Lab Members

Post-doctoral fellows

Thiago Bruce 

I am Post doc in Dinsdale´s Lab. I was born in Brazil and have PhD in genetics, Msc in Biotechnology and graduate in microbiology (2004). I have genuine interest in topics related to microbial molecular biology. I have been involved in research related to characterization and bioprospecting of microbial diversity. I had opportunity to handle with diverse approaches to characterize microbial communities from a variety of environments, searching for biocatalysts of industrial interest.Currently, im involved with Genotype to Phenotype Project. The lack of high-throughput phenotypic data is hindering our ability to describe the metabolic potential of microbes based on their genome annotation and our ability to predict gene complements from phenotypic analyses.The overall goal of this project is to improve our capability to reliably predict phenotype from genotype for microbial life across the bacterial kingdom. this project will result in genomic sequences, annotation and microbial metabolic models.

 

 Shaili Johri

Shaili Johri

I have a background in molecular genetics and conservation biology. My major research focus is to develop non-invasive tools for monitoring and conservation of wildlife populations. During my tenure at the University of Washington, Seattle I led a project to develop non-invasive monitoring methods to study ecological impacts of apex predator recovery. I developed a Real Time PCR and High Resolution Melt curve based method for species identification of large carnivores from scat.
As part of the project at UW, we used detection dogs for sampling of scat from seven large carnivores in high wolf density areas of Northeast Washington. This allowed high sample numbers which are necessary for comprehensive analyses in ecological studies. As part of this study we were able to determine  distribution of large carnivores by season, species interactions and resource use as well as impact of wolf recovery on human-wildlife conflicts.
I recently received a grant from the Society for Conservation Biology-Marine Section for biodiversity indexing of sharks in India. I am currently involved in developing a species identification method for -sharks, rays and chimaeras using portable sequencers.
Secondly, I am interested in developing microbiomes as a non-invasive monitoring tool for wildlife populations. I am currently involved in studying microbiomes from killer whales and sharks to determine the effect of contaminants like persistent organic pollutants and heavy metals on the health of these marine species.

PhD students 

 Michael Doane

I am a fourth year Ph.D student in the Dinsdale lab. I received my B.S from the University of Illinois at Urbana-Champaign in Integrative Biology. I started the Master’s program at SDSU in 2012, transitioning then into the Ecology Ph.D program in 2014. The Ecology doctoral degree at SDSU is a joint program with the University of California-Davis. My research focuses on the microbial communities that live on the skin of sharks. The shark species under investigation include common thresher sharks (Alopias vulpinus), whale sharks (Rhincodon typus), and leopard sharks (Triakis semifasciata). Sharks have a unique skin surface only found among the shark group that is covered by teeth-like structures call dermal denticles. The organized dermal denticle pattern of shark skin reduces fluid friction, a property that allows sharks to move with greater efficiency through the water; but this surface pattern also embodies characteristics that influence the settlement of small life forms, including bacteria. Some questions my work aims to address are 1) how is microbial community diversity distributed across shark species and 2) does microbial community diversity on the skin vary across gradients of spatial and temporal scales. My research interests center microbial community ecology, microbial biodiversity and ecosystem function.

 

Megan Morris

I joined the Dinsdale Lab in 2012 after receiving my BS in Biology from SDSU in 2011. I am currently a Ph.D. student in the Joint Doctoral Program in Ecology with SDSU and UC Davis. My dissertation research focuses on the microbial ecology of kelp forests, and microbial associations with giant kelp Macrocystis pyrifera. I apply metagenomics to describe the kelp forest microbial communities in great detail, examining their composition and functional roles within the ecosystem.

 

Lais Lima

I enrolled the Joint Doctoral Program in Ecology at SDSU/UC Davis in the fall 2016. Before I joined the Dinsdale lab, I received my Bachelor in Biological Sciences (University of Brasilia, 2011) and defended a Master’s in Marine Ecology (Federal Fluminense University, 2015) in Brazil, where I was born and raised. As a coral reef ecologist, I published my master’s thesis on the population ecology of an endemic coral species from Brazil advised by Dr. Ricardo Coutinho (IEAPM/UFF) and also conducted research on coral physiology in Bermuda, advised by Dr. Samantha de Putron (BIOS). The aim of my PhD dissertation is to investigate the relationships between the holobiont physiological processes and the associated microbiome. I expect to address this aim by conducting in situ and laboratorial experiments in Caribbean coral reefs and in coastal ecosystems in California. The first part of my field and lab work will be conducted in the summer 2017 in Bermuda. In collaboration with the Bermuda Institute of Ocean Sciences (BIOS), I am sampling the coral microbiome across reef zones and subjecting corals from distinct thermal environments to heat-water treatments to assess whether the microbiome component enhances coral thermal resilience.  As a joint doctoral student, I am spending the 2017-2018 academic year at UC Davis under the Area of Emphasis “Ecotoxicology/Physiological Ecology”.
More information about my research interests and publications: https://www.researchgate.net/profile/Lais_Lima5


Douglas Beattie

I am a visiting PhD candidate from the University of New South Wales, Australia. My research focuses on the role of viruses infecting the Sydney kelp Ecklonia radiata and the Californian giant kelp Macrocystis pyrifera. These are both primary habitat-forming brown alga along temperate rocky coastlines, and ongoing diebacks and disease have raised concern over the long-term health of these ecosystems and economic and commercial endeavors which rely on them. Most medical or agricultural studies into viruses need the virus of interest to be isolated and grown on its own to enable further investigation. In contrast, we sequence the viral particles extracted directly from the kelp tissue. This provides genetic snapshots or Metagenomes of this community, where we can explore how different virus genes are affecting the health of the kelp.

 

Graduate Students 

Dnyanada Pande 

I joined the Dinsdale lab in 2015. I did my BS in Microbiology and my MS in Bioinformatcs from India and currently I am pursuing my MS in the Bionformatics and Medical Informatics program. I am working on improving the annotation of viral metagenomes using signature genes and motifs. Ultimately, this would be used to improve the assembly and reconstruction of complete genomes.

 

Rebecca de Wardt

Rebecca de WardtWhen you grow up in Colorado, it is hard not to fall in love with camping, backpacking, hiking, and snowboarding.  My love of the outdoors has grown into a sense of duty to protect the worlds’ incredible and unique ecosystems.  This led me to attain a B.S. in Biology from the University of Colorado.  My studies as an undergrad piqued my interest in sustainability and biomimicry.  Currently, I am working towards attaining a M.S. in Cell and Molecular Biology.  My main research project focuses on linking genotypes to phenotypes through experimental analysis and metabolic modeling software.  The overarching goal of this project is to provide researches with a publicly available metabolic modeling tool to aid in understanding and bioengineering not well characterized bacterial species.  I am also working on tide pool microbiomes and am interested in their effects on host and ecological systems as well as exploring how microbiome signatures can be used as ecological bioindicators.

 

Tucker Lopez

 Marine microbes aid in the nutrition, reproduction, chemical defense, and immunity of associated organisms in marine ecosystems. As anthropogenic activity increases in coastal regions worldwide, marine microbial communities are shifting from symbiotic to pathogenic, causing further environmental detriment. Although the microbial genomic adaptations resulting from anthropogenic disturbance have been described, few studies have supported the genomic adaptation with evidence of phenotypic adaptations as well. My research explores the phenotypic adaptations in bacterial strains resulting from anthropogenic influence. Bacterial strains were isolated from four kelp forest regions offshore San Diego, California with different levels of anthropogenic disturbance. Because studies have shown that anthropogenic perturbations induce genomic changes in microbes, including transport of pollutant compounds out of the cell and utilization of contaminants as energy sources, we hypothesized that microbial strains isolated from higher anthropogenic disturbance areas would show phenotypic markers carbon, sulfur, phosphorous and nitrogen utilization. Utilization usage is tested using a 96-well phenotypic array plate with 72 carbon nutrient sources 24 sulfur, 10 phosphorus and 54 nitrogen  nutrient sources. Strains across the four kelp forest sampling locations, Catalina, Pt. Loma, La Jolla, & San Diego Bay have been tested to-date. The 96-well phenotypic array results are currently being analyzed to determine the nutrients that are being utilized among the Vibrio strains isolated from our areas of interest. As a result of this study, we will be better able to predict the changes that will occur in microbial communities, which has implications on the health of the associated environment and macro-organisms. This study is relevant as anthropogenic perturbations continue to increase in frequency and magnitude worldwide.

 

Undergraduate Students 

Abigail Turnlund

 I am an undergraduate majoring in Biology with an emphasis in Marine Biology at San Diego State University. Before attending San Diego State University, I first got involved in marine science by working at the Seymour Marine Discovery Center at Long Marine Lab at UC Santa Cruz. There I loved working with their swell sharks and plan on pursuing shark research in graduate school. Currently I am helping out with two projects in the lab, one looking at the role of microbes on sharks and the other linking genotypes to phenotypes for marine bacterial strains through experimental analysis.

 

Taylor Dillon

I am an undergraduate studying Biology with an emphasis in Marine Biology and I have a minor in Sustainability at San Diego State University. I first peeked an interest in the marine sciences when I was hired on as a marine science instructor at the Mission Bay Aquatic Center. After a long summer of teaching children about marine life and conservation, I was hooked on the idea of becoming a marine biologist. After joining the Green Love club at SDSU, I have also found a love for sustainability and conservation. I’m really interested in how sustainable practices can better suit marine species, habitats, and ecosystems.  I am now a 5th year senior finishing up my undergraduate classes, volunteering, and getting ready for graduate school!


Dominic Cavalli

I am an undergraduate majoring in Biology with an emphasis in Cellular and Molecular Biology at San Diego State University. My interest in Marine Biology began in middle school when I competed in an ROV competition. From there I went to Monterey Academy of Oceanographic Science (MAOS) for high school. Currently I am working on project looking at the metabolic models of bacterial strains by testing bacterial usage of different carbon, nitrogen, phosphorus, and sulfur substrates.