As I announced over a year ago, I have a website featuring the protists (protozoans and algae) that one can find in freshwater (ponds, reservoirs, drains...) in Singapore. The pages are illustrated with pictures (photomicrographs) and videos, and are organized as a guidebook (inspired by the Singapore Science Centre nature guidebooks that I grew up with).
With my collection of videos, though, I wanted to put them together into a documentary-style film, and I finally found time to do it this summer.
Hidden Lives (SD) from brandon seah on Vimeo.
This was made with iMovie '08, with music sourced from ccMixter. Feel free to share, with credits! Read more about the motivation here.
Showing posts with label protists. Show all posts
Showing posts with label protists. Show all posts
Monday, June 03, 2013
Saturday, March 23, 2013
Pretty Protozoa
While browsing the web I came across a tumblog called "Pretty Protozoa", which regularly posts scientifically interesting or visually attractive images of protists. Most of them seem to be from scientific publications or scientists' websites, but are properly credited to the original authors, as far as I can tell.
Another great protist blog worth mentioning is The Ocelloid, and its predecessor Skeptic Wonder, both maintained by a grad student at Indiana University. She writes with plenty of enthusiasm, she definitely knows a lot about all sorts of protists, and the blog is often illustrated by her own micrographs.
Another great protist blog worth mentioning is The Ocelloid, and its predecessor Skeptic Wonder, both maintained by a grad student at Indiana University. She writes with plenty of enthusiasm, she definitely knows a lot about all sorts of protists, and the blog is often illustrated by her own micrographs.
Monday, April 09, 2012
Plankton Chronicles
The word "plankton" literally means "wanderer", and these floating wanderers of the ocean have a strange and alien beauty that has fascinated generations of biologists.
The Plankton Chronicles project uses modern microscopy and videography to make this world accessible to the average armchair explorer. They've produced a series of videos highlighting different planktonic organisms, using a technique called dark field optics, where objects are made visible by the light that they scatter, appearing light against a dark background.
The project is a collaboration between the Tara Oceans Expedition and the Oceanographical Observatory at Villefranche-sur-Mer.
One of the episodes, on planktonic protists (of course!), is embedded below:
I came by the site by way of this TED Talk by Tierney Thys:
The Plankton Chronicles project uses modern microscopy and videography to make this world accessible to the average armchair explorer. They've produced a series of videos highlighting different planktonic organisms, using a technique called dark field optics, where objects are made visible by the light that they scatter, appearing light against a dark background.
The project is a collaboration between the Tara Oceans Expedition and the Oceanographical Observatory at Villefranche-sur-Mer.
One of the episodes, on planktonic protists (of course!), is embedded below:
I came by the site by way of this TED Talk by Tierney Thys:
Sunday, January 01, 2012
Are they embryos or not?
Once again, news about fossils (I promise that I'm not turning this into a paleontology blog).
They found that dead Thiomargarita look nothing like the Doushantuo fossils: because of their internal vacuole, they collapse readily. And so it seems that the "giant bacterium" theory is quite unlikely.
But does that mean that they're embryos? Another research group (sharing at least one team member as the previous group), this time publishing in Science, claims that they aren't, based on the patterns of cell division that they found by peering into the fossils using X-ray tomographic microscopy. (Blog post on Scientific American)
Reassuringly, they found structures that they interpret to be eukaryotic cell nuclei within the compartments. It's worth quoting their "criteria for biogenicity" to appreciate the reasoning that goes on "under the hood":
But the pattern of cell division that they observed wasn't like metazoan embryos. Embryos undergo a period of "palintomic division", where the overall size of the cell mass doesn't change but is simply subdivided into more and more cells. At some point, however, morphogenesis takes over and higher-order structures such as epithelial sheets start to form. In these fossils, they found no such differentiation. The pattern they found was instead of further and further undifferentiated cell division, and in some cases protrusions containing lots of small cells. Perhaps these might be propagules waiting to be released into the environment, they hypothesize.
In the title of their paper, the researchers interpret the Doushantuo microfossils to be a kind of "protist". The term is used as a grab-bag for all eukaryotes that are not plants, animals, or fungi. That is to say, they think it's an eukaryote, but don't quite know what kind. More observations will probably be necessary, and perhaps we may never know what it is.
Yet they're still valuable, because you don't always need to be able to slap a name on something to learn interesting things about it. These microfossils still represent an interesting example of multicellularity. It may or may not be the complex multicellularity exhibited by animals and plants, but it still gives a glimpse into the morphological organization that can be achieved by "simpler" living organisms.
Sources
The Doushantuo Formation in China is one of the most important sites for pre-Cambrian microfossils. These date back to before the Cambrian Explosion of animal life in prehistoric seas, exactly where you'd want to go looking if you were interested in the origins of animal diversity. What's important about Doushantuo is that the fossils recovered are microscopic and preserve fine structural detail, the original cells having been replaced by phosphate minerals.
Many of the Doushantuo microfossils were interpreted as fossilized animal embryos encased within ornamented walls (see image below, via Ministry of Science and Technology, China). If so, they would represent some of the earliest evidence for metazoan (i.e. multicellular animal) life. It is a particularly appealing idea, because they would then pre-date the known adult animal fossils.
But as always, fossilized forms are notoriously difficult to interpret, especially globs of microscopic spheres. Some others have suggested that they could be giant bacteria, analogous to the modern Thiomargarita namibiensis, which achieves its great size by accumulating nitrate in a big vacuole in the cell, which it uses as a source of energy.
To investigate this hypothesis, one group of scientists decided to go with the approach of experimental taphonomy. Taphonomy is the science that studies the process of fossilization, so essentially what they did was to kill the giant bacteria Thiomargarita and also some sea urchin embryos, and then see what they looked like as they decayed.
Well, that was the plan, anyway. According to their paper (recently published in the Proceedings of the Royal Society, B):
Attempts to kill the bacteria in a consistent manner using strongly reducing conditions induced with beta-mercaptoethanol (BME) were ineffective. ... Consequently, we relied on a decay pathway from the natural taphonomic spectrum in the population.I.e. "we couldn't kill the bugs, so we fished out the dead ones from the mud instead."
They found that dead Thiomargarita look nothing like the Doushantuo fossils: because of their internal vacuole, they collapse readily. And so it seems that the "giant bacterium" theory is quite unlikely.
But does that mean that they're embryos? Another research group (sharing at least one team member as the previous group), this time publishing in Science, claims that they aren't, based on the patterns of cell division that they found by peering into the fossils using X-ray tomographic microscopy. (Blog post on Scientific American)
Reassuringly, they found structures that they interpret to be eukaryotic cell nuclei within the compartments. It's worth quoting their "criteria for biogenicity" to appreciate the reasoning that goes on "under the hood":
The nucleus-like bodies fulfill relevant criteria for biogenicity: Their occurrence is consistent and repeated (12 of the 14 specimens have one such body in each cell); they are regularly positioned in the cells within any single individual (central to the cells in four of the specimens, peripherally in the others); they have a consistently globular shape; and the volumetric ratio between bodies and cells corresponds to that of nuclei and cells in eukaryotes (fig. S6 and table S1). Furthermore, one specimen (Fig. 2 and fig. S1, D to H) has two elongated and one dumbbell-shaped nucleus-like body, suggesting that they are in the process of division.In an observational science, as opposed to an experimental science, like paleontology, the standard of proof (to borrow the legal term) is more akin to "preponderance of evidence" (used in civil cases) than "beyond a reasonable doubt" (used in criminal cases). This is not to criticize the validity of their work, but just a comment on the practical limits of knowledge.
But the pattern of cell division that they observed wasn't like metazoan embryos. Embryos undergo a period of "palintomic division", where the overall size of the cell mass doesn't change but is simply subdivided into more and more cells. At some point, however, morphogenesis takes over and higher-order structures such as epithelial sheets start to form. In these fossils, they found no such differentiation. The pattern they found was instead of further and further undifferentiated cell division, and in some cases protrusions containing lots of small cells. Perhaps these might be propagules waiting to be released into the environment, they hypothesize.
In the title of their paper, the researchers interpret the Doushantuo microfossils to be a kind of "protist". The term is used as a grab-bag for all eukaryotes that are not plants, animals, or fungi. That is to say, they think it's an eukaryote, but don't quite know what kind. More observations will probably be necessary, and perhaps we may never know what it is.
Yet they're still valuable, because you don't always need to be able to slap a name on something to learn interesting things about it. These microfossils still represent an interesting example of multicellularity. It may or may not be the complex multicellularity exhibited by animals and plants, but it still gives a glimpse into the morphological organization that can be achieved by "simpler" living organisms.
Sources
- JA Cunningham et al. Experimental taphonomy of giant sulphur bacteria: implications for the interpretation of the embryo-like Ediacaran Doushantuo fossils. Proceedings of the Royal Society, B. Online before print, 7 Dec 2011. doi: 10.1098/rspb.2011.2064
- T Huldtgren, JA Cunningham et al. Fossilized nuclei and germination structures identify Ediacaran "animal embryos" as encysting protists. Science 334 (6063): 1696-1699. 23 Dec 2011. doi: 10.1126/science.1209537
Sunday, October 16, 2011
The world's largest virus
Back in January I blogged about how the physical constraint of capsid size may be forcing some viruses to squeeze their genomes into such a compact state that their genes overlap. Now we visit the other end of the scale to the largest virus yet discovered, appropriately called Megavirus chilensis, found in ocean waters off the coast of Chile.
As one of the paper's coauthors told BBC News, "You don't need an electron microscope to see it; you can see it with an ordinary light microscope." Each virus particle is about 680 nm across, or just under a micrometer, making it just barely visible as specks by light microscopy. They're structurally interesting, bearing a covering of fibers ("hair") all over the surface, and a five-pronged star-shaped structure on one vertex that the authors have called a "stargate", which the virus uses to release its nuclear material into the host cytoplasm.
As one of the paper's coauthors told BBC News, "You don't need an electron microscope to see it; you can see it with an ordinary light microscope." Each virus particle is about 680 nm across, or just under a micrometer, making it just barely visible as specks by light microscopy. They're structurally interesting, bearing a covering of fibers ("hair") all over the surface, and a five-pronged star-shaped structure on one vertex that the authors have called a "stargate", which the virus uses to release its nuclear material into the host cytoplasm.
Saturday, October 08, 2011
Slime is going places
In college I kept a pet in my dorm room, possibly against regulations. However, it didn't make any noise, didn't poop all over the place, and didn't need to be fed every single day. When it got too troublesome to take care of it, I simply cut off a piece of it to keep, and killed the rest. Before you think I'm some kind of cruel monster, here's a photo of my pet.
Slime molds are amazing creatures. They're neither plant nor fungus nor animal, but are protists, the "eukaryotic leftovers". The one I had is called Physarum polycephalum, and is a common organism used for demonstrations in schools and biology classes. It's bright yellow, big, grows fast, and is easy to revive from a dormant culture. Slime molds come in two "flavors": the plasmodial molds like Physarum which are essentially giant single cells, and the cellular ones which are an aggregate of numerous individual amoeboid cells.
The New York Times science section, which has possibly the best science reporting of any mainstream newspaper, recently featured an article by Carl Zimmer on slime molds and why they're exciting to current biology research (via Twitter).
He highlights Physarum and its ability to solve "mazes" where the objective is to connect up different particles of food scattered on a substrate. This research won a team of Japanese researchers the prize in Transportation Planning for the tongue-in-cheek Ig Nobels in 2010 (and before in 2008). What the organism does is to spread its plasmodium outwards (much like the photo above) until it encounters these food particles, and then retract those parts of the plasmodium which are on barren areas leaving behind thicker "veins", connecting the food particles with each other and with the exploring front of the plasmodium. The link to transportation? When the particles are scattered in an arrangement resembling the major centers of the Tokyo metropolitan area, the resulting plasmodial vein network is quite similar to a map of the Tokyo rail network!
It sounds relatively easy to design an optimal transport network but such design actually requires a whole lot of trade-offs and is not straightforward. However I wouldn't go quite as far as hire them as transport engineers. The Japanese team used the mold's behavior as a template to come up with an algorithm for making such networks. The computational model is more easily controlled!
In addition to Physarum the other molds mentioned include the cellular slime mold Dictyostelium, which has a long and distinguished history of use as a lab organism for studying simple multicellularity. It's interesting to evolutionary science because to make its fruiting bodies (which release spores for dispersal), some of the slime mold cells in the colony have to sacrifice themselves to form the stalk, which leaves no descendants. This is an example of a cooperative behavior, which is puzzling from an evolutionary standpoint because it should theoretically collapse in a maelstrom of cheating for individual benefit.
In the wild the diversity of slime molds has not been given as much attention as other organisms, but they have their own distinctive beauty. They come in many colors and shapes, but require some patience to find, by peering closely at decaying wood and leaf litter. There are slime molds in Singapore too, and I've posted a gallery of beautiful images taken by Serena Lee of the Botanic Gardens to the Protists in Singapore webpage. One particularly striking one is Diachea leucopodia, which has an iridescent black fruiting body borne on a white stalk (above). The diversity of slime molds from the tropics is poorly understood, with many species that look like temperate ones but may or may not be the same thing.
These creatures are often sidelined because of their taxonomic obscurity, and maligned because of their unfortunate name. Let's help to spread a better appreciation for them among the nature-loving public!
 |
| Slime mold Physarum polycephalum growing outwards to feed on oat flakes. |
Slime molds are amazing creatures. They're neither plant nor fungus nor animal, but are protists, the "eukaryotic leftovers". The one I had is called Physarum polycephalum, and is a common organism used for demonstrations in schools and biology classes. It's bright yellow, big, grows fast, and is easy to revive from a dormant culture. Slime molds come in two "flavors": the plasmodial molds like Physarum which are essentially giant single cells, and the cellular ones which are an aggregate of numerous individual amoeboid cells.
The New York Times science section, which has possibly the best science reporting of any mainstream newspaper, recently featured an article by Carl Zimmer on slime molds and why they're exciting to current biology research (via Twitter).
He highlights Physarum and its ability to solve "mazes" where the objective is to connect up different particles of food scattered on a substrate. This research won a team of Japanese researchers the prize in Transportation Planning for the tongue-in-cheek Ig Nobels in 2010 (and before in 2008). What the organism does is to spread its plasmodium outwards (much like the photo above) until it encounters these food particles, and then retract those parts of the plasmodium which are on barren areas leaving behind thicker "veins", connecting the food particles with each other and with the exploring front of the plasmodium. The link to transportation? When the particles are scattered in an arrangement resembling the major centers of the Tokyo metropolitan area, the resulting plasmodial vein network is quite similar to a map of the Tokyo rail network!
It sounds relatively easy to design an optimal transport network but such design actually requires a whole lot of trade-offs and is not straightforward. However I wouldn't go quite as far as hire them as transport engineers. The Japanese team used the mold's behavior as a template to come up with an algorithm for making such networks. The computational model is more easily controlled!
In addition to Physarum the other molds mentioned include the cellular slime mold Dictyostelium, which has a long and distinguished history of use as a lab organism for studying simple multicellularity. It's interesting to evolutionary science because to make its fruiting bodies (which release spores for dispersal), some of the slime mold cells in the colony have to sacrifice themselves to form the stalk, which leaves no descendants. This is an example of a cooperative behavior, which is puzzling from an evolutionary standpoint because it should theoretically collapse in a maelstrom of cheating for individual benefit.
 |
| Diachea leucopodia fruiting bodies, from MacRitchie Reservoir area in Singapore. |
These creatures are often sidelined because of their taxonomic obscurity, and maligned because of their unfortunate name. Let's help to spread a better appreciation for them among the nature-loving public!
Monday, August 29, 2011
Protists in Singapore - New Website!
Last month I featured photos of some protozoans that I found in a pond on the NUS campus (part 1, part 2). Even though it's somewhere right in the middle of the city, there's plenty of wild life to see if you're lucky enough to have a microscope to see it with.
Those images and plenty more are now on a new website that I've put together, Protists in Singapore, hosted at Wordpress. My aim is to highlight these under-appreciated organisms, which most nature enthusiasts have overlooked.
The guide itself is organized by the different groups of protists that one might commonly encounter. Navigate using the menu bar underneath the banner at the top of the page.
In addition to the named groups of protists, there are two other pages: Interactions, which highlights examples of interactions between different organisms, and By-catch, which features organisms other than protists, such bacteria and animals, that can also be observed in the same habitats.
A typical page will have both photographs and videos (hosted at Vimeo), as well as a short description.
Write in at the Contact page to let me know whether you found it useful!
Those images and plenty more are now on a new website that I've put together, Protists in Singapore, hosted at Wordpress. My aim is to highlight these under-appreciated organisms, which most nature enthusiasts have overlooked.
The guide itself is organized by the different groups of protists that one might commonly encounter. Navigate using the menu bar underneath the banner at the top of the page.
In addition to the named groups of protists, there are two other pages: Interactions, which highlights examples of interactions between different organisms, and By-catch, which features organisms other than protists, such bacteria and animals, that can also be observed in the same habitats.
A typical page will have both photographs and videos (hosted at Vimeo), as well as a short description.
Write in at the Contact page to let me know whether you found it useful!
Tuesday, July 26, 2011
Singapore Protozoans Part 2 - A Murky Pond
After looking at today's sample (from a small pond in the botany garden at NUS) under the microscope I think I might hesitate to stick my hands into warm murky pond water again. It's absolutely crawling with bacteria, and to illustrate what I mean by crawling I've even got a video:
On the bright side, that means there's plenty of protists grazing on all these bacteria, including lots of small bacterivorous ciliates, and gliding euglenids (photo below). I really think that they look like twisted potato chips, don't you too? Diatom and dinoflagellates were common, but I saw more empty tests and frustules than living cells.
One of the highlights was a big amoeba which had really awesome cytoplasmic streaming and which moved by blebbing outwards in a way which is easier to show than to describe in words.
See the full set of photographs on Flickr. [Update 6/9/11 - I've moved all the photos to my new protist website and the Flickr album is no longer available.]
Bacteria moving from brandon seah on Vimeo.
On the bright side, that means there's plenty of protists grazing on all these bacteria, including lots of small bacterivorous ciliates, and gliding euglenids (photo below). I really think that they look like twisted potato chips, don't you too? Diatom and dinoflagellates were common, but I saw more empty tests and frustules than living cells.
  |
| "Potato chip" euglenids with flagellum that points in the direction of motion. |
One of the highlights was a big amoeba which had really awesome cytoplasmic streaming and which moved by blebbing outwards in a way which is easier to show than to describe in words.
Large Amoeba from brandon seah on Vimeo.
See the full set of photographs on Flickr. [Update 6/9/11 - I've moved all the photos to my new protist website and the Flickr album is no longer available.]
Singapore Protozoans Part 1
 |
| Heliozoan from Kranji Reservoir. Each unit on the graticule scale is 2.5 microns. |
Microscope, murky water, a camera, and free time.
Lately I've been volunteering at Darren Yeo's new freshwater biology lab, but Maxine, the graduate student whose project I'm supposed to help with, has been busy with the Honours fieldtrip to Pulau Tioman and with getting sick (get well soon!) In the meantime, I've found that her plankton net samples from Kranji Reservoir are teeming with interesting and picturesque protozoa!
Today I captured some shots of microscopic aquatic life to share online, and you can browse the full set on Flickr [update 6/9/11 - I've moved all the media to my new protist website and the album is no longer available]. The picture above shows an organism called a heliozoan. The long radiating arms, called axopods, appear to be beaded with dew drops, which are actually organelles involved in prey capture called extrusomes. The spherical cell body itself is covered in a layer of spicules, which seem like a fuzzy layer of hair, but reveal finely ornamented detail under electron microscopy.
These pictures were taken in a fairly primitive way: by balancing a camera in front of the eyepiece of the microscope. The microscope was set up for brightfield illumination, but I closed down the condenser aperture to improve contrast, in the absence of any better option. Still, there's enough detail to recognize lots of protozoans and to tell a good story.
When I've got a decent bunch of these pictures and descriptions, I'd like to eventually put up a photographic guide to common protozoans in Singapore. That might help to address some of the 'macrobe' bias in the natural history scene here, by showing the beauty hidden in the very small.
As a bonus here's a video of ciliates squirming in the carcass of a dead planktonic crustacean. The bright droplets are oil globules, which the ciliates are feeding on (ingested oil globules are also visible within their cytoplasm). Outside the animal carcass you can see another ciliate which has been left out of the feeding frenzy, and is trying to find its way in....
Saturday, May 14, 2011
"Primitive" fungi discovered... in a pond!
The microbial world is ubiquitous (there are microbes everywhere!) and vast (there remains so much to be discovered). Basic discoveries are made on a fairly regular basis, and new taxonomic groups of microorganisms are routinely identified when people sequence DNA from the environment.
We don't necessarily have to go to exotic locations like hot springs or the deep sea to discover something new. A new group of "primitive" fungi has recently been described from samples taken from a variety of locations around the world, including a pond in Devon near Exeter University in the UK, where the scientists worked.
This group, called the cryptomycota (not capitalized, because it's not yet officially described according to the rules of taxonomy), has characteristics which make it apparently a 'missing link' between the fungi and other eukaryotic microbes. Sequences of a number of genes place it as a sister group to the rest of the fungi; that is to say, on the family tree of the fungi, it branches off at the very base of the tree.
Although the term "primitive" is often used for groups that fall out at the base of phylogenetic trees, like the cryptomycota, it's important to note that they don't necessarily resemble the ancestors of these groups in every respect. That is to say, just because one branch of your family split off many generations ago from your own lineage, it's not true that this branch more closely resembles your great-great-grandparents. Likewise with other living organisms.
However, in this case, the cryptomycota are called a 'missing link' precisely because they have some characters which were presumed to be present in the ancestors to fungi. They have flagella, which are absent in all 'true' fungi except the chytrids. In fact, chytrid fungi were originally not considered to be true fungi, because they had a flagellated stage in their life cycle. Aside from the cryptomycota, the chytrids are the next-most-basal group of fungi. Furthermore, in every intro biology class we learn that fungi have a chitinous cell wall. These are lacking in the cryptomycota, and presumably also lacking in the precursor to fungi, because it's a feature that's unique to the 'true fungi'.
As before, it's important to point out that the term 'missing link' is often misinterpreted. Just as the word 'primitive' has commonsense connotations of being somehow worse off than the 'advanced' species, the same goes for 'missing links'. In the context of systematics, what it refers to is the fact that some species retain traits that are present in ancestral species (either known from fossil evidence or inferred by reconstruction), and their having a mixture of 'derived' and 'primitive' characters provides additional confirmation for how we reconstruct the phylogenetic relationships of these related species.
Also notable is how these fungi were identified. It's fairly routine now to study microbes from the environment without needing to culture them in the lab. Sequences of a well-known gene, such as the ribosomal RNA genes, can be produced from DNA extracted from the environment, and then compared with known sequences in databases, to see 'what's out there'. Novel sequences identified in this way can be related to actual cells under a microscope, by labeling them with probes that specifically target these unique parts of their ribosomal RNA, a method called in-situ hybridization. That's what's shown above in the micrograph, where the probe labeled with a green fluorescent molecule demonstrates that these peculiar flagellated cells were the mysterious fungus-like sequences that the scientists kept finding in environmental samples.
So the lesson here is: There's plenty out there waiting to be found, even in stagnant nondescript ponds! As DNA sequencing gets cheaper and labeling techniques become more convenient, I'm sure that we'll be hearing much more news like this, about cool new microbes that many years ago would have been impossible to identify or classify.
Sources:
Jones et al. "Discovery of novel intermediate forms redefines the fungal tree of life." Nature (published online: 11 May 2011) doi:10.1038/nature09984
BBC News
We don't necessarily have to go to exotic locations like hot springs or the deep sea to discover something new. A new group of "primitive" fungi has recently been described from samples taken from a variety of locations around the world, including a pond in Devon near Exeter University in the UK, where the scientists worked.
This group, called the cryptomycota (not capitalized, because it's not yet officially described according to the rules of taxonomy), has characteristics which make it apparently a 'missing link' between the fungi and other eukaryotic microbes. Sequences of a number of genes place it as a sister group to the rest of the fungi; that is to say, on the family tree of the fungi, it branches off at the very base of the tree.
Although the term "primitive" is often used for groups that fall out at the base of phylogenetic trees, like the cryptomycota, it's important to note that they don't necessarily resemble the ancestors of these groups in every respect. That is to say, just because one branch of your family split off many generations ago from your own lineage, it's not true that this branch more closely resembles your great-great-grandparents. Likewise with other living organisms.
However, in this case, the cryptomycota are called a 'missing link' precisely because they have some characters which were presumed to be present in the ancestors to fungi. They have flagella, which are absent in all 'true' fungi except the chytrids. In fact, chytrid fungi were originally not considered to be true fungi, because they had a flagellated stage in their life cycle. Aside from the cryptomycota, the chytrids are the next-most-basal group of fungi. Furthermore, in every intro biology class we learn that fungi have a chitinous cell wall. These are lacking in the cryptomycota, and presumably also lacking in the precursor to fungi, because it's a feature that's unique to the 'true fungi'.
 |
| Fluorescence microscopy image of cryptomycota. Flagella are labeled with an antibody (red), the nuclei with a fluorescent stain (blue), and the ribosomal RNA labeled with an in-situ hybridization probe (green). Via BBC News. |
Also notable is how these fungi were identified. It's fairly routine now to study microbes from the environment without needing to culture them in the lab. Sequences of a well-known gene, such as the ribosomal RNA genes, can be produced from DNA extracted from the environment, and then compared with known sequences in databases, to see 'what's out there'. Novel sequences identified in this way can be related to actual cells under a microscope, by labeling them with probes that specifically target these unique parts of their ribosomal RNA, a method called in-situ hybridization. That's what's shown above in the micrograph, where the probe labeled with a green fluorescent molecule demonstrates that these peculiar flagellated cells were the mysterious fungus-like sequences that the scientists kept finding in environmental samples.
So the lesson here is: There's plenty out there waiting to be found, even in stagnant nondescript ponds! As DNA sequencing gets cheaper and labeling techniques become more convenient, I'm sure that we'll be hearing much more news like this, about cool new microbes that many years ago would have been impossible to identify or classify.
Sources:
Jones et al. "Discovery of novel intermediate forms redefines the fungal tree of life." Nature (published online: 11 May 2011) doi:10.1038/nature09984
BBC News
Wednesday, May 19, 2010
Protistology Bibliography
For those who are interested in microbial eukaryotes (a.k.a. protists, protozoa, algae...), I've uploaded a reading bibliography that I prepared this past semester. Suggestions welcome.
Friday, September 28, 2007
Space bacteria
Bacteria (Salmonella typhimurium) flown in space on the shuttle were shown to be more virulent than the control strains held on Earth.
What I found pretty neat was something that one of the researchers said: "Wherever humans go, microbes go; you can't sterilise humans. Wherever we go, under the oceans or orbiting the Earth, the microbes go with us, and it's important that we understand... how they're going to change."
This is a good reminder that microbes, the prokaryotes but also the protists, play extremely important ecological roles in the environment and within other organisms, that we frequently overlook because of their small size. Concepts which seem 'exotic', such as parasitism, 'alternative' metabolisms, and even perhaps the ecology of soil bacteria, are actually more commonplace than we think.
In terms of sheer number and biomass, the microbes are the rule, not the exception, and they're everywhere. Even in space flight, the pinnacle of human technological achievement, we've still not figured out how to deal with the 'problem' of microbial hitch-hikers.
Perhaps we shouldn't think of them as problems to be eliminated. After all, they've been with us since the beginning and have had a hand in our own evolution (for example vitamins produced by gut bacteria which our own metabolisms cannot produce). They've pretty much become part of us, and attempting to eliminate them would be a sign of hubris and only put our own selves in the way of illness.
PNAS article link.
What I found pretty neat was something that one of the researchers said: "Wherever humans go, microbes go; you can't sterilise humans. Wherever we go, under the oceans or orbiting the Earth, the microbes go with us, and it's important that we understand... how they're going to change."
This is a good reminder that microbes, the prokaryotes but also the protists, play extremely important ecological roles in the environment and within other organisms, that we frequently overlook because of their small size. Concepts which seem 'exotic', such as parasitism, 'alternative' metabolisms, and even perhaps the ecology of soil bacteria, are actually more commonplace than we think.
In terms of sheer number and biomass, the microbes are the rule, not the exception, and they're everywhere. Even in space flight, the pinnacle of human technological achievement, we've still not figured out how to deal with the 'problem' of microbial hitch-hikers.
Perhaps we shouldn't think of them as problems to be eliminated. After all, they've been with us since the beginning and have had a hand in our own evolution (for example vitamins produced by gut bacteria which our own metabolisms cannot produce). They've pretty much become part of us, and attempting to eliminate them would be a sign of hubris and only put our own selves in the way of illness.
PNAS article link.
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