Posts Tagged ‘microbes’

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.

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Ocean Sampling Day 2015

July 2, 2015

Skidaway Institute participates in worldwide ocean snapshot

June 29, 2015

Scientists at the University of Georgia Skidaway Institute of Oceanography joined researchers around the globe in a worldwide Ocean Sampling Day on Sunday, June 21, the summer solstice.

This was the second year Skidaway researchers have participated in the Ocean Sampling Day event. The first was conducted last year, also on the summer solstice. The event focuses on simultaneous sampling of microbes in ocean, coastal and Great Lakes waters.

This year, 191 marine research locations—from the Rothera Research Station in Antarctica to Göteborg University in Sweden—participated. The sampling program supports international missions to provide information on the diversity of microbes, their function and their potential economic benefits.

“It’s a global effort to take a snapshot of microbes across the world’s oceans at the same time, on the same day, in this case, the summer solstice,” said Skidaway Institute professor Marc Frischer.

The Skidaway Institute team transfers a water sample from the Skidaway River during Ocean Sampling Day.

The Skidaway Institute team transfers a water sample from the Skidaway River during Ocean Sampling Day.

Frischer cited the significance of the project by describing microbes as the “engines of our planet” and said half the oxygen in the atmosphere is produced by microbes in the ocean.

Skidaway Institute scientists collected samples at two locations. One team collected and processed samples from the Skidaway River estuary immediately adjacent to the Skidaway Institute campus. That also served as part of an ongoing water-quality monitoring program Skidaway Institute has supported for more than 25 years. A second group teamed up with scientists from the National Oceanic and Atmospheric Administration Gray’s Reef National Marine Sanctuary and collected samples from Gray’s Reef. The 14,000-acre marine sanctuary is located about 17 miles off the Sapelo Island coast.

“We helped Gray’s Reef by collecting and processing their samples in the way they needed to be done,” Frischer said. “You really need a laboratory for that, and we were able to provide that.”

One goal of the global project is to note the commonalities and the differences among the microbial communities around the globe. Some of those differences were seen just in the samples collected at Gray’s Reef and at the Skidaway campus, two sites only 40 miles apart.

“We generally observe a larger number of smaller organisms out in the ocean, which makes sense because they are adapting to a system with lower nutrients,” Frischer said. “We also saw a different kind of photosynthetic organisms since there is much more light available in the ocean compared to rather turbid waters in our estuary.”

Much of the fieldwork at both Skidaway Institute and Gray’s Reef was handled by undergraduate college students gaining research experience at Skidaway Institute this summer. These included students from UGA and Savannah State University’s Research Experience for Undergraduates program.

All samples and data were sent to Bremen, Germany, for DNA extraction and sequencing to ensure maximum comparability. The resulting data will be made publicly available as soon as quality checks are finished. These cumulative samples, related in time, space and environmental parameters, will provide insights into fundamental rules describing microbial diversity and function and contribute to the blue, or oceanic, economy through the identification of novel, ocean-derived biotechnologies.

Ocean Sampling Day was jointly coordinated by Jacobs University in Bremen, Germany, and the University of Oxford in the U.K. and is part of the European Union-funded Ocean of Tomorrow research project Micro B3.

“It is really important to have a global perspective,” Frischer said. “We are glad we can participate in what they are now calling “gigascience” where we are collecting a snapshot from all over the world. It is amazing!”

Additional information on the global Ocean Sampling Day project is available at www.microb3.eu/osd.

 

 

Warming climate may release vast amounts of carbon from long-frozen Arctic soils

April 24, 2015

While climatologists are carefully watching carbon dioxide levels in the atmosphere, another group of scientists is exploring a massive storehouse of carbon that has the potential to significantly affect the climate change picture.

Aron Stubbins

Aron Stubbins

University of Georgia Skidaway Institute of Oceanography researcher Aron Stubbins is part of a team investigating how ancient carbon, locked away in Arctic permafrost for thousands of years, is now being transformed into carbon dioxide and released into the atmosphere. The results of the study were published in Geophysical Research Letters.

The Arctic contains a massive amount of carbon in the form of frozen soil—the remnants of plants and animals that died more than 20,000 years ago. Because this organic material was permanently frozen year-round, it did not undergo decomposition by bacteria the way organic material does in a warmer climate. Just like food in a home freezer, it has been locked away from the bacteria that would otherwise cause it to decay and be converted to carbon dioxide.

“However, if you allow your food to defrost, eventually bacteria will eat away at it, causing it to decompose and release carbon dioxide,” Stubbins said. “The same thing happens to permafrost when it thaws.”

Scientists estimate there is more than 10 times the amount of carbon in the Arctic soil than has been put into the atmosphere by burning fossil fuels since the start of the Industrial Revolution. To look at it another way, scientists estimate there is two and a half times more carbon locked away in the Arctic deep freezer than there is in the atmosphere today. Now, with a warming climate, that deep freezer is beginning to thaw and that long-frozen carbon is beginning to be released into the environment.

“The study we did was to look at what happens to that organic carbon when it is released,” Stubbins said. “Does it get converted to carbon dioxide or is it still going to be preserved in some other form?”

Stubbins and his colleagues conducted their fieldwork at Duvanni Yar in Siberia. There, the Kolyma River carves into a bank of permafrost, exposing the frozen organic material. This worked well for the scientists, as they were able to find streams that consisted of 100 percent thawed permafrost. The researchers measured the carbon concentration, how old the carbon was and what forms of carbon were present in the water. They bottled it with a sample of the local microbes. After two weeks, they measured the changes in the carbon concentration and composition and the amount of carbon dioxide that had been produced.

A bank of permafrost thaws near the Kolyma River in Siberia.

“We found that decomposition converted 60 percent of the carbon in the thawed permafrost to carbon dioxide in two weeks,” Stubbins said. “This shows the permafrost carbon is definitely in a form that can be used by the microbes.”

Lead author Robert Spencer of Florida State University added, “Interestingly, we also found that the unique composition of thawed permafrost carbon is what makes the material so attractive to microbes.”

The study also confirmed what the scientists had suspected: The carbon being used by the bacteria is at least 20,000 years old. This is significant because it means that carbon has not been a part of the global carbon cycle in the recent past.

“If you cut down a tree and burn it, you are simply returning the carbon in that tree to the atmosphere where the tree originally got it,” Stubbins said. “However, this is carbon that has been locked away in a deep-freeze storage for a long time.

“This is carbon that has been out of the active, natural system for tens of thousands of years. To reintroduce it into the contemporary system will have an effect.”

The carbon release has the potential to create what scientists call a positive feedback loop. This means as more carbon is released into the atmosphere, it would amplify climate warming. That, in turn, would cause more permafrost to thaw and release more carbon, causing the cycle to continue.

“Currently, this is not a process that shows up in future (Intergovernmental Panel on Climate Change) climate projections; in fact, permafrost is not even accounted for,” Spencer said.

“Moving forward, we need to find out how consistent our findings are and to work with a broader range of scientists to better predict how fast this process will happen,” Stubbins said.

In addition to Stubbins and Spencer, the research team included Paul Mann from Northumbria University, United Kingdom; Thorsten Dittmar from the University of Oldenburg, Germany; Timothy Eglinton and Cameron McIntyre from the Geological Institute, Zurich, Switzerland; Max Holmes from Woods Hole Research Center; and Nikita Zimov from the Far-Eastern Branch of the Russian Academy of Science.

26 Hours on the Marsh — November edition

November 6, 2014

Associate Professor Aron Stubbins led a 26 hour sampling program on the marsh. The team, including Thais Bittar, Robert Spencer, Zachary Tait, Megan Thompson, Alison Buchan, and Drew Steen, spent the day and night monitoring a day in the life of the microbes, gases and organic carbon molecules that form the biogeochemical milieu of the marsh. This work is part of two National Science Foundation projects involving professors and students from Skidaway Institute of Oceanography, University of Tennessee – Knoxville, and Florida State University.

Cutting edge techniques are being employed to watch the marsh creek in real time over 18 months. The sampling event shown in the time lapse video is the fall rendition of four seasonal sampling events that are recording the daily life of the creek. Manual sampling is required so that we can collect live bacteria and gas (such as carbon dioxide) samples that need to be processed by hand, immediately upon collection. The bacteria collected are being genetically characterized, so we know who was in the creek at different times of day (DNA). Then we will also determine which genes were active (RNA). This tells us what the bacteria present in the marsh were doing throughout the day.

We also record the changes in dissolved organic carbon throughout the day. Dissolved organic carbon is a major part of the global carbon cycle and so understanding its cycling is important with respect to understanding how natural carbon cycling responds to and plays a role in climate change. For the microbes in the creek, the dissolved organic carbon (DOC) is food. So by looking at which bacteria are there (DNA), what they are doing (RNA), and what types of food is present (DOC), we hope to gain a more complete understanding of the miniature world within every drop of creek water. The daily routines of these tiny bacteria and dissolved organic molecules shape the marsh ecosystem and play important roles in determining the current and future climate of our planet.

Skidaway Institute joins international project to sample the world’s waters

June 26, 2014

Scientists at the University of Georgia Skidaway Institute of Oceanography participated in Ocean Sampling Day—an ambitious, international project to produce a single-day snapshot of microbial populations around the world. On Saturday, June 21, researchers collected water samples at 185 global sites, ranging from Antarctica to the Arctic Ocean and from New Zealand to Iceland.

This was the first global, simultaneous sampling of microbes in ocean, coastal and Great Lakes waters. The sampling program will support international missions to provide information on the diversity of microbes, their functions and their potential economic benefits.

Skidaway Institute scientists collected water at two locations. One team collected and processed samples from the Skidaway River, which is immediately adjacent to the Skidaway Institute campus. This activity will also be part of an ongoing water-quality monitoring program that Skidaway Institute has supported for more than 25 years. A second group teamed up with scientists from NOAA’s Gray’s Reef National Marine Sanctuary and collected samples from Gray’s Reef. The 14,000-acre marine sanctuary is located approximately 17 miles off the coast of Georgia’s Sapelo Island.

Kevin McKenzie and Tina Walters collect samples from the Skidaway Institute dock in the Skidaway River.

Kevin McKenzie and Tina Walters collect samples from the Skidaway Institute dock in the Skidaway River.

“Simultaneous sampling provides a reference for direct comparison between different types of ecosystems,” said Skidaway Institute scientist Marc Frischer, who supervised Skidaway Institute’s activities. “The observation of similarities and differences between ecosystems provides a context for understanding how complex natural aquatic ecosystems work.”

Scientists at all the sites used the same protocol to collect and process their samples. The samples will be analyzed at Jacobs University in Bremen, Germany. However, shipping liters of water would be both impractical and expensive. So the Skidaway Institute collection team of Tina Walters, Kevin McKenzie and LaGina Frazier ran the water through filters fine enough to collect the microbes and other particulates in the water. The filters, which are about the size of a lipstick tube, were then frozen to minus 80 degrees Celsius and shipped to Germany where they will be analyzed.

“It is important that this program provides a standard method for sample collection and analysis,” Frischer said. “Having a standard set of methods makes it easier to make direct comparisons.”

According to Frischer, the Ocean Sampling Day project will advance scientists’ understanding of the diversity and role of microbes in aquatic environments. Microbes, such as viruses, bacteria, algae, fungi and microzooplankton, account for the majority of biomass and genetic diversity of life on Earth and they play critical roles in all living systems.

“Because microbes play such a central role in ecosystem function, a deeper understanding of them in aquatic systems will advance our understanding of every aspect of these systems,” Frischer said. “It is hard to predict direct benefits, but the information we gain will certainly be relevant to many issues that are of concern, including climate change, fisheries, water quality, human impacts, discovery of novel pharmaceuticals, and diseases of important fishery organisms.”

The Ocean Sampling Day project was coordinated jointly by Jacobs University and the University of Oxford, U.K. The effort was launched under the umbrella of the European-funded project Micro B3, which aims to boost marine research and innovation opportunities.

Additional information on the global Ocean Sampling Day project is available at http://www.microb3.eu/osd.

Spring In Barrow April 23 – May 4, 2011

April 25, 2011

23 April 2011

Dr. Marc Frischer

Hi All, it’s back to Barrow Alaska for another sampling adventure.  As I’ve discussed before in this blog, the intent of our project is to reach a new and quantitative understanding concerning how microbes (bacteria and phytoplankton) may respond to climate induced changes in the Arctic.

Although there is a very strong consensus among scientists that the world’s climate is changing (For more information, see the footnote at the bottom of this posting.), particularly in the Polar Regions, our understanding of how the organisms will respond is quite limited.  At the base of the food web are the microbes and these are the primary focus of our investigations. These tiny organisms are responsible for at least half of the oxygen production (and consumption) on the planet, almost all of the nutrient regeneration, and are the food that support the diet of everything including, to name a few,  fish, seals, whales, and humans.  In other words, it’s very important that we understand how these microscopic organisms will respond to ongoing climate change, especially here in the Arctic.

To answer these questions we are visiting the Arctic three times a year in the winter, spring, and summer, to make measurements of a large number of microbial parameters and to conduct experiments that will help us understand how the microbes may be affected by climate change.  We are sampling at different seasons to account for the astounding amount of seasonal variation that occurs naturally during a year.  We can’t sample in the fall because that would interfere with whaling activities that are an important cultural component of the community in Barrow Alaska where our studies are being conducted.

Our team includes scientists from the Skidaway Institute of Oceanography, the University of Georgia, and the Virginia Institute of Marine Sciences.  In addition, on this trip a middle school teacher (Lolli Garay) from the Red School in Houston, Texas and an artist (Adriane Colburn) from the University of Georgia are joining us in an effort to help communicate and share information about our efforts and results outside of the science community.

This springtime trip will be the fourth in our 3-year project and the second (and last) time during this project that we will sample during the spring.

The Trip – Saturday 23 April, 2011

Although this is our fourth trip to Barrow Alaska and so a lot of what we are doing is starting to become routine, it still took a lot of planning to get ready for this trip.  Since our return in February from our last trip, in addition to processing the winter samples, we’ve been busy planning and organizing the logistics for this trip.  Victoria Baylor took charge of most of this effort.

My graduate student from Savannah State University, Zac Tait, is also planning to start some new experiments related to his thesis research, so that took some additional planning efforts.

Finally we were ready.  This time we took a different route through Chicago to travel the 6,000 plus miles to Barrow.

Map of route from Savannah GA to Barrow, AK.

This route gets us to Barrow in a single day, but what a day!  The way back will be worse though, with a 10-hour layover in Anchorage and another 5-hour layover in Chicago.  But the route wasn’t without benefits as we were able to get a Chicago Hotdog for lunch.

Lunch at Gold Coast Hot Dogs in Chicago’s O’Hare airport.

Unfortunately, Zac lost his luggage along the way.  Besides his clothes, Zac packed a number of important pieces of equipment in his bag so we’re really hoping it’s not lost forever.  We made it to Barrow’s Will Rogers airport after a spectacular flight over Alaska’s Northslope passing over the frozen Yukon River and following the pipeline into Prudhoe Bay.

Alaska’s North Slope from the air.

Alaska pipeline from the air.

We arrived in Barrow in the early evening on Saturday but as we stepped off the plane it was immediately apparent how different it was compared to the winter.  First of all, it was sunny!  Last time we were here the sun was just appearing after 3 months of being absent.  Although there was light, it was perpetual twilight time.  Today there was 18 hours of sun and its light from about 2 am to 11:30 pm and on May 11, a week after we depart the sun will be up for 24 hours a day until the next sunset on August 1st.  Its also considerably warmer though still well below freezing.  Right now its -4°F (-20°C).  There are also other very visible changes.  The sea ice is beginning to break-up and is piled-up on the beach as a result of past storms.  The snow on the streets is also beginning to melt (because of all the sunlight) and the roads are dusty rather than snowy.

Other evidence of the long winter are several ice and snow carvings that have appeared around town, some rivaling Mount Rushmore but with a more Arctic theme.

Ice carvings in downtown Barrow.

Polar bear ice carving along the coastal road.

But, despite the change of season returning to Barrow was a bit like coming home.  We were picked-up at the airport by Tony Kaleak and Frantz Brower who are members of our logistic support group, UMIAQ.  Tony and Brower (no one calls him Frantz) updated us on the recent gossip and many organizational changes that have occurred since we were last in town and got us checked in to our living and working quarters.  The rest of the group won’t arrive until tomorrow evening so we set about surveying our equipment and space and planning for the next day.

Around 8pm we called it quits got some dinner at our favorite Barrow restaurant “Arctic Pizza” and tried to sleep.  It was tough though since the sun didn’t set until 11:30 and rose again around 2am.

Off to Alaska!

August 25, 2010

Professor Marc Frischer and research technician Victoria Baylor are traveling to Point Barrow, Alaska for field work on their project to study the effects of global climate change on the coastal environment there.

Dr. Frischer will be blogging about their adventures. Here is the first report.

Notes from the Arctic — We’re on our way!  August 23 & 24th, 2010.

Today was a travel day.  After months of planning, preparation, ordering supplies, and shipping we’re finally off.  This will be our second sampling trip to Barrow Alaska, the most northern point in the continental US.  Our goal is to collect information concerning the response of the organisms at the very base of the food web (the microbes) to climate change.  Arctic ecosystems are considered to be the most sensitive environments to the effects of climate change.

The journey itself is an adventure.  Victoria Baylor and I left Savannah on Monday August 23,  early in the morning traveling to Atlanta, Minneapolis, Anchorage, Fairbanks, Prudhoe Bay, and finally to Barrow — racking up nearly 5,000 frequent flier miles along the way.

Marc Frischer (right) with friend in Anchorage hotel lobby

It never ceases to amaze me how big our country is and yet, at the same time, how fragile it is. This is certainly one of the great paradoxes of our times.  Amazingly, with the exception of a few minor delays that we’ve all come to expect whenever we travel by air, the trip itself was thankfully uneventful.

Sunset in Anchorage

After arriving in Barrow and being greeted by the rest of our team who had arrived earlier, we spent the next 14 hours readying our equipment and laboratories for the first sampling expedition tomorrow. Our team, in addition to Victoria and myself, includes Debbie Bronk, Quinn Roberts, and Rachel Sipler from the Virginia Institute of Marine Sciences, and Tara Connelly and Karrie Sines from the University of Georgia. Our goal is to sample coastal water just a couple of miles offshore at a standard station we have previously established.  The last time we were here in April, we had to access our site on snow machines and had to drill a hole in the ice to sample the water below.

Now in August, the ice is melted and we’ll be traveling to our site in a small boat charted from a native whaling captain. Currently the temperature in Barrow is in the upper 40’s (F) and, at least for now, sunny. For sure, one thing that really slaps you in the face up here is the extreme climate.

Stay tuned for more, the fun really begins tomorrow!

Marc Frischer

Students grow bacteria gardens

October 26, 2009

Often students grow vegetable gardens for a science project, but some local students took on an entirely different task. They grew bacteria cultures. It was one of several educational activities at Skidaway Institute of Oceanography’s annual open house — Skidaway Marine Science Day — on Saturday, October 10.

The bacteria project was the brainchild of Skidaway Institute scientist Marc Frischer and student assistant LaGina Frazier.

Marc Frischer (right) and LaGina Frazier at their Skidaway Marine Science Day exhibit

Marc Frischer (right) and LaGina Frazier at their Skidaway Marine Science Day exhibit

“Microbes get a bad rap,” said Frazier, who is also a biology student at Savannah State University. “We wanted to show the students that bacteria are all around them, and most bacteria are beneficial.”

Visitors to the Frischer lab exhibit at Skidaway Marine Science Day were given a cotton swab and told to wipe it anything they wanted to collect some bacteria. A total of 98 students participated. They roamed the campus, swabbing plants, trees, buildings and each other.

After a quick demonstration, Frazier and the Frischer lab volunteers let the students “streak” (spread) their sample onto a culture dish. Each dish had an ID number which was given to the student. Following the collection, Frazier grew the bacteria cultures in Skidaway Institute’s microbiology lab. After a week, the cultures were photographed and posted on Skidaway Institute’s Web site. The participants used their ID number to view their dish and compare their results with the other participants.

One student's fast-growing bacteria culture

One student's fast-growing bacteria culture

“The great thing about using our Web site is the students don’t have to come back out here to see the results of their exercise,” said Frazier. “They can see the results of their microbe collection by visiting our Web site.”

Frazier said she could tell the students obtained a wide variety of different microbes just from a visual inspection. There are no plans to test the cultures any further and specifically indentify each one.

“We hope this exercise taught the students a little about a part of their world they can’t usually see with the naked eye,” said Frazier. “Maybe some of them may be inspired to study science seriously as they advance in school.”

The results of the project can be seen here.