Metagenomics probes a gutless wonder

The last week has seen the appearance of two interesting reports on the use of linkurl:metagenomics;https://www.the-scientist.com/article/display/23800/ to probe the biology of microbial communities ? reports that demonstrate the emerging power of this technique to untangle metabolic mysteries in organisms that cannot be grown in the lab. The first, linkurl:published Sept. 17;http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature05192.html in __Nature__, involves the annelid worm, __Olav

By | September 25, 2006

The last week has seen the appearance of two interesting reports on the use of linkurl:metagenomics;https://www.the-scientist.com/article/display/23800/ to probe the biology of microbial communities ? reports that demonstrate the emerging power of this technique to untangle metabolic mysteries in organisms that cannot be grown in the lab. The first, linkurl:published Sept. 17;http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature05192.html in __Nature__, involves the annelid worm, __Olavius algarvensis__. __O. algarvensis__ has neither mouth, gut, nor anus, and instead relies upon a series of obligate bacterial endosymbionts for its existence. Ed Rubin of the DOE Joint Genome Institute (JGI), and Nicole Dubilier at the Max Planck Institute for Marine Microbiology, Bremen, Germany, identified and sequenced four cosymbionts, using metagenomics to demonstrate how these organisms interact with each other, and with their host. Sequence analysis identifies the four cosymbionts as members of either the gamma- or delta-proteobacteria, and their genetic complements belie their biochemistry. Sequence homology suggests, for instance, these two bacterial classes feed each other in a cycle of reduced and oxidized sulfur metabolites. The gamma-proteobacteria can use energy derived from the reduction of sulfide -? which comes from the delta symbionts -- to drive carbon fixation, a pathway to provides its host with needed nutrients. The worm, in turn, provides the bacteria with nitrogen in the form of urea and ammonia, among other things ? an observation that demonstrates how this gutless wonder was able to eliminate its excretory system, the lone annelid known to have done so. The second study, linkurl:published Sept. 24;http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt1247.html in __Nature Biotechnology__, uses metagenomics to investigate two "enhanced biological phosphorus removal (EBPR) sludge communities," which are used in bioremediation programs. Philip Hugenholtz, also of the JGI, led the study, which demonstrates that these communities are dominated by a single organism, __Candidatus Accumulibacter phosphatis__, whose composite genome was sequenced and analyzed in the report. Among the interesting findings: __A. phosphatis__ can evidently run the citric acid cycle under anaerobic conditions, a feat the authors attribute to a novel quinol-NAD(P) reductase, which again, is pinpointed via sequence homology. "This protein appears to be a fusion of a cytochrome b/b6 with five transmembrane helices and a soluble NAD(P)? and flavin-binding domain, a domain configuration that is currently unique in public sequence databases." The significance of this finding: running the citric acid cycle in anaerobic mode would give __A. phosphatis__ the energy resources to climb to the top of the EBPR sludge heap, so to speak, and outgrow its competitors. That?s a pretty nifty real-world deduction from a metagenomics study, isn?t it?

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