Expeditions and Outreach

    Western Society of Naturalists Conference 2019

    Can you tell we like sharks?

    The Dinsdale lab spent Halloween at the 100th annual meeting of the Western Society of Naturalists (WSN) in Ensenada, Baja California, Mexico. WSN is the premier professional society for marine ecology on the west coast, and they meet every year to present the latest developments in the field from microbes to megafauna. Our lab had a strong showing; we learned a lot, made some new friends, and spread the genomic gospel of the holy holobiont far and wide.We had some great talks from 
    our fearless leader and charistmatic macrobe, Liz (global whale shark metagenomes), our model metagome modeler Lais (PhD, modeling coral metagenome networks and coral microbiome physiology), and our massively spectacular mass spectrometer expert Asha (PhD, charcterizing shark blood metabolites)!

    We also had wonderful posters from our devil weed demystifier Hayden (undergrad, Sargassum horneri's effect on giant kelp photochemistry), 
    our demersal demographer Isabella (undergrad, Chondrichthyan range expansion in western India), and our phylosymbiotic ph-riend Emma (undergrad, categorizing the microbiome of round rays against sharks and teleosts)

    We also received an honorable mention for best poster from our shark wrangler, captain Colton (M.S., characterizing the leopard shark microbiome)!

    We cannot wait for WSN 2020!

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    Coastal Marine Sciences Institute Research Symposium at UC Davis, 2018

    Graduate student Lais Lima presented her research at the Coastal Marine Sciences Institute Research Symposium at University of California, Davis on May 8, 2018. Lais is a PhD candidate in Ecology and is completing her courses at UC Davis. Her research focuses on coral reefs and its associated microbes!

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    National Center for Genome Analysis Support (NCGAS) Spring Workshop on de Novo Transcriptome Assembly, 2018

    Graduate students Rebecca de Wardt and Megan Morris attended the National Center for Genome Analysis Support (NCGAS) Spring Workshop on de Novo Transcriptome Assembly held April 30 - May 1 at Indiana University, Bloomington IN. At the workshop they learned about computational resources and bioinformatics pipelines for transcriptomic data, and also caught up with Dinsdale Lab alumna Bhavya Papudeshi, who now works for NCGAS and helped run the workshop.


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    The Dinsdale Lab 'Spring Breaks' in Catalina!

    While some use spring break as a time to vacation, the Dinsdale Lab took advantage of the week off from classes and teaching to squeeze in a much-needed research expedition. One of the many projects that the lab works on is investigating the microbial ecology of southern Californian temperate kelp forests, including those at Santa Catalina Island. However, over the past few years, the pristine kelp forests have been invaded by Sargassum horneri and the native kelp have not fully recovered. As a result, the ecosystem and the organisms that live there are at risk. Dr. Dinsdale along with some of her undergraduate and graduate students spent three full days at the USC Wrigley Marine Institute on Catalina Island to collect and process samples to better understand the interactions between native and invasive algae and their microbial communities. This study aims to provide us with more insight on the role of microbial communities in the recovery of the kelp forest ecosystem.



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    SDSU Coastal Marine Institute (CMIL) Marine Science Day, 2018

    The Marine Science Day was held at the Coastal and Marine Institute Laboratory (CMIL) on 18th March 2018, where students from SDSU and CMIL showcase current research and many educational activities related to marine ecology and conservation. The theme for this year was 'Science has  Solutions' and Dinsdale lab participated by organising fun activities for the kids.
    Dr. Elizabeth Dinsdale also gave a talk at the event highlighting the research in the lab.

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    Student Research Symposium (SRS), 2018

    Students from Dinsdale lab were able to present their research at the annual Student Research Symposium at SDSU.

    Undergraduate student Rhaya Alkafaji presents her research on different stress response genes in the environment.
    Undergraduate student Dominic Cavalli presenting a poster on the substrate utilization patterns in bacteria.
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    15th Annual Rocky Mountain Bioinformatics Conference, 2017

    Dnyanada presents her research at the ICSB meeting!

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    Ecological Society of America (ESA), 2017

    Megan presents her research at ESA 2017!

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    SDSU Coastal Marine Institute (CMIL), Marine Science Day 2017

    Dinsdale lab takes part in the annual Marine Science Day that is hosted at the CMIL. This is a free event open to the public that showcases some of the current research at SDSU, the facilities at CMIL. Dinsdale Lab actively took part this year with educational activities on microbial ecology.

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    Student Research Symposium, SRS 2017

    Dinsdale Lab members presented their research at the Student Research Symposium, SRS 2017 on campus.

    CONGRATS to Megan Morris who won the Presidents Award.

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    Ecological Metagenomics (BIOL 562)- Fish Sampling

    Dr.Dinsdale teaches the Ecological Metagenomics Course every Spring semester providing her students with hands on training on sequencing. The class entails collection, library preparation, sequencing and metagenomics analysis. This Spring 2017 semester, the class collected fish microbiome from Mission Bay.

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    CSU Biotechnology Symposium, CSUPERB 2017

    CSUPERB Symposium was held in Santa Clara between Jan 5-7th, 2017. Two students from Dinsdale lab presented their posters and received travel grants to attend the conference. The conference focused on biotech product innovation across CSU campuses.

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    International Symposium of Microbial Ecology (ISME), 2016

    Liz Dinsdale and six of her students presented their research at the 2016 ISME conference held in Montreal. All of us received travel grants from COAST (California State University), FARRIS/EPEF (San Diego State University) or ISME travel grants.

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    Marine Ecology and Microbiology Sydney Trip

    This past June I was able to attend the Marine Ecology and Microbiology class run by Elizabeth Dinsdale and Rob Edwards in Sydney Australia!


    During this trip we surveyed two different rocky intertidal zone locations in Sydney Harbor.

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    Shark skin microbial communities

    Leopard sharks aggregating in Big Fisherman's Cove - USC Wrigley Field Station on Santa Catalina Island.





    Sampling the microbes from the skin surface of a juvenile whale sharks in La Paz, Mexico
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    Student Research Symposium 2016

    Dinsdale Lab members presenting their research at the Student Research Symposium on campus.


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    Tidepool Sampling -Metagenomics Class 2016

    Dr.Dinsdale teaches an Ecological Metagenomics class at SDSU focusing on training students in next generation sequencing. Students gather samples from tidepools, sequence and apply bioinformatics to draw conclusions on the microbial community present within the tidepools.


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    California Kelp Forest Sampling

    The Dinsdale lab has been collecting metagenomes from the San Diego Bay, Kelp Forest every month and analysing the microbes asssicated with the kelp Macrocystis pyrifera. Through observing this activity across a long time series will provide us valuable insights into microbial functioning on kelp forest through time and across a suite of environmental parameters. The lab has been collecting samples from both San Diego Bay and Catalina Island frequently and analysing both the bacterial and viral particles from the metagneomes.

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    2015 American Elasmobranch Society meeting in Reno,Nevada

    The American Elasmobranch Society (AES) is a group dedicated to research focused on advancing the understanding for shark biology. This meeting is often held in conjunction with the annual Joint Meeting of Ichthyology and Herpetology. This past year (2015) I present my work entitled 'Revealing a physiological role of shark skin through microbial community analysis' at the Reno, Nevada meeting.

    Michael Doane presented his research "Revealing a physiological role of shark skin through microbial community analysis" at the American Elasmobranch Society, Reno, NV 2015.


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    2015 CMIL Marine Science Day

    San Diego State University Coastal and Marine Institute (CMIL) hosts a Marine Science Day event that attracts between 500-700 visitors to the CMIL each year. Dinsdale lab participates in this event every year  to highlight some of the research work being conducted by SDSU researchers in San Diego.


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    2015 Student Research Symposium

    Student Research Symposium is a public forum where SDSU students present their research and creative activities.


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    2014 Feb Whale shark sampling in La Paz, Mexico -

    Mike from Dinsdale lab went to La Paz, Mexico for Whale shark sampling with Dr. Deni Ramirez, founder of the organization Tiburon Ballena Mexico (Whale shark Mexico). See address below for more information about Dr. Ramirez's work with Whale sharks in La Paz.


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    2014 Research Expedition to Indonesia

    Matthew, Megan, Kevin, Michael and Dr. Dinsdale, along with members of Dr. Rob Edwards lab, Genivaldo Gueiros and Daniel Cuevas went to Indonesia in April 2014. The aim of the visit was to discuss possible collaborations with Diponegoro University in Semarang (on island of Java) and Hasanuddin University in Makasar (island of Sulawesi). While there, the group had the opportunity to learn about local customs, talk to Indonesian students, present research work and to also see the amazing coral reef systems of this area. Below you can see a few of the great pictures from the time spent in Indonesia.


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    2014 June Abrolhos Archipelago Expedition

    Members of the Dinsdale lab: Dr Liz, Kevin, Mike and John went to Abrolhos Archipelago on June 2014. This expedition was in collaboration between SDSU and Universidade Federal do Rio de Janeiro in order to look for microbial communities associated to coral reefs.

    caudal jubarte PAB2 DSCF2350

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    2014 Kelp Sampling in Catalina Island,CA

    On April 2014, Dr Liz, Matthew, Megan, Mike and Giselle (exchange student from UFRJ) collected microbial samples from Kelp forests off coast of Catalina Island.

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    2012 Science Outreach in San Diego, CA


    Every year, the Dinsdale Lab participates in the Coastal and Marine Institute Laboratory Open House through SDSU's Marine Ecology and Biology Student Association.

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    California Sea Lion Genome Sequencing and Annotation


    We have sequenced the Sea Lion Genome thanks to the alumni of SDSU's BIO596 class. Assembly and annotation of this massive Eukaryotic genome (~24 billion bp sequenced) is underway under Liz's supervision. More information about this project can be found on our California Sea Lion Genome website.


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    2011 Research Expedition to Abrolhos, Brazil


    Matt, Liz, and Rob went to the Abrolhos Islands as part of a collaboration with Universidad Federal do Rio de Janeiro. Water column and coral reef metagenomes and chemical samples were collected to assess the health of the Abrolhos holobiont.

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    2010 Sampling Expedition out of Valdivia, Chile

    Nori, Matt and Liz went to Chile as part of a collaboration with the Centro de Estudios Cientificos (CECS), Valdivia, Chile. Metagenomes and microbial abundance counts were collected on a transect from Arica at sea-level to the Atacama Desert at 14,000 feet.

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    2009 Research Expedition off Iquique, Chile

    Alejandra, Julia and Nori went on the third annual Oxygen Minimum Zone expedition. Marine metagenomes, abundance counts, and dissolved organic carbon samples were collected as part of the international effort to characterize the low-oxygen environment.

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    Metagenomic Analysis of Oxygen Minimum Zone Viral Communities

    Annual percentage oxygen saturation at 200m depth

    Part of an international collaboration: ETSP OMZ.
    OMZs are coastal marine areas that contain a hypoxic layer of <20 µM of dissolved oxygen. In the ETSP OMZ, microbes (small Eukaryotes, Bacteria, Archaea, and Viruses) metabolize nitrogen, carbon, and sulfur in the absence of oxygen. Sampling over three consecutive years, we have found that the ratio of virus-like particles to microbes fluctuates wildly in the anoxic layers and, unusually, reaches a 1:1 at some depths. Analysis of the prophage and viral communities from these unique marine habitats are in progress. These two viral metagenomes exhibit distinct community structures, indicating successful induction of OMZ prophages. Further analysis includes fine-grained investigation of the OMZ viral and prophage metabolism compared to the microbes.


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    Copper Tolerance of Kelp-Associated Bacteria

    Kelp forests are one of the most widespread and productive of all ecosystems. They provide habitat and nutrition to diverse communities of microorganisms, invertebrates, and mammals. Many kelp forests are dominated byMacrocystis pyrifera, a species of large brown algae that produce negatively charged polysaccharides on their cell surfaces. The polysaccharides allow Macrocystis to accumulate heavy metals such as copper, normally an essential element involved in cellular pathways. Brown algae in environments with higher levels of heavy metals, such as those near human activity, accumulate toxic levels of copper by producing larger amounts of polysaccharides. Toxic amounts of copper can then bioaccumulate up the food chain.

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    Microbial Ecology of the Alaskan Tundra

    Collaboration with Dr. David Lipson, Department of Ecology, SDSU

    In arctic peat soils, iron reduction is an important pathway for respiration in anaerobic environments. We are interested in the factors that contribute to CO2 and CH4 fluxes from the arctic soil ecosystem, especially the microbial communities. We are investigating metagenomes acquired from different depths of our research site on the Arctic Coastal plain near Barrow, Alaska. The soil  bacterial metagenomes were acquired from depths of 0 – 10m, 10-20m, 20-30m and 30-40m from the research site. Once the soil DNA was extracted, sequenced and assembled, they were uploaded onto the MG – RAST server (Metagenome - Rapid Annotation using Subsystems Technology) and annotated. I am currently comparing these metagenomes to look for similarities and more importantly, the differences and track the major metabolic pathways and functions at each depth in the Arctic tundra.


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