Effects of eutrophication of ecosystems

Anthropogenic activities are increasing. Activities include urban, agricultural, and industrial land development. The activity has resulted in the eutrophication of numerous fresh-water ecosystems worldwide. The excess of nutrients, such as phosphorus and nitrogen increase the growth rate of phytoplankton resulting in the formation of dense populations (i.e., algae blooms). 

Algae blooms, cyanobacterial blooms, have been shown to pose environmental and social
problems (Vargas-Montero and Freer 2004; Haande et al. 2007; Stone and Bress 2007; Zhang et al. 2007). 

Blooms reduce water quality and the recreational value of aquatic ecosystems (Rahman at al. 2005; Smith and Lester 2006).

 Cyanobacterial species produce potent toxins, which pose serious health risks to both human and animals (Codd et al. 2005).

qPCR

 

Quantitative real-time PCR technologies (what is Taqman qPCR):

 

https://www.ncbi.nlm.nih.gov/probe/docs/techqpcr/

Quantitative real-time PCR (qrt-PCR) is a good option to generate ‘real-time’ data regarding the presence of harmful algal species. The major goal of a qrt-PCR project is to design and test a qrt-PCR assay that will accurately identify and estimate marine algal species. 

Quantification is performed during the exponential phase of the PCR, where amplification efficiency is maximum. In real-time PCR, amplicon formation is monitored after each cycle by measuring a fluorescence signal.

An amplicon is a piece of DNA or RNA that is the source and/or product of natural or artificial amplification or replication events. It can be formed using various methods including polymerase chain reactions (PCR) or natural gene duplication.

In qrt-PCR, the increase in fluorescence observed during the reaction will be proportional to the starting quantity of the target molecule. Fluorescence can be generated by using fluorescent probes such as TaqMan®. Since there is a correlation between the cycle number at which the amplicon is initially detected (threshold cycle, Ct) and the starting amount of target molecules, it is possible to calculate the amount of target sequence in an unknown sample by using a standard reference curve generated using DNA extracted from a known number of cultured cells. 

Postdoctoral Molecular Researcher position at Northwest Indian College

 

As a Postdoc and Molecular Researcher at Northwest Indian College on the Lummi main campus at the Salish Sea Research Center (SSRC), I will monitor harmful agal bloom species (Alexandrium catenella, Azadinium poporum, and Pseudo-nitzschia multiseries) in the Bellingham and Lummi Bays (Washington State) using molecular techniques. 

Protocols for monitoring harmful algal bloom species will used in inform the local Lummi Nation. This project will provide food and data sovereignty for the Lummi Nation and Lummi Natural Resources deparment about annual harmful algal blooms. 

Gooseberry Point along the Bellingham Bay

 

Career update for years 2008-2020

Background:

LSAMP-Bridge to the Doctorate cohort VI.

As I have not updated this blog since I was a Master's student at the University of New Mexico (Image above taken in 2008) working with Professor Laura Crossey on the biogeochemistry of the Tierra Amarilla Anticline in northern New Mexico, I thought it was a good idea to catch up on my background. As a biogeochemist, I have used and become an expert in a variety of different imaging and spectroscopy tools. 

(from left to right) Brandi Cron, Professor Brandy Toner, Robert Atticus Kamermans and Aubrey Dunshee taking a photo break with Robert Atticus Kameramans at BL 12.3.2 at the Advanced Light Source.

As a Ph.D. candidate at the University of Minnesota (image above taken in 2017), I gained expertise characterizing abiotic and biotic mineral precipitates in deep-sea hydrothermal vents, using Scanning Transmission X-ray Microscopy, X-ray Absorption Near Edge Structure (XANES) and X-ray diffraction.

Pennsylvania State University geosciences professor Julie Cosmidis and postdoctoral fellow Brandi Kamermans prepare to change out samples on the SM beamline. Photo is from the Canadian Light Source.

Most recently, I have been using Scanning Transmission X-ray Microscopy, Raman, and Scanning Electron Microscopy at the Pennsylvania State University Material Characterization Laboratory to characterize both elemental sulfur and organics produced by Sulfuricurvum kujiense, in an effort to distinguish chemical versus microbial induced mineral production. 

This week I was ambitious and decided to drill four of my samples for Uranium dating. I only got two done, with lots of support from Eileen Embid. (The drill is pictured above)




There are studies that have already assessed the timing of travertine accumulation in the Rio Salado, the Grand Canyon, and Springerville, AZ (Sower et al., 2008; Embid et al., in prep.; Crossey et al., 2009). My study focuses specifically on the active spring deposits in the Tierra Amarilla anticline, just south of the Rio Salado and their correlation with results from the surrounding area.

To better understand the paleohydrologic processes and to estimate the growth record of the mound system, geologic mapping and U-series geochronology is being incorporated. The active and extinct mound springs we propose to study are morphologically similar to mounds elsewhere in the southwestern U.S., including in Springerville, AZ and the Grand Canyon.

U-series chronology of travertine samples will be determined in the Radiogenic Isotope Laboratory at the University of New Mexico. The chemistry lab and mass spectrometry lab are class 100 clean labs. The travertine samples will be cut and drilled samples will be obtained along growth bands with an automated drill. The carbonate powder, typically around 200 mg, will be dissolved in HNO3 and spiked with a mixed 229Th-233U-236U spike. You can see my fresh travertine powder above and Eileen is putting in a vial for safe keeping until January when we will run the samples in the lab.


The Micromass Sector 54 thermal ionization mass spectrometer with a high-abundance sensitivity filter will be utilized for all U and Th measurements (Rasmussen, 2001). The timing of travertine accumulation will be determined and than correlated with nearby accumulations (Springerville, AZ and Grand Canyon). We will define the time interval over which these springs have been active and these dates will relate to the surrounding region and the incision rates of the Rio Salado. We hypothesize that this region will provide unique dates that do not correlate with the Grand Canyon or the Springerville area (i.e., controls are local).

Eileen Embid just finished her Master's at UNM working with travertine from Springerville,AZ. If you want to see more information on her and the other graduate students in our research group here is our link: http://epswww.unm.edu/facstaff/lcrossey/PersonalPage/students.html

"Studies of simpler and more stable systems make it easier to observe patterns that may influence the way we think about more complex systems."

If you were ever curious about how certain bacteria survived the Cretaceous-Paleogene global extinction (extinction of the dinosaurs) read the following:
Astrobiology, vol. 9, Number 6, 2009, Harriet Jones, et al., Experiments on Mixotrophic Protists and Catastrophic Darkness.
In this paper several experiments were done to test the effect that 6 months of darkness and exposure to controlled amounts of DOC would do to mixotrophic bacteria. Turns out, they eat each other's dead bodies in order to survive. I am trying to imagine what a human would do if it was locked up with controlled nutrients with 1000's of other humans in the dark for 6 months... and I'm thinking "Zombies"? I guess we are not too far from the root of the tree, huh?

YSI Sonde

Two weeks ago I deployed two YSI sondes into the travertine mound spring located at the northern most point of the Tierra Amarilla anitcline. I left the instruments in the springs for three days. They recorded measurements of DO, pH, temperature, and conductivity every 2 minutes; one at 1m depth and the other at 5m depth. The goal for our research is to synchronously measure all parameters in these springs to hopefully predict what and how these springs are altered by climate and/or seismic events. In order to properly assess the data that I have from the Sonde deployments I need to incorporate diel cycling, hydrologic cycling, and maybe lunar cycling. I have a link to the GOSA wesite. The paper I'm currently reading refers to temperature measurements that were taken from Upper Geyser Basin in Yellowstone National Park with an instrument similar to ours. It was found that GEIs are lengthened when the water discharge is low. They also conclude that the GEIs are effected not only by the water that is provided by the warm subsurface, but also by the colder water that is provided by the geyser surface. The GOSA link is also an interesting link for anyone who wants to know more about how geysers work:
http://www.geyserstudy.org/
Also, here is a link to the USGS real-time water data for Firehole River: http://waterdata.usgs.gov/wy/nwis/uv/%20?site_no%20=%2006037500&agency_cd%20=%20USGS measurements include temperature fluctuations and discharge rates.
I might be able to use these data for an interpretation for my 1m vs. 5m depth measurements. So far it look as though the 1m depth water is retaining surface and subsurface water (recycling the water before discharging it to the outside of the mound), whereas the 5m depth water is constantly refueling from the subsurface. Or at least this is what I hypothesize.