A5091470163- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Environmental DNA in Biodiversity Studies
- Protist diversity and phylogeny
- Methane Hydrates and Related Phenomena
- Research Data Management Practices
- Bacteriophages and microbial interactions
- Scientific Computing and Data Management
- Gene expression and cancer classification
- Plant Pathogens and Fungal Diseases
- Biomedical Text Mining and Ontologies
- Gut microbiota and health
- Species Distribution and Climate Change
- Genetics, Bioinformatics, and Biomedical Research
- Marine and coastal ecosystems
- Wastewater Treatment and Nitrogen Removal
- Microbial Natural Products and Biosynthesis
- RNA and protein synthesis mechanisms
- Marine Biology and Ecology Research
- Microbial Metabolic Engineering and Bioproduction
- Probiotics and Fermented Foods
- Molecular Biology Techniques and Applications
- Identification and Quantification in Food
- RNA modifications and cancer
- Environmental Monitoring and Data Management
University of Bremen
2011-2023
Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung
2019-2023
Constructor University
2012-2021
Universidad de la República
2021
University of Arizona
2021
University of Copenhagen
2021
Universitätsmedizin Greifswald
2020
Staats- und Universitätsbibliothek Bremen
2020
Max Planck Institute for Marine Microbiology
2010-2019
University of Newcastle Australia
2018
SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit 288 717 large rRNA sequences. Since initial description project, substantial new features have been introduced, including advanced quality control...
16S ribosomal RNA gene (rDNA) amplicon analysis remains the standard approach for cultivation-independent investigation of microbial diversity. The accuracy these analyses depends strongly on choice primers. overall coverage and phylum spectrum 175 primers 512 primer pairs were evaluated in silico with respect to SILVA 16S/18S rDNA non-redundant reference dataset (SSURef 108 NR). Based this evaluation a selection 'best available' Bacteria Archaea three size classes (100–400, 400–1000, ≥1000...
Sequencing ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction, nucleic acid based detection and quantification microbial diversity. The ARB software suite with its corresponding rRNA datasets has been accepted by researchers worldwide as a standard tool large scale analysis. However, rapid increase publicly available sequence data recently hampered maintenance comprehensive curated knowledge databases. A new system, SILVA (from Latin silva , forest),...
SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains supplementary online services. provides manually curated taxonomy all three life, based on representative phylogenetic trees small- large-subunit rRNA genes. This article describes improvements has undergone in last 3 years. Specifically we are focusing curation...
Abstract Motivation: In the analysis of homologous sequences, computation multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like ribosomal RNA (rRNA) where already millions sequences are publicly available and individual studies can easily produce hundreds thousands new sequences. Methods have been developed to cope with such numbers, but further improvements needed meet accuracy requirements. Results: this study, we present SILVA...
UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets formal fungal barcode-the nuclear ribosomal internal transcribed spacer (ITS) region-and offers all ∼1 000 public ITS sequences reference. These are clustered into ∼459 species hypotheses assigned digital object identifiers (DOIs) to promote unambiguous reference across studies. In-house third-party curation annotation have resulted in more than 275...
Abstract Summary: JSpecies Web Server (JSpeciesWS) is a user-friendly online service for in silico calculating the extent of identity between two genomes, parameter routinely used process polyphasic microbial species circumscription. The measures average nucleotide (ANI) based on BLAST+ (ANIb) and MUMmer (ANIm), as well correlation indexes tetra-nucleotide signatures (Tetra). In addition, it provides Tetra Correlation Search function, which allows to rapidly compare selected genomes against...
We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of Minimum Information about Any (x) Sequence (MIxS). The a Single Amplified Genome (MISAG) Metagenome-Assembled (MIMAG), including, but not limited to, assembly quality, estimates completeness contamination. These can be used in combination with other GSC checklists, including (MIGS), Metagenomic (MIMS), Marker Gene (MIMARKS). Community-wide...
Phytoplankton blooms characterize temperate ocean margin zones in spring. We investigated the bacterioplankton response to a diatom bloom North Sea and observed dynamic succession of populations at genus-level resolution. Taxonomically distinct expressions carbohydrate-active enzymes (transporters; particular, TonB-dependent transporters) phosphate acquisition strategies were found, indicating that Bacteroidetes, Gammaproteobacteria, Alphaproteobacteria are specialized for successive...
ABSTRACT Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes was used to investigate the phylogenetic composition of bacterioplankton communities several freshwater and marine samples. An average about 50% cells were detected by for domains Bacteria Archaea , these, half could be identified at subdomain level a set group-specific probes. Beta subclass proteobacteria constituted dominant fraction systems, accounting 16% (range, 3 32%) cells, although they...
ABSTRACT The culturability of abundant members the domain Bacteria in North Sea bacterioplankton was investigated by a combination various cultivation strategies and cultivation-independent 16S rRNA-based techniques. We retrieved rRNA gene (rDNA) clones from environmental DNAs determined situ abundance different groups genera fluorescence hybridization (FISH). A culture collection 145 strains established plating on oligotrophic medium. Isolates were screened FISH, amplified ribosomal DNA...
ABSTRACT In a search for cosmopolitan phylogenetic clusters of freshwater bacteria, we recovered total 190 full and partial 16S ribosomal DNA (rDNA) sequences from three different lakes (Lake Gossenköllesee, Austria; Lake Fuchskuhle, Germany; Baikal, Russia). The comparison with the currently available rDNA data set showed that our fall into 16 clusters, which otherwise include bacterial primarily soil, but not marine, origin. Six were affiliated α, four β, one was γ subclass Proteobacteria...
Pirellula sp. strain 1 (“ Rhodopirellula baltica ”) is a marine representative of the globally distributed and environmentally important bacterial order Planctomycetales . Here we report complete genome sequence member this independent phylum. With 7.145 megabases, has largest circular sequenced so far. The presence all genes required for heterolactic acid fermentation, key interconversion C1 compounds, 110 sulfatases were unexpected aerobic heterotrophic isolate. Although proteinaceous cell...
Abstract Background In the emerging field of environmental genomics, direct cloning and sequencing genomic fragments from complex microbial communities has proven to be a valuable source new enzymes, expanding knowledge basic biological processes. The central problem this so called metagenome-approach is that cloned often lack suitable phylogenetic marker genes, rendering identification clones are likely originate same genome difficult or impossible. such cases, analysis intrinsic...
A process of global importance in carbon cycling is the remineralization algae biomass by heterotrophic bacteria, most notably during massive marine blooms. Such blooms can trigger secondary planktonic bacteria that consist swift successions distinct bacterial clades, prominently members Flavobacteriia, Gammaproteobacteria and alphaproteobacterial Roseobacter clade. We investigated such spring phytoplankton southern North Sea (German Bight) for four consecutive years. Dense sampling...
Summary A basic problem of the metagenomic approach in microbial ecology is assignment genomic fragments to a certain species or taxonomic group, when suitable marker genes are absent. Currently, (G + C)‐content together with phylogenetic information and codon adaptation for functional mostly used assess relationship different fragments. These methods, however, can produce ambiguous results. In order evaluate sequence‐based methods fragment identification, we extensively compared C)‐contents...
Summary Members of the Bacteroidetes , formerly known as Cytophaga‐Flavobacteria‐Bacteroides (CFB) phylum, are among major taxa marine heterotrophic bacterioplankton frequently found on macroscopic organic matter particles (marine snow). In addition, they have been shown to also represent a significant part free‐living microbial assemblages in nutrient‐rich microenvironments. Their abundance and distribution pattern combination with enzymatic activity studies has led notion that organisms...
This viewpoint paper explores the potential of genomics technology to provide accurate, rapid, and cost efficient observations marine environment. The use such approaches in next generation monitoring programs will help achieve goals legislation implemented world-wide. Genomic methods can yield faster results from monitoring, easier more reliable taxonomic identification, as well quicker better assessment environmental status waters. A summary genomic that are ready or show high for...