The Taxonomy of Cow Farts

The organism in the above picture (from Garrity & Holt 2001) may not look particularly remarkable, but this is a very important microbe. This is a thin section of Methanobrevibacter ruminantium, a member of the group of archaebacteria known as the Methanobacteriales (methanogens). Methanobacteriales get their name because they grow by reacting carbon and hydrogen to produce methane. They are found in a variety of habitats, though all are strict anaerobes (they die if exposed directly to oxygen). As suggested by its name, Methanobrevibacter ruminantium was described from the rumen (part of the digestive system) of cattle; it or closely related strains are also known from sheep, and even from the crop of the hoatzin, the South American bird that is the world's closest thing to a flying cow. These are the organisms that make cattle fart.

Climate change is a major issue in modern society, and a lot of questions have been raised about how to mitigate its effects. The most familiar factor in climate change is the burning of fossil fuels, but something else that has been subjected to scrutiny is the role of livestock. Anyone who has spent much time in the company of cattle will tell you that they belch and fart continuously. Methane emissions from livestock may not produce the same volume of greenhouse gases worldwide as fossil-fuel burning, but they still cause concern because methane is a significantly more potent greenhouse gas (litre for litre) than carbon dioxide. Methane production can also siphon off 10% or more of the energy contained in the livestock's feed, energy that might otherwise go towards putting on weight, making it a concern for the farmer as well as for the environment. As a result, the question has been raised of whether it would somehow be possible to get the world's cattle to effectively put a cork in it.

Unfortunately, it is not as simple as wiping the methanogens from the cattle's system, because they do have a very important role to play. The digestive system of cattle and other ruminants contains a whole ecosystem of micro-organisms that serve to break down the cellulose and other parts of the cattle's food that it can't digest alone. Ciliates in the rumen that break down cellulose excrete hydrogen gas, in the way that we breathe out carbon dioxide as a result of our own respiratory processes. But just as we would not be able to keep functioning if the concentration of carbon dioxide in a room got too high, these cellulose-digesting microbes become sluggish as the concentration of hydrogen in the gut increases. By converting the hydrogen to methane, the methanogens keep the rumen sweet-smelling and fresh (at least by ciliate standards). Without this process of hydrogen removal, the cattle themselves would not survive long.

Comparison of methanogen populations in low-methane (left) and high-methane (right) cattle, from Zhou et al. (2009).

And this is where taxonomy becomes important. I've been talking as if there is only a single methanogen species in cattle. This is not the case. Methanobrevibacter ruminantium is one of at least five Methanobrevibacter species known from cattle rumens, together with a number of methanogen species belonging to other genera (Zhou et al. 2009). And not all these methanogens are equal in the amount of methane they produce. Zhou et al. (2009) compared the methanogen flora in cattle that absorbed a high ratio of nutrients from their food, and produced relatively little methane, with that in cattle that were less efficient digesters and that produced more methane. They found that while members of both groups contained similar total numbers of methanogens, they differed in taxonomic composition. In the high-efficiency cattle, M. ruminantium made up a higher proportion of the gut flora, while other methanogens such as Methanobrevibacter sp. 'AbM4' increased in abundance in low-efficiency cattle.

Now obviously, there's a lot this doesn't tell us. We don't know whether the high-efficiency cattle produce less methane because of the differences in their methanogen flora, or whether the methanogen flora is different because the cattle are more efficient digesters. If the former, then maybe cattle could be inoculated against undesirable methanogens and the less injurious methanogens encouraged. If the latter, then maybe breeding would have to come into it. Or the methanogen flora could differ due to differences in the cellulose-digesting flora, in which case control measures would have to act at that level. Whatever the reasons, the simple fact that there are different species involved is yet another reminder: even if we're talking about climate, taxonomy matters.

REFERENCES

Garrity, G. M., & J. G. Holt. 2001. Phylum AII. Euryarchaeota phy. nov. In: Boone, D. R., R. W. Castenholz & G. M. Garrity (eds) Bergey’s Manual of Systematic Bacteriology, 2nd ed., vol. 1. The Archaea and the Deeply Branching and Phototrophic Bacteria, pp. 211-355. Springer.

Zhou, M., E. Hernandez-Sanabria & L. L. Guan. 2009. Assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies. Applied and Environmental Microbiology 75 (20): 6524-6533.

How to Kill Tropical Fish

A short while ago I was contacted by Ava of The Reef Tank, a site for keepers of tropical marine aquaria, asking if I would contribute something for their in-house blog. I did once keep a tropical (freshwater) aquarium, but sadly the main thing I learnt from the experience was that putting too much fish in the tank early on leads to their rapid demise due to the buildup of toxic nitrogen compounds (eventually, I discovered the attractive yet indestructable White Cloud mountain minnow). So I presented Ava with a piece on the bacteria responsible for maintaining the nitrogen cycle in fish tanks, and you can read it here.

The Nature of Nanoarchaeum

Ignicoccus cell with four 'Nanoarchaeum' cells attached. Scale bar = 1 μm. Image from Huber et al. (2002) via MicrobeWiki.

The Archaea have received a great deal of attention in recent years as the supposed Third Domain of life. They are a group of prokaryotes that differ from all others (the Eubacteria) in a number of significant ways - they have a RNA-protein translation system more similar to that of eukaryotes than Eubacteria, they lack the murein that makes up the cell wall of most Eubacteria, and they have a unique tetraether cell membrane that differs from that of the other domains. The study of Archaea has also been influenced by the association of most cultured representatives with extreme environments as thermophiles or halophiles, though environmental PCR studies suggest that Archaea may be much more abundant in the general environment than the cultured diversity suggests (Forterre et al., 2002).

Compared to the dog's breakfast that is our current understanding of eubacterial phylogeny, the phylogeny of Archaea seems much clearer. Most studies indicate a basal division of cultured Archaea between two major clades, the Crenarchaeota and Euryarchaeota. Crenarchaeota is the smallest of the two groups and the cultured representatives are all hyperthermophiles, though again PCR samples indicate uncultured mesophilic examples. The Euryarchaeota are much more diverse, including halophiles and methanogens as well as thermophiles. Environmental PCR sequences suggesting archaeal taxa lying outside these two major clades, and one group of them has received the provisional name of Korarchaeota, but until these taxa are properly characterised their existence remains uncertain.

So far, the only well-characterised archaeum that has been suggested to lie outside the two main clades is 'Nanoarchaeum equitans'* (Huber et al., 2002). 'Nanoarchaeum' is a minute (400 nm) organism that lives in hyperthermophilic environments as an obligate associate of another archaeum, Ignicoccus. Attempts to culture 'Nanoarchaeum' independently have failed - even growth on a medium of puréed Ignicoccus or separated from an Ignicoccus culture by a semipermeable membrane proved impossible. 'Nanoarchaeum' can only grow in direct cell-to-cell contact with living Ignicoccus. 'Nanoarchaeum' also has the one of the smallest genomes of any organism known, with only about 490,000 base pairs. For comparison, the human genome includes about 3000,000,000 base pairs, that of a lungfish 130,000,000,000 base pairs, and that of the largest known virus, Mimivirus, 1200,000.

*I haven't italicised 'Nanoarchaeum' because it's not yet a technically valid taxon. To be valid, a prokaryote name requires publication or validation in the International Journal of Systematic and Evolutionary Microbiology, and this doesn't seem to have happened for 'Nanoarchaeum'. Because of the stringent culture requirements of the Prokaryote Code of Nomenclature, 'Nanoarchaeum' may not be eligible for validation, though it may be recognisable as a Candidatus, the Prokaryote Code's provisional class for a taxon that cannot be cultured independently but can be well-characterised environmentally.

The reduced genome of 'Nanoarchaeum' is reflective of its inability to synthesise many of the metabolites it requires to survive, which it draws instead from its Ignicoccus host. This is not unusual among parasitic organisms, though 'Nanoarchaeum' is unusual among super-reduced parasites in its extracellular rather than intracellular position relative to the host, probably as a consequence of the general absence of phagocytosis among prokaryotes. 'Nanoarchaeum' is also comparable to other super-reduced parasites in another way. When it was first described, analysis of ribosomal genes suggested a position for 'Nanoarchaeum' divergent from all other Archaea, which lead to its promotion as a new archaeal phylum. However, studies of comparable eukaryotic parasites have indicated that they have usually undergone exceedingly rapid evolution that has exaggerated their differences from their more mediocre relatives. Ribosomal genes in particular seem to be very prone to such long-branch distortion. The prime example in recent years has been the Microsporidia, intracellular parasites that were once thought on the basis of ribosomal genes to be one of the earliest-diverging branches of eukaryotes, but have since been reinterpreted as highly-evolved fungi.


Phylogenetic analysis results from Brochier et al. (2005) showing association between 'Nanoarchaeum' and Thermococcales. Unconstrained unrooted maximum likelihood trees of (a) elongation factor EF-1α, (b) elongation factor EF-2, (c) subunit A of topoisomerase VI, and (d) Bayesian tree of reverse gyrase. Bold numbers at nodes are bootstrap values; the other numbers are the Bayesian posterior probabilities. Scale bars represent the number of changes per position for a unit branch length.

With this in mind, I was not overly surprised to see the results of Brochier et al. (2005). Brochier et al. took a slightly different tack to understanding the phylogeny of 'Nanoarchaeum' - as well as using a wider range of genes, Brochier et al. also calculated the open reading frames (ORFs) of the entire 'Nanoarchaeum' genome (an ORF is a section of the genome that could potentially code for a protein) and compared them to those of other Archaea. The ORF analysis found that 'Nanoarchaeum' shared the majority of its ORFs with Euryarchaeota, and was particularly similar to members of the order Thermococcales. This result was corroborated by a number of the gene analyses. The basal position of 'Nanoarchaeum' in the ribosomal trees would therefore appear to be due to long-branch attraction, possibly exacerbated by lateral gene transfer with its Crenarchaeota host.

REFERENCES

Brochier, C., S. Gribaldo, Y. Zivanovic, F. Confalonieri & P. Forterre. 2005. Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales? Genome Biology 6: R42.

Forterre, P., C. Brochier & H. Philippe. 2002. Evolution of the Archaea. Theoretical Population Biology 61 (4): 409-422.

Huber, H., M. J. Hohn, R. Rachel, T. Fuchs, V. C. Wimmer & K. O. Stetter. 2002. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417: 63-67.