A5065083991- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Methane Hydrates and Related Phenomena
- Photosynthetic Processes and Mechanisms
- Protist diversity and phylogeny
- Legume Nitrogen Fixing Symbiosis
- Plant-Microbe Interactions and Immunity
- ATP Synthase and ATPases Research
- Mitochondrial Function and Pathology
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Gut microbiota and health
- Probiotics and Fermented Foods
- 3D Printing in Biomedical Research
- Algal biology and biofuel production
- Plant Pathogens and Fungal Diseases
- Bacteriophages and microbial interactions
- Plant Pathogens and Resistance
- Digital Imaging for Blood Diseases
- Paleopathology and ancient diseases
- Isotope Analysis in Ecology
- Mycorrhizal Fungi and Plant Interactions
- Archaeology and ancient environmental studies
- Insect symbiosis and bacterial influences
- Anaerobic Digestion and Biogas Production
Royal Netherlands Institute for Sea Research
2018-2024
University of Amsterdam
2023-2024
Utrecht University
2018-2022
Max Planck Institute for Plant Breeding Research
2015-2021
The University of Texas at Austin
2016-2021
ORCID
2020
Max Planck Society
2013
Abstract The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology evolution environmental host-associated microbiomes. Here we applied this approach to >10,000 collected diverse habitats covering all Earth’s continents oceans, including human animal hosts, engineered environments, natural agricultural soils, capture extant microbial, metabolic functional potential. This comprehensive catalog includes 52,515 metagenome-assembled...
Significance All plants carry distinctive bacterial communities on and inside organs such as roots leaves, collectively called the plant microbiota. How this microbiota diversifies in related species is unknown. We investigated diversity of root Brassicaceae family, including three Arabidopsis thaliana ecotypes, its sister halleri lyrata , Cardamine hirsuta . show that differences profiles between these hosts are largely quantitative host phylogenetic distance alone cannot explain observed...
Rhizobia are a paraphyletic group of soil-borne bacteria that induce nodule organogenesis in legume roots and fix atmospheric nitrogen for plant growth. In non-leguminous plants, species from the Rhizobiales order define core lineage microbiota, suggesting additional functional interactions with hosts. this work, genome analyses 1,314 isolates along amplicon studies root microbiota reveal evolutionary history nitrogen-fixing symbiosis bacterial order. Key genes were acquired multiple times,...
Microbes in Guaymas Basin (Gulf of California) hydrothermal sediments thrive on hydrocarbons and sulfur experience steep, fluctuating temperature chemical gradients. The functional capacities communities inhabiting this dynamic habitat are largely unknown. Here, we reconstructed 551 genomes from hydrothermally influenced, nearby cold belonging to 56 phyla (40 uncultured). These comprise 22 unique lineages, including five new candidate phyla. In contrast findings hydrocarbon seeps,...
Abstract Large reservoirs of natural gas in the oceanic subsurface sustain complex communities anaerobic microbes, including archaeal lineages with potential to mediate oxidation hydrocarbons such as methane and butane. Here we describe a previously unknown phylum, Helarchaeota, belonging Asgard superphylum for hydrocarbon oxidation. We reconstruct Helarchaeota genomes from metagenomic data derived hydrothermal deep-sea sediments hydrocarbon-rich Guaymas Basin. The encode methyl-CoM...
Deep-sea hydrothermal vents are hotspots for productivity and biodiversity. Thermal pyrolysis circulation produce fluids rich in hydrocarbons reduced compounds that stimulate microbial activity surrounding sediments. Several studies have characterized the diversity of Guaymas Basin (Gulf California) sediment-inhabiting microorganisms; however, many identified taxa lack cultures or genomic representations. Here, we resolved metabolic potential community-level interactions these diverse...
Summary In Arabidopsis roots, the transcription factor MYB 72 plays a dual role in onset of rhizobacteria‐induced systemic resistance ( ISR ) and plant survival under conditions limited iron availability. Previously, it was shown that coordinates expression gene module promotes synthesis excretion iron‐mobilizing phenolic compounds rhizosphere, process is involved both acquisition signaling. Here, we show volatile organic VOC s) from ‐inducing Pseudomonas bacteria are important elicitors ....
Abstract In the ongoing debates about eukaryogenesis—the series of evolutionary events leading to emergence eukaryotic cell from prokaryotic ancestors—members Asgard archaea play a key part as closest archaeal relatives eukaryotes 1 . However, nature and phylogenetic identity last common ancestor remain unresolved 2–4 Here we analyse distinct marker datasets an expanded genomic sampling evaluate competing scenarios using state-of-the-art phylogenomic approaches. We find that are placed, with...
Abstract The nature of the last universal common ancestor (LUCA), its age and impact on Earth system have been subject vigorous debate across diverse disciplines, often based disparate data methods. Age estimates for LUCA are usually fossil record, varying with every reinterpretation. LUCA’s metabolism has proven equally contentious, some attributing all core metabolisms to LUCA, whereas others reconstruct a simpler life form dependent geochemistry. Here we infer that lived ~4.2 Ga...
Abstract Recent field and laboratory experiments with perennial Boechera stricta annual Arabidopsis thaliana suggest that the root microbiota influences flowering time. Here we examined in long-term time-course bacterial of arctic-alpine Arabis alpina natural controlled environments by 16S rRNA gene profiling. We identified soil type residence time plants as major determinants explaining up to 15% variation, whereas environmental conditions host genotype explain maximally 11% variation. When...
Abstract The recently discovered DPANN archaea are a potentially deep-branching, monophyletic radiation of organisms with small cells and genomes. However, the monophyly early emergence various clades their role in life’s evolution debated. Here, we reconstructed analysed genomes an uncharacterized archaeal phylum ( Candidatus Undinarchaeota), revealing that its members have and, while being able to conserve energy through fermentation, likely depend on partner for acquisition certain...
Small acidophilic archaea belonging to Micrarchaeota and Parvarchaeota phyla are known physically interact with some Thermoplasmatales members in nature. However, due a lack of cultivation limited genomes on hand, their biodiversity, metabolisms, physiologies remain largely unresolved. Here, we obtained 39 from acid mine drainage (AMD) hot spring environments around the world. 16S rRNA gene based analyses revealed that were only detected AMD habitats, while also others including soil, peat,...
Core gene phylogenies provide a window into early evolution, but different sets and analytical methods have yielded substantially views of the tree life. Trees inferred from small set universal core genes typically supported long branch separating archaeal bacterial domains. By contrast, recent analyses broader non-ribosomal suggested that Archaea may be less divergent Bacteria, estimates inter-domain distance are inflated due to accelerated evolution ribosomal proteins along branch....
Abstract The timing of early cellular evolution, from the divergence Archaea and Bacteria to origin eukaryotes, is poorly constrained. ATP synthase complex thought have originated prior Last Universal Common Ancestor (LUCA) analyses genes, together with ribosomes, played a key role in inferring rooting tree life. We reconstruct evolutionary history synthases using an expanded taxon sampling set develop phylogenetic cross-bracing approach, constraining equivalent speciation nodes be...
Ocean plastic pollution is a severe environmental problem but most of the that has been released to ocean since 1950s unaccounted for. Although fungal degradation marine plastics suggested as potential sink mechanism, unambiguous proof by fungi, or other microbes, scarce. Here we applied stable isotope tracing assays with 13C-labeled polyethylene measure biodegradation rates and trace incorporation plastic-derived carbon into individual cells yeast Rhodotorula mucilaginosa, which isolated...
Organic matter degradation in marine environments is essential for the recycling of nutrients, especially under conditions anoxia where organic tends to accumulate. However, little known about diversity microbial communities responsible mineralization absence oxygen, as well factors controlling their activities. Here, we determined active heterotrophic prokaryotic community sulphidic water column Black Sea, an ideal model system, a tight coupling between carbon, nitrogen and sulphur cycles...
Abstract Geothermal environments, such as hot springs and hydrothermal vents, are hotspots for carbon cycling contain many poorly described microbial taxa. Here, we reconstructed 15 archaeal metagenome-assembled genomes (MAGs) from terrestrial spring sediments in China deep-sea vent Guaymas Basin, Gulf of California. Phylogenetic analyses these MAGs indicate that they form a distinct group within the TACK superphylum, thus propose their classification new phylum, ‘Brockarchaeota’, named...
Significance Much of Earth’s volcanism occurs in the deep sea, yet little is known about microbial communities inhabiting such extreme and dynamic systems. Using a multidisciplinary approach to study distinct hydrothermal systems at Brothers submarine arc volcano, we provide insights into how community composition function reflect subtly different fluid chemistries resulting from subsurface interactions with alteration mineral assemblages. These variations can be traced hydrogeologic history...