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Project Progress

During this past year we have continued our studies on the bacteria that contain homologs for alpha- and beta-tubulin. Our most recent paper is a comparative genomic study. The genomes of the tubulinate bacterium, Prosthecobacter dejongeii of the phylum Verrucomicrobia and a member of the related phylum, Planctomyetes, named Gemmata Wa-1 were compared to the Eucarya. Since both of these organisms have been implicated as evolutionary progenitors of the Eucarya, a blast search was made against a group of 347 eukaryotic signature proteins (Staley et al., 2005). The results of that investigation cast doubt on these two phyla as being ancestors of the Eucarya. We have also found that the Planctomycetes contain six homologs for C-1 genes that encode enzymes involved in the oxidation of formaldehyde. Previously these genes were reported only in the methanogens of the Archaea and the methane-oxidizing members of the Bacteria that are in the phylum, Proteobacteria. The phylogeny of these six deduced proteins indicates that the Planctomycetes occupy an intermediate position between these two other phyla suggesting they may have played a role in their inter-Domain horizontal gene transfer (Chistoserdova, 2004).

In continuation of our low temperature work, we reported that “Psychromonas ingrahamii” grows at —12°C, the lowest temperature reported for for a bacterium with an authenticated growth curve (Breezee et al., 2004). We are now comparing this organism with its south polar counterpart which is a member of this same species (Staley et al., in preparation).

Our research has recently become focused on the Black Sea as a model for the early evolution of life and metabolism. Inasmuch as the Black Sea is the largest anoxic basin on Earth, its redox profile serves as an excellent place to study the evolution of metabolism and microbial life. We have begun our investigations by looking at a novel reaction, the anammox (anaerobic ammonia oxidation) reaction in which ammonia is oxidized anaerobically as an energy source and nitrite is the electron acceptor. Importantly, the anammox reaction is carried out by a group within the Planctomycetes phylum. We are also looking at denitrification (Oakley et al, in prepartion), thiodenitrification and nitrogen fixation. Using PCR with primers for the Planctomycetes-specific 16S rDNA, we have constructed a profile of this phylum across the suboxic zone of the Black Sea and identified the redox zone of the anammox bacteria (Oakley et al., submitted; Kirkpatrick et al., in prepartion). These results also reveal novel clades within the Planctomycetes whose function is not yet understood. Our goal is to determine what the activities are of each of the novel clades and also determine which organisms are responsible for dentrification, thiodenitrification and nitrogen fixation.