A5041789974- Microbial Community Ecology and Physiology
- Protist diversity and phylogeny
- Genomics and Phylogenetic Studies
- Bacteriophages and microbial interactions
- Marine and coastal ecosystems
- Bacterial Infections and Vaccines
- Photosynthetic Processes and Mechanisms
- Viral Infections and Immunology Research
- Wastewater Treatment and Nitrogen Removal
- Environmental DNA in Biodiversity Studies
- Vibrio bacteria research studies
- Aquatic Ecosystems and Phytoplankton Dynamics
- Advanced biosensing and bioanalysis techniques
- Methane Hydrates and Related Phenomena
- Biocrusts and Microbial Ecology
- Atmospheric chemistry and aerosols
- Diatoms and Algae Research
- Marine Biology and Ecology Research
- Virus-based gene therapy research
- Extracellular vesicles in disease
- Pneumonia and Respiratory Infections
- Animal Virus Infections Studies
- Bacterial Genetics and Biotechnology
- Microbial Fuel Cells and Bioremediation
- Plant Virus Research Studies
Wellesley College
2019-2025
Massachusetts Institute of Technology
2015-2024
University of California, Riverside
2024
Alvernia University
2022
University of Washington
2022
University of Groningen
2022
Stanford University
2006-2012
Cyanobacterial Diversity What does it mean to be a global species? The marine cyanobacterium Prochlorococcus is ubiquitous and, arguably, the most abundant and productive of all living organisms. Although our eyes seas look uniform, bacterium ocean's bulk plethora microhabitats, by large-scale single-cell genomic analysis uncultured cells, Kashtan et al. (p. 416 ; see Perspective Bowler Scanlan ) reveal that has diversified match. This “species” constitutes mass subpopulations—each with...
Many heterotrophic bacteria are known to release extracellular vesicles, facilitating interactions between cells and their environment from a distance. Vesicle production has not been described in photoautotrophs, however, the prevalence characteristics of vesicles natural ecosystems is unknown. Here, we report that cultures Prochlorococcus, numerically dominant marine cyanobacterium, continuously lipid containing proteins, DNA, RNA. We also show carrying DNA diverse abundant coastal...
Recent advances in understanding the ecology of marine systems have been greatly facilitated by growing availability metagenomic data, which provide information on identity, diversity and functional potential microbial community a particular place time. Here we present dataset comprising over 5 terabases data from 610 samples spanning diverse regions Atlantic Pacific Oceans. One set metagenomes, collected GEOTRACES cruises, captures large geographic transects at multiple depths per station....
Hydrocarbons are ubiquitous in the ocean, where alkanes such as pentadecane and heptadecane can be found even waters minimally polluted with crude oil. Populations of hydrocarbon-degrading bacteria, which responsible for turnover these compounds, also throughout marine systems, including unpolluted waters. These observations suggest existence an unknown widespread source hydrocarbons oceans. Here, we report that strains two most abundant cyanobacteria, Prochlorococcus Synechococcus, produce...
Treating Arabidopsis roots with exogenous auxin results in dramatic changes cellular processes including de novo induction of lateral which later emerge through the overlying cells. Microarray experiments reveal approximately 80 genes that are substantially up-regulated root over first 12 h following treatment. We hypothesize observed increase expression pectate lyase family leads to degradation pectin-rich middle lamellae, allowing cells parent separate cleanly. Differences degree pectin...
The marine cyanobacterium Prochlorococcus is the numerically dominant photosynthetic organism in oligotrophic oceans, and a model system microbial ecology. Here we report 27 new whole genome sequences (2 complete closed; 25 of draft quality) cultured isolates, representing five major phylogenetic clades Prochlorococcus. sequenced strains were isolated from diverse regions facilitating studies drivers diversity-both lab field. To improve utility these genomes for comparative genomics, also...
Prochlorococcus and Synechococcus are the dominant primary producers in marine ecosystems perform a significant fraction of ocean carbon fixation. These cyanobacteria interact with diverse microbial community that coexists them. Comparative genomics cultivated isolates has helped address questions regarding patterns evolution diversity among microbes, but can be is miniscule compared to wild. To further probe these groups extend utility reference sequence databases, we report data set single...
PCR amplification and sequencing of marker genes are a low-cost technique for monitoring prokaryotic eukaryotic microbial communities across space time but will work optimally only if environmental organisms match primer sequences exactly. In this study, we evaluated how well primers globally distributed short-read oceanic metagenomes.
Archaea play an important role in nitrification and are, thus, inextricably linked to the global carbon nitrogen cycles. Since initial discovery of ammonia monooxygenase α-subunit (amoA) gene associated with archaeal metagenomic fragment, amoA sequences have been detected a wide variety nitrifying environments. Recent sequencing efforts revealed extensive diversity within different habitats. In this study, we examined over 8000 from literature public databases effort understand ecological...
Abstract Prochlorococcus is the smallest oxygenic phototroph in ocean, where it can be found great abundance throughout euphotic zone mid‐latitude waters. Populations of this picocyanobacterium have been observed below zone, but viability these cells unclear. To explore tolerance to extended light‐deprivation, we subjected multiple strains varying periods darkness and examined their ability recover when placed back light. Some recovered after 35 h while others could not; variability was not...
Sea spray is the largest aerosol source on Earth. Bubble bursting mechanisms at ocean surface create smaller film burst and larger jet drop particles. This study quantified effects of particle chemistry depositional ice nucleation efficiency laboratory-generated sea aerosols under cirrus-relevant conditions. Cultures Prochlorococcus, most abundant phytoplankton species in global ocean, were used as a model organic aerosols. We showed that particles generated from lysed Prochlorococcus...
Summary Extracellular vesicles are small (~50–200 nm diameter) membrane‐bound structures released by cells from all domains of life. While abundant in the oceans, their functions, both for themselves and emergent ecosystem, remain a mystery. To better characterize these particles – prerequisite determining function we analysed lipid, protein, metabolite content produced marine cyanobacterium Prochlorococcus . We show that exports diverse array cellular compounds into surrounding seawater...
Prochlorococcus and Synechococcus are the most abundant photosynthesizing organisms in oceans. Gene content variation among picocyanobacterial populations separate ocean basins often mirrors selective pressures imposed by region's distinct biogeochemistry. By pairing genomic datasets with trace metal concentrations from across global ocean, we show that capacity for siderophore-mediated iron uptake is widespread low-light adapted deep chlorophyll maximum layers of iron-depleted regions...
Phage satellites are mobile genetic elements that propagate by parasitizing bacteriophage replication. We report here the discovery of abundant and diverse phage were packaged as concatemeric repeats within naturally occurring particles in seawater. These same phage-parasitizing found integrated genomes dominant co-occurring bacterioplankton species. Like known satellites, many marine encoded genes for integration, DNA replication, interference, capsid assembly. Many also contained...
We introduce the Global rRNA Universal Metabarcoding Plankton database (GRUMP), which consists of 1194 samples that were collected from 2003-2020 and cover extensive latitudinal longitudinal transects, as well depth profiles in all major ocean basins. DNA unfractionated (> 0.2um) seawater was amplified using 515Y/926R universal three-domain gene primers, simultaneously quantifying relative abundance amplicon sequencing variants (ASVs) bacteria, archaea, eukaryotic nuclear 18S, plastid...
Horizontal gene transfer (HGT) is enabled in part through the movement of DNA within two broad groups small (<0.2 µm), diffusible nanoparticles: extracellular vesicles (EVs) and virus-like particles (VLPs; including viruses, agents, phage satellites). The information enclosed these structures represents a substantial portion HGT potential available planktonic ecosystems, but whether some genes might be preferentially transported one type nanoparticle versus another unknown. Here we use...
Microbes evolve within complex ecological communities where biotic interactions impact both individual cells and the environment as a whole. Here we examine how cellular regulation in marine cyanobacterium Prochlorococcus is influenced by heterotrophic bacterium, Alteromonas macleodii, under different light conditions. We monitored transcriptome of Prochlorococcus, grown either alone or coculture, across diel light:dark cycle stress extended darkness-a condition that would experience when...