Michelle Jungbluth- Ph.D.
- Adjunct Assistant Professor at San Francisco State University
Michelle Jungbluth
- Ph.D.
- Adjunct Assistant Professor at San Francisco State University
About
17
Publications
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164
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Introduction
My work investigates ecosystem health and population ecology of marine and estuarine zooplankton and larval fishes. I primarily approach my research questions utilizing novel 'omics based methods, like targeted qPCR, DNA barcoding, or high-throughput sequencing, and am active in the field of environmental DNA, community metabarcoding, and dietary DNA.
Current institution
Additional affiliations
December 2018 - September 2020
May 2017 - June 2019
March 2016 - September 2016
Education
January 2013 - December 2016
January 2010 - December 2012
August 2003 - June 2007
Publications
Publications (17)
Copepod nauplii are important in plankton food web dynamics, but limited information is available about their ecology due to methodological challenges. Reported here is a new molecular method that was developed, optimized, and tested in laboratory and field samples that uses quantitative PCR (qPCR) to identify and estimate the abundance of nauplii...
Environmental DNA (eDNA) and RNA (eRNA) metabarcoding has become a popular tool for assessing biodiversity from environmental samples, but inconsistent documentation of methods, data and metadata makes results difficult to reproduce and synthesise. A working group of scientists have collaborated to produce a set of minimum reporting guidelines for...
Zooplankton in estuaries provide an important link between primary production and fish. Resource managers in the San Francisco Estuary have several initiatives designed to increase phytoplankton production, expecting zooplankton increases to follow. However, it is not always clear if an increase in phytoplankton biomass will lead to an increase in...
Despite the importance of early life‐history stages to ecosystem processes, challenges in the identification of the larval stages of species continue to slow progress in understanding the dynamics of marine ecosystems. A quantitative polymerase chain reaction‐based method was developed and tested for estimating the species‐specific biomass of juven...
Abstract Food limitation can dampen the survival and growth of fish species during early development. To investigate prey diversity important to the planktivorous larval longfin smelt (Spirinchus thaleichthys) and Pacific herring (Clupea pallasii) from the San Francisco Estuary, we used DNA metabarcoding analysis of the cytochrome oxidase I gene on...
Food limitation can dampen survival and growth of fish during early development. To investigate prey diversity important to the planktivorous larval longfin smelt (Spirinchus thaleichthys) and Pacific herring (Clupea pallasii) from the San Francisco Estuary, we used DNA metabarcoding analysis of the cytochrome oxidase I gene on the guts of these fi...
In 2016, a massive bloom of the chain-forming diatom Aulacoseira granulata occurred in the upper San Francisco Estuary, California, with chlorophyll concentrations up to 75 μg Chl L −1. In this study, quantitative PCR was used to investigate consumption of the bloom organism by the numerically dominant zooplankter Pseudodiaptomus forbesi (Copepoda:...
Abyssal plains are among the most biodiverse yet least explored marine ecosystems on our planet, and they are increasingly threatened by human impacts, including future deep seafloor mining. Recovery of abyssal populations from the impacts of polymetallic nodule mining will be partially determined by the availability and dispersal of pelagic larvae...
Here, we present a range of interactions, which we term “cryptic interactions.” These are interactions that occur throughout the marine planktonic foodweb but are currently largely overlooked by established methods, which mean large‐scale data collection for these interactions is limited. Despite this, current evidence suggests some of these intera...
Copepod naupliar grazing estimates often appear to represent an insignificant fraction of prey community mortality, despite high naupliar abundances and weight-specific ingestion rates. To address this seeming paradox, the impact of incubation time on grazing by nauplii of the subtropical copepod Parvocalanus crassirostris on natural prey assemblag...
The ingestion rates of Parvocalanus crassirostris and Bestiolina similis mid-stage (N3 and N4) nauplii feeding on a natural prey assemblage from a subtropical embayment were measured to evaluate differences in prey preferences and estimate the trophic impact of grazing by each species. During the 2 wk period of our experiments, the in situ 2-35 μm...
Kāne'ohe Bay, Hawai'i, USA, an oligotrophic subtropical coastal embayment, is a stable ecosystem dominated by picophytoplankton through most of the year (dry state). After heavy rains, macronutrients from high stream flow result in elevated phytoplankton biomass and change the community to one dominated by diatoms (wet state). However, the effect o...
The effect of the dinoflagellate, Alexandrium fundyense, on relative expression of glutathione S-transferase (GST) transcripts was examined in the copepod Calanus finmarchicus. Adult females were fed for 5-days on one of three experimental diets: control (100% Rhodomonas spp.), low dose of A. fundyense (25% by volume, 75% Rhodomonas spp.), and high...
Ethanol is one of the most commonly used fixatives for zooplankton samples in molecular studies, despite known problems with this method. Alternative preservation solutions are desired that would reliably preserve DNA over medium to long time scales (months to years). This study tested the efficacy of acetone as a bulk fixative for DNA preservation...
Copepod communities in lagoons and embayments on subtropical islands in the Pacific Ocean are geographically isolated from other populations along continents and other islands. Nevertheless, taxonomic identifications suggest that many of these species are cosmopolitan. The genetic diversity of planktonic copepod species in a subtropical embayment,...
Questions
Questions (3)
I've always used 95% non-denatured ethyl alcohol as a preservative for genetic analyses of aquatic zooplankton samples, and am debating whether it might be worth trying to switch the DESS solution (DMSO Na-EDTA solution, Dawson et al 1998) given the challenges in dealing with flammable solutions in lab, storage long term, and in the field, and DESS can apparently be stored long term at room temperature, whereas Ethanol-preserved samples are best stored at least chilled if not frozen for longer term storage. But, that requires special freezers that are safe for storage of flammables, and space runs out quickly.
Does anyone know of limitations of using DESS solution for preservation for genetic work? Have any opinions and/or experience to share?
I am having some major challenges in PCR amplifying DNA from mixed community samples using degenerate primers that have inosine bases in them. The same samples amplify fine with a regular TAQ polymerase (lovely bright bands, good Sanger sequences), but as soon as I try the High Fidelity type, I have no amplification or extremely low levels with a range of DNA concentrations. I worry that the polymerases are mainly incompatible with the inosine bases in the primers, as some high fidelity polymerases explicitly state they are incompatible with inosines, but not all polymerases state this problem in their guides. Therefore I do not know if it is a universal problem with high fidelity polymerases or just problems with certain brands. So far my tests suggest it is the former.
So far I have tried:
Kapa HiFi (regular, and Hot start, Fidelity and GC buffer)
Phusion HiFi mastermix - did not amplify
Platinum SuperFI master mix - notes a problem with inosines, did not amplify
With Kapa HiFi (regular, not hot start), I was able to get a faint band after 40 cycles by adding 100 ng DNA/10 uL reaction, GC Buffer, and BSA. Adding less DNA = no bands. It seems crazy to add so much DNA and still get very little amplification, this is the mitochondrial COI gene (multiple copies). With a regular TAQ (MangoMix, and AmpliTaq Gold) I get strong amplification of my target sequence by adding only ~5 ng DNA/reaction, all other things remaining equal.
Ultimately I will do Illumina MiSeq on the indexed product to sequence diverse COI amplicons, so I should really have a high fidelity polymerase doing the amplification.
Thank you in advance for sharing your experience in this area.
I have not worked with inosine bases before and did not expect it to be such a problem! I am using someone's published primers, tried using their methods as much as possible, but they did not use a high fidelity polymerase in either of their publications (though they recommend doing so in the earlier of the two pubs!). Perhaps they tried and also failed - reasons there should be a journal of failed methods!
These are copepod grazing experiments, where the particle size spectra and abundance were measured with a coulter counter particle counter in initial samples, and final control (no grazer) and treatment (with grazers) bottles.
This is a new area for me, any help is greatly appreciated.
