551 research outputs found
Relative abundance of prokaryotes in sediments of the Håkon Mosby mud volcano (Z1-Z3, all habitats)
No full textCARD-FISH was performed as previously described in Ruff et al., (2013; doi:10.1371/journal.pone.0072627) with the following modifications. 4-6 µl of 25-fold diluted sediment were used for filtration. Archaeal cell walls were permeabilized with 0.1M HCl for 2 min to detect ANME-3 cells, or Proteinase K solution (15 µg ml-1 (Merck, Darmstadt, Germany) in 0.05 M EDTA (pH 8), 0.1 M Tris-HCl (pH 8), 0.5 M NaCl) for 2-4 min at room temperature for all other archaea. Bacterial cell walls were permeabilized with lysozyme solution (1000kU/ml) for 60 min at 37°. Cells were stained with DAPI (1µg/ml), embedded in mounting medium and counted in 40-60 independent microscopic fields using an Axiophot II epifluorescence microscope (Carl Zeiss, Jena, Germany)
Metadata und statistic analysis of archaeal and bacterial sequences originating from sediments of the Håkon Mosby mud volcano (all habitats)
No full textDNA extraction was carried out as described on the MICROBIS project pages (http://icomm.mbl.edu/microbis ) using a commercially available extraction kit. We amplified the hypervariable regions V4-V6 of archaeal and bacterial 16S rRNA genes using PCR and several sets of forward and reverse primers (http://vamps.mbl.edu/resources/primers.php). Massively parallel tag sequencing of the PCR products was carried out on a 454 Life Sciences GS FLX sequencer at Marine Biological Laboratory, Woods Hole, MA, following the same experimental conditions for all samples. Sequence reads were submitted to a rigorous quality control procedure based on mothur v30 (doi:10.1128/AEM.01541-09) including denoising of the flow grams using an algorithm based on PyroNoise (doi:10.1038/nmeth.1361), removal of PCR errors and a chimera check using uchime (doi:10.1093/bioinformatics/btr381). The reads were taxonomically assigned according to the SILVA taxonomy (SSURef v119, 07-2014; doi:10.1093/nar/gks1219) implemented in mothur and clustered at 98% ribosomal RNA gene V4-V6 sequence identity. V4-V6 amplicon sequence abundance tables were standardized to account for unequal sampling effort using 1000 (Archaea) and 2300 (Bacteria) randomly chosen sequences without replacement using mothur and then used to calculate inverse Simpson diversity indices and Chao1 richness (doi:10.2307/4615964). Bray-Curtis dissimilarities (doi:10.2307/1942268) between all samples were calculated and used for 2-dimensional non metric multidimensional scaling (NMDS) ordinations with 20 random starts (doi:10.1007/BF02289694). Stress values below 0.2 indicated that the multidimensional dataset was well represented by the 2D ordination. NMDS ordinations were compared and tested using Procrustes correlation analysis (doi:10.1007/BF02291478). All analyses were carried out with the R statistical environment and the packages vegan (available at: http://cran.r-project.org/package=vegan), labdsv (available at: http://cran.r-project.org/package=labdsv), as well as with custom R scripts. Operational taxonomic units at 98% sequence identity (OTU0.03) that occurred only once in the whole dataset were termed absolute single sequence OTUs (SSOabs; doi:10.1038/ismej.2011.132). OTU0.03 sequences that occurred only once in at least one sample, but may occur more often in other samples were termed relative single sequence OTUs (SSOrel). SSOrel are particularly interesting for community ecology, since they comprise rare organisms that might become abundant when conditions change.16S rRNA amplicons and metagenomic reads have been stored in the sequence read archive under SRA project accession number SRP042162
Editorial: microbial communities and metabolisms involved in the degradation of cellular and extracellular organic biopolymers
No full text© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ruff, S. E. Editorial: microbial communities and metabolisms involved in the degradation of cellular and extracellular organic biopolymers. Frontiers in Microbiology, 12, (2022): 802619, https://doi.org/10.3389/fmicb.2021.802619.Most organic matter on Earth occurs in the form of macromolecules and complex biopolymers, which include the building blocks of every organism. Plant, animal, fungal, and microbial cells largely consist of macromolecules belonging to four compound classes: proteins, polysaccharides, nucleic acids, and lipids (Figure 1). The percentage of these compounds per dry weight can vary greatly between lineages, but also between individuals of the same species or developmental stages of the same organism. Living and lysing cells release a substantial quantity and variety of macromolecules to the environment. These compounds often contain nitrogen, phosphorus, and sulfur, in addition to carbon, and are thus ideal food sources for heterotrophic organisms. Although the degradation of biopolymers and macromolecules has received considerable attention, many knowledge gaps remain, particularly in very complex ecosystems such as soils and sediments
Concentrations of select dissolved anions in porewater retrieved by Rhizon sampling from hydrothermal sediments of the Guaymas Basin in 2016
No full textThe Guaymas Basin hydrothermal vents in the Gulf of California have been visited during RV Atlantis mission AT37-06 in December 2016. Aim of this mission was to understand element fluxes and microbially driven reactions at the diffusive vent sites. The submarine ALVIN and push cores were used to sample undisturbed sediments at specific locations covering different temperature and geochemical regimes. From these cores porewater was sampled using Rhizons. Here we present concentrations of select anions in the porewater. We measured the concentrations of sulfate, sulfide, chloride, ammonia, phosphate and silicate
Archaeal and bacterial diversity at different sites as determined by 16S rRNA gene analysis
No full textArchaeal and bacterial diversity at different sites as determined by 16S rRNA gene analysi
Microbial community ecology of marine methane seeps
No full textThe detailed investigation of microbial communities, e.g. of soil or hydrothermal vent ecosystems, greatly improved our understanding of the diversity, habitat preferences and functions of microorganisms and their impact on global element cycles. The aim of this thesis was a detailed analysis of the diversity, abundance and distribution of micoorganisms at marine methane seeps and the mechanisms that govern community assembly at these sites. The seep ecosystems were investigated using geochemical analyses, gene libraries, pyrosequencing, community fingerprinting and fluorescence in situ hybridization. Cold seep ecosystems hosted distinct microbial communities that differed from those of the surrounding seabed and were unique microbial habitat patches in the deep sea. The communities also greatly differed between seeps, covered broad ranges of richness and evenness and showed high degrees of endemism. However, despite the differences all seeps were inhabited by certain organisms the cold seep microbiome - including key functional clades of anaerobic methane oxidizing archaea (ANME) and sulfate-reducing bacteria. Additionally, aerobic methanotrophs and thiotrophs were found at all seeps where oxygen was present. These key functional clades seemed to be influenced by environmental parameters, such as temperature, fluid flux, sediment depth and faunal activity. Bioirrigation by ampharetid tubeworms, for instance, created a habitat for aerobic Methylococcales, whereas vesicomyid clams seemed to favor the establishment of the clade ANME-2c. Thus, niche-based processes played an important role for the community assembly at seep ecosystems. However, most of the seeps seemed to be clearly dominated by a few, globally distributed operational taxonomic units at 97% 16S rRNA gene identity (OTU0.03) of each key functional clade. Some of these OTU0.03 were rare at some seep ecosystems and abundant at others. Moreover, some findings suggested that rare organisms became abundant because the environmental conditions at the seep changed supporting the importance of species sorting at seep communities. Finally, the succession of microbial communities and the emergence of ecosystem function at a cold seep were monitored showing that it may take years to develop fully functioning communities that efficiently remove the potential greenhouse gas methane. Overall this work may help to resolve the mysteries of microbial community ecology at cold seep ecosystems
Silné souvislé Steinerovské podgrafy s malým počtem Steinerovských vrcholů
No full textTitle: Strongly Connected Steiner Subgraphs with Small Number of Steiner Vertices Author: Tamás Dávid Kemény Department: Department of Applied Mathematics Supervisor: Dr. Andreas Emil Feldmann, Department of Applied Mathematics Abstract: Two well-established methods of dealing with hard optimization problems have been to develop approximation and parameterized algorithms. Recent results have shown that for some problems, it is only by combining these two approaches, into so-called pa- rameterized approximation algorithms, that we are able to efficiently find solutions that are of reasonable quality. This is the viewpoint from which we study the problem known as the Strongly Connected Steiner Subgraph problem, where a set of terminal vertices of an edge-weighted directed graph needs to be strongly-connected in the cheapest way possible. Keywords: Strongly Connected Steiner Subgraphs, Parameterized Algorithms, Approxi- mation Algorithms, Bidirected Graphs iiiKatedra aplikované matematikyDepartment of Applied MathematicsFaculty of Mathematics and PhysicsMatematicko-fyzikální fakult
Performing Emil Hartmann – The Importance of Musical Contextualisation: A practice-based research project
No full textWhen embarking on a journey of preparing a musical work for performance, a contextualisation process is undertaken which informs the performer/s of the factors which govern the parameters of the work. In this study, the author performed Emil Hartmann’s piano trio op. 10 as a part of an integrated master’s degree program. As the composer was not a part of mainland European musical society, information on his life and work was difficult to access, which presented the performer with a contextualisation problem. This study aimed to highlight the process of contextualisation, in the absence of sufficient literary material, through the lens of Emil Hartmann’s piano trio op. 10. The research used a three-pronged methodological approach in order to construct the narrative around Hartmann’s life and composition. Through a structured process of using practice-based research to analyse the creative process undertaken by the practitioners, alongside a micro-historical and analytical methodology, the study builds layers of understanding to inform Hartmann’s narrative, and thus provides interpretational insight into the execution of the work. The research finds that, although it is possible to interpret a musical work based on the musical score, there are layers of depth which cannot be accessed without a contextual understanding of the composer and the conditions in which the composition was written. Through forming the narrative on Emil Hartmann and his piano trio, the research uses the methodology to highlight a method which can be undertaken in the absence of contextual knowledge, and thus presents a contextual understanding of Emil Hartmann’s narrative. With the constructed knowledge, the author uses the findings based on the methodological approaches to weave a narrative around the life of Emil Hartmann. Applying the information discovered in the findings, interpretational approaches are discussed to inform future performances of the work.Thesis (MMus) -- Faculty of Humanities, Music and Musicology, 202
Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations
No full textSaad S, Bhatnagar S, Tegetmeyer H, Geelhoed JS, Strous M, Ruff SE. Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations. ENVIRONMENTAL MICROBIOLOGY. 2017;19(12):4866-4881.For the anaerobic remineralization of organic matter in marine sediments, sulfate reduction coupled to fermentation plays a key role. Here, we enriched sulfate-reducing/fermentative communities from intertidal sediments under defined conditions in continuous culture. We transiently exposed the cultures to oxygen or nitrate twice daily and investigated the community response. Chemical measurements, provisional genomes and transcriptomic profiles revealed trophic networks of microbial populations. Sulfate reducers coexisted with facultative nitrate reducers or aerobes enabling the community to adjust to nitrate or oxygen pulses. Exposure to oxygen and nitrate impacted the community structure, but did not suppress fermentation or sulfate reduction as community functions, highlighting their stability under dynamic conditions. The most abundant sulfate reducer in all cultures, related to Desulfotignum balticum, appeared to have coupled both acetate- and hydrogen oxidation to sulfate reduction. We describe a novel representative of the widespread uncultured candidate phylum Fermentibacteria (formerly candidate division Hyd24-12). For this strictly anaerobic, obligate fermentative bacterium, we propose the name (U)Sabulitectum silens' and identify it as a partner of sulfate reducers in marine sediments. Overall, we provide insights into the function of fermentative, as well as sulfate-reducing microbial communities and their adaptation to a dynamic environment
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