A5066244533- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Bacteriophages and microbial interactions
- Marine and coastal ecosystems
- Protist diversity and phylogeny
- Methane Hydrates and Related Phenomena
- Marine Biology and Ecology Research
- Environmental DNA in Biodiversity Studies
- Oceanographic and Atmospheric Processes
- Metabolomics and Mass Spectrometry Studies
- Geology and Paleoclimatology Research
- Marine Bivalve and Aquaculture Studies
- Vibrio bacteria research studies
- Photoreceptor and optogenetics research
- Gut microbiota and health
- Cancer Genomics and Diagnostics
- Plant and Fungal Interactions Research
- Cell Image Analysis Techniques
- Evolution and Genetic Dynamics
- Insect symbiosis and bacterial influences
- Scientific Computing and Data Management
- CRISPR and Genetic Engineering
- RNA and protein synthesis mechanisms
- interferon and immune responses
- Coral and Marine Ecosystems Studies
University of Hawaiʻi at Mānoa
2015-2025
University of Hawaii System
2014-2023
ORCID
2021
Virginia Tech
2017
Massachusetts Institute of Technology
2007-2015
Parsons (United States)
2012
University of California, Berkeley
2007
Up and down go the cyanobacteria Plankton move together in strikingly coordinated daily patterns, sinking at night to avoid being eaten rising surface daylight photosynthesize. Otteson et al. found similar activity patterns even smallest of planktonic organisms, such as photosynthetic bacteria (see Perspective by Armbrust). Because it's hard take regular samples open ocean, authors built a robotic sampler set it adrift for several days mid-Pacific. The captured showed immediate responses...
Sinking particles are a critical conduit for the export of organic material from surface waters to deep ocean. Despite their importance in oceanic carbon cycling and export, little is known about biotic composition, origins, variability sinking reaching abyssal depths. Here, we analyzed particle-associated nucleic acids captured preserved sediment traps at 4,000-m depth North Pacific Subtropical Gyre. Over 9-month time-series, Bacteria dominated both rRNA-gene rRNA pools, followed by...
Significance Microbial communities regulate the cycling of energy and matter in environment, yet how they respond to environmental change is not well-known. We describe here a day life wild planktonic microbial species using robotic sampling coupled with genome-wide gene expression analysis. Our results showed that closely related populations, as well very different bacterial archaeal species, displayed remarkably similar time-variable synchronous patterns over 2 d. suggest specific cues may...
Significance Microbes drive biogeochemical cycles across the globe, collectively playing a central role in shaping biosphere. Despite their immense importance, situ activities of communities microbes, particular uncultivated lineages “microbial dark matter,” remain poorly elucidated. In this study, we report that common temporal and ecological dynamics underpin disparate marine microbial communities, providing first evidence trans-Pacific diurnal transcriptional patterns these may regulate...
Sinking particles mediate the transport of carbon and energy to deep-sea, yet specific microbes associated with sedimenting in ocean's interior remain largely uncharacterized. In this study, we used particle interceptor traps (PITs) assess nature particle-associated microbial communities collected at a variety depths North Pacific Subtropical Gyre. Comparative metagenomics was differences taxa functional gene repertoires PITs containing preservative (poisoned traps) compared...
Significance Marine microbial communities exert a large influence on ocean ecosystem processes, and viruses in these play key roles controlling abundances, nutrient cycling, productivity. We show here that dominant the open persist for long time periods many appear tightly locked coordinated diel oscillations with their bacterial hosts. The persistent structure of viral assemblages, as well synchronized daily hosts, are part result regular diurnal coupling host replication cycles....
Significance All three domains of life—Eukarya, Bacteria, and Archaea—are known to inhabit the marine water column from surface waters great depth. Planktonic Archaea are comprised two dominant groups—the Thaumarchaeaota Euryarchaeota. The Thaumarchaeota contain characteristic biomarker lipids as tetraethers that thought be diagnostic for this group, used paleotemperature proxies, since these well preserved in sediments. In study, we show planktonic Euryarchaeota produce same types archaeal...
Oxygen minimum zones (OMZs) are natural physical features of the world's oceans. They create steep physiochemical gradients in water column, which most notably include a dramatic draw down oxygen concentrations over small vertical distances (<100 m). Microbial communities within OMZs play central roles ocean and global biogeochemical cycles, yet we still lack fundamental understanding how microbial biodiversity is distributed across OMZs. Here, used metagenomic sequencing to investigate...
Viruses are the most abundant biological entities on Earth and play key roles in host ecology, evolution, horizontal gene transfer. Despite recent progress viral metagenomics, inherent genetic complexity of virus populations still poses technical difficulties for recovering complete genomes from natural assemblages. To address these challenges, we developed an assembly-free, single-molecule nanopore sequencing approach, enabling direct recovery genome sequences environmental samples. Our...
In the open ocean, elevated carbon flux (ECF) events increase delivery of particulate from surface waters to seafloor by severalfold compared other times year. Since microbes play central roles in primary production and sinking particle formation, they contribute greatly export deep sea. Few studies, however, have quantitatively linked ECF with specific microbial assemblages that drive them. Here, we identify key taxa functional traits on deep-sea particles correlate positively events....
Abstract Microbial communities are critical to ecosystem dynamics and biogeochemical cycling in the open oceans. Viruses essential elements of these communities, influencing productivity, diversity, evolution cellular hosts. To further explore natural history ecology open-ocean viruses, we surveyed spatiotemporal double-stranded DNA (dsDNA) viruses both virioplankton bacterioplankton size fractions North Pacific Subtropical Gyre, one largest biomes on planet. Assembly clustering viral...
Bacteria and archaea are central to the production, consumption, remineralization of dissolved particulate organic matter contribute critically carbon delivery, nutrient availability, energy transformations in deep ocean. To explore environmentally relevant genomic traits sinking-particle-associated versus free-living microbes, we compared habitat-specific metagenome-assembled genomes recovered throughout water column North Pacific Subtropical Gyre. The prokaryotes were compositionally,...
Abstract Sinking particles and particle-associated microbes influence global biogeochemistry through particulate matter export from the surface to deep ocean. Despite ongoing studies of microbes, viruses in these habitats remain largely unexplored. Whether, where, which might contribute particle production open investigation. In this study, we analyzed 857 virus population genomes associated with sinking collected over three years sediment traps moored at 4000 m North Pacific Subtropical...
Abstract Mesoscale eddies have been shown to support elevated dinitrogen (N 2 ) fixation rates (NFRs) and abundances of N ‐fixing microorganisms (diazotrophs), but the mechanisms underlying these observations are not well understood. We sampled two pairs mesoscale cyclones anticyclones in North Pacific Subtropical Gyre 2017 2018 compared our with seasonal patterns from Hawaii Ocean Time‐series (HOT) program. Consistent previous reports, we found that NFRs were anomalously high for this...
Abstract Few microbial time-series studies have been conducted in open ocean habitats having low seasonal variability such as the North Pacific Subtropical Gyre (NPSG), where surface waters experience comparatively mild variation. To better describe this habitat, we analyzed rRNA amplicon and shotgun metagenomic data over two years at Hawaii Ocean Time-series Station ALOHA. We postulated that relatively stable habitat might reveal different environmental factors influence planktonic...
Abstract Background Oceanic microbiomes play a pivotal role in the global carbon cycle and are central to transformation recycling of energy ocean’s interior. SAR324 is ubiquitous but poorly understood uncultivated clade Deltaproteobacteria that inhabits entire water column, from ocean surface waters its deep Although some progress has been made elucidating potential metabolic traits dark ocean, very little known about ecology capabilities this group euphotic twilight zones. To investigate...
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...
Combined metagenomic and metatranscriptomic datasets make it possible to study the molecular evolution of diverse microbial species recovered from their native habitats. The link between gene expression level sequence conservation was examined using shotgun pyrosequencing community DNA RNA marine environments, forest soil.Across all samples, expressed genes with transcripts in sample were significantly more conserved than non-expressed sets relative best matches reference databases. This...
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...