Posts Tagged ‘biology’

UGA Skidaway Institute scientists study microbial chemical warfare

April 18, 2017

In the battlefield of the microbial ocean, scientists have known for some time that certain bacteria can exude chemicals that kill single-cell marine plants, known as phytoplankton. However, the identification of these chemical compounds and the reason why bacteria are producing these lethal compounds has been challenging.

Now, University of Georgia Skidaway Institute of Oceanography scientist Elizabeth Harvey is leading a team of researchers that has received a $904,200 grant from the National Science Foundation to fund a three-year study into the mechanisms that drive bacteria-phytoplankton dynamics.

Researcher Elizabeth Harvey examines a part of her phytoplankton collection.

Understanding these dynamics is important, as phytoplankton are essential contributors to all marine life. Phytoplankton form the base of the marine food chain, and, as plants, produce approximately half of the world’s oxygen.

“Bacteria that interact with phytoplankton and cause their mortality could potentially play a large role in influencing the abundance and distribution of phytoplankton in the world ocean,” Harvey said. “We are interested in understanding this process so we can better predict fisheries health and the general health of the ocean.”

This project is a continuation of research conducted by Harvey and co-team leader Kristen Whalen of Haverford College when they were post-doctoral fellows at Woods Hole Oceanographic Institution. They wanted to understand how one particular bacteria species impacted phytoplankton.

A microscopic view of a population of phytoplankton

“We added the bacteria to the phytoplankton and the phytoplankton died,” Harvey said. “So we became very interested in finding the mechanism that caused that mortality.”

They identified a particular compound, 2-heptyl-4-quinlone or HHQ, that was killing the phytoplankton. HHQ is well known in the medical field where it is associated with a bacterium that can cause lung infections, but it had not been seen before in the ocean. The team will conduct laboratory experiments to determine the environmental factors driving HHQ production in marine bacteria; establish a mechanism of how the chemical kills phytoplankton; and use field-based experiments to understand how HHQ influences the population dynamics of bacteria and phytoplankton.

“This project has the potential to significantly change our understanding of how bacteria and phytoplankton chemically communicate in the ocean.” Harvey said.
The project will also include a strong education component. The researchers will recruit undergraduate students, with an effort to target recruitment of traditionally under-represented groups, to participate in an intense summer learning experience with research, field-based exercises and some classroom work.

“The idea is for the students to return to their home institutions at the end of the summer, but to continue to work with us on this project,” Harvey said. “This will be a unique opportunity to offer students cross disciplinary training in ecology, chemistry, microbiology, physiology and oceanography.”

In addition to Harvey and Whalen, the research team includes David Rowley of the University of Rhode Island.

NOTE:  A complementary video with an interview with Dr. Harvey is available at http://www.skio.uga.edu/news/videos/

 

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Diving Deep Into Phytoplankton: How Tiny Ocean Organisms Help You Breathe — An Interview With GPB

March 21, 2017

You can hear Dr. Elizabeth Harvey’s interview with Georgia Public Broadcasting here.

“You may have learned in school that photosynthesis is how plants use sunlight to turn water into hydrogen and carbon dioxide, its food, and oxygen, which it releases into the air for all of us to breathe. But photosynthesis doesn’t just happen on land – it happens in the ocean.

Phytoplankton are tiny, single-celled algae basically, that live in the ocean,” explained Liz Harvey, Assistant Professor of Marine Science at University of Georgia’s Skidaway Institute of Oceanography, which is located on Skidaway Island. “They conduct photosynthesis just like land plants, trees and grass do, and they are prolific. They grow everywhere in the ocean.”

“There’s lots of different types of phytoplankton, they can do lots of different things,” Harvey continued. “But I think if you take one thing home, it’s that phytoplankton are important  as they produce about fifty percent of the oxygen that you breathe. Land plants produce about half and then phytoplankton produce about half. These tiny little microscopic organisms are actually very, very important for helping to sustain life on earth. “

Producing half of earth’s supply of oxygen is only half of this organism’s job.

“Phytoplankton are eaten quite regularly and serve as food for other small organisms, which are then eaten by larger organisms which eventually lead up to fish, whales and sharks and all the really cool things that we think about when we think about the ocean,” Harvey said. “Although I would think phytoplankton are really cool too! So they serve a very important purpose to sustain the health and viability of fisheries. That’s another reason why we’re so concerned about what they’re doing, where they are, what types of phytoplankton are around – because they serve this purpose in supporting the larger fisheries as a whole.”

Tiny but voracious marine organism studied — video

February 8, 2017

Tiny but all-consuming marine organism focus of UGA Skidaway Institute study

February 8, 2017
Marc Frischer

Marc Frischer

Doliolids are tiny marine animals rarely seen by humans outside a research setting, yet they are key players in the marine ecosystem, particularly in the ocean’s highly productive tropical and subtropical continental margins, such as Georgia’s continental shelf. University of Georgia Skidaway Institute of Oceanography scientist Marc Frischer is leading a team of researchers investigating doliolids’ role as a predator in the marine food web.

Doliolids are small, barrel-shaped gelatinous organisms that can grow as large as ten millimeters, or about four tenths of an inch. They are not always present in large numbers, but when they bloom they can restructure the marine food web, consuming virtually all the algae and much of the smaller zooplankton.

A doliolid with a cluster of juvenile doliolids on its tail. Actual size is approximately three millimeters, or one eighth inch.

A doliolid with a cluster of juvenile doliolids on its tail. Actual size is approximately three millimeters, or one eighth inch.

“The goal of this particular study is to find out what the doliolids are eating quantitatively,” Frischer said. “This is so we can understand where they fit in the food web.”

Scientists know from laboratory experiments what doliolids are capable of eating, but they don’t know what they actually do eat in the wild. They are capable of eating organisms as small as bacteria all the way up to much larger organisms.

“What they are eating and how much are they eating from the smorgasbord that is available to them, that is the question,” Frischer said. “We are investigating how much of those different prey types they are really eating out there across the seasons.”

The project involves intensive field work, including 54 days of ship time on board UGA Skidaway Institute’s Research Vessel Savannah. During the cruises they conduct trawls using special plankton nets to collect the doliolids. They also collect water samples to understand the conditions where the doliolids thrive.

Graduate students Lauren Lamboley and Nick Castellane deploy a plankton net from the Research Vessel Savannah.

Graduate students Lauren Lamboley and Nick Castellane deploy a plankton net from the Research Vessel Savannah.

“We take the doliolids and the water samples back to the laboratory, and that is where the magic begins,” Tina Walters, Frischer’s laboratory manager said.

Because the animals are gelatinous and very delicate, the researchers cannot use classical microscopic techniques to dissect the animals and analyze their gut content. Instead they extract DNA from the animals’ gut and use sequence-based information to determine what the doliolid ate.

“We go through a process called quantitative PCR,” Walters said. “So even though we can’t see the prey in a doliolid’s gut, because the prey have unique DNA sequences, we can identify and quantify them using a molecular approach.”

The three-year project is funded by a $725,000 grant from the National Science Foundation and will run until February 2018. Frischer’s collaborator on the project is Deidre Gibson from Hampton University. Gibson received her Ph.D. from the University of Georgia in 2000, and did much of her graduate research at Skidaway Institute with Professor Gustav Paffenhöfer.  In addition to Walters, Savannah State University graduate student Lauren Lamboley is part of the team, along with a number of students at Hampton University. Several undergraduate research interns have also participated in the project, gaining hands-on research experience. Frischer is also working with the Institute for Interdisciplinary STEM Education at Georgia Southern University to engage K-12 teachers by inviting them to participate in the research cruises.

New imaging lab in the news

January 23, 2017

There was a nice article in Saturday’s Savannah Morning News regarding a new imaging lab at UGA Skidaway Institute.

http://savannahnow.com/news/2017-01-20/automated-microscopes-aid-crucial-ocean-work-skidaway

UGA Skidaway Institute develops cutting-edge microbial imaging laboratory

December 7, 2016

A team of researchers from the University of Georgia Skidaway Institute of Oceanography has received a $226,557 grant from the National Science Foundation to acquire state-of-the-art imaging equipment to investigate microorganisms from the tiniest viruses to larger zooplankton. The equipment will be housed in UGA Skidaway Institute’s new Laboratory for Imaging Microbial Ecology, or LIME.

Researcher Elizabeth Harvey leads the research team that also includes UGA Skidaway Institute scientists Julia Diaz, Marc Frischer, James Nelson and James Sanders.

The equipment will improve Skidaway Institute’s capability to conduct field and laboratory experiments by automating many viewing methods.

“Anyone who uses a microscope will tell you that it is both tedious and time consuming,” Harvey said. “This equipment will allow us to enumerate and analyze microbes and other planktonic organisms much faster, and will allow us to do more large-scale projects than we could in the past.”

UGA Skidaway Institute researchers Tina Walters, Marc Frischer and Karrie Bulski practice running zooplankton samples on the FlowCam, a new instrument that is part of LIME.

UGA Skidaway Institute researchers Tina Walters, Marc Frischer and Karrie Bulski practice running zooplankton samples on the FlowCam, a new instrument that is part of LIME.

Much of the equipment will also have imaging capability so researchers will be able to do more detailed measurements on the size and shape of the tiny organisms and how that might relate to the health of an ecosystem.

Marine microbes are an essential component of all marine ecosystems and they play central roles in mediating biogeochemical cycling and food web structure.

“They are the things that drive all other processes in the ocean,” Harvey said. “They play a really important role in the way nutrients, oxygen and carbon are cycled through the ocean. We care a lot about those processes because they impact our climate, fisheries and the ocean’s overall health.”

A sampling of phytoplankton   imaged by the LIME's FlowCam.

A sampling of phytoplankton imaged by the LIME’s FlowCam.

The benefits of LIME will be shared beyond Skidaway Institute’s science team. Harvey envisions it as a regional center for microbial imaging, available to any other researchers who need the capability.

“Anyone is welcome to come here and get trained to use them,” she said. “They just need to contact me and we can make arrangements.”

Some of the equipment is already in place, while other pieces have not been delivered. Harvey anticipates all the equipment being functional by mid-2017.

Fall black gill cruise rolls out new research

November 10, 2016

The University of Georgia Skidaway Institute of Oceanography entered the fourth year of its black gill research program with a daylong cruise on board the Research Vessel Savannah and the introduction of a new smartphone app that will allow shrimpers to help scientists collect data on the problem.

Led by UGA scientists Marc Frischer, Richard Lee, Kyle Johnsen and Jeb Byers, the black gill study is being conducted in partnership with UGA Marine Extension and Georgia Sea Grant, and is funded by Georgia Sea Grant.

Black gill is a condition Georgia shrimpers first noticed in the mid-1990s. Many shrimpers have blamed black gill for poor shrimp harvests in recent years, but until Frischer began his study, almost nothing was known about the condition. Now the researchers know black gill is caused by a parasite—a single-cell animal called a ciliate—although the exact type of ciliate is still a mystery.

The October cruise had three goals. The first was simply to collect data and live shrimp for additional experiments.

 

“We were able to collect enough live shrimp in good shape to set up our next experiment,” Frischer said. “We are planning on running another direct mortality study to investigate the relationship between temperature and black gill mortality. This time, instead of comparing ambient temperature to cooler temperatures as we did last spring and summer, we will investigate the effects of warming.”

Researchers Marc Frischer (UGA Skidaway Institute), Brian Fluech and Lisa Gentit (both UGA Marine Extension and Georgia Sea Grant) examine shrimp for signs of black gill.

Researchers Marc Frischer (UGA Skidaway Institute), Brian Fluech and Lisa Gentit (both UGA Marine Extension and Georgia Sea Grant) examine shrimp for signs of black gill.

If his hypothesis is correct, Frischer believes researchers would expect that raising fall water temperatures to warmer summer levels in a laboratory setting will induce black gill associated mortality in the shrimp caught in the fall.

Those studies will be compared to those that are being conducted in South Carolina in a slightly different manner. Frischer expects the results should be similar.

“However, as it goes with research, we are expecting surprises,” Frischer continued. “We also collected a good set of samples that will contribute to our understanding of the distribution and impact of black gill.”

A second goal was to introduce and begin field testing a new smartphone application developed by Johnsen. The app is intended to be a tool that will allow shrimp boat captains and recreational shrimpers to assist the researchers by filling some of the holes in the data by documenting the extent of black gill throughout the shrimp season. The Georgia Department of Natural Resources conducts surveys of the shrimp population up and down the coast throughout the year. However, those surveys do not provide the researchers with the rich data set they need to really get an accurate assessment of the black gill problem.

A sample screen shot of the black gill smartphone application.

A sample screen shot of the black gill smartphone application.

“Instead of having just one boat surveying the prevalence of black gill, imagine if we had a dozen, or 50 or a hundred boats all working with us,” Frischer said. “That’s the idea behind this app.”

The fishermen will use the app to document their trawls and report their data to a central database. Using GPS and the camera on their smartphone, they will record the location and images of the shrimp catch, allowing the researchers to see what the shrimpers see. If repeated by many shrimpers throughout the shrimping season, the information would give scientists a much more detailed picture of the prevalence and distribution of black gill.

“The app is complete and available on the app store, but we are still in the testing stages,” Johnsen said. “We want to make sure that it will be robust and as easy to use on a ship as possible before widely deploying it.”

Recruiting, training and coordinating the shrimpers will be the responsibility of UGA Marine Extension and Georgia Sea Grant.

“I think it should be entirely possible to at least have a small group of captains comfortable and ready to start using it when the 2017 season begins,” Frischer said.

Johnsen is excited about the app for what it can provide to the shrimping and research community, but also the implications it has for using apps to involve communities in general.

“There is still work to be done to improve the usability of these systems,” he said. “But I’m confident that we are going to see an increasing number of these ‘citizen science’ applications going forward.”

The final aim of the cruise was to bring together diverse stakeholders, including fishery managers, shrimpers and scientists, to spend the day together and share ideas.

“This was a good venue for promoting cross-talk among the stakeholder groups,” Frischer said. “I had many good conversations and appreciated the opportunity to provide a few more research updates.”

Georgia DNR's Pat Geer sorts through the marine life caught in a trawl net.

Georgia DNR’s Pat Geer sorts through the marine life caught in a trawl net.

Frischer says he thinks the communication and cooperation among the various stakeholder groups has improved dramatically since the beginning of the study. He recalled that when the study began in 2013, tensions were high. Shrimpers were angry and demanded that something be done to address the problem of black gill. Meanwhile, fishery managers were unclear if black gill was even causing a problem and frustrated that no one could provide them any reliable scientific advice. The research community had not been engaged and given the resources to pursue valid investigations.

“In 2016, we still have black gill. The fishery is still in trouble, but it does feel like we are at least understanding a bit more about the issue,” Frischer said. “Most importantly, it is clear that all of us are now working together.

“My feeling is that the opportunity for us to spend a day like that together helps promote understanding, communication and trust among the shrimpers, managers and researchers.”

Marc Frischer on morning radio program Thursday & Friday

July 28, 2016

Marc at WTKS w

Dr. Marc Frischer was a guest on the WTKS Radio morning show this morning to talk about black gill in shrimp. Thanks to Bill Edwards and Laura Picone for the invitation. They also taped a second interview which will be aired tomorrow morning. In Savannah, it’s 1290 on the AM dial.

Savannah newspaper article features UGA Skidaway Institute and R/V Savannah

July 5, 2016

The Savannah Morning News published a nice article over the weekend on the Rivers to Reefs teacher development program produced by Gray’s Reef National Marine Sanctuary. Although the Rivers to Reefs is not a Skidaway Institute program, the last day of the experience was on board the Research Vessel Savannah. The ship and Skidaway scientist Marc Frischer are prominently featured. Here is a link to the article and also to a slide show on the SMN Web site. Kudos to Dash Coleman for an excellent article and beautiful pictures.

http://savannahnow.com/education-news-news/2016-07-02/georgia-teachers-get-muddy-drenched-and-familiar-fish-trip-savannah

Photo Slide Show:

http://savannahnow.com/slideshow/2016-06-30/rivers-reefs-2016-expedition-grays-reef-national-marine-sanctuary#slide-1

UGA Skidaway Institute team studies nutrient levels in Georgia’s coastal estuaries

June 6, 2016

How much of a nutrient load is too much for Georgia’s coastal rivers and estuaries? A research team from University of Georgia Skidaway Institute of Oceanography is helping Georgia’s Environmental Protection Division answer that question. Their primary focus is on the estuary at the mouth of the Ogeechee River, where the researchers are measuring nutrient concentrations and other water properties to determine how they change as they flow through the estuary.

The nutrients are chemicals like nitrates and phosphates typically introduced into the rivers by agricultural runoff, storm water or sewage effluents, and the natural decay of organic matter in the river. When present in high concentrations, the nutrients act as fertilizer, promoting excessive growth of marine plants, especially microscopic marine plants called phytoplankton.

Researcher Kate Doyle lowers a sensor package into the water to measure salinity, temperature and depth.

Researcher Kate Doyle lowers a sensor package into the water to measure salinity, temperature and depth.

Elsewhere on the East Coast, excessive nutrients in estuaries have been linked to toxic algal blooms that can cause fish kills or shellfish closures. Death and decay of algal blooms by bacteria can drive oxygen concentrations down to levels that are unhealthy for other marine life. These are not presently known to be significant problems in Georgia’s waters, but scientists and regulators do not know what the thresholds are for developing water quality problems.

“The Georgia EPD wants to know how much nitrogen is coming down the river and whether it has any consequences when it gets to the estuary,” said UGA Skidaway Institute scientist William Savidge. “It doesn’t really matter if you have high nutrient concentrations if it is not having a harmful effect.”

The EPD is interested in these issues because they are mandated by the Environmental Protection Agency to set limits on nutrient levels for Georgia’s estuaries. Savidge describes the mandate as a difficult problem for several reasons.

“There is not any current and systematic information on nutrient conditions in most of the estuaries,” he said, “nor is there much information on the consequences of nutrient availability in the estuaries, and it’s those consequences that are the most important.”

They are currently mapping the biological and chemical properties of the Ogeechee River estuary each season to assess the nutrient changes throughout the year and to see what effects can be seen in the river and the estuary. Twice every quarter for the last year, the researchers have followed the incoming tide and sampled the river continuously as they moved upstream from the mouth of the estuary to fresh water. They used an onboard set of sensors to obtain continuous surface measurements of temperature, salinity, dissolved oxygen, chlorophyll (indicative of phytoplankton), turbidity and colored dissolved organic matter. In addition to the continuous surface measurements, the team stopped periodically and collected water samples from the bottom and throughout the water column. The product of each of these expeditions was a detailed map of conditions on the river, and when and where they are changing.

Researcher Lixin Zhu filters larger-volume surface water samples collected from the flow-through system to analyze for dissolved organic carbon.

Researcher Lixin Zhu filters larger-volume surface water samples collected from the flow-through system to analyze for dissolved organic carbon.

As they expected, Savidge and his team observed a wide range of conditions depending on the season. Nutrient inputs tend to be highest in the spring when agricultural fields are fertilized.

“Nutrient delivery is high in the spring, but we don’t have a high chlorophyll concentration in the Ogeechee River because, presumably, the nutrients are being washed off into the coastal ocean before any effect is noticed,” Savidge said

On the other hand, chlorophyll levels — which indicate phytoplankton population — are highest in the summer. Low summer river flow means water remains in the system longer. When combined with more sunlight and warmer temperatures, this slow flow this allows more time for the microscopic plants to grow.

In addition to sampling the Ogeechee River, the team is also conducting a smaller sampling project in the Altamaha River for comparison purposes.

Field work on the project will end in June, and Savidge expects to report the team’s findings to Georgia EPD by mid-summer.

“The Georgia EPD is going to have to balance the potential negative risks of nutrient loading versus the economic consequences of restricting nutrient additions,” Savidge said. “If, for example, most of the nutrient additions are agricultural, and that is creating problems downstream, the Georgia EPD may be forced by EPA to regulate nutrient additions, either by restricting how much fertilizer is placed on fields or mandating larger buffer zones around rivers and creeks.”

In addition to Savidge, the research team includes UGA Skidaway Institute scientists Jay Brandes and Aron Stubbins, research associate Kate Doyle and graduate student Lixin Zhu. UGA researchers Brock Woodson and Mandy Joye are also contributing.