torsten, 1983-
(författare)
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Microbial adaptations and controlling mechanisms of surface-associated microhabitat heterogeneity in aquatic systems
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Habitat heterogeneity is a driving factor for speciation and ecosystem functioning and is well studied in macro-ecology. Yet our understanding of microbial adaptations, and governing processes is incomplete. The here presented thesis aims at giving us a better understanding of patterns in micro-heterogeneity, and microbial adaptations to such heterogeneity with particular focus on surface-dominated, aquatic habitats. The most prominent microbial adaptation to surface associated mode of life is biofilm formation. Biofilms rely heavily on type IV pili. These pili systems are well studied in Bacteria, but largely unknown in Archaea. Therefore, the first part of this thesis focuses on resolving genetic and structural feature of the type IV like aap-pilus of the thermo-acidophilic Sulfolobus acidocaldarius. We found the aap-pilus to be indispensible for biofilm formation, and to be unparalleled in variability of its quaternary structure and cross regulation with other filaments. The second part of this thesis investigates particle colonization in the water column, focusing on diatoms as a model system, allowing an in situ assessment of different stages of particle colonization, and potential particle-specificity of the associated bacterial community. Opposing reports from marine systems, we did not observe diatom-specificity in the associated bacterial community. Instead we found bacterial community subsets, one likely originating from sediment resuspension, and the other being controlled by biofilm-forming populations (e.g. Flexibacter), able to attach to newly formed particle surfaces and subsequently facilitate secondary colonization by other bacteria. Finally, the habitat heterogeneity in top-layers of lake sediments were investigated in experimental microcosms. Cell-specific oxygen consumption rates were determined, to assess microbial activity across different scales. Individual activity rates differed strongly across all investigated scales, likely due to spatially heterogeneous distribution of nutrients with differing quality. Vice versa, the influence of microbial activity on micro-habitat-heterogeneity was investigated. We correlated sediment redox-state with bacterial community composition and populations. Our results indicate that habitat heterogeneity is generally beneficial for microorganism, and greater heterogeneity results in greater bacterial diversity. However, this heterogeneity-diversity relationship is limited and microorganisms actively stabilize their immediate redox environment to a preferred, community-specific, stable state, if cell abundances exceed a minimum threshold.
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| 7. |
- Jeske, Jan Torsten, 1983-, et al.
(författare)
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Microscale decoupling of sediment oxygen consumption and microbial biomass in an oligotrophic lake
- 2016
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Ingår i: Freshwater Biology. - : Wiley. - 0046-5070 .- 1365-2427. ; 61:9, s. 1477-1491
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Tidskriftsartikel (refereegranskat)abstract
- Sediments of aquatic ecosystems are hotspots for biological activity. Here, we address the question if, within surface sediments, oxygen consumption is linearly related to cell abundance. In addition, we identify habitat-specific factors influencing underlying microbial processes. Sediment microcosms were established from three sites within oligotrophic Lake angstrom nnsjon, Sweden, to use microsensors for measuring oxygen profiles and estimate spatially resolved oxygen consumption rates at the water-sediment interfaces. To evaluate differences between habitats, we measured sediment carbon content and C:N:P as a proxy for diagenetic state and organic matter bioavailability. Epifluorescence microscopy was used to assess the microscale distribution and size of surface-colonising microorganisms. There was no linear correlation between oxygen consumption rates and microbial cell abundances. Cell-specific respiration rates were highest in the profundal compared to the littoral- and inflow-sediment microcosms, whereas vertical variability in all these parameters was highest at the inflow, intermediate in the littoral and least variable in profundal sediments. Illumina sequencing of spatially resolved 16SrRNA genes was used to test for possible influence of bacterial diversity on spatially resolved oxygen consumption rates. Bacterial -diversity decreased over depth at each site, but was also lower in sediments from the most active profundal zones of the lake compared to the inflow. We suggest that bacteria in profundal sediments mainly use highly oxidised organic compounds, resulting in overall low growth yield despite high metabolic activity. In the lake inflow and the littoral, more reduced organic substrates of terrestrial origin are used at lower rates but with higher yield.
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| 9. |
- Richert, Inga, et al.
(författare)
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Bacterial communities in a tar-contaminated lake sediment
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Organic anthropogenic pollutants, such as polycyclic aromatic hydrocarbons (PAHs) are widespread in nature and even low concentrations can be harmful for many organisms. To assess if also microbiota residing in freshwater sediments respond to such contaminants a lake sediment adjacent to the former discharge of a factory that conducted tar distillation in the early 20th century in central Sweden were studied. We compared the bacterial community composition (BCC) at sites affected by high tar loads to BCC in a linked, but pristine sediment, and a downstream site that is likely influenced by regular diffusive loads of PAHs. PAH and VOC (Volatile Organic Carbon) concentrations were analyzed whereas sediment aliquots were used for molecular identification of the local BCC. Here we took the opportunity to compare the bacteria abundance-data retrieved from two distinct approaches; two OTU tables were generated based on either paired-end MiSeq Illumina 16S rRNA gene amplicon sequencing or direct HiSeq Illumina-based metagenome sequencing of sediment DNA extracts. Both methods revealed that the high PAH loads adjacent to the tar factory significantly alters the BCC compared to the less affected sites, even though they both partly result in contrasting outcome. The highly contaminated sediments hosted a bacterial community that was low in richness, featuring taxa known to colonize habitats with high PAH loads. For instance the relative abundance of Sphingomonadales and Burkhoderiales, both orders, within the phylum Proteobacteria, increased relative to the pristine site as well as Acidimicrobiales, one subclass of Actinobacteria. Interestingly the sediment downstream of the former factory outlet was colonized by bacteria which were very similar in community composition to the pristine site upstream of the factory outlet, implying a capacity of the natural sediment microbiota to cope with low levels of PAH contamination.
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| 10. |
- Richert, Inga, 1982-
(författare)
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Environmental filtering of bacteria in low productivity habitats
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Microbes fulfill important ecosystem functions by contributing as drivers of global nutrient cycles. Their distribution patterns are mainly controlled by environmental heterogeneities. So far, little is known about the mode of action of particular environmental drivers on the microbiota, particularly in low productivity habitats.The aim of this thesis was to investigate the relationships between local environmental drivers and the microbial responses at the level of communities, individuals and realized function, using three structurally different model habitats sharing the feature of overall low productivity. Using a hypothesis-based approach and extensive 16S rRNA amplicon mapping of bacterioplankton colonizing the polar Southern Ocean, I identified how the seasonal formation of open-water polynyas and coupled phytoplankton production affected the diversity of surface bacterial communities and resulted in a cascading effect influencing the underlying dark polar water masses. Additional laboratory experiments, with cultures exposed to light, resulted in reduction in alpha diversity and promoted opportunistic populations with most bacterial populations thriving in the cultures typically reflected the dominants in situ.Furthermore it was experimentally tested how induced cyclic water table fluctuations shaping environmental heterogeneity in a constructed wetland on temporal scale, by directly affecting redox conditions. Twelve months of water table fluctuations resulted in enhanced microbial biomass, however a shift in community composition did not lead to a significant increase in pollutant removal efficiency when compared to a static control wetland. I detected phyla that have previously been proposed as key players in anaerobic benzene break-down using a protocol that was developed for single cell activity screening using isotope-substrate uptake and microautoradiography combined with taxonomic identification based on fluorescent in situ hybridization targeting the 16S rRNA. Eventually, I provide an example of how anthropogenic pollution with polyaromatic hydrocarbons induced a strong environmental filtering on intrinsic microbial communities in lake sediments.In conclusion, my studies reveal that microorganisms residing in low productivity habitats are greatly influenced by environmental heterogeneity across both spatial and temporal scales. However, such variation in community composition or overall abundance does not always translate to altered community function.
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