Alexander Bartholomäus
A5051680155- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Environmental DNA in Biodiversity Studies
- RNA and protein synthesis mechanisms
- Methane Hydrates and Related Phenomena
- RNA modifications and cancer
- Gut microbiota and health
- COVID-19 Clinical Research Studies
- CO2 Sequestration and Geologic Interactions
- biodegradable polymer synthesis and properties
- Recycling and Waste Management Techniques
- Microplastics and Plastic Pollution
- Geology and Paleoclimatology Research
- RNA Research and Splicing
- Plant-Microbe Interactions and Immunity
- Plant Disease Resistance and Genetics
- SARS-CoV-2 and COVID-19 Research
- Microbial Metabolism and Applications
- Protist diversity and phylogeny
- Molecular Biology Techniques and Applications
- Anaerobic Digestion and Biogas Production
- Biocrusts and Microbial Ecology
- Bioinformatics and Genomic Networks
- Bacteriophages and microbial interactions
- Climate change and permafrost
GFZ Helmholtz Centre for Geosciences
2020-2025
University of Potsdam
2015-2024
Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung
2024
Universität Hamburg
2015-2021
Heinrich Heine University Düsseldorf
2021
Fast and reliable detection of patients with severe heterogeneous illnesses is a major goal precision medicine1,2. Patients leukaemia can be identified using machine learning on the basis their blood transcriptomes3. However, there an increasing divide between what technically possible allowed, because privacy legislation4,5. Here, to facilitate integration any medical data from owner worldwide without violating laws, we introduce Swarm Learning-a decentralized machine-learning approach that...
Messenger RNA acts as an informational molecule between DNA and translating ribosomes. Emerging evidence places mRNA in central cellular processes beyond its major function entity. Although individual examples show that specific structural features of regulate translation transcript stability, their role throughout the bacterial transcriptome remains unknown. Combining three sequencing approaches to provide a high resolution view global secondary structure, efficiency abundance, we unraveled...
Environmental stress is detrimental to cell viability and requires an adequate reprogramming of cellular activities maximize survival. We present a global analysis the response Escherichia coli acute heat osmotic stress. combine deep sequencing total mRNA ribosome-protected fragments provide genome-wide map at transcriptional translational levels. For each type stress, we observe unique subset genes that shape stress-specific response. Upon temperature upshift, mRNAs with reduced folding...
Abstract ARGONAUTE-2 and associated miRNAs form the RNA-induced silencing complex (RISC), which targets mRNAs for translational degradation as part of RNA interference pathway. Despite essential nature this process cellular function, there is little information on role RISC components in human development organ function. We identify 13 heterozygous mutations AGO2 21 patients affected by disturbances neurological development. Each identified single amino acid result impaired shRNA-mediated...
Abstract Metagenomics became a standard strategy to comprehend the functional potential of microbial communities, including human microbiome. Currently, number metagenomes in public repositories is increasing exponentially. The Sequence Read Archive (SRA) and MG-RAST are two main for metagenomic data. These databases allow scientists reanalyze samples explore new hypotheses. However, mining from them can be limiting factor, since metadata available these often misannotated, misleading,...
The concept of a ‘plastisphere microbial community’ arose from research on aquatic plastic debris, while the effect plastics communities in soils remains poorly understood. Therefore, we examined inhabiting two debris ecosystems with regard to their diversity and composition relative plastic-free same area using 16S rRNA amplicon sequencing. Furthermore, studied plastic-colonizing potential bacteria originating both study sites as measure surface adhesion UV-weathered polyethylene (PE)...
The microbiota is attributed to be important for initial soil formation under extreme climate conditions, but experimental evidence its relevance scarce. To fill this gap, we investigated the impact of in situ microbial communities and their interrelationship with biocrust plants compared abiotic controls on arid semiarid soils. Additionally, assessed response bacterial change. Topsoil subsoil samples from sites Chilean Coastal Cordillera were incubated 16 weeks diurnal temperature moisture...
Desert environments constitute one of the largest and yet most fragile ecosystems on Earth. Under absence regular precipitation, microorganisms are main ecological component mediating nutrient fluxes by using soil components, like minerals salts, atmospheric gases as a source for energy water. While previous studies microbial ecology desert have focused surface environments, little is known about life in deeper sediment layers. Our study extending limited knowledge communities within...
Permafrost underlies 25% of the land surface area northern hemisphere and stores approximately a third world's organic soil carbon (C). When permafrost thaws, C that was frozen in suspended state decomposition rejoins active layer can be respired by microbial organisms within as CO2 or CH4. As climate warming advances, thaw is likely to occur more abrupt (seasons decades) timelines opposed generally better understood gradual (decades centuries). Abrupt increase emissions over shorter time...
Translation is a central cellular process and optimized for speed fidelity. The of translation single codon depends on the concentration aminoacyl-tRNAs. Here, we used microarray-based approaches to analyze charging levels tRNAs in Escherichia coli growing at different growth rates. Strikingly, observed non-uniform aminoacylation complex media. In contrast, minimal medium, level aminoacyl-tRNAs more uniform rises approximately 60%. Particularly, tRNA(Ser), tRNA(Cys), tRNA(Thr) tRNA(His)...
Abstract Sedimentary DNA-based studies revealed the effects of human activity on lake cyanobacteria communities over last centuries, yet we continue to lack information longer timescales. Here, apply high-resolution molecular analyses sedimentary ancient DNA reconstruct history throughout Holocene in a north-eastern Germany. We find substantial increase abundance coinciding with deforestation during early Bronze Age around 4000 years ago, suggesting increased nutrient supply by local...
As most eukaryotic genomes are yet to be sequenced, the mechanisms underlying their contribution different ecosystem processes remain untapped. Although approaches recovering Prokaryotic have become common in genome biology, few studies tackled recovery of from metagenomes. This study assessed reconstruction microbial using 6000 metagenomes terrestrial and some transition environments EukRep pipeline. Only 215 metagenomic libraries yielded bins. From a total 447 bins recovered 197 were...
Abstract Background In arid and semiarid environments, microbial activity is restricted by low water availability high evapotranspiration rates, soil development limited. Under humid conditions, such limitations can be overcome, accelerating pedogenesis processes. Our study aims to broaden our understanding of under a climate change scenario toward conditions identify the microorganisms that help transform initial soils from sites. We characterized pedogenetic processes how their gene...
Emerging evidence places small proteins (≤50 amino acids) more centrally in physiological processes. Yet, their functional identification and the systematic genome annotation of cognate open-reading frames (smORFs) remains challenging both experimentally computationally. Ribosome profiling or Ribo-Seq (that is a deep sequencing ribosome-protected fragments) enables detecting actively translated (ORFs) empirical coding sequences (CDSs) using in-register translation pattern that characteristic...
Abstract Background Tracing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission chains is still a major challenge for public health authorities, when incidental contacts are not recalled or perceived as potential risk contacts. Viral sequencing can address key questions about SARS-CoV-2 evolution and may support reconstruction viral networks by integration molecular epidemiology into classical contact tracing. Methods In collaboration with local we set up an...
Strain NGK65T, a novel hexadecane degrading, non-motile, Gram-positive, rod-to-coccus shaped, aerobic bacterium, was isolated from plastic polluted soil sampled at landfill. NGK65T hydrolysed casein, gelatin, urea and catalase-positive. It optimally grew 28 °C, in 0-1% NaCl pH 7.5-8.0. Glycerol, d-glucose, arbutin, aesculin, salicin, potassium 5-ketogluconate, sucrose, acetate, pyruvate were used as sole carbon sources. The predominant membrane fatty acids iso-C16:0 followed by iso-C17:0...
Abstract Background Metagenomics is an expanding field within microbial ecology, microbiology, and related disciplines. The number of metagenomes deposited in major public repositories such as Sequence Read Archive (SRA) Metagenomic Rapid Annotations using Subsystems Technology (MG-RAST) rising exponentially. However, data mining interpretation can be challenging due to mis-annotated misleading metadata entries. In this study, we describe the Marine Metagenome Metadata Database...
Every year, millions of deaths are associated with the increased spread antimicrobial resistance genes (ARGs) in bacteria. With increasing urbanization global population, ARGs urban bacteria has become a more severe threat to human health. In this study, we used metagenome-assembled genomes (MAGs) recovered from 1,153 metagenomes multiple locations investigate fate and occurrence Additionally, analyzed these on plasmids estimated virulence bacterial species. Our results showed that multidrug...
The Atacama Desert in Chile is one of the driest and most inhospitable places on Earth. To analyze diversity distribution microbial communities such an environment, important challenging steps DNA extraction. Using commercial environmental extraction protocols, a mixture living, dormant, dead cells microorganisms extracted, but separation different pools almost impossible. overcome this problem, we applied novel method soils across west-east moisture transect to distinguish between...
Microorganisms are known to be natural agents of biocorrosion and mineral transformation, thereby potentially affecting the safety deep geological repositories used for high-level nuclear waste storage. To better understand how resident microbial communities terrestrial biosphere may act on mineralogical geochemical characteristics insulating clays, we analyzed their structure potential metabolic functions, as well site-specific mineralogy element composition from dedicated Mont Terri...
Long-term stability of underground CO2 storage is partially affected by microbial activity but our knowledge these effects limited, mainly due to a lack sites. A consistently high flux mantle-derived makes the Eger Rift in Czech Republic natural analogue storage. The seismically active region and H2 produced abiotically during earthquakes, providing energy indigenous communities.To investigate response ecosystem levels H2, we enriched microorganisms from samples 239.5 m long drill core Rift....
Abstract Background Metagenomic data can shed light on animal-microbiome relationships and the functional potential of these communities. Over past years, generation metagenomics has increased exponentially, so availability reusability present in public repositories. However, identifying which datasets associated metadata are available is not straightforward. We created Animal-Associated Metagenome Metadata Database (AnimalAssociatedMetagenomeDB - AAMDB) to facilitate identification reuse...