The story of a predator that, upon eating a certain food, suddenly becomes a peaceful plant. Sort of.

Free-living versus symbiotic

A working definition for symbiosis is two or more species that live and interact. Mutualism means that each derives a certain benefit from the other, or at most causing no harm to each other. Their relationship is that of “give and take”. For example cleaning fish serve other fish by cleaning off parasites and getting protection, food and rides in return. Sometimes the mutualistic symbionts have practically fused into a single functional organism. The Portuguese Man o’ War is a colony of four different organisms which form a composite jellyfish;  None of the individuals which can exist in a free-living form. Lichen is a colony of two: a photosynthetic partner providing sugars, and a fungus providing other nutrients as well as preventing the dehydration of the photosynthetic partner.

Lichen, from "Art Forms of Nature" / E. Haeckel

The Endosymbiotic Hypothesis

The endosymbiotic hypothesis maintains that eukaryotes evolved from  symbiotic interactions between bacteria. There is plenty of evidence for that in  chloroplasts and mitochondria: they have their own DNA; their membranes, their DNA,  their ribosomes all resemble those of bacteria. The relationship between a eukaryotic cell and its mitochondria is heavily mutualistic: the cell gets ATP, the mitochondria / chloroplasts (M/C) get.. well, to live and reproduce, which they cannot do outside a living cell. Over time, M/C have have lost most of their genomic material to the host: many of the proteins needed to construct an M/C are not encoded in the M/C but in the host’s nucleus, and transported to the M/C.  This is probably as intimately connected as two organisms can get, before you cannot tell that they were two separate organisms before they fused into an organism and an organelle. Indeed, the threshold set for distinguishing between an endosymbiont and an organelle lies in protein import. According to this working definition, once an endosymbiont starts importing proteins, it is no longer considered an endosymbiont and becomes an organelle.  As with any working definition, if you scratch the surface a bit you will find cases where this rule does not apply well. Viruses are a case in point, acquiring host proteins and actually acting as a vector transferring them between hosts.

Vegging out

Two researchers have shown a striking example of   endosymbiosis forming  now:  in 2005 Noriko Okamoto an  Isao Inouye reported on a unicellular organism called Hatena. Hatena (“enigma” in Japanese) leads a curious life cycle. Hatena is a single-cell organism, swimming around in the water, using a little feeding apparatus to eat cells and organic material smaller than itself.  At some point, it would feed on another unicellular algae, the Nephroselmis. Once Hatena swallows Nephroselmis, it does not digest it. Rather, Nephrosolmis makes itself comfortable home inside Hatena. The alga starts growing inside Hatena: it grows to about 10 times its original size, filling up most of Hatena. The alga also seems to lose most of its own organelles, except for the chloroplast. The chloroplast actually grows bigger.

Hatena changes too as a result. Before ingesting the alga, it has a rather complex “mouth”, or feeding apparatus. After ingesting the algae, this mouth disappears only to be replaced by an eyespot from the algae. The eyespot is a light sensing organelle, a very primitive eye, that guides algae to light sources. In this case, it also guides the host, Hatena, to light. Hatena has obviously stopped feeding, and least through its mouth. It is now swimming to the light, letting the alga photosynthesize its food for both of them.

I get the plant, you get the steakhouse coupons

Hatena reproduces by binary fission. So once it splits itself,  what happens to the symbiotic alga? Well, one daughter cell gets the alga, and the other gets to be a predator… at least until it eats another alga. So here we are, looking at a fascinating evolutionary snapshot: two creatures, they can live apart or together. One is a predator,but is ready to be a plant under the right circumstances; the other is not quite an organelle of the first yet, but definitely on its way.

Right: Hatena with chloroplast, and without. Left: the red bit on the top of the cell marks the eyespot.

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OKAMOTO, N., & INOUYE, I. (2006). Hatena arenicola gen. et sp. nov., a Katablepharid Undergoing Probable Plastid Acquisition Protist, 157 (4), 401-419 DOI: 10.1016/j.protis.2006.05.011

The Schmidt Lab is interested in upland soils are the Earth’s largest methane sink. In agricultural soil this capacity decreases: less methanotrophs. They estimate it takes 75 years for a microbial community to recover once agricultural soil stops being tended.They have shown a clear decrease in methanotrophs in agricultural soil, but it is not clear why the decrease occur.

Another interesting find in his lab was a technological one; they found an artifact in 454 sequencing: artificially replicated sequences. He estimated that about 10-30% of sequence replications found in his 454 runs are due to this artifact. The Schmidt lab actually wrote software to correct this, and they made it publicly usable via a web site.

Shannon Williamson from JCVI talked about marine viruses. Her group isolated bacteriophages (viruses that infect bacteria) using a combined filtering and bacteriocidal approach. When they analyzed the resulting  viral metagenome, they found genes that are homologous to known bacterial genes, yet cluster together in a “viral” branch of the tree. The most interesting explanation would be that some of these genes have been appropriated by the viruses to maintain the host while viral replication takes place. It is hard to rule out simple horizontal gene transfer though, since those viral genes were not compared with bacterial metagenomes from where the original samples were taken, but with known genomes only. Then again, how do you get a “bacterial only” metagenomic samples with no viral contaminants (including lysogenic phages)?

Eric Allen from the Scripps Institute of Oceanography talked about the metagenomics of extreme halophiles taken from Lake Tyler in Australia. Extreme halophiles live in very saline waters,. An interesting argument he made was for the tractability of such a system, due to the small number of species. He showed a cool slide of  a stick-figure standing at the bottom of a staircase, with the stairs themselves getting progressively higher, representing different microbial habitats ordered by their complexity.  The bottom stair was very low, and that was the acid mine drainage system. Acid mine drainage kills almost everything, and there are less than 10 microbial species that have been identified in this habitat. The next stair, slightly higher, was that of extreme halophiles, more complex than acid mine drainage, yet still species-poor. The top stair, twice as high as the stick figure itself was soil metagenomics: >10,000 species and quite insurmountable! One cool thing about extreme haliophiles is their shapes: many have regular geometric shapes: diamond shaped, or squares.

Square microbe! from Bolhuis et al. BMC Genomics 2006 7:169 doi:10.1186/1471-2164-7-169

The second day was opened by James Collins,  assistant director for directorate of biological sciences at the NSF. He talked about  NSF’s need to keep its finger on the pulse of biology: the field is in flux both due to new technologies that open up new questions, and changes in the biosphere itself due to global climate change: we are going through the largest mass extinction since the KT (dinosaur) one.

One cool figure that he had illustrated “trans-disciplinary” versus “interdisciplinary” vs. “multidisciplinary” vs. “separate disciplines”; reproduced here from memory. I guess that taking such complex human activities and interactions and placing them into Venn diagrams holds an appeal to my need to simplify and categorize.

Cross-talk between scientific disciplines.

Then the floor was opened for discussion.  Seemed like almost everyone agreed that the more genomes the better, and they would like to see more genomes and metagenomes coming up. A heated discussion then opened as to how funds should be allocated within this rather nebulous goal. To me it is clear that all levels of genomic annotation are currently insufficient. Some estimate gene calling error rate in whole genomes to be > 30%! I won’t even try to think about how high the error rate might be in metagenomes.  Computational Function Prediction is problematic too (I should know, I have been organizing a function prediction meeting for the past 4 years).  Perhaps we need more money for developing high throughput experimental methods as we continue with the bioinformatics. As much as I hate to say it, the curve that represents advances in bioinformatics annotation methods seems to be not as steep as it was five years ago.

The last talk I attended was by Nancy Moran from Arizona University. Nancy is a co-author of a paper I really like in PLoS Biology that talks about insect symbionts.The Glassy Winged Sharpshooter is an insect that feeds on tree sap. It harbors two bacterial symbionts: one supplies the vitamins to the host, whereas the other produces the essential amino acids. their genomes are very much in accord with those functions, each actually lacking the pathways the other provides, and feeding off each other’s products as well as feeding the host.

Another cool insect symbiont is the aptly named Hamiltonella defensa. This microbe protects pea aphids from parasitic wasp larva. The wasp lays its  eggs in the live aphid, and in an aphid that does not have H. defensa that larva would hatch and eat the aphid alive from the inside-out. But good-ol’ defensa kills the larva when it hatches in the aphid. (Or bad-ol’ defensa if you view aphids as a pest).  H. defensa is transmitted between insects (horizontally) as well to the next generations (vertically). Interestingly enough, some of these toxins are not encoded by the genome of H. defensa, but by a phage, APSE, that infects the bacteria. Aphids that carry the bacteria survive better than aphids that don’t, and those that carry the bacteria which, in turn, carry the virus survive even better.

I will let Jonathan Swift finish this one for me:

"So nat'ralists observe, a flea
Hath smaller fleas that on him prey,
And these have smaller fleas that bite 'em,
And so proceed ad infinitum."

Now excuse me while I shampoo my kids for head lice and boil wash all their clothes & beddings.