Meyerdierks, Anke
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Meyerdierks, Anke
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Meyerdierks, Anke
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Item-typ:Veröffentlichung, Assessing the Genetic Potential of Uncultivated Sulfate Reducing Bacteria(2010-09-01); ; ; The anaerobic oxidation of methane with sulfate (AOM) removes more than 90% of the methane produced in marine sediments. The process is mediated by consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). Previous studies focusing on the archaeal part of ANME/SRB consortia yielded as yet only a fragmentary understanding of this process. Additionally, whereas ANME clades have been repeatedly studied with respect to phylogeny, key genes, and genomic capabilities, little is known about their sulfate-reducing partner. Thus, in order to change this situation, this thesis focused on SRB associated with AOM.In the first part of this thesis, SRB associated with Archaea from the ANME-2 clade were investigated. Sequences of bacterial 16S rRNA genes retrieved from ANME-2/SRB enrichment cultures supported a previous hypothesis that ANME-2 associated SRB belong to the SEEP-SRB1 group within the deltaproteobacterial Desulfosarcina/Desulfococcus (DSS) group. Using fluorescence in situ hybridization (FISH) and probes for newly defined SEEP-SRB1 subgroups (a-f), bacteria from the SEEP-SRB1a subgroup were identified as the dominant sulfatereducing partners in ANME-2 consortia in samples from six different AOM sites. In contrast to their abundance as ANME-2 partners, single SEEP-SRB1a cells were very rare (<1%) in all but one of the examined samples. This suggested a highly adapted if not even obligate syntrophic lifestyle of the SEEP-SRB1a group in ANME-2 consortia. Additionally, SEEP-SRB1a was also detected as an alternative partner of archaea of the ANME-3 clade which was previously described to be predominantly associated with SRB of the Desulfobulbus group.In the second part of this thesis, the diversity of SRB in AOM habitats was investigated using aprA and dsrAB, key genes of sulfate-reduction, as functional markers. AprA and DsrAB diversity in different samples from methanotrophic microbial mats from the Black Sea as well as in two enrichment cultures from sediment above gas hydrates at Hydrate Ridge was lower compared to not enriched Hydrate Ridge sediment. Clone libraries were dominated by sequences affiliated with Desulfobacteraceae. Sequences within this group featured a considerable diversity. Most of the retrieved sequences affiliated with clusters that possessed no cultured representative. One AprA cluster was identified to represent SEEP-SRB1a by using a combination of FISH and fluorescence-activated cell sorting.In the third part of this thesis, it was attempted to obtain knowledge about the genetic potential of SEEP-SRB1a. Since no pure cultures of SEEP-SRB1a existed, a metagenomic approach was used. For this, DNA from an enrichment culture dominated by ANME-2 and SEEP-SRB1a was used for constructing a large-insert fosmid library and for performing next-generation pyrosequencing. Altogether, 570 Mbp of sequence data was thus generated which could be assembled into longer contigs. In total, 9,075 contigs could be mapped onto the genome of Desulfococcus oleovorans Hxd3, the closest fully sequenced relative of SEEPSRB1a, and thereby could be assigned to SEEP-SRB1a. Two contigs carrying putative SEEP-SRB1a apr and dsr genes, provided a first glimpse of the genetic potential of these bacteria.Dissertation303 127 - Some of the metrics are blocked by yourconsent settings
Item-typ:Veröffentlichung, Molecular Ecology of Free-Living Chemoautotrophic Microbial Communities at a Shallow-sea Hydrothermal Vent(2012-03-26); ; ; Deep-sea hydrothermal systems are unique habitats for microbial life with primary production based on chemosynthesis. They are considered to be windows to the subsurface biosphere. Their far more accessible shallow-sea counterparts are valuable targets to study the effects of hydrothermal activity on geology, seawater chemistry and microorganisms. Such an area of shallow-sea hydrothermal venting is observed approximately 2.5 km east off Panarea Island (Sicily, Italy). This system is characterized by fluid temperatures of up to 135°C, gas emissions dominated by CO2 and precipitation of elemental sulfur on the seafloor. It is quite well studied, yet, only very few studies exist on its microbial ecology. This thesis is therefore targeting the microbiology of sediment cores as part of an interdisciplinary project which combines geological, geochemical, biomarker and molecular biological investigations. It was intended to correlate the environmental parameters with the taxonomic composition and the metagenomes of the microbial community thereby gaining insights into the interaction of geosphere and biosphere. All samples were taken at Hot Lake, an oval-shaped (~10 by 6 meters) shallow (~2.5 m deep) depression at 18 m below sea level. The sediments in this depression are strongly affected by hydrothermal activity. In situ temperatures at 10 cm below sea floor of 36°C and 74°C were measured at two different sites within Hot Lake. Based on the physico-chemical parameters, a thermodynamic modeling was performed which revealed sulfur oxidation and sulfur reduction to be exergonic at Hot Lake. Microbial community structures of different sediment layers were first screened by automated rRNA intergenic spacer analysis (ARISA). Based on the ARISA fingerprints, a total of eight bacterial and archaeal 16S rRNA gene libraries were constructed from surface to bottom layers of sediments to gain more insights into microbial diversity. Comparative sequence analyses revealed a dominance of sequences affiliated with Epsilonproteobacteria, Deltaproteobacteria and Bacteroidetes. In the surface sediments, sequences close to anoxygenic phototrophic Chlorobi were also detected. In the bottom sediments, thermophilic bacteria such as Thermodesulfobacteria spp. were found. Hyperthermophilic Archaea sequences related to Desulfurococcaceae and Korarchaeota were retrieved from 74°C hot sediment. Based on the most closely related cultured representatives, it could be deduced that the majority of microorganisms in Hot Lake sediments have a sulfur-dependent metabolism, including sulfide oxidation, sulfur reduction or sulfate reduction. Fluorescence in situ hybridization showed the dominance of Bacteria in all depths of sediments. With increasing depth and temperature, the abundance of Archaea increased relatively to that of Bacteria. Metagenomic analyses revealed that Epsilonproteobacteria were dominating surface sediments of Hot Lake where they gain energy from sulfur metabolism to fix CO2 by the reductive tricarboxylic acid (rTCA) cycle. This is consistent with findings reported from deep-sea hydrothermal vent systems. The results have led to the conclusion that mixing between hydrothermal fluids and seawater results in distinctly different temperature gradients and ecological niches in Hot Lake sediments. Overall, the correlation of geochemical profiles, IPL analyses, characterization of the microbiological community and metagenomic analyses provided strong evidence for a sulfur-dominated metabolism in the surface sediments of Hot Lake.Dissertation268 130 - Some of the metrics are blocked by yourconsent settings
Item-typ:Veröffentlichung, Diversity and function of microbial communities in sediments from different deep-sea habitats(2010-04-16); ; ; Deep-sea floors are diverse environments that range from permanently cold (desert-like plains) to hot systems (hydrothermal vents). In hot systems, primary productivity is performed by microbial communities which use chemical energy generated by geological processes (lithotrophy). This energy transfer from mantle to the ocean is as yet poorly understood, and the diversity and activity of microbes at these sites is therefore an interesting target for microbial ecologists. However, the vast majority of all globally distributed deep-sea sediments is permanently cold. The distribution of microorganisms in deep-sea floors and the factors controlling it at small and large scales are important for the understanding of the mechanisms that regulate biodiversity. During this thesis, hydrothermally influenced sediments of the peridotite-hosted Logatchev hydrothermal vent field were investigated in an interdisciplinary study to reveal the diversity and activity of the associated microbial communities. In situ microprofiles showed that these sediments were controlled by diffusive transport, instead of previously reported advective processes. White mats on top of these sediments resemble Beggiatoa-mats from the basalt- hosted field in the Guaymas Basin. However, fluorescence in situ hybridization revealed that the overlying sulfur-mats were dominated by filamentous Epsilonproteobacteria or a vibrioid Arcobacter-type. The microbial community of the surface layer was predominantly composed of Epsilonproteobacteria (7-21%), Deltaproteobacteria (20-21%), and Bacteroidetes (19- 20%). Comparative 16S rRNA gene sequence analyses identified various bacteria related to those found in basaltic systems. The presence of an active microbial community in these sediment surface layers was confirmed by high oxygen consumption rates. Geochemical analyses detected metal-sulfides in the sediments, elemental sulfur in the mats and an intensive sulfide flux from below. Ex situ incubations and turnover rate experiments revealed that sulfide is consumed and that sulfate-reduction is performed by the surface sediment microbial community. This was consistent with the detection of aprA-genes and soxB-genes, which are both key genes of the sulfur cycle. Further metabolic capabilities such as denitrification and CO2-fixation were indicated by primary analysis of metagenomic data retrieved by pyrosequencing. So far, our analyses suggest that sulfur cycling is one of the driving forces for primary production and biomass formation in surface sediments of the ultramafic-hosted Logatchev hydrothermal vent fields. Therefore, major differences in microbial composition between basalt- and peridotite-hosted fields were not detected. Hydrothermally influenced sediments from the Mid-Atlantic Ridge and permanently cold sediments from three basins of the eastern South Atlantic Ocean were investigated to examine the ability of microorganisms to disperse in the deep-sea. Besides spatial distance, the structuring effect of the physical barrier Walvis Ridge, which separates the Cape Basin from the other two basins, was determined. The analysis of 16S rRNA gene sequences of the deep- sea sediments revealed phylotypes affiliated with Gammaproteobacteria, Deltaproteobacteria and Acidobacteria, which were present in all three basins. The distribution of these shared phylotypes seemed to be influenced neither by the Walvis Ridge nor by different deep water masses, suggesting a high dispersal capability, as also indicated by low distance decay relationships. In contrast, the comparison of the total bacterial diversity of the cold sediments as well as of the hydrothermally influenced sediments revealed significant differences between the microbial communities. Within the Logatchev field and therefore for small distances (<10 km) microbial biogeography was primarily controlled by environmental heterogeneity. In contrast, the analysis of the permanently cold sediments revealed that at intermediate (10 3000 km) and large scales (>3000 km), both factors influenced bacterial diversity, indicating a complex interplay of local contemporary environmental effects and dispersal limitation.Dissertation290 155 - Some of the metrics are blocked by yourconsent settings
Item-typ:Veröffentlichung, Molecular ecology of deep-sea hydrothermal plumes(2022-06-13); ; ; Hydrothermal plumes are considered ephemeral habitats in the deep-sea and are reported to serve as hotspots for microbial biomass. The chemolithoautotrophic microbial communities form the basis of the food web in the resource-limited deep-sea and contribute to biogeochemical cycles over larger spatial scales. Despite their influence on biogeochemistry, a comprehensive analysis of microbial clades inhabiting hydrothermal plumes, their metabolism and distribution in the open-ocean is lacking. In this thesis, I investigated the communities of ten hydrothermal plumes, located in the Atlantic and Pacific oceans, originating at different depths and characterized by distinct chemical conditions. In these plumes, the dynamics and ecological function of the dominant microbial clades were investigated and ecological niches subsequently described. The first study identified and described the niches of three new SUP05 species in three sulfur rich plumes. The niche partitioning between SUP05 species was shown to be driven by depth and minor variations in environmental parameters. Based on differences in species distribution between vent sites and open-ocean, we propose that plumes serve as growth chambers for SUP05 species, from which they are released into the surrounding water. The investigation of four plumes originating from hydrothermally active volcanoes in the South Pacific Ocean elucidated a dominance of the alkane-degrading Alcanivorax. Results of our analysis, revealed a niche partitioning driven by depth and the complexity of hydrocarbons. We hypothesized that the Alcanivorax genus could be used as an indicator of environmental perturbations, such as hydrocarbon leakage from the seabed. Finally, the third study characterized the microbial community of four hydrothermal plumes in the Mid-Atlantic Ridge (MAR). The prominent taxa in these hydrogen-rich plumes were the SUP05 clade and Sulfurimonas. The high abundance of Sulfurimonas and SUP05 pointed towards a niche partitioning between the two clades, potentially driven by oxygen and hydrogen concentrations. The results of this thesis provide valuable information on the ecology of microbial communities inhabiting diverse hydrothermal plumes, their metabolisms and their ecological niches. With this, I show how we can move towards predictive ecology of plume communities. Furthermore, the data collected and analyzed from plumes in this study, considerably expands the currently available plume data and can serve as a valuable resource in future studies.Dissertation380 253