Social bacteria and asocial eukaryotes

The end of 2007 brought us draft genome sequences of two eukaryotic microorganisms, Babesia bovis and Malassezia globosa, as well as complete genomes of the ammonia-oxidizing archaeal chemoautotroph Nitrosopumilus maritimus, and several environmental bacteria (Table 1). In terms of genome size, this list covers both sides of the spectrum: the 245 kb genome of an obligate insect symbiont Sulcia muelleri is the second smallest microbial genome sequenced so far, whereas the 13 033 kb chromosome of the social myxobacterium Sorangium cellulosum breaks the record as the largest bacterial genome – and the largest DNA molecule in the prokaryotic world.

Table 1.

Recently completed microbial genomes (October–November 2007).

Species name	Taxonomy	GenBank accession	Genome size, bp	Proteins (total)	Sequencing centrea	Reference
New organisms
Babesia bovis	Eukaryota,Apicomplexa	AACB02000000	8 200 000	6470	Washington State U.	Brayton et al. (2007)
Malassezia globosa	Eukaryota,Basidiomycota	AAYY00000000	8 900 000	4285	Procter & Gamble	Xu et al. (2007)
Caldivirga maquilingensis	Crenarchaeota	CP000852	2 077 567	1963	JGI	Unpublished
Nitrosopumilus maritimus	Crenarchaeota	CP000866	1 645 259	1798	JGI	Unpublished
Frankia sp. EAN1pec	Actinobacteria	CP000820	8 982 042	7191	JGI	Normand et al. (2007)
Salinispora arenicola	Actinobacteria	CP000850	5 786 361	4917	JGI	Unpublished
Sulcia muelleri	Bacteroidetes	CP000770	245 530	227	U. Arizona	McCutcheon and Moran (2007)
Herpetosiphon aurantiacus	Chloroflexi	CP000875, CP000876, CP000877	6 346 587 339 639 99 204	5278	JGI	Unpublished
Acaryochloris marina	Cyanobacteria	CP000828, CP000838–CP000846	8 361 599 (total)	8383	WashU	Unpublished
Alkaliphilus oremlandii	Firmicutes	CP000853	3 123 558	2836	JGI	Unpublished
Clostridium phytofermentans	Firmicutes	CP000885	4 847 594	3902	JGI	Unpublished
Lactobacillus helveticus	Firmicutes	CP000517	2 080 931	1625	Teagasc	Unpublished
Azorhizobium caulinodans	α-Proteobacteria	AP009384	5 369 772	4717	U. Tokyo	Unpublished
Bartonella tribocorum	α-Proteobacteria	AM260525, AM260524	2 619 061 23 343	2154	U. Basel	Saenz et al. (2007)
Brucella canis	α-Proteobacteria	CP000872, CP000873	2 105 969 1 206 800	3251	JGI, VBI	Unpublished
Dinoroseobacter shibae	α-Proteobacteria	CP000830–CP000835	1 159 772 total	1093	JGI	Unpublished
Burkholderia multivorans	α-Proteobacteria	CP000868–CP000871	7 008 622 total	6262	JGI	Unpublished
Delftia acidovorans	α-Proteobacteria	CP000884	6 767 514	6040	JGI	Unpublished
Desulfococcus oleovorans	δ-Proteobacteria	CP000859	3 944 167	3265	JGI	Unpublished
Sorangium cellulosum	δ-Proteobacteria	AM746676	13 033 779	9384	Bielefeld U.	Schneiker et al. (2007)
Petrotoga mobilis	Thermotogae	CP000879	2 169 548	1898	JGI	Unpublished
New strains
Methanococcus maripaludis C6	Euryarchaeota	CP000867	1 744 193	1826	JGI	Unpublished
Prochlorococcus marinus str. MIT 9211	Cyanobacteria	CP000878	1 688 963	1855	JCVI	Unpublished
Staphylococcus aureus ssp. aureusUSA300_TCH1516	Firmicutes	CP000730, CP000731, CP000256	2 872 915 27 041 3 125	2688	Baylor	Highlander et al. (2007)
Salmonella enterica ssp. arizonae serovar 62:z4,z23:--	γ-Proteobacteria	CP000880	4 600 800	4511	WashU	Unpublished
Salmonella enterica ssp. enterica serovar Paratyphi B str. SPB7	γ-Proteobacteria	CP000886	4 858 887	5601	WashU	Unpublished
Shewanella balticaOS195	γ-Proteobacteria	CP000891–CP000894	5 547 544 (total)	4688	JGI	Unpublished

^aSequencing centre names are abbreviated as follows: Baylor, Baylor College of Medicine, Houston, TX, USA; Bielefeld U., Center for Biotechnology, Bielefeld University, Bielefeld, Germany; JCVI, J. Craig Venter Institute, Rockville, MD, USA; JGI, US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA; Procter & Gamble, The Procter and Gamble Co., Miami Valley Innovation Center, Cincinnati, OH, USA; Teagasc, Moorepark Food Research Centre, Moorepark, Fermoy, County Cork, Ireland; U. Basel, Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland; U. Arizona, University of Arizona, Tucson, AZ, USA; U. Tokyo, University of Tokyo Biotechnology Research Center, Bunkyo-ku, Tokyo, Japan; VBI, Virginia Bioinformatics Institute at Virginia Polytechnic Institute and State University, Blacksburg, VA, USA; Washington State U., Washington State University, Pullman, WA, USA; WashU, Washington University Genome Sequencing Center, St Louis, MO, USA.

Babesia bovis is an apicomplexan parasite of cattle that is closely related to two other animal pathogens, Theileria parva and Theileria annulata, whose genomes have been sequenced in 2005. It is also related to such human pathogens as malaria-causing Plasmodium spp. and Toxoplasma gondii, the causative organism of human toxoplasmosis. Like Plasmodium spp., B. bovis infects and eventually lyses erythrocytes, causing anaemia. Studies of B. bovis infection, besides helping protect the livestock, could lead to a better understanding of malaria. The description of B. bovis genome sequence (Brayton et al., 2007) includes a detailed three-way comparison of the genomes and deduced protein sets of B. bovis, Plasmodium falciparum and T. parva. An interesting conclusion from this comparison is that the number of nuclear-encoded proteins targeted to the apicoplast (a plastid-like organelle of apicomplexans that is a potential target for antiparasite drugs) might be much smaller than previously believed. If true, this would have important consequences for future drug design. The knowledge of the genomic sequence will also boost the efforts towards creation of antibabesian vaccines.

Genomes of the basidiomycetes Malassezia globosa and Malassezia restricta are certain to attract attention of those who suffer from dandruff, a nasty skin flaking condition that reportedly occurs in 30–95% of the human population (Xu et al., 2007). These fungi also cause a more serious skin disease, referred to as seborrheic dermatitis. Analysis of M. globosa genome revealed a large number of secreted hydrolases (phospholipases, aspartyl proteases), but an apparent absence of a fatty acid synthase gene. This observation correlated with the experimental data on lipid requirement for growth of M. globosa. A somewhat unexpected result of the phylogenetic analysis of M. globosa proteins was that its nearest neighbour is apparently a plant pathogen, corn smut fungus Ustilago maydis (Xu et al., 2007).

Speaking about eukaryotic genomes, it might be appropriate to mention publication of the draft genome of the domestic cat Felis catus (Pontius et al., 2007). After all, this decidedly asocial eukaryote shares with us its home – and many microorganisms.

Compared with the tiny – for eukaryotic organisms – genomes of B. bovis and M. globosa, the genome of the soil myxobacterium S. cellulosum looks like a monster: at more than 13 Mbp, it is almost as large and encodes as many proteins as those two combined (Schneiker et al., 2007). Furthermore, it is composed of a single chromosome, in contrast to the genome of B. bovis that consists of four chromosomes of 2.62, 2.59, 1.73 and 1.25 Mbp in length (Brayton et al., 2007), and the genome of M. globosa that apparently consists of eight even smaller chromosomes (Xu et al., 2007). The chromosome of S. cellulosum turned out to be even longer than the initial estimate of 12.2 Mbp (Pradella et al., 2002) and is currently the largest DNA molecule known in the prokaryotic world, far surpassing the previous record, the 10 Mbp chromosome of Solibacter usitatus.

In the current classification, S. cellulosum belongs to the family Polyangiaceae in the order Myxococcales of the δ-Proteobacteria. Myxococcus xanthus and Anaeromyxobacter dehalogenans, whose genomes have been sequenced earlier (Goldman et al., 2006), belong to a different family, Myxococcaceae. Stigmatella aurantiaca, whose unfinished genome is available in GenBank (Accession No. AAMD00000000), is assigned to the family Cystobacteraceae. However, all these organisms are closely related and belong to the same order Myxococcales or ‘fruiting gliding bacteria’. The latter name captures three most prominent features of the group: (i) movement by gliding that includes ‘social’ and ‘adventurous’ motility, (ii) ability to form multicellular fruiting bodies with all the complex intercellular communication that is required for this process, and (iii) the fact that despite their large genome sizes, complex signalling and regulatory systems and a sophisticated social life, these organisms are still typical bacteria. The properties of myxobacteria, including S. cellulosum, have been subject of numerous reviews, including an opening paper in the inaugural issue of this journal (Reichenbach, 1999).

Unlike M. xanthus and A. dehalogenans that are remarkable for their predatory lifestyle and aryl-halorespiration, respectively, S. cellulosum has attracted attention primarily by its ability to degrade cellulose and produce a great variety of secondary metabolites with antibacterial and antifungal activity. This organism was first described as Polyangium compositum in 1904, renamed Sorangium compositum in 1924 and received its current name in 1936 (Imshenetski and Solntseva, 1937). The sequenced strain S. cellulosum So ce56 was isolated in 1985 in Germany from a soil sample containing decaying plant material, which had been collected near Cipajung in Indonesia. Genome analysis of S. cellulosum revealed more than 3000 proteins (34.7% of the total) that had no significant similarity to predicted proteins in the public databases (Schneiker et al., 2007). Efforts to deduce their functions through genomic context-based methods, including so-called phylogenomic maps, also proved unsuccessful, making S. cellulosum the largest source of unannotated bacterial proteins. A comparison of S. cellulosum and M. xanthus genomes revealed an almost complete lack of synteny. Like M. xanthus, S. cellulosum encoded a very complex system of signal transduction proteins that included more than 140 histidine kinases and more than 300 eukaryotic-type serine/threonine/tyrosine protein kinases, comprising more than 3% of all predicted proteins (Schneiker et al., 2007). In accordance with its lifestyle, S. cellulosum encoded only five chemotaxis transducers (MCPs), four times less than M. xanthus, but had a larger fraction of genes involved in carbohydrate metabolism. A significant part of the analysis was dedicated to the enzymes of secondary metabolism, particularly polyketide synthases and non-ribosomal peptide synthases. The genes responsible for synthesis of chivosazol, etnangien and myxochelin have been identified, and several more gene clusters encoding polyketide synthase and/or non-ribosomal peptide synthase domains have been found in the genome. Characterization of these genes could result in discovery of entirely new antibiotics. In addition, comparative analysis of signalling systems of M. xanthus and S. cellulosum could shed light on the mechanism of their social behaviour.

The list of newly sequenced genomes (Table 1) includes two members of the Crenarchaeaota. Caldivirga maquilingensis is a hyperthermoacidophile, originally isolated from a hot spring located on the side of Mount Maquiling, Laguna, in the Philippines (Itoh et al., 1999). It grows in a wide range of temperature and pH values with optimal growth at 85°C and pH around 4.0. This organism is a heterotroph that can utilize gelatin, peptone and other protein substrates as carbon sources. It can grow both anaerobically and microaerobically, but requires sulfur, thiosulfate or sulfate as electron acceptors. Caldivirga maquilingensis forms a separate branch in the family Thermoproteaceae, which also includes the genus Pyrobaculum with its four completed genomes. Comparison of C. maquilingensis genome with those from Pyrobaculum spp. is expected to shed light on the mechanisms of aerotolerance in hyperthermophilic archaea and their choice of terminal electron acceptors.

Nitrosopumilus maritimus strain SCM1 was isolated in 2005 from a marine tropical fish tank at the Seattle aquarium and was the first cultivated non-thermophilic crenarchaeon, a representative of the vast community of crenarchaea inhabiting cold oxic ocean waters (Könneke et al., 2005). In addition, N. maritimus was the first ammonia-oxidizing archaeal chemoautotroph obtained in pure culture. Its ability to use bicarbonate and ammonia as sole sources of carbon and energy is apparently widespread in the open ocean (Ingalls et al., 2006; Coolen et al., 2007).

The two members of the phylum Actinobacteria in the current list illustrate the diversity of the group. The soil nitrogen-fixing symbiotic actinobacterium Frankia sp. strain EAN1pec is the third representative of that genus with a completely sequenced genome. All three genomes were sequenced in 2006 in the course of a large Franco-American project and described in a paper (Normand et al., 2007) that is already freely available online. However, genome of the strain EAN1pec, the largest of the three, included some gaps corresponding to regions with sequence repeats and high GC content. These gaps have now been filled and the genome has been released in the finished form. More information on Frankia and actinorhizal plants is available at http://web.uconn.edu/mcbstaff/benson/Frankia/FrankiaHome.htm

The second actinobacterium in the list is Salinispora arenicola, a marine organism that is found in tropical and subtropical marine sediments around the world at the depth of up to 1100 m (Mincer et al., 2005; Jensen and Mafnas, 2006). The genus Salinispora includes numerous marine isolates but only one other validly described species, Salinispora tropica (Maldonado et al., 2005), whose genome was released by the JGI 6 months earlier (Udwary et al., 2007). Genomes of two more strains, one from S. arenicola and one from S. tropica, are currently in the works. Salinispora spp. grow only in the presence of seawater or on sodium-enriched media (Mincer et al., 2002; Maldonado et al., 2005), which makes them obligate marine bacteria and points to a very interesting evolutionary history. Another reason for sequencing Salinispora spp. is their complex secondary metabolism. Many Salinispora isolates produce biologically active compounds that inhibit proliferation of tumour cells and are promising candidates for anticancer therapy. These include rifamycin-like compounds, cyclopenta[a]indene glycosides and halogenated macrolides. One of such compounds, salinosporamide A (Protein Data Bank entry 2FAK, see http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=11110244 for a chemical formula), is a potent inhibitor of the 20S proteasome that is currently in phase I clinical trials for the treatment of cancer. Salinispora arenicola produces various macrolide polyketides, such as saliniketals A and B (inhibitors of ornithine decarboxylase) and arenicolides A, B and C (Williams et al., 2007a,b), whose biosynthetic pathways will now be investigated using the genomic sequence.

Sulcia muelleri was described in 2005 as an obligate bacterial symbiont of the glassy-winged sharpshooter (Homalodisca coagulata), a 12-mm-long leafhopper that feeds on xylem fluid of a wide range of plants (Moran et al., 2005). Unlike previously known obligate insect symbionts, it is not a γ-proteobacterium but a member of the phylum Bacteroidetes that functions as a co-symbiont with the γ-proteobacterium Baumannia cicadellinicola. The complete genome sequence of B. cicadellinicola and partial genome sequence of S. muelleri have been determined, leading to the suggestion that these two bacteria have complementary metabolic capabilities (Wu et al., 2006). The genome sequence of S. muelleri has now been completed, using a combination of pyrosequencing with even shorter reads of 33 bases in length generated by an Illumina/Solexa Genome Analyzer (McCutcheon and Moran, 2007). Genome sequence of S. muelleri made it possible to analyse its metabolism in detail and verify the idea of the metabolic interdependence of S. muelleri, B. cicadellinicola and the sharpshooters. Indeed, S. muelleri was found to encode biosynthetic pathways for all essential amino acids, but not purines, pyrimidines, vitamins and cofactors, whereas B. cicadellinicola can produce vitamins and cofactors, purines and pyrimidines but not amino acids and the host cells cannot produce either of these. These shared functions ensure that neither cell can exist without the others and force them all to co-evolve (McCutcheon and Moran, 2007). Given that intracellular bacterial symbionts from the Bacteroidetes lineage were also found in cicadas, leafhoppers, treehoppers, spittlebugs and planthoppers (Moran et al., 2005), such tripartite symbioses may be widespread in nature.

Herpetosiphon aurantiacus was first isolated in 1961 from the slimy coating of Chara sp. growing in Birch Lake in Minnesota and described as a separate organism in 1968, based on isolation of similar strains from well water and cow dung in Iowa, hot springs in California and Mexico and from marine shores of France, Eire, Lagos and Samoa (Holt and Lewin, 1968). Closely related strains were later isolated from bulking activated sludge at communal and industrial sewage treatment plants in southern Germany (Trick and Lingens, 1984). Herpetosiphon aurantiacus is a Gram-negative aerobic filamentous gliding bacterium that belongs to the phylum Chloroflexi, also referred to as green non-sulfur bacteria, or GNS group, and has an unusual cell wall, typical for those organisms. The cells divide by transverse septum formation, forming long flexible filaments that consist of numerous cells and can be 0.2–0.5 mm in length. Unlike its relatives, such as Chloroflexus aurantiacus and Roseiflexus castenholzii, H. aurantiacus does not produce bacteriochlorophyll and is unable to perform anoxygenic photosynthesis. The genome sequence should provide insights into the specific growth patterns of H. aurantiacus, as well as into its unusual ability to kill a wide variety of bacteria by lysing their colonies (Quinn and Skerman, 1980) and to produce unique secondary metabolites (Nett et al., 2006).

Acaryochloris marina is a relatively well-studied model organism that was first isolated in 1993 from algae squeezed out of Lissoclinum patella, a colonial ascidian collected from the marine coast of the Palau Islands in the western Pacific Ocean (Miyashita et al., 1996). It had an unusual morphology and an unusual photosynthetic pigment, chlorophyll d, seen previously only in red algae. However, 16S rRNA analysis clearly showed that A. marina is a member of Cyanobacteria (Miyashita et al., 2003). Furthermore, chlorophyll d of red algae was shown to be produced by A. marina-like bacteria, associated with algal cells (Murakami et al., 2004). Spectral properties of chlorophyll d allow A. marina to use far-red light for photosynthesis, defining its unique ecological niche underneath the coral-reef ascidians (Kühl et al., 2005).

Among the four low-G+C Gram-positive bacteria in the current list, there are two interesting representatives of the family Clostridiaceae. One of them, Alkaliphilus oremlandii strain OhILAs, is yet another example of a bacterium whose complete genome sequence had been released even before the organism was formally described. This bacterium was isolated from sediments of the Ohio River near Pittsburgh, Pennsylvania, using a medium with 10 mM arsenate and 20 mM lactate, and was originally referred to as Clostridium sp. OhILAs (Fisher et al., 2008). The organism used arsenate or thiosulfate as terminal electron acceptors and tolerated up to 50 mM of arsenate. Accordingly, it was named Clostridium oremlandii after Ronald S. Oremland, an investigator with the US Geological Survey and a member of the Editorial Board of this journal, who had been studying bacterial use of arsenate for many years (Oremland and Stolz, 2003; 2005). Finally, 16S rRNA sequence clearly identified this bacterium as a member of the genus Alkaliphilus, despite its ability to grow only in a relatively narrow pH range of 8.0–8.8. About a year ago, A. oremlandii attracted attention of the general public with its ability to degrade 3-amino-4-hydroxybenzene arsonic acid (trade name: Roxarsone, see http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5104), a compound that is added to the broiler chicken feed to prevent coccidiosis (an infection by the apicomplexan protist Eimeria spp.), but also stimulates chicken growth and improves pigmentation (Stolz et al., 2007). In these experiments, most of the roxarsone ended up reduced to 3-amino-4-hydroxybenzene arsonic acid, but a significant fraction was apparently degraded further releasing inorganic arsenic, a well-known poison and a human carcinogen. The idea that roxarsone, which has been abandoned in Europe since 1999 but is still being added to the feed of ∼70% of broilers in the USA, could end up contaminating soil and groundwater with arsenate is quite unsettling. Several major firms have stopped using roxarsone or pledged to do that, but the continued use of organoarsenic compounds and the ability of clostridia to degrade them are certain to remain a subject of much controversy.

The second Clostridium, C. phytofermentans, is an obligately anaerobic mesophilic cellulolytic bacterium, isolated from forest soil in central Massachusetts. It is capable of fermenting a variety of complex carbohydrates, including cellulose, pectin, polygalacturonic acid, starch and xylan, to ethanol, acetate, CO₂ and H₂ (Warnick et al., 2002). Production of ethanol as the major end-product of fermentation makes C. phytofermentans an attractive organism for biofuel production. A comparison of its genomic sequence with that of Clostridium thermocellum, released by the JGI a year ago, should help understand its peculiar metabolism and increase ethanol production by other cellulolytic bacteria.

Lactobacillus helveticus, first described in 1919 by Orla-Jensen, is a moderately thermophilic lactic acid bacterium, used in production of cheese. It belongs to the Lactobacillus acidophilus subgroup of lactobacilli and is characterized by a diminished capacity to ferment sugars. Lactobacillus helveticus is primarily used in starter cultures in the manufacture of Swiss-type and long-ripened Italian cheeses, such as Emmental, Gruyère and Provolone. The sequenced strain DPC 4571 is a Swiss cheese isolate that has been selected for a number of highly desirable traits including rapid autolysis, reduced bitterness and increased flavour notes (Hickey et al., 2007). The genome sequence of L. helveticus revealed a high level of synteny with L. acidophilus, numerous IS elements and an apparent loss of genes that contribute to the colonization of the intestinal mucosa in probiotic lactobacilli (Callanan et al., 2008).

Two of the four α-proteobacterial genomes in the current list come from obligate parasites: Bartonella tribocorum is an intraerythrocytic pathogen of rats, while Brucella canis, as the name suggests, is the causative agent of canine brucellosis. The other two represent interesting environmental microorganisms. The nitrogen-fixing bacterium Azorhizobium caulinodans strain ORS571 is a member of so-called fast-growing group of rhizobia. This organism was first isolated in 1981 from nitrogen-fixing nodules formed on the stem of the tropical legume Sesbania rostrata, commonly found in freshwater swamps in Africa, by the scientists from the Laboratoire de Microbiologie des Sols, Office de la Recherche Scientifique et Technique Outre-Mer in Dakar, Senegal (Dreyfus and Dommergues, 1981), and could be counted among the greatest discoveries ever made by that office. Azorhizobium caulinodans could grow in pure culture using N₂ as the sole nitrogen source and, unlike other rhizobia, readily nodulated legume stems (Elmerich et al., 1982; Dreyfus et al., 1983), offering a convenient experimental model to study mechanisms of nodulation and nitrogen fixation. In the past 20 years, A. caulinodans has been used as model organism in numerous studies. One of such studies revealed that, in addition to forming nodules, this bacterium could colonize xylem of S. rostrata roots (O'Callaghan et al., 1997). Colonization of root xylem by A. caulinodans was subsequently shown for Arabidopsis, rice and tomato, suggesting that root xylem could provide a suitable niche for endophytic nitrogen fixation (Gopalaswamy et al., 2000; Stone et al., 2001). Recently, a transposon mutagenesis study of the mechanisms of the maturation and maintenance of N₂-fixing nodules identified novel symbiosis-related genes in A. caulinodans (Suzuki et al., 2007). This must have prompted sequencing of its genome, which will now further boost the use of A. caulinodans as a model organism. Stem nodulation, bacterial colonization of xylem and nodulation in the absence of nod genes (Giraud et al., 2007) show that bacteria-plant symbiosis is even more complex than we used to think.

The key properties of another environmental α-proteobacterium, Dinoroseobacter shibae, are perfectly reflected in its name. The genus name identifies it as a member of the marine Roseobacter clade; the first two syllables reflect its isolation from cultivated marine dinoflagellates. The species name has been assigned after Professor Tsuneo Shiba of the University of Tokyo Otsuchi Marine Research Centre, who discovered the marine aerobic anoxygenic phototrophs and provided the first description of this important group of bacteria (Shiba et al., 1979). Cultures of D. shibae grown in the dark accumulate the carotenoid pigment spheroidenone (http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5366412) and are characterized by intense colour, from pink to wine-red (Biebl et al., 2005). They also contain bacteriochlorophyll a and are able to perform aerobic anoxygenic photosynthesis. Still, D. shibae is a heterotroph that can use acetate, succinate, fumarate, malate, lactate, citrate, glutamate, pyruvate, glucose, fructose and glycerol as carbon sources. The genome sequence of D. shibae should allow further analysis of these poorly studied microorganisms.

The soil bacterium Delftia acidovorans has been first described in the PhD thesis of L.E. den Dooren de Jong (1926) with ∼40 other Pseudomonas soil isolates and named Pseudomonas acidovorans. Very similar strains have been described as Pseudomonas desmolytica, Pseudomonas indoloxidans and Pseudomonas testosteroni. These strains were subsequently re-classified as β-proteobacteria and combined under the name Comamonas acidovorans. Finally, in 1999, this organism received its current name, ‘referring to the city of Delft, the site of isolation of the type species, and in recognition of the pioneering role of Delft research groups in the development of bacteriology’ (Wen et al., 1999). Representatives of this species have been found in a variety of environments, including soil, river sediment, activated sludge, wastewater and even drinking water. They have extremely versatile metabolism and degrade a wide variety of pollutants. The sequenced strain D. acidovorans DSM 14801 was isolated at a communal sewage treatment plant in Germany and shown to utilize 4-(4-sulfophenyl)-hexanoate (Schleheck et al., 2004). This and other strains of D. acidovorans are attractive candidates for use in bioremediation.

The two remaining bacteria in the current list are both obligate anaerobes isolated from oil production plants. Desulfococcus oleovorans is a sulfate-reducing δ-proteobacterium that was isolated using hexadecane as the sole carbon source. This organism could grow on alkanes from C₁₂ to C₂₀, 1-hexadecene, 1-hexadecanol, 2-hexadecanol, palmitate and stearate using sulfate as terminal electron acceptor (Aeckersberg et al., 1991). It has been proposed that reduction of sulfate in oil by D. oleovorans and related bacteria could be responsible for the accumulation of sulfide in oil deposits and oil production plants (Rueter et al., 1994).

Petrotoga mobilis is a moderately thermophilic member of the phylum Thermotogae. This bacterium was isolated from hot production waters of a North Sea oil reservoir and grows optimally at 58–60°C (Lien et al., 1998). The JGI Thermotogales project sequenced the genome of P. mobilis primarily for comparing it with the genomes of Fervidobacterium nodosum and Thermosipho melanesiensis, whose optimal growth temperature is 10°C higher, and Thermotoga maritima and Thermotoga petrophila, whose optimal growth temperature is 20°C higher. Such a comparison could provide valuable clues to the hyperthermophilic adaptations within this ancient clade.

Several other recently sequenced genomes come from important pathogens. Burkholderia multivorans is a member of the Burkholderia cepacia complex, an opportunistic pathogen that colonizes lungs of patients with cystic fibrosis, aggravating the condition and sometimes causing fatal necrotizing pneumonia.

Two new strains of Salmonella enterica have been sequenced in the course of the Enterobacterial genome project at the Washington University School of Medicine (http://genome.wustl.edu/sub_genome_group.cgi?GROUP=3&SUB_GROUP=3). Salmonella enterica ssp. IIIa (arizonae) serovar 62:z4,z23:-- (common name: Salmonella Arizonae) is a reptile isolate that can infect turkeys and occasionally causes gastroenteritis in humans, while S. enterica ssp. enterica serovar Paratyphi B str. SPB7 (common name: Salmonella Paratyphi B) infects only humans, causing a typhoid-type fever.

Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen that is spreading around the world. To get a better understanding of this growing threat, researchers at the Baylor College of Medicine sequenced genomes of two paediatric isolates of S. aureus strain USA300, one of the most virulent strains that causes superficial and invasive infections in children and adults (Highlander et al., 2007). A comparison of methicillin-resistant and methicillin-sensitive isolates did not reveal any major differences in gene order and plasmid content, indicating that the differences in virulence of these strains are not due to acquisition of specific virulence factors. The authors suggest that pathogenicity differences between S. aureus strains are largely determined by sequence polymorphisms (Highlander et al., 2007).

Finally, there has been an interesting development in the area of genome annotation. For a number of years, function of one of the most widespread ‘conserved hypothetical’ genes remained ambiguous. This gene, referred to as ygjD (gcp) in Escherichia coli, ydiE in Bacillus subtilis, QRI7 and Kae1 in yeast, and OSGEP and OSGEPL1 in humans, is one of the very few to be encoded in every sequenced genome (with the exception of highly degraded genomes of Carsonella ruddii and, now, S. muelleri). Until recently, the only key to its function was an experimental paper showing that in Pasteurella haemolytica A1, the product of this gene was a glycoprotease, specific for O-sialoglycoproteins (Abdullah et al., 1991), which is how this gene is currently annotated in most public databases. That function did not seem appropriate for such a widespread gene, which prompted us to place it as No. 1 in our ‘top 10’ list of ‘known unknown’ proteins that should be priority targets for further experimental study (Galperin and Koonin, 2004). In a recent paper in Nucleic Acids Research, a group of French scientists led by Patrick Forterre reported the absence of protease activity in the archaeal (Pyrococcus abyssi) orthologue of this protein. Instead, the expressed protein could bind DNA and exhibited an apurinic endonuclease activity (Hecker et al., 2007). It still was not immediately clear what biological role would require presence of this protein in every organism on this planet, but interaction with DNA sounds far more plausible than hydrolysis of glycoproteins.