A5083972342- Coral and Marine Ecosystems Studies
- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Aquaculture disease management and microbiota
- Ichthyology and Marine Biology
- Marine and coastal plant biology
- Marine Biology and Ecology Research
- Ion-surface interactions and analysis
- Gut microbiota and health
- Laser-induced spectroscopy and plasma
- Ocean Acidification Effects and Responses
- Diamond and Carbon-based Materials Research
- Plant and animal studies
- Syphilis Diagnosis and Treatment
- Bacteriophages and microbial interactions
- HIV Research and Treatment
- Marine and coastal ecosystems
- Microbial Metabolism and Applications
- Immune Cell Function and Interaction
- Marine Sponges and Natural Products
- Microbial Natural Products and Biosynthesis
- Microplastics and Plastic Pollution
- Coastal wetland ecosystem dynamics
- Identification and Quantification in Food
- Fish Biology and Ecology Studies
Lawrence Livermore National Laboratory
2021-2024
Stanford University
2019-2020
San Diego State University
2016-2020
University of California, Davis
2020
Universidade Federal do Rio de Janeiro
2017
Mayo Clinic in Florida
2015
Mayo Clinic in Arizona
2015
University of California Davis Medical Center
2008-2010
Global climate change includes rising temperatures and increased pCO2 concentrations in the ocean, with potential deleterious impacts on marine organisms. In this case study we conducted a four-week incubation experiment, tested independent combined effects of temperature partial pressure carbon dioxide (pCO2), microbiomes foundation species, giant kelp Macrocystis pyrifera, surrounding water column. The microbiome responded differently to each stressors. microbiome, condition caused an...
Microbial dispersal is essential for establishment in new habitats, but the role of vector identity poorly understood community assembly and function. Here, we compared microbial function floral nectar visited by legitimate pollinators (hummingbirds) robbers (carpenter bees). We assessed effects visitation on abundance composition culturable bacteria fungi their taxonomy using shotgun metagenomics chemistry. also metagenome-assembled genomes (MAGs) Acinetobacter, a common highly abundant...
A small percentage of human immunodeficiency virus (HIV)-infected individuals, termed elite controllers, are able to spontaneously control HIV replication in blood. As the gastrointestinal mucosa is an important site transmission and as well CD4+ T-cell depletion, it understand nature immune responses occurring this compartment. Although role HIV-specific CD8+ mucosal tissues has been described, few studies have investigated T cells. In study, we assessed rectal 28 "controllers" (viral load...
Abstract Background The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical physiological differences, including skin properties. of is covered in dermal denticles, whereas are scales mucous rich. divergence time among these two fish groups hypothesized to result predictable variation symbionts. Here, using shotgun metagenomics, we test if patterns diversity the...
Host-associated microbial communities are shaped by extrinsic and intrinsic factors to the holobiont organism. Environmental microbe-microbe interactions act simultaneously on community structure, making microbiome dynamics challenging predict. The coral is essential health of reefs sensitive environmental changes. Here, we develop a dynamic model determine structure associated with surface mucus layer (SML) corals using temperature as an factor network factor. was validated comparing...
Previous studies have suggested that polyfunctional mucosal CD8(+) T-cell responses may be a correlate of protection in HIV controllers. Mucosal breadth and/or specificity also contribute to defining protective responses. In this study, rectal Gag, Env, and Nef were mapped at the peptide level four subject groups: elite controllers (n = 16; viral load [VL], <75 copies/ml), viremic 14; VL, 75 2,000 noncontrollers >10,000 antiretroviral-drug-treated subjects 8; copies/ml). all groups,...
Microbiome/host interactions describe characteristics that affect the host's health. Shotgun metagenomics includes sequencing a random subset of microbiome to analyze its taxonomic and metabolic potential. Reconstruction DNA fragments into genomes from metagenomes (called metagenome-assembled genomes) assigns unknown taxa/function facilitates discovery novel organisms. Genome reconstruction incorporates sequence assembly sorting assembled sequences bins, characteristic genome. However,...
A detailed evaluation of eight bacterial isolates from floral nectar and animal visitors to flowers shows evidence that they represent three novel species in the genus Acinetobacter . Phylogenomic analysis closest relatives these new are apis , boissieri nectaris previously described associated with bees, but high genome-wide sequence divergence defines as species. Pairwise comparisons average nucleotide identity compared known is extremely low (<83 %), thus confirming samples...
Bacterial remineralization of algal organic matter fuels growth but is rarely quantified. Consequently, we cannot currently predict whether some bacterial taxa may provide more remineralized nutrients to algae than others. Here, quantified incorporation algal-derived complex dissolved carbon and nitrogen in fifteen co-cultures growing with the diatom Phaeodactylum tricornutum at single-cell level using isotope tracing nanoSIMS. We found unexpected strain-to-strain cell-to-cell variability...
Life in the ocean will increasingly have to contend with a complex matrix of concurrent shifts environmental properties that impact their physiology and control life histories. Rhodoliths are coralline red algae (Corallinales, Rhodophyta) photosynthesizers, calcifiers, ecosystem engineers therefore represent important targets for acidification (OA) research. Here, we exposed live rhodoliths near-future OA conditions investigate responses photosynthetic capacity, calcium carbonate production,...
As coral reef habitats decline worldwide, some reefs are transitioning from coral- to algal-dominated benthos with the exact cause for this shift remaining elusive. Increases in abundance of microbes water column has been correlated an increase disease and reduction cover. Here we investigated how multiple organisms influence microbial communities surrounding column. Our study consisted a field assessment above replicate patches dominated by single macro-organism. Metagenomes were...
The coral holobiont is comprised of a highly diverse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. surface mucus layer (SML) microbiome very sensitive external changes, it constitutes the direct interface between host environment. Here, we investigate whether bacterial taxonomic functional profiles in SML are shaped by local reef zone explore their role health ecosystem functioning. analysis was conducted using metagenomes...
Shifts in microbiome community composition can have large effects on host health. It is therefore important to understand how perturbations, like those caused by the introduction of exogenous chemicals, modulate composition. In poison frogs within family Dendrobatidae, skin exposed alkaloids that sequester from their diet and use for defense. Given demonstrated antimicrobial these frog alkaloids, compounds may be structuring microbial community. To test this, we first characterized...
The epidermis of Chondrichthyan fishes consists dermal denticles with production minimal but protein-rich mucus that collectively, influence the attachment and biofilm development microbes, facilitating a unique epidermal microbiome. Here, we use metagenomics to provide taxonomic functional characterization microbiome Triakis semifasciata (leopard shark) at three time-points collected across 4 years identify links between microbial groups host metabolism. Our aims include (1) describing...
Marine microbes mediate key ecological processes in kelp forest ecosystems and interact with the macroalgae. Pelagic biofilm-associated macroalgal propagules at multiple stages of recruitment, yet these interactions have not been described for M. pyrifera. Here we investigate influence from coastal environments on recruitment giant kelp, Macrocystis Through repeated laboratory experiments tested effects altered pelagic microbial abundance settlement development microscopic pyrifera during...
We present the complete mitochondrial genome of Sharpnose/Granulated Guitarfish Glaucostegus granulatus, obtained with whole shotgun sequencing genomic DNA. The 16,547 bp long circular consisted 13 protein-coding genes, 22 tRNA 2 rRNA and a non-coding control region. A few genes ended incomplete stop codons. Phylogenetic analysis provided strong support for specimen to be identified as G. granulatus improved resolution phylogeny within genus such placing thouin in sister group typus. This is...
Outdoor cultivation of microalgae has promising potential for renewable bioenergy, but there is a knowledge gap on the structure and function algal microbiome that coinhabits these ecosystems. Here, we describe assembly mechanisms, taxonomic structure, metabolic bacteria associated with Microchloropsis salina cultivated outdoors. Open mesocosms were inoculated cultures either free or coincubated one two different strains alga-associated sampled across five time points taken over multiple...
Microbiomes are vast communities of microbes and viruses that populate all natural ecosystems. Viruses have been considered the most variable component microbiomes, as supported by virome surveys examples high genomic mosaicism. However, recent evidence suggests human gut is remarkably stable compared to other environments. Here we investigate origin, evolution, epidemiology crAssphage, a widespread virus. Through global collaboratory, obtained DNA sequences crAssphage from over one-third...
Coral reef health is tightly connected to the coral holobiont, which association between animal and a diverse microbiome functioning as unit. The holobiont depends on key services such nitrogen sulfur cycling mediated by associated bacteria. However, these microbial may be impaired in response environmental changes, thermal stress. A perturbed lead bleaching disease outbreaks, have caused an unprecedented loss cover worldwide, particularly correlated warming ocean. mechanisms of under high...
The high lateral resolution and sensitivity of the NanoSIMS 50 50L series dynamic SIMS instruments has enabled numerous scientific advances over past 25 years. Here we report on NanoSIMS-HR, first major upgrade to series, analytical tests in a suite sample types, including an aluminum containing silicon crystals, microalgae plant roots colonized with arbuscular mycorrhizal fungi. Significant improvements have been made Cs ion source, voltage (HV) control, stage reproducibility, other aspects...
The high lateral resolution and sensitivity of the NanoSIMS 50 50L series dynamic SIMS instruments has enabled numerous scientific advances over past 25 years. Here we report on NanoSIMS-HR, first major upgrade to series, analytical tests in a suite sample types, including an aluminum containing silicon crystals, microalgae plant roots colonized with arbuscular mycorrhizal fungi. Significant improvements have been made Cs ion source, voltage (HV) control, stage reproducibility, other aspects...
Microbiomes confer beneficial physiological traits to their host, but microbial diversity is inherently variable, challenging the relationship between microbes and contribution host health. Here, we compare architectural complexity of epidermal microbiome from 74 individual whale sharks (Rhincodon typus) across five aggregations globally determine if network properties may be more indicative microbiome-host relationship. On premise that are expected exhibit biogeographic patterns distantly...