Stories tagged bacteria

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.

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!

Sep
18
2010

Dyson hand dryer
Dyson hand dryerCourtesy Mr T in DC

How you dry your hands matters

Dyson, who makes a new type of "airblade" hand dryer, funded research which showed regular hot-air hand dryers could make your hands "germier".

When volunteers kept their hands still, the dryers reduced skin bacteria numbers by around 37 per cent compared to just after washing. But the count rose by 18 per cent when volunteers rubbed their hands under one of the machines. Paper towels proved the most efficient, halving the bacterial count even though volunteers rubbed their hands. That's because the towels actually scrape off the bacteria. Journal of Applied Microbiology

This mesage brought to you by ...

Reading this research paper made me think it was a commercial message written by the Dyson advertising department.

Jan
03
2010

Pretty bacteria: Do not be fooled by the pastel colors- these things will kill you.
Pretty bacteria: Do not be fooled by the pastel colors- these things will kill you.Courtesy esterase
I bet regular bacteria have posters of their favorite superbug hung on their bedroom walls. I mean superbugs are just so much cooler than regular bacteria; they’re kind of the bad boys of the bacteria world. Regular bacteria do what they are told: they keel over when exposed to disinfectants and antibiotics. But not those rebellious superbugs. Superbugs have some kind of genetic mutation that allows them to survive in hostile, antimicrobial environments. Basic principles of natural selection come into play: the mutant bacterium survives in the presence of the antibiotic/disinfectant and then goes on to produce other bacteria with the same mutation, ultimately creating a new resistant colony. In this scenario, exposure to the antimicrobial agent (the antibiotic or disinfectant) is imperative. However, scientists now think that another scenario exists; one in which exposure is not required. In a recent study, these scientists found that the use of disinfectants in hospitals can lead to bacterial resistance to antibiotics, even if the bacteria haven’t been exposed to the antibiotics.

Researchers from the National University of Ireland added increasing amounts of disinfectant to petri dishes full of Pseudomonas aeruginosa (a bug that causes pneumonia in hospital patients, among other things) and the bug became immune not only to the disinfectant, but also to ciprofloxacin- the antibiotic used to treat the bug. Superbugs are essentially using their exposure to disinfectants as “teachable moments” for resisting antibiotics.

This is significant because now it seems that bacteria have one less hurdle to overcome in their mission to cause serious harm to patients (that’s not really their “mission,” I say that for dramatic effect). If superbugs can resist the disinfectant slathered on the countertops and doorknobs of hospitals, it’s possible that they could go on to infect patients who “for some reason” won’t respond to the antibiotics. Man, regular bacteria must be so jealous.

Nov
01
2009

Richard Lenski (top) and Jeffrey Barrick view bacteria cultures in Lenski's lab.: They have watched the bacteria's DNA evolve over 40,000 generations.
Richard Lenski (top) and Jeffrey Barrick view bacteria cultures in Lenski's lab.: They have watched the bacteria's DNA evolve over 40,000 generations.Courtesy Michigan State University / photo by G.L. Kohuth

Sometimes you’ll hear people cast doubts on evolution because no one has ever seen it happen. As if that’s some sort of great insight. No one has eve “seen” atomic fusion, either, but the fact that the Sun was shining this morning is pretty strong evidence that, yep, it happens. No one has ever “seen” gravity. Seen gravity’s effects, sure. But seen gravity itself? Like Ms. Ono once asked, Who Has Seen The Wind?

Evolution used to be in the same boat. The effects of evolution are visible everywhere, in every cell of every living thing on the planet. But seeing the actual process of evolution? That was another matter.

Until now. Scientists at Michigan State University (go Spartans!) have been growing bacteria in bottles for the past 21 years. Every so often, they would freeze a sample for later study. Well, “later” is now. DNA sequencing and computer analysis have advanced to the state where they can readily map the genome of each sample. And guess what? The bugs evolved exactly as evolution says they should. Mutations in the genome pop up at random intervals. Mutations that help the bug survive—like make more efficient use of food, or fend off disease—get passed on to future generations, and eventually spread through the entire colony.

Twenty-one years may not seem like enough time for a species to change. But, as Mia Sorvino said in the truly awful 1997 movie Mimic, think generations, not time. In the two decades of study, the little bacteria went through 40 thousand generations—the equivalent of roughly 800,000 years in human terms. Plenty of opportunity for evolution to do it’s thang.

And the experiment continues. Understanding mutations in bacteria might help us understand the mutations that lead to some forms of cancer. In recent generations, the rate of mutation has increased; the scientists would like to know why.

Richard Lenski, the scientist heading up the research, has put together a video explaining his work.

Feb
12
2009

These guys have been eating bacteria all day: That's all it takes!
These guys have been eating bacteria all day: That's all it takes!Courtesy Dave Austria
Hey y’all! Get a earful of this: Russian scientists claim to have found bacteria living in the superfrost that may be able to significantly extend our lifespans!

Whoa!

Oh, also, “superfrost” isn’t the word the original article used. In fact, “superfrost” isn’t a real word in the first place. The perpetually frozen sandy soil the bacteria were found in is actually called “permafrost.” I just invented the word “superfrost” because it was kind of cool in this post’s title. I also used the fake word to honor the original article, which contains an amount of information somewhere between zero and almost zero.

Maybe I shouldn’t have gotten my hopes up over a quasi-science article coming from a the Daily Mail, considering that the other stories on the page feature shots of the octuplet mother’s explosive looking belly, and Chris Brown leering over Rhianna’s shoulder… but it seems so cool! Seriously, this is sci-fi stuff!

What I can tell is this: Russian scientists were digging in an area of Siberia known for its abundance of wooly mammoth remains. Among the biological materials they recovered was a species of bacteria that appears to live in the permafrost. Finding it was an accident.

After doing a partial DNA analysis, the scientists determined that they were working with a unique type of bacteria. I don’t know if this means it’s a new species, genus, family, order, class, phylum, or kingdom… whatever. Probably not important, right, Daily Mail?

What’s interesting about the bacterium is that it appears to be very, very old. Three to five million years old, according to the article.

Say what, Daily Mail? Say what?!

I mean… What? Check out the wikipedia page on long-living organisms. With the exception of this weird jelly fish that could potentially live forever (we won’t get into it), 3-5 million years puts everything else on the list to shame. By far.

I’m guessing that the age was estimated based on the age of the associated mammoth remains in the area (they’re about 4.8 million years old), but how they know that the bacteria were alive at the same time as the mammoths isn’t explained.

Some scientists have made claims that certain bacteria might be able to remain in stasis for millions of years before being revived. But those claims are disputed, and, anyway, we’re talking about bacteria trapped in amber or salt deposits, not permafrost (which, despite the “perma,” has probably been considerably more dynamic over the last 5 million years than most amber).

If the bacteria were in stasis, which wasn’t suggested in the helpful article, that wouldn’t explain what the Russian scientists did with the bacteria next: they put it in some mice.

We aren’t talking gene therapy here, either. All the article says is that the mice were “vaccinated with the bacterium extract.”

That makes sense, right? I mean, I know turtles and parrots live a really long time, so if I’m always eating turtle soup and parrot cake, so I’m pretty much guaranteed to live a long time, right? And if I supplement that diet by shooting up some alligator (into my veins with a needle, say), I’ll be alive forever!

I don’t know. Somebody help me out here. Why would vaccinating yourself with a bacterium imbue you with properties of that bacterium? Wouldn’t it just help your immune system figure out how to kill that organism? I was vaccinated with weakened mumps virus, but, as far as I know, I don’t have the ability to make anyone’s face inflate on cue, nor did the process transform me into a protein shell full of bits of DNA.

Nonetheless, after their inoculation with the bacteria, the mice demonstrated “growth of physical, mental, and sexual activity” into their old age. Female mice were even able to give birth at an age equivalent to a human 70-year-old.

That’s freaking amazing, isn’t it? So, hmm… here at the Daily Mail, we seem to have an exclusive story on this awesome biological breakthrough. What should we title this story? What… should… we… call… it? I know! “'Pre-historic Viagra' found in Siberian mammoth DNA could boost your sex life and let you live longer”

Duh. I mean, it says in the article that the bacteria and the mammoths, though they were found in the same area, are not believed to be linked to each other, but nothing else makes sense, so why should the headline? Mammoth DNA! Pre-historic Viagra! Print it!

How frustrating. This seems awesome, but until I can get some better, and possibly less fake, information, I have to file it under “Thhhbbtttbbbtbb.” Fudge.

The flu and cold season is upon us, and with it the regular reminders to wash your hands. Check out this story – that tells you how many specific types of bacteria the average hand carries around at any particular time. And gals, you have even more reason to wash your hands than guys.

Studies have shown that, contrary to popular belief, mayonnaise actually inhibits the growth of bacteria and thus reduces the risk of food poisoning.

As the Mississippi flood waters recede, a new threat is rising. Public health officials in Iowa are warning people about the health risks associated with cleaning up their water-damaged homes, farms and buildings. Bacteria thrives in the water, and could lead to a number of diseases, and can contaminate well water. Water-logged buildings are a haven for mold, which can cause serious problems for allergy and asthma sufferers.