Stories tagged microbes

Yup, it's Friday.
So let's not beat around the bush.

Science FridayCourtesy Science Friday

This week,

"Malcolm Beck was farming organically in the 1950s, and that's how he got into compost. What started out as a little manure pile on his farm became a 40-acre compost-processing business five decades later. Beck sold his company, Garden Ville, but still works there and is constantly experimenting with different fertilizer formulas--from bat guano to earthworm tea.

When San Antonio’s Malcolm Beck got into the compost business over fifty years ago, many people had never heard of compost, Beck says. Beck began making it for his organic farm and found that his compost more profitable than produce. Science Friday stopped by for a tutorial in the art of composting.

Malcolm Beck's website

RV Melville
RV MelvilleCourtesy WHOI
Being on a ship exploring the oceans: how cool is that?! If you can't be on the ship, or maybe you get seasick and don't want to be, check out videos from a real oceanography expedition.

An entire series is now on Science 360: The Knowledge Network. YouTube videos are filtered from some classrooms. Since Science 360 is sponsored by the National Science Foundation, their videos have passed a high academic standard and are not filtered.

Marine Microbes: Come see videos about us!
Marine Microbes: Come see videos about us!Courtesy C-MORE
The Center for Microbial Oceanography (C-MORE), headquartered at the University of Hawai`i, conducted the BiG RAPA oceanographic expedition. The C-MORE scientists sailed from Chile to Easter Island, making discoveries about micro-life in one of the least explored areas of the world's ocean.

Welcome aboard!

May
18
2011

R/V Hespérides, docked at Aloha Tower in Honolulu, Hawai`i
R/V Hespérides, docked at Aloha Tower in Honolulu, Hawai`iCourtesy C-MORE
How would you like to be aboard a ship, circumnavigating the globe, collecting samples from the world’s ocean?

That’s exactly what Spanish oceanographers are doing on their Malaspina Expedition aboard the Research Vessel, R/V Hespérides. Scientists and crew left southern Spain in December, reached New Zealand in mid-April, and recently arrived in Hawai`i. The expedition's primary goals are to:

  • build upon the historic 1789-1794 Malaspina expedition to promote interest in marine sciences among the Spanish public, particularly the nation’s youth
  • collect oceanographic and atmospheric data -- chemical, physical and biological – that will help evaluate the impact of global change
  • explore the variety of marine life, including microbes, especially those living in the deep sea
  • CTD: As this oceanographic instrument is lowered over the side of a ship, each gray Niskin “bottle” can be electronically triggered to collect a seawater sample from a different ocean depth.
    CTD: As this oceanographic instrument is lowered over the side of a ship, each gray Niskin “bottle” can be electronically triggered to collect a seawater sample from a different ocean depth.Courtesy C-MORE
    In connection with the latter two goals, the Malaspina scientists met with their colleagues at the Center for Microbial Oceanography: Research and Education (C-MORE). The two groups of scientists are working together. "We can exchange data on the local effects, what's happening around the Hawaiian Islands, and they can tell us what's happening in the middle of the Pacific," said Dr. Dave Karl, University of Hawai`i oceanography professor and Director of C-MORE.

    The Malaspina-C-MORE partnership is the kind of cooperation that can help solve environmental problems which stretch beyond an individual nation’s borders. The R/V Hespérides has now left Honolulu on its way to Panama and Colombia. From there, the scientists expect to complete their ocean sampling through the Atlantic Ocean and return to Spain by July. Buen viaje!

May
02
2011

the ocean's 5 major gyres
the ocean's 5 major gyresCourtesy NOAA
We often talk about the ocean ecosystem. And, indeed, there is really just one, world-wide ocean, since all oceans are connected. An Indian Ocean earthquake sends tsunami waves to distant coasts. Whitecaps look as white anywhere in the world. The ocean swirls in similar patterns.

However, oceanographers do find differences from place to place. For example, let’s take a closer look at the chemistry of two swirls, or gyres as they’re more properly called. Scientists have found a micro difference between the North Atlantic Gyre and the North Pacific Gyre. The Atlantic generally has really low levels of phosphorus, measurably lower than the North Pacific Gyre.

the element phosphorus among its neighbors in the Periodic Table of the Elements
the element phosphorus among its neighbors in the Periodic Table of the ElementsCourtesy modified from Wikipedia
Phosphorus is a very important element in living things. For example, it’s a necessary ingredient in ATP (adenosine tri-phosphate), the energy molecule used by all forms of life. Phosphorus is picked up from seawater by bacteria. All other marine life depends upon these bacteria, either directly or indirectly, for P. Therefore, if you’re bacteria living in the impoverished North Atlantic Gyre, you’d better be really good at getting phosphorus.

And they are!

Oceanographers at the Center for Microbial Oceanography: Research and Education (C-MORE) at the University of Hawai`i have made an important discovery. C-MORE scientists Sallie Chisholm, based at the Massachusetts Institute of Technology and her former graduate student Maureen Coleman, now a scientist at the California Institute of Technology, have been studying two species of oceanic bacteria. Prochlorococcus is an autotrophic bacterium that photosynthesizes its own food; Pelagibacter, is a heterotrophic bacterium that consumes food molecules made by others.

Pacific HOT and Atlantic BATS Stations: Microbial samples were collected at each location.
Pacific HOT and Atlantic BATS Stations: Microbial samples were collected at each location.Courtesy C-MORE
Drs. Chisholm and Coleman took samples of these two kinds of bacteria from both the Atlantic and Pacific Ocean. The Atlantic samples were collected by the Bermuda Atlantic Time-Series (BATS) program. The Pacific samples were collected in the North Pacific Gyre (about 90 miles north of Honolulu) by the Hawai`i Ocean Time-Series (HOT) program. The scientists discovered surprising differences in the genetic code of the bacteria between the two locations:

  • First of all, the Atlantic populations of both bacterial species have more phosphorus-related genes compared to their Pacific cousins. (Picture Atlantic microbes in Superman outfits with a big "P" on their chests!)
  • Secondly, in the Atlantic, Prochlorococcus has different kinds of P-related genes compared to Pelagibacter. Perhaps this means the two microbial species have evolved over time to use different phosphorus sources, to avoid competing with one another for this limited resource.

Drs. Chisholm and Coleman have discovered important micro differences between bacteria of the same species in two oceanic gyres. Now we can better understand how these microbes are working to recycle an important nutrient beneath the whitecaps.

Reference: October 11, 2010 issue of the Proceedings of the National Academy of Sciences

Apr
13
2011

Earth, our place in space
Earth, our place in spaceCourtesy NASA
Life scientists study…well, life. They want to know everything about living things on planet Earth. One of the first things biologists want to know is who’s here. What kinds of plants and animals live in a forest? --or in a field? –or in the ocean?

If you’re an oceanographer who studies marine mammals, perhaps you’d go to sea on a ship with a good pair of binoculars and hunt for whales. As you focused your binoculars you’d be able to see different kinds of whale species. As you looked closer, for example at Humpback Whales, you'd see that each individual whale has a different black-white pattern on its tail. You might even take a biopsy, a small sample of whale flesh, and do a more detailed study of genetic differences among individual Humpbacks.

But what if you’re a microbial oceanographer? You sure can't use binocs to hunt for microbes! How can you study individual differences among tiny creatures that are only one-one-hundredth the width of a human hair? How do you hunt and capture single-celled bacteria, like Prochlorococcus, the most common bacterial species in the world’s ocean?

Invent something!

laser-based micro-fluidic system
laser-based micro-fluidic systemCourtesy C-MORE
Young scientists, Sebastien Rodrigue and Rex Malmstrom, at the Center for Microbial Oceanography: Research and Education (C-MORE) were doing research in Dr. Sallie Chisholm’s C-MORE lab at the Massachusetts Institute of Technology when they adapted a “laser-based micro-fluidic system” used commonly by medical researchers, for the study of marine bacteria. With this method they could put each individual tiny Prochlorococcus cell into its own little pool of seawater.

And then the excitement began.

Prochlorococcus
ProchlorococcusCourtesy Dr. Anne Thompson, MIT
Even in scanning microscope photographs, each Prochlorococcus looks like just another teeny, tiny balloon; we can't see any individual differences. However, Sebastien and Rex used fast and inexpensive genetic methods and discovered an extraordinary variety of individual differences among Prochlorococcus. Of course the variety among these microbes doesn't have to do with tail patterns, like whales. Prochlorococcus vary in their method of getting nutrients, like iron, out of seawater.

So what? Why do we care?

We care A LOT because microbes like Prochlorococcus are operating at the nitty gritty level of cycling not only iron, but also other elements in the ocean. Like carbon. That's right, as in carbon dioxide accumulating in our atmosphere -- and ocean -- causing climate change and associated problems. The more we understand about individual differences among oceanic microbes, the more we'll understand how they influence and respond to changes in Earth's climate.

Jan
28
2011

ocean micro-plastic: These samples were collected from the surface water of the North Pacific Ocean by the SUPER expedition in 2008.
ocean micro-plastic: These samples were collected from the surface water of the North Pacific Ocean by the SUPER expedition in 2008.Courtesy C-MORE
Who hasn’t heard that plastic in the ocean is trouble?

  • Plastic has been found clogging the stomachs of dead albatross and other ocean birds.
  • Plastic ropes and traps have entangled marine life, causing more death.
  • As a long-lasting chemical, plastic floating in the ocean provides long-distance rafts that may move aggressive alien marine life to new areas.
  • Plastic may provide a “sticky” surface where toxins can accumulate, becoming a concentrated source of poison for marine consumers.
  • A "Great Pacific Garbage Patch" has been reported to be an "island the size of Texas" floating in the North Pacific Ocean...but is this really true? Continue reading to find out!

Yep, plastic in the ocean is bad news; so let’s put scientific energy into studying and solving the problem.

manta trawl: The trawl is hoisted above the stern deck of the RV Kilo Moana.
manta trawl: The trawl is hoisted above the stern deck of the RV Kilo Moana.Courtesy C-MORE
In 2008 C-MORE, the Center for Microbial Oceanography: Research & Education headquartered at the University of Hawai`i, with assistance from the Algalita Marine Research Foundation, embarked on an oceanographic expedition aboard the RV Kilo Moana, which means "oceanographer" in Hawaiian. The goal of the expedition, dubbed SUPER (Survey of Underwater Plastic and Ecosystem Response Cruise), was to measure the amount of micro-plastic in the ocean. In addition, oceanographers took samples to study microbes and seawater chemistry associated with the ocean plastic. The Kilo Moana sailed right through the area known as the “Great Pacific Garbage Patch,” between Hawai`i and California.

Early results: there was no garbage patch/island. Once in a while something like a barnacle-covered plastic buoy would float past the ship, but mostly the ocean looked really clean and empty of any kind of marine debris.

manta trawl: The net is being pulled slowly through the ocean's surface water.
manta trawl: The net is being pulled slowly through the ocean's surface water.Courtesy C-MORE
But wait! Scientists looked closer and were amazed. Every single one of the more than a dozen manta trawls, filtering the surface seawater for an hour and a half each, brought up pieces of micro-plastic! Some were as small as 0.2 millimeter, mixed among zooplankton!

Other expeditions have reported similar results (for example, Scripps Institution of Oceanography's 2009 SEAPLEX expedition and Sea Education Association's North Atlantic Expedition 2010): no Texas-size garbage patches, but plenty of plastic marine debris to worry about. The data seem to show that most of the plastic is in the form of small pieces spread throughout upper levels of water at some locations around the world's ocean. In these areas, the ocean is like a dilute soup of plastic.

Dr. White: examining the results of a manta tow
Dr. White: examining the results of a manta towCourtesy C-MORE
C-MORE researcher Dr. Angelicque (Angel) White, assistant professor of oceanography at Oregon State University (OSU) was a scientist on board the SUPER expedition. In recent interviews, (for example: the Corvallis Gazette-Times and Seadiscovery.com) Dr. White cautions us to view the complex plastic marine debris problem accurately. Furthermore, new results will soon be published by C-MORE about microbial diversity and activity on plastic pieces.

In the meantime, as Dr. White says, “…let’s keep working on eliminating plastics from the ocean so one day we can say the worst it ever became was a dilute soup, not islands. “

Plastic in the ocean is trouble. How can you be part of the solution?

Dec
09
2010

Surveying Microbes at Sea
Surveying Microbes at SeaCourtesy C-MORE
There are microbes…and then there are micro-microbes. Oceanographers on C-MORE’s BiG RAPA oceanographic expedition are finding bacteria the size of one-one-millionth of a meter in the oligotrophic (low nutrient), open-ocean of the Southeast Pacific, far from the productive waters off the coast of Chile. But that’s not all; some scientists are looking for the even smaller marine viruses in gallons of filtered seawater. Meet some of these micro-microbes in these video reports:
Prochlorococcus
ProchlorococcusCourtesy Dr. Anne Thompson, MIT

  • Microbe Diversity, Part 1: Prochlorococcus, the most common bacterium in the world’s oceans; nitrogen-fixing bacteria that provide a usable form of nitrogen “fertilizer” for other photosynthesizers
  • Microbe Diversity, Part 2: picophytoeukaryotes with different colored pigments; viruses, which are parasites on other living things

Yes indeed, microbial oceanographers are taking home quite a collection from the South Pacific Ocean. In less than a week the good ship RV Melville will arrive at Rapa Nui (Easter Island), and scientists will step onto land for the first time in almost a month. They and their oceanographic samples will return to C-MORE laboratories around the U.S. The oceanographers are also returning with new hypotheses buzzing around in their heads. Now it’s time for them to take the next step in the Scientific Method: data analysis!

surveying microbes at sea
surveying microbes at seaCourtesy C-MORE
Microbial oceanographers on C-MORE’s BiG RAPA oceanographic expedition have transited from the coast of Chile to 1000 miles offshore. No longer are the scientists in rich, productive coastal water. Now the ship is in clear-blue, open-ocean seas. Learn why Dr. Angel White from Oregon State University says the change is like going from the Amazon to the Sahara Desert in this video of BiG RAPA’s discoveries.

Color these waves red!
Color these waves red!Courtesy C-MORE
You’ve probably seen all sorts of colors in the ocean: deep-blue, turquoise-blue, light-green, brown, even gray on a gray day. But red? Microbial oceanographers on C-MORE's (Center for Microbial Oceanography: Research and Education) BiG RAPA oceanographic expedition have seen a red ocean off the coast of Chile! Huh?! Learn what a plankton net is, and then see what caused the strange red color.

Nov
26
2010

surveying microbes at sea
surveying microbes at seaCourtesy C-MORE
Dr. Dan Repeta from the Woods Hole Oceanographic Institution (WHOI) is C-MORE’s Chief Scientist on the BiG RAPA expedition, which is conducting research off the coast of Chile. Dr. Repeta and his team of scientists are sampling the underwater microbial environment using a variety of instruments, including a water collector called a CTD (see educational resource below). Two interesting results have turned up in the CTD data:

  1. chlorophyll -- The greatest amount of the green pigment, representing floating microscopic plants in the sea known as phytoplankton, was found about 30 meters below the sea surface. (That's where oceanographers expect the most chlorophyll. Perhaps phytoplankton living at that depth must produce more chlorophyll in order to capture the lower light intensities, just like leaves are usually darker green if they're growing on a land plant in the shade). However, a surprise awaited oceanographers at 60 meters. At that depth, they discovered an unusual “secondary, deeper chlorophyll max," something not seen many other places in the world.
  2. Oxygen -- This gas enters the ocean primarily at the surface, from the air and also from phytoplankton photosynthesis. Bacteria and other heterotrophs consume the O2 as they metabolize. Therefore, oxygen is expected to decrease with depth. At BiG RAPA's Station 1 oxygen not only fell; it fell all the way to near zero.

Dr. Angel White and the CTD
Dr. Angel White and the CTDCourtesy Eric Grabowski, C-MORE
"Sea It Live" in some BiG RAPA videos. Join Dr. Angel White from Oregon State University as she demonstrates the CTD rosette. Then join Dr. Repeta for his Chief Scientist Station 1 Update .
______________________
*Educational resource = C-MORE Science Kit Ocean Conveyor Belt's Powerpoint, "Lesson 3: Using Data to Explore Ocean Processes "