Saturday, June 30, 2007

Cilliate kleptoplasty

Chloroplasts, like mitochondria, have their own chromosomal DNA. This is, of course, evidence for the endosymbiotic theory of the origin of chloroplasts. It is also useful because it allows researchers to use the DNA to identify the source of the chloroplasts present in kleptoplastic organisms. This is a fairly standard method and is the way that Gast et al 2007 determined the source of the chloroplasts in the Antartic dinoflagellates discussed in a previous post.

In a paper (pdf) a few years ago in Limnology and Oceanography, McManus et al. used the chloroplasts present in the kleptoplastic tide-pool ciliates, Strombidium oculatum and Strombidium styliferseen to help reveal an interesting life history. The chloroplasts were from the large multicellular macroalgae Enteromorpha clathrata which raised the question of how these unicellular cilliates were able to acquire macroalgal chloroplasts.

McManus et al. found that the cilliates don't appear to be grazing directly on the large strands of the mature algae but on the small motile reproductive cells, called zoospores, mature algal strands release.

In addition to chloroplasts, the zoospores contain a pigmented eyespot. As the photo above (from the paper's figure 1) demonstrates, the kleptoplastic cilliates contain a pigmented eyespot similar to the ones possessed by the zoospores. This suggests that the Strombidium cilliates also owe their phototaxic abilities to the alga cells they ingest.

Some other interesting points about these cilliates:
  • They are tidal organisms and live by the rhythm of the tides, becoming active during low tide when tidal pools are calm, and then attach to surfaces and encyst during high tide, presumably to prevent them from being washed out to sea and away from their food.
  • They appear to be obligate mixotrophs, unable to grow in the dark or in the absence of algal food.
Complete reference:
McManus, G. B., H. Zhang, and S. Lin. 2004. Marine planktonic ciliates that prey on macroalgae and enslave their chloroplasts. Limnol. Oceanogr. 49:308-313.

Tuesday, June 26, 2007

8 random facts meme

I have been tagged by John Dennehy (aka the Evilutionary biologist) in this 8 random facts meme. The rules are:
  • We have to post these rules before we give you the facts.
  • Players start with eight random facts/habits about themselves.
  • People who are tagged need to write their own blog about their eight things and post these rules.
  • At the end of your blog, you need to choose eight people to get tagged and list their names.
  • Don’t forget to leave them a comment telling them they’re tagged, and to read your blog.

1. When I saw I'd been tagged for this, my first though was: how big a population of facts do I need to generate in order to make sure that the list of 8 will seem random?

2. I own more that one microscope.

3. I have never known what I wanted to be when I grow up (I still don't).

4. I love the change of seasons and do my best to never complain about the weather.

5. There is a definite trend in the size of the organisms I've studies since college: penguins > tilapia > phytoplankon > bacteria ... ?

6. My dog's name is Larry

7. I live on an island off the the coast (if Spalding Grey can say that about Manhattan, I can say it about Aquidneck Island)

8. I am pretty sure this is not a random list but we'll have to check with Larry to be certain.

So many people have already done this so for the last part, I'll steal this from Tara: anyone who's not been hit already, feel free to consider yourself tagged.

Monday, June 25, 2007

In the Bay 24 Jun 2007

Dactyliosolen fragilissimus, a chain forming diatom, one of the most abundant species of phytoplankton in the bay.

Thursday, June 21, 2007

Building a better biofuel

Biofuels offer the promise of reducing our dependence on fossil fuels. The most widely used biofuel is ethanol made by the biological fermentation of corn. This process is not as green as many would like to believe because a substantial amount of energy (in the form of fossil fuel) is used in the production process. So ,the net gain is not great. Also, ethanol itself is not a terribly good fuel as it is very volatile, is not very energy dense and absorbs water.

A better biofuel would be one that does not rely on an important food crop, has a higher energy density and can be produced with as little energy input as possible. In todays issue of Nature, Román-Leshkov et al present a letter in which they report on a process by which the are able to produce 2,5-dimethylfuran (DMF) from the sugar fructose.

DMF is a better fuel than ethanol and interest in it is not new. What is new in this report is the ability to produce DMF in an industrial process requiring much less energy than previously reported methods.

The environmental impacts of this material have not been well studied and the source of fructose for the production of DMF remains an important issue but this type of innovative thinking has a place in our efforts to move away from dependence on fossil fuels.

Complete citation:
Roman-Leshkov, Y., C. J. Barrett, Z. Y. Liu, and J. A. Dumesic. 2007. Production of dimethylfuran for liquid fuels from biomass-derived carbohydrates. Nature 447:982-985.

Cow burps and global warming

Methane is a greenhouse gas and methane released into the atmosphere contributes to global climate change. Compared to CO2, relatively little methane is released but it is ~ 20 times more effective at absorbing energy than CO2 so its contribution is significant. There are both human influenced and natural sources of methane. These including rice patties, swamp gasses, termites and ruminants such as cows.

My friend (and a reader of this blog) Marek Kirs send me this link to a story on NPR about attempts to reduce the amount of methane produced by cows. The idea is to adjust the types of food they eat or even manipulate their gut microbial community to eliminate the methanogenic organisms responsible for the gas production.

One of the points the researchers make is that the production of methane is the result of incomplete oxidation of food eaten by the cows. So, the elimination of methanogenesis could result in increases production of meat and milk from these animals. Cattle food conversion ration are around 12%, and any increases would likely be small but the idea is to have enough of an increase to offset any increased cost to the producers.

Wednesday, June 20, 2007

Gut bacteria metabolic diversity

Another paper exploring microbial diversity of the human gut has been released in PLoS Biology. It is open source so go read it for yourself! There is also a summary article on the data intended for a lay audience. The data presented in the paper is very interesting. They sequenced the genomes of two gut bacteria, Bacteroides vulgatus and Bacteroides distasonis, and contrasted their metabolic potential (the genes present in the genome) with the well studied species Bacteroides thetaiotaomicron. This comparison does provide some evidence that niche specialization plays a role in maintaining the diversity of the gut microbiota.

The importance of studying the gut microbiota is summed up nicely in the beginning of the author summary:

"Our microbial partners provide us with certain features that we have not had to evolve on our own. In this sense, we should consider ourselves to be a supraorganism whose genetic landscape includes both our own genome as well as the genomes of our resident microbes, and whose physiologic features are a synthesis of human and microbial metabolic traits."

I would have worded the first sentence differently as saying 'have not had to" sounds a bit too teleological to me.

I am also troubled by their use (later in the introduction) of the term "top-down selection" in reference to host driven selective forces that they argue are responsible for maintaining a high degree of functional redundancy in the gut community. I am not aware that the term top-down selection, as used by the broader ecology community, is considered a force for the maintenance of ecosystem stability.

The end of the paper lists a set open questions that it would be very nice to have answers to:
"Do we share an identifiable core “microbiome”? If there is such a core, how does the shell of diversity that surrounds the core influence our individual physiologic properties? How is the human microbiome evolving (within and between individuals) over varying time scales as a function of our changing diets, lifestyle, and biosphere? Finally, how should we define members of the microbiome when microbes possess pan-genomes (all genes present in any of the strains of a species) with varying degrees of “openness” to acquisition of genes from other microbes?"

Sunday, June 17, 2007

Bacterial predators

With the rise of antibiotic resistance in important bacterial pathogens, attention is being focused on alternative treatments for bacterial infections. The most prominent among these is phage therapy. Another potential antimicrobial agent is the predatory bacteria Bdellovibrio and related species

I am not sure how likely it is that these bacteria will ever find use as therapeutic agents, but they are pretty amazing organisms and they definitely have the potential to be used in this way.

Bdellovibrio have a truly predatory life style. They require specific species of gram negative bacteria to grow. The cells are small and highly motile. When they encounter a susceptible host cell, they attach themselves to the outer surface of the cell, bore a hole in the cell wall and push themselves into the periplasmic space (the space between the outer membrane and cytoplasmic membrane of gram negative bacteria). Once there the cell is killed and its contents consumed. Bdellovibrio reproduces within the cell and once the contents of the prey are consumed, the daughter cells will burst out of the shell of the dead prey cell and head off to find other targets.

Thursday, June 14, 2007


DNA sequencing has revolutionized biology. Not too long ago obtaining the sequence of an individual gene was a big deal. Now sequencing entire genomes is becoming routine. To obtain the sequence of an organism's entire genome, the genome is broken into fragments and many many fragments are sequenced individually using a PCR based method. In the standard process, the sequence generated from each fragment is about 500 to 1,000 bases long. To generate the sequence of the genome, computers are used to align all of the data and identify contiguous sequences that can then be assembled. In order to be confident in the data (errors are made in the process), the entire genome is sequenced multiple times. At least 4 to 5 x coverage is considered necessary for good data.

A typical bacterial genome of 3.5 mega-bases sequenced to 5x coverage amounts to over 21,000 individual sequencing runs. For organisms (such as humans) which have multiple chromosomes each chromosome is sequenced individually. With about 3 billion bases in the human genome and 10x coverage, the data contained in the human genome project represents an enormous amount of sequencing and alignment effort.

A relatively new innovation called 454 sequencing has sped up the process. 454 is still based on PCR but it is much faster as the sequence is read as the PCR progresses. The trade off to the increased speed is that each individual read is somewhat shorter making assembly more challenging.

One 454 application that is becoming more and more widespread is the sequencing of multiple strains of a species of bacteria. In this type of application the genome of one strain is already known. The assembly of the genome of each successive strain is facilitated by the use of the original strains sequence as a template.

454 sequencing was used to determine James Watson's genome. The whole genome was assembled in two months at a cost of $1 million. The assembly was almost certainly accelerated by aligning short reads of Watson's DNA with the pre-existing human genome sequence.

image from the tutorial found on 454 life sciences web page

Monday, June 11, 2007


Kleptoplasty is a wonderful term. It is used to describe the behavior of a group of organisms that are able to ingest algal cells and degrade the cells, but not the chloroplasts contained within the cells. The chloroplasts remain functional for some period of time during which the photosynthetic products generated by the sequestered chloroplasts are utilized by the new 'host'.

On the left is a figure from a paper by Gast et al. in the journal Enviornmental Microbiology from earlier this year showing a kleptoplastic dinoflagellate isolated from the Ross Sea in Antartica (the paper is in a free issue of the journal so go read the whole thing).

In addition to being a very interesting behavior from an ecological perspective, kleptoplasty is of evolutionary interest because the capacity to grow autotrophically by photosynthesis arose within dinoflagellates by the retention of chloroplasts from ingested algal cells. This ability appears to have arisen multiple times within dinoflagellates because not all contain chloroplasts from the same type of algal cell.

Sunday, June 10, 2007

African deforestation

The rainforest of the Congo Basin in Central Africa is the second largest in the world. It covers millions of square kilometers and spans 6 different countries (including Gabon where I spent 2 years). As with other tropical rain forests this region is home to substantial biodiversity. Here in the US we hear a great deal about deforestation in the Amazon, less is heard about the African rainforests.

The most recent issue of the journal Science contains a brief report documenting the extent of deforestation and increases in commercial logging in the Congo Basin. The information was acquired by analyzing almost 30 years of satellite data for changes in forest cover and the appearance of new logging roads. The objectives of the report were to highlight the lack of good data on the extent of deforestation in the Congo Basin, present the data acquired from the available satellite data and demonstrate the value of the satellite data as a tool to assess changes in land use and document the extent of logging.

*added on edit: Here is some more information about the article and here is the figure from the paper showing the extent of the deforestation. Note how much of the area still has >75% forest cover.

Saturday, June 09, 2007

adopt a cheetah

A recent report in Proceeding of the Royal Society describes the genetic relationship among cheetah litter mates. They found that almost half the litters were comprised kittens of mixed paternity. Female cheetah parole a territory of 300-400 km2 and this allows them to interact with more than one male during a single reproductive cycle. This is a behavior that they share with the common cat. A summary of the paper can be found here.

One finding that struck me was that within the 47 litters surveyed, they found 3 instances of adoption by mother cheetahs of unrelated kittens. This finding has been described previously and there are several ideas as to the potential selective advantage this behavior. My first question is given the huge territories these cats parole, how on earth do the new mothers find orphaned kittens?

Thursday, June 07, 2007

Plant-bacteria communication

In a previous post I mentioned that the nitrogen fixation performed by leguminous plants is the result of a symbiosis between the plants and bacteria. In this relationship, the plants create an environment within their roots (called nodules) where the bacteria take up residence. In exchange for energy provided by the plant, the bacteria fix atmospheric nitrogen that is then made available to the plant. Allowing bacteria access to the interior of the root is a potentially risky act on the part of the plant. So, a mechanism to exclude all bacteria except for the desired nitrogen fixer has developed and the symbiotic relationships are species specific. Each plant has specific bacterial symbionts. In the early stages of the establishment of the root nodule, signals are exchanged between the plant roots and bacteria in the soil. First, the plants release phytochemicals that attract the desired bacteria. The target bacteria are attracted by the phytochemicals and these chemicals induce the bacteria to release their own compounds called nod factors. The nod factors, in turn are sensed by the plant. Detection of the appropriate nod factor will induce the plant to initiate the process of allowing the bacteria access to the interior of the root where the nodule will form.

In the latest PNAS, Fox et al. report that many common pesticides inhibit the formation of root nodules by interfering with communications between the plants and bacteria.

While the significance of this in the environment is not known, it has the potential to be of concern because the use of crop rotations that include plants (such as soy or alfalfa) that are capable of enriching the nitrogen content of the soil is one important way to reduce the use of fertilizer (and energy) in modern agriculture.

Wednesday, June 06, 2007

In the bay 6 June 2007

One word: SNAILS! They were abundant last time and there are even more of them out there this week.

I know a fair amount about phytoplankton and am pretty good at identifying them. See the list of previous students here. When I came up with the idea of posting microscope images take of samples from the bay here on mixotrophy, I was ( and still am) planning on focusing on phytopankton. Of course this time of year, the zooplankton population is high and all of these little heterotrophs are busy grazing on the phytoplankton. This keeps phytoplankton cell abundance low. As a result, I am not seeing much of what I was planning on photographing. There are plenty of zooplankton to look at of course. The problem is, identifying zooplankton is much harder for me. Getting good live pictures is also a challenge because they move around.

I did get a few nice images though. Here is another larvae viewed in bright field. It is the nauplius stage of some type of crustation (I think).

This is the same view in dark field:

Tuesday, June 05, 2007

Computing power!

Check out this video on meta-imaging from a recent TED conference. Phil Plait at BA was struck by the reconstruction of Notre Dame and its potential for use within astronomy. The whole presentation is incredible. I wonder how powerful a computer he was using. With image resolution so high the memory needs must also be huge. Here is a link to the photosynth software. Of course I am using a mac so I can't download it.

Monday, June 04, 2007

Nitrogen fixation

Industrial agriculture is highly dependent on a ready supply of labile nitrogen fertilizer for high yields. Roughly half of all the nitrogen used in agriculture is in the form of ammonia (NH3) synthesized using the Haber-Bosch process. In this process, atmospheric nitrogen in the form of N2 gas is mixed with hydrogen gas at high temperature (500 oC) and pressure (200 atm) in the presence of an iron catalyst. That's 500 oC and 200 atm. Very hot and very high pressure.

Bacteria (and archaea) are also capable of converting nitrogen gas to ammonium (often referred to as 'fixing nitrogen') but they do it at normal temperatures and under 1 atmosphere of pressure. In these organisms the process is also energy intensive but the energy is supplied in the form of ATP and the catalyst is an enzyme complex containing 2 proteins, dinitrogenase and dinitrigenase reductase. This capacity is found in both bacteria and archaea in diverse environments including the root nodules of so called nitrogen fixing plants such as clover and soy. Bacteria, not the plants, fix the nitrogen.

There are many blog worthy aspects of microbial nitrogen fixation. I have created a label for this topic and intend to explore some of them here in the future.

Sunday, June 03, 2007

Ancient life?

An item in a list of news reports over at Primordial Blog caught my eye this evening. It is a report in CBC News about a paper in the most recent issue of the journal Geology describing what is believed to be ichnofossils in 3.5 billion years pillow basalts from Australia.

Ichnofossils, or trace fossils are not the remains of organisms themselves but tracks left by organisms that become preserved. In this case the traces are tunnels in the volcanic rock presumably left by microorganisms as they degraded the rock to mobilize nutrients contained within. The images on the left are from a 1998 report (Fisk, M. R., Giovannoni, S. J. & Thorseth, I. H. (1998) Alteration of Oceanic Volcanic Glass: Textural Evidence of Microbial Activity. Science, 281, 978-980.) describing these tunnels from oceanic basalts. The scale bars are 50 and 10 microns long in the top and bottom panels respectively.

There is some controversy over whether these tunnels are due to the activity of microbes or are the result of some poorly understood form of abiotic chemical weathering. These images are not easy to get as the rock has to be cut into think slices with a diamond saw and then polished to allow light through. The sections that were used to take the images shown here were 30 microns thick.

Saturday, June 02, 2007

MDR mobility

There is much talk in the blogsphere about this idiot who knowingly exposed a huge number of people to a multi drug resistant strain of TB. f you are interested, Tara Smith over at Aetiology has several posts (1,2,3 & 4 so far) on the topic including links to other discussions and information.

Instead of commenting on that situation I thought I'd call attention to a recent paper by Tim Welch and others in Plos One about a plasmid inferring multi drug resistance that has been found to be present quite common in our food supply.

This plasmid is of concern because it was isolated from a strain of the plague bacteria, Yersinia pestis, back in the mid 1990s. Since then it has not turned up in Y. pestis again but this new paper reports finding related plasmids in the fish pathogen Yersinia ruckeri and in a strain of the food born pathogen Salmonella. The picture on the left shows the relationship between the three plasmids.

The inner circle shows the conserved backbone indicating that the plasmids isolated from three different species of bacteria have a recent, common origin. They all have the genes necessary to be self mobilizing but they differ in the number of drug resistance genes they carry, ranging from 9 to 13.

using data from the conserved backbone Welch et al. screened a large number of MDR strains of Salmonella, E. coli and Klebsiella sp. isolated from agricultural products and found that the majority of the resistant strains harbor a relative of this plasmid.

From the paper:
The discovery of these MDR IncA/C plasmids in evolutionarily distinct pathogens attests to recent genetic exchange, either directly between these bacterial species or through bacterial intermediates, and it suggests that overlap in the ecological niches of these organisms is sufficient to permit past or future plasmid transmission.

we present evidence that a common plasmid backbone is prevalent among E. coli, Klebsiella sp. and multiple Salmonella serotypes isolated from retail meats in the US, and among some food animal isolates of E. coli. Our data imply that high levels of MDR in the causative agent of plague may rapidly evolve naturally...

Friday, June 01, 2007

In the bay 30 May 2007 II

Snail larvae. The water was loaded with these. Probably the periwinkle Littorina littorea. An invasive species introduced to Canada from Europe in the 1800. It is abundant on rocky shores throughout New England. I am not sure how far south they are found.

Here are 2 pictures:

Side view of the shell. the blurring at the top right of the image is due to the movement of cilia along the edge of their feeding apparatus called a velum.

End on view:

the picture is fuzzy but you can see the extended velum and the cilia along the edge.

And a video: