PT Unknown
AU Voskuhl Dr., L
TI Unraveling mechanisms of microbial community assembly using naturally replicated microbiomes
PD 03
PY 2022
DI 10.17185/duepublico/76080
LA en
DE Umweltmikrobiologie; Mikrobiologie; Mikrobielle Ökologie
AB In the field of microbial ecology, it is challenging to study mechanisms that affect microbial communities in situ. Primarily, this is due to the high complexity of environmental data. Scientist have always to deal with several unknown parameters while handling environmental samples. However, the Pitch Lake water droplets provide extraordinary model systems that are anthropogenically unaffected and naturally occurring. The microliter-sized water droplets are dispersed in the heavy oil of the Pitch Lake in Trinidad and Tobago and contain different and complex microbial community compositions. They provide a naturally less complicated system because numerous droplets can be sampled at the same time, each representing an independent natural replicate, and because on the first view all droplets have been exposed to the same environmental conditions within the oil reservoir. In this thesis, multiple microbial communities inhabiting the Pitch Lake water droplets were studied to unravel basic mechanisms that play a role in microbial community assembly and how these shape microbial communities. Dispersal was excluded as possible assembly process for the water droplets. A fluid-dynamics model applied to the Pitch Lake oil predicted that it is highly unlikely that droplets fuse amongst themselves. Individual cells are unlikely to disperse between the water droplets due to the low water activity of the oil. Computational modelling manifested that ecological drift and speciation on basis of 16S rRNA amplicon sequences are unimportant for the microbial assembly processes in the Pitch Lake droplet microbial communities. Because dispersal, ecological drift and speciation processes were ruled out we conclude that mainly selection has shaped the microbial community patterns determined by 16S rRNA gene amplicon sequencing. Indeed, we provide experimental evidence that selection is shaping the communities. Ion chromatography measurements of single water droplets demonstrated that geochemistry within the water droplets is variable and that chloride, potassium and sulfide are selective parameters which significantly influence microbial communities in terms of composition and diversity. Statistical analyses were applied to prove that the Pitch Lake microbial communities respond threshold-regulated rather than gradually to the droplet’s chloride concentrations. Once, chloride concentrations exceeded 57.3 mM, the microbial community composition abruptly shifted to less diverse and more uneven. Besides, the water droplets were further characterized as densely populated microhabitats of actively oil degrading microbial communities. Each droplet community was inhabited by a rather large core community constituting 68 ± 20 % of the total community consisting of 18 OTUs. For investigating the life in a water droplet following methods were applied: computer tomography 3D-imaging of water droplets entrapped in oil, quantitative real-time PCR for the determination of the 16S rRNA gene copy numbers, microscopic cell counting, ATP-measurement, LIVE/DEAD staining, biofilm visualization, anaerobic cultivation and reverse VII stable isotope labeling for detection of microbial CO2 production. Moreover, such water droplet microhabitats were proved to also occur in two other heavy oil seeps located in the USA and by that thousands of kilometers away from the Pitch Lake in Trinidad and Tobago. Before it was not clear if the water droplets were unique for the heavy oil of the Pitch Lake or a more general characteristic of heavy oil reservoirs. These water droplets were shown to enlarge the total surface at which oil degradation can take place inside an oil reservoir and thus far away from the oil-water-transition-zone (OWTZ). The OWTZ is located below an oil reservoir and was up to now recognized as the major location where oil biodegradation is taking place. We observed high in situ formate concentrations of ~ 2.37 mM in half of the investigated water droplets. We investigated if the high formate concentrations might inhibit sulfate reduction and if this observation can be extrapolated to sulfate-reducing microorganisms. For this we combined the observations from the Pitch Lake water droplets with laboratory experiments on sulfate-reducing strains. The results demonstrated that high formate concentrations can slow down the growth rates or delay the onsets of growth and sulfate reduction depending on the organism’s energy metabolism. This helped to conclude that the sulfate-reducing microorganisms in the Pitch Lake water droplets are most likely inhibited by formate. These are interesting results because sulfate reducing organisms produce hydrogen sulfide which causes lower oil quality and corrosion of oil pipelines. By that oil industry is confronted with a lot of costs, which they try to decrease by targeted inhibition of sulfate reducing organisms. The application of formate during oil production might display a cost-efficient and environmentally friendly alternative to other inhibition methods of microbial sulfate-reduction. The work presented in this thesis advances the knowledge on the water droplet microhabitats entrapped in heavy oil. It emphasizes that the water droplets provide a very interesting natural model system for studying undisturbed and environmentally less complex microbial communities that are mainly driven by selective parameters and respond threshold-regulated to salinity. Selection alone can produce core communities that represent a large proportion of the total community but with varying abundances of single core members. Moreover, in future studies natural environments might be considered as more heterogeneous in terms of geochemical properties. The results imply that also water droplets should be considered in future calculations regarding our worldwide oil biodegradation rates and thus the economically available oil deposits.
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