A5070974187- Microbial Community Ecology and Physiology
- Protist diversity and phylogeny
- Marine and coastal ecosystems
- Genomics and Phylogenetic Studies
- Advanced Proteomics Techniques and Applications
- Evolution and Genetic Dynamics
- Wastewater Treatment and Nitrogen Removal
- Metabolomics and Mass Spectrometry Studies
- Microbial Fuel Cells and Bioremediation
- Evolutionary Game Theory and Cooperation
- Chemical Analysis and Environmental Impact
- Electrostatics and Colloid Interactions
- Methane Hydrates and Related Phenomena
- Geochemistry and Elemental Analysis
- Environmental DNA in Biodiversity Studies
- Radioactive contamination and transfer
- Marine Bivalve and Aquaculture Studies
- Materials Engineering and Processing
- Bacterial Genetics and Biotechnology
- Marine Biology and Ecology Research
- Bacteriophages and microbial interactions
- Aquatic Ecosystems and Phytoplankton Dynamics
- CRISPR and Genetic Engineering
- Nematode management and characterization studies
- Genetics and Neurodevelopmental Disorders
Swiss Federal Institute of Aquatic Science and Technology
2020-2024
ETH Zurich
2022-2024
University of Southern California
2023-2024
Southern California University for Professional Studies
2024
Johnson University
2024
Rutgers, The State University of New Jersey
2024
Advanced Pharma
2024
Woods Hole Oceanographic Institution
2017-2023
Massachusetts Institute of Technology
2018-2023
Abstract. Trichodesmium is a globally important marine microbe that provides fixed nitrogen (N) to otherwise N-limited ecosystems. In nature, fixation likely regulated by iron or phosphate availability, but the extent and interaction of these controls are unclear. From metaproteomics analyses using established protein biomarkers for nutrient stress, we found iron–phosphate co-stress norm rather than exception colonies in North Atlantic Ocean. Counterintuitively, nitrogenase enzyme was more...
How the growth rate of a microbial population responds to environmental availability chemical nutrients and other resources is fundamental question in microbiology. Models this response, such as widely used Monod model, are generally characterized by maximum half-saturation concentration resource. What values should we expect for these concentrations, how they depend on resource? We survey response data across wide range organisms resources. find that concentrations vary orders magnitude,...
Abstract. Ocean warming alongside changes to the natural and anthropogenic supply of key nutrient resources such as nitrogen, phosphorus trace metals is predicted alter magnitude stoichiometry nutrients that are essential for maintaining ocean productivity. To improve our ability predict how marine microbes will respond a changing environment, we need better understand assemblages acquire nutrients. We combined observations zonal gradients across North Atlantic subtropical gyre state...
Abstract. Microbial enzymes alter marine biogeochemical cycles by catalyzing chemical transformations that bring elements into and out of particulate organic pools. These processes are often studied through enzyme rate-based estimates nutrient-amendment bioassays, but these approaches limited in their ability to resolve species-level contributions enzymatic rates. Molecular methods including proteomics have the potential link specific populations overall community rate; this is important...
Two-component sensory (TCS) systems link microbial physiology to the environment and thus may play key roles in biogeochemical cycles. In this study, we surveyed TCS of 328 diverse marine bacterial species. We identified lifestyle traits such as copiotrophy diazotrophy that are associated with larger numbers system genes within genome. compared species 1,152 reference from a variety habitats found evidence extra response regulators genomes. Examining location along circular genome, also...
We present METATRYP version 2 software that identifies shared peptides across the predicted proteomes of organisms within environmental metaproteomics studies to enable accurate taxonomic attribution during protein inference. Improvements include ingestion complex sequence assembly data categories (metagenomic and metatranscriptomic assemblies, single cell amplified genomes, metagenome assembled genomes), prediction least common ancestor (LCA) for a peptide multiple organisms, increased...
The colony-forming cyanobacteria Trichodesmium spp. are considered one of the most important nitrogen-fixing genera in warm, low nutrient ocean. Despite this central biogeochemical role, many questions about their evolution, physiology, and trophic interactions remain unanswered. To address these questions, we describe pangenomic potential via significantly improved genomic assemblies from two isolates 15 new >50% complete metagenome-assembled genomes hand-picked, colonies spanning Atlantic...
ABSTRACT Trichodesmium is a globally distributed cyanobacterium whose nitrogen-fixing capability fuels primary production in warm oligotrophic oceans. Like many photoautotrophs, serves as host to various other microorganisms, yet little known about how this associated community modulates fluxes of environmentally relevant chemical species into and out the supraorganismal structure. Here, we utilized metatranscriptomics examine gene expression activities microbial communities with erythraeum...
The keystone marine nitrogen fixer Trichodesmium thrives in high-dust environments. While laboratory investigations have observed that colonies can access the essential nutrient iron from dust particles, less clear are biochemical strategies underlying particle-colony interactions nature. Here we demonstrate engage with mineral particles wild distinct molecular responses. We encountered particle-laden at a sampling location Southern Caribbean Sea; microscopy and synchrotron-based imaging...
Resource availability dictates how fast and much microbial populations grow. Quantifying the relationship between growth resource concentrations makes it possible to promote, inhibit, predict activity. Microbes require many resources, including macronutrients (e.g., carbon nitrogen), micronutrients metals), complex nutrients like vitamins amino acids. When multiple resources are scarce, as occurs in nature, microbes may experience colimitation which more than one limits simultaneously....
Proteins are critical in catalyzing chemical reactions, forming key cellular structures, and regulating processes. Investigation of marine microbial proteins by metaproteomics methods enables the discovery numerous aspects biogeochemical However, these datasets present big data challenges as they often involve many samples collected across broad geospatial temporal scales, resulting thousands protein identifications, abundances, corresponding annotation information. The Ocean Protein Portal...
While the ecological role that
Abstract Microbial communities perform key ecosystem processes collectively. One such process is the degradation of carbohydrate polymers, which are dominant pool organic carbon in natural environments. Carbohydrate polymers often degraded a stepwise manner. Individual steps performed by different microbial species, form trophic cascades with at bottom and fully oxidised top. It widely believed that these hierarchically organised, where organisms each level rely on levels below. However,...
How the growth rate of a microbial population responds to environmental availability chemical nutrients and other resources is fundamental question in microbiology. Models this response, such as widely-used Monod model, are generally characterized by maximum half-saturation concentration resource. What values should we expect for these concentrations, how they depend on resource? We survey response data across wide range organisms resources. find that concentrations vary orders magnitude,...
Abstract We present METATRYP version-2 software that identifies shared peptides across organisms within environmental metaproteomics studies to enable accurate taxonomic attribution of during protein inference. Improvements include: ingestion complex sequence assembly data categories (metagenomic and metatranscriptomic assemblies, single cell amplified genomes, metagenome assembled genomes), prediction the Least Common Ancestor (LCA) for a peptide multiple organisms, increased performance...
The physiology and ecology of particle-associated marine bacteria are growing interest, but our knowledge their aggregation behavior mechanisms controlling association with particles remains limited. We have found that a isolate, Alteromonas sp. ALT199 strain 4B03, the related type-strain A. macleodii 27126 both form large (>500 μm) aggregates while in rich medium. A non-clumping variant (NCV) 4B03 spontaneously arose lab, whole genome sequencing revealed partial deletion gene encoding...
Resource availability dictates how fast and much microbial populations grow. Quantifying the relationship between growth resource concentrations makes it possible to promote, inhibit, predict activity. Microbes require many resources, including macronutrients (e.g., carbon nitrogen), micronutrients metals), complex nutrients like vitamins amino acids. When multiple resources are scarce, as frequently occurs in nature, microbes may experience colimitation which more than one simultaneously...