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Found 7 results.

Project: OTC-Genomics

Estuaries and coasts are characterized by ecological dynamics that bridge the boundary between habitats, such as fresh and marine water bodies or the open sea and the land. Because of this, these ecosystems harbor ecosystem functions that shaped human history. At the same time, they display distinct dynamics on large and small temporal and spatial scales, impeding their study. Within the framework of the OTC-Genomics project, we compiled a data set describing the community composition as well as abiotic state of an estuary and the coastal region close to it with unprecedented spatio-temporal resolution. We sampled fifteen locations in a weekly to twice weekly rhythm for a year across the Warnow river estuary and the Baltic Sea coast. From those samples, we measured temperature, salinity, and the concentrations of Chlorophyll a, phosphate, nitrate, and nitrite.

Biocrust and sediment characteristics of biological soil crusts in coastal sand dunes in northern Germany

This dataset comprises environmental parameters for biological soil crusts in coastal sand dunes in northern Germany. Biological soil crusts (biocrusts) are autonomous ecosystems consisting of prokaryotic and eukaryotic microorganisms growing on the topsoil. They colonize global climatic zones, including temperate dunes. This study examined changes in the community structure of biocrust phototrophic organisms along a dune chronosequence at the Baltic Sea compared to an inland dune in Northern Germany. The community composition and their shift between different successional stages of dune development were related to physico-chemical sediment properties. A vegetation survey followed by species determination and sediment analyses were conducted. The sampling took place on the 25th of April and on the 5th of May 2020. The samples were collected at a costal dune area, namely the Schaabe spit on the island Rügen, Mecklenburg Wester-Pomerania, Germany, and in an inland dune area at Verden (Aller), Lower Saxony, Germany. Biocrust samples were taken along one transect per study site. Each transect followed a natural succession gradient in the dune area. Along each transect, the different successional dune stages were visually identified and further named as dune subsites. At each subsite, a sampling plot of 1 m2 was established and used for further vegetation analyses, biocrust and sediment sampling. Along the Schaabe spit transect four subsites with one sampling plot each were established and three subsites were established in the inland dune in Verden. For the vegetation survey seven different functional groups were defined describing the overall surface coverage: Thin (1-3 mm) green algae-dominated biocrusts were defined as early successional stages. Later successional stages, in which the green algae biocrusts became slightly thicker (3-8 mm) and moss-covered, were defined as the intermediate successional biocrust stage. Moss-dominated biocrusts and those who additionally lichenized characterized the mature successional stages of biocrusts. Vascular plants, and litter (dead material, i.e., pine needles, leaves, and branches) were two of the non-cryptogamic but still biotic functional groups. Bare sediment was the only abiotic functional group. The predefined functional groups were recorded within each plot according to the point intercept method by Levy and Madden (1933). Each of the seven sampling plots was divided into 16 equal subplots (0.0625 m2). A 25 cm x 25 cm (0.0625 m2) grid of 25 intersections was placed randomly into 4 of these subplots. Within each sub-plot, the functional groups were recorded by 25 point measurements according to the approach of Williams et al. (2017). That allowed 100 point measurements per sampling plot (1 m2).

Morphological determination of the phototrophic community composition of biological soil crusts in coastal sand dunes in northern Germany

This dataset comprises the microbial community composition of biological soil crusts in north-German sand dunes. For this we obtained enrichment cultures of phototrophic microorganisms, by placing fragments of biocrusts of the same Petri dishes as used for sequencing, in Petri dishes with Bold Basal (1N BBM) agarized medium (Bischoff and Bold 1963). Cultures were grown under standard laboratory conditions: with a 12-hour alteration of light and dark phases and irradiation of 25 μmol photons m-2 s-1 at a temperature 20 ± 5 ºС. Microscopic study of these raw cultures began in the third week of cultivation. Morphological examinations were performed using Olympus BX53 light microscope with Nomarski DIC optics (Olympus Ltd, Hamburg, Germany). Micrographs were taken with a digital camera (Olympus LC30) attached to the microscope, and processed by the Olympus software cellSens Entry. Direct microscopy of rewetted samples was performed in parallel with cultivation for evaluation of dominating species of algae and cyanobacteria in the original samples. Morphological identification of the biocrust organisms was based mainly on Ettl and Gärtner (2014) for green microalgae, and on Komárek (2013) for cyanobacteria, as well as on some monographs and papers devoted to taxonomic revisions of the taxa of interest (Darienko and Pröschold 2019). Moss and lichens samples were air-dried after collection. For determination, a microscope with a maximum magnification of 400x was used. Morphological identification of mosses followed Frahm and Frey (2004) with taxonomical reference to (Hodgetts et al. 2020). Lichens were determined according to Wirth et al. (2013). Morphologically critical species of the genus Cladonia where additionally analyzed by thin-layer chromatography according to (Culberson and Ammann 1979) in solvent system A.

Microbial community composition of biological soil crusts in coastal sand dunes in northern Germany

This data collection comprises environmental data and taxonomic parameters of the investigated biocrusts of sampling sites in coastal and inland sand dunes in northern Germany. Sampling took place in spring 2020 and winter 2021. Biocrusts and uppermost sediment samples were collected along dune successional gradients and sequenced by LGC Genomics Ltd. Corresponding sequence data of biocrust organisms are archived at the European Nucleotide Archive.

16S analysis (pyrosequencing), Hainich grassland VIPs 2008

Original data comes from a project which takes or took place as part of the DFG priority program "Exploratories for large-scale and long-term functional biodiversity research". The data is stored together with descriptive metadata, in combination called a dataset, in the project repository (https://www.bexis.uni-jena.de). Species information was extracted from that original dataset. The second paragraph is part of the metadata of the original dataset. 16S analysis of the diversity in Hainich grassland

Einsatz von molekularen Methoden fuer die mikrobielle Oekologie und biologische Sicherheitsforschung

Das wissenschaftliche Gesamtziel der Arbeiten ist das funktionale Verstaendnis der genetischen, mikrobiellen und oekologischen Prozesse beim Einsatz von Mikroorganismen in der Umwelt. Um einem kausalen Verstaendnis der Struktur und Funktion natuerlicher mikrobieller Lebensgemeinschaften naeher zu kommen, muss zuerst die organismische Struktur der Lebensgemeinschaft methodisch definiert werden. Mit einer breiten Methodenpalette fuer die mikrobielle Strukturanalyse soll gewaehrleistet sein, dass einerseits ein schneller Ueberblick ueber die mikrobielle Lebensgemeinschaft erhalten werden kann, um die raeumlich-zeitliche Dynamik mikrobieller Strukturen in der Umwelt verfolgen zu koennen, und andererseits ein sehr detailliertes Bild der raeumlichen und taxonomischen Struktur auf der Ebene der einzelnen Bakterienzelle durch den Einsatz von Gen- und Immunsonden gewonnen werden kann. Um zu einem funktionalen, modellhaften Verstaendnis dieser mikrobiellen Strukturen zu gelangen, werden eine Reihe ausgewaehlter Modellsysteme mit zunehmender biologischer Komplexitaet eingesetzt. Die Laboruntersuchungen werden durch oekosystemare Messungen mit denselben analytischen Ansaetzen komplementiert, um das im Labor ermittelte funktionalen Verstaendnis auf die Reaktionen der tatsaechlichen Umwelt zu erweitern. Hierdurch wird ein dichtes Netz funktionaler Zusammenhaenge geknuepft, das die Reaktionen der Umwelt auf das Einbringen von Mikroorganismen vorhersagbar machen soll.

Hochaufloesende automatische Identifizierung von Mikroorganismen (Fortsetzungsantrag), Hochaufloesende automatische Identifizierung von Mikroorganismen (Erstantrag)

Eine multidisziplinaere Arbeitsgruppe aus 10 verschiedenen Forschungslaboratorien entwickeln verschiedene Verfahren zur schnellen Identifizierung von Mikroorganismen am Bsp. der Gruppe der Pseudomonaden. Als analytisches Instrumentar werden Techniken aus der molekularen Genetik , Immunologie und analytischen Chemie eingesetzt, um Nukleinsaeuren, Proteine, Lipide, komplexe makromolekulare Profile und Antigene zu analysieren. Die Ergebnisse der einzelnen Methoden werden verglichen und hinsichtlich ihrer Moeglichkeiten der Bakterienidentifikation, -detektion und -quantifizierung evaluiert. Darueberhinaus dienen diese Methoden der schnellen strukturellen und funktionellen Charakterisierung verschiedener Bakteriengemeinschaften an natuerlichen oder kontaminierten Standorten 1.) Erstellung von 16S rRNA Gensequenz Datenbanken zur phylogenetischen Analyse von Pseudomonaden. 2.) Neueinteilung der Pseudomonaden aufgrund ihrer unterschiedlichen polaren Lipide 3.) Entwicklung von gattungsspezifischen und artspezifische Antikoerpern zur schnellen Identifizierung von Pseudomonaden. 4.) Identifizierung von Pseudomonaden aufgrund ihrer niedermolekularen RNA-Profile.

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