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Archaeal Genomics

Archaeal Tree of Life Project (PI: Iain Anderson)

Archaea is the least well characterized of the three domains of life. Yet, they share many important features with eukaryotes and are the key in both the understanding of the development of the eukaryotic cell and of the origins and nature of the last common ancestor. So far only a handful of organisms from this domain of life have been completely sequenced, and several key biological and evolutionary questions remain unanswered. The Archaeal Genomics group is leading the projects of sequencing and analysis of several key archaeal organisms with important phylogenetic positions or significant biological applications.

There are currently two projects approved for sequencing a group of six (CSP-2006), a group of five (LSP-2007) and a group of 10 (CSP 2010) Archaeal genomes selected for their phylogenetic diversity and their ability to complement the genomes already published, thereby providing a fuller understanding of the major Archaeal phyla. The 21 new Archaeal genome sequences will enable researchers to determine the set of genes common to all Archaea and gene sets defining the major subdivisions of the Archaea, leading to a greater understanding of the biology and evolution of this domain. The list of the eleven selected organisms is presented below, together with their individual properties.

	GOLD ID	Organism	JGI Program	Status	Temperature	Size ± 0.2Mbp	G+C%	Publication
1.	Gc01209	Ferroglobus placidusDSM 10642	CSP-2006	complete	Hyperthermophile	1.9Mb	43	in preparation
2.	Gc01350	Staphylothermus hellenicus P8	LSP-2007	complete	Hyperthermophile	1.6Mb	36	in preparation
3.	Gc00952	Halorubrum lacusprofundi ATCC 49239	CSP-2006	complete	Psychrophile Halophile	4.3Mb	58	PLoS ONE
4.	Gc00506	Methanocorpusculum labreanum Z	CSP-2006	complete	Mesophile	2.3 Mb	50	PLoS ONE
5.	Gc00512	Methanoculleus marisnigri JR1	CSP-2006	complete	Mesophile	2.2 Mb	61.2	PLoS ONE
6.	Gc01304	Methanohalobium evestigatumZ-7303	LSP-2007	complete	Thermophile	~3.0Mb	37	in preparation
7.	Gc00511	Staphylothermus marinus F1	CSP-2006	complete	Hyperthermophile	1.7Mb	35	BMC Genomics
8.	Gc00473	Thermofilum pendens Hrk5	CSP-2006	complete	Thermophile	2.2 Mb	57	J. Bacteriology
9.	Gi05846	Halosimplex carlsbadense 2-9-1	CSP-2010	in production	Halophile
10.	Gi05998	Halovivax ruber XH-70	CSP-2010	in production	Halophile		65
11.	Gi06001	Natronolimnobius baerhuensis IHC-005	CSP-2010	awaiting DNA	Halophile		59
12.	Gi05999	Natrinema pellirubrum157	CSP-2010	in production	Halophile		70
13.	Gi06000	Natronobacterium gregoryi SP2	CSP-2010	awaiting DNA	Halophile		65
14.	Gi05997	Halostagnicola larseniiXH-48	CSP-2010	in production	Halophile		61
15.	Gc01807	Halopiger xanaduensis SH-6	CSP-2010	complete	Halophile		63	in preparation
16.	Gi09602	Natronorubrum tibetenseDSM 13204	CSP-2010	awaiting DNA	Halophile
17.	Gi05740	Haladaptatus paucihalophilusDX253	CSP-2010	awaiting DNA	Halophile		60
18.	Gi05996	Halosarcina pallida BZ256	CSP-2010	awaiting DNA	Halophile		65
Abandoned Projects
		Acidianus sulfidivorans JP7	LSP-2007	abandoned	Thermophile	1.9Mb	31.1
		Geogemma barossii	LSP-2007	abandoned	Hyperthermophile	1.8Mb	52.5
		Halococcoides aestuarii	LSP-2007	abandoned	Mesophile	1.8Mb
		Methanobacterium formicicum MF	LSP-2007	abandoned	Mesophile	1.8Mb	41
		Natronorubrum bangenseA33	CSP-2010	abandoned	Halophile		60
		Stetteria hydrogenophila	LSP-2007	abandoned	Hyperthermophile

1. Acidianussulfidivvorans JP7 is a thermoacidophilic member of the order Sulfolobales capable of growing aerobically or anaerobically.It was isolated from a hydrothermal site in Papua New Guinea.Its temperature growth range is 50-80 ˚C and it can grow at pH as low as 0.3, substantially lower than other Sulfolobales.It is capable of oxidizing ferrous iron and sulfur compounds, producing ferric iron and sulfuric acid which are leaching agents for mineral sulfide ores.JP7's combination of growth properties makes it suitable as a bioleaching agent for mineral sulfide ores as bioleaching is more effective at higher temperatures, and low pH prevents the formation of precipitates that can inhibit the process (Plumb and Franzmann, 2004).

2. Ferroglobus placidus is an anaerobic, hyperthermophilic member of the order Archaeoglobales with a versatile metabolism.It was isolated from hydrothermally heated marine sediment It grows at neutral pH with a temperature optimum of 85 ˚ C (Hafenbradl et al., 1996).The electron acceptors it can use include nitrate and thiosulfate, while ferrous iron, hydrogen, and sulfide can serve as electron donors (Hafenbradl et al., 1996).Unlike all other known Archaeoglobales, it does not reduce sulfate.When growing on nitrate, the nitrite produced can be further reduced to N₂O; therefore this is the first anaerobic denitrifier to be found (Vorholt et al., 1997). F. placidusis the first anaerobic hyperthermophile found to oxidize ferrous iron (Hafenbradl et al., 1996). F. placidusis also capable of oxidizing acetate and aromatic compounds using ferric iron as the electron acceptor (Tor et al., 2001; Tor and Lovley, 2001).It is the first archaeon and the first thermophile found to carry out the anaerobic oxidation of acetate and of aromatic compounds.

3. Staphylothermus hellenicus was isolated from a shallow hydrothermal vent in Greece.Its close relative S. marinus, which was isolated from a hydrothermal site on the Italian coast and from a deep hydrothermal vent, has been sequenced by JGI.It is of interest to compare the two genomes to determine how similar the two species are at the genomic level, since they were isolated at geographically close sites.S. marinus appears to use different enzymes for sulfur reduction than other anaerobic Crenarchaeaota, and it is of interest to determine the sulfur reduction mechanisms of S. hellenicus for comparison.

4. Stetteria hydrogenophila

5. Halorubrum lacusprofundi is a psychrophile isolated from Deep Lake, a hypersaline lake in Antarctica.H. lacusprofundi can grow between 0oC and 42oC with optimal growth at 31oC (Franzmann et al., 1988).H. lacusprofundi differs from the already sequenced Halobacterium sp. NRC-1 (Ng et al., 2000) in that it can grow on a variety of carbon sources including glucose, mannose, acetate, and ethanol, while NRC-1 has a more limited metabolic capacity and has not been shown to use sugars.The other sequenced halophile, Haloarcula marismortui, on the other hand has been shown to use a variety of sugars (Baliga et al., 2004).H. lacusprofundi, as a psychrophile, provides a contrast to both sequenced halophiles, and comparison of the three will highlight adaptations to low temperature.These results can be compared with those of psychrophilic methanogens (Saunders et al. 2003) to determine whether they use similar mechanisms for cold adaptation.A third halophile genome also helps to determine the gene set defining halophiles.

6. Methanobacterium formicicum is a mesophilic methanogen from the order Methanobacteriales.The neotype strain, MF, was isolated from a sewage sludge digestor in Urbana, Illinois (Bryant and Boone, 1987).It can grow with H2 + CO2 or formate.This species has also been found in landfills (Fielding et al., 1988), freshwater sediments, the rumen of cattle, and as endosymbionts in anaerobic protozoa (Boone, 2001).M. formicicum has been a model organism among methanogens for studies of formate utilization and hydrogenases (Schauer and Ferry, 1980; Schauer and Ferry, 1986; Baron and Ferry, 1989).Studies have also been carried out comparing M. formicicum with thermophilic members of the genus Methanobacterium to determine effects of growth temperature on protein composition (Fabry et al., 1989; Li et al., 2000).

7. Methanocorpusculum labreanum Z is a mesophile isolated from surface sediments of Tar Pit Lake at the La Brea Tar Pits in Los Angeles, California.Unlike M. marisnigri it does not utilize ethanol or secondary alcohols as electron donors for methanogenesis.Instead it has a much more limited repertoire of methanogenic substrates, limited to H2/CO2 and formate. Thus it provides a contrast to the more flexible metabolism of M. marisnigri.As discussed in section 1, having two genomes from the Methanomicrobiales will allow comparative studies to proceed.

8. Methanoculleus marisnigri JR1 is a mesophile isolated from marine sediments of the Black Sea.Members of the genus Methanoculleus are commonly found in bioreactors treating wastewater and sewage and in landfills.One of the unusual features of Methanoculleus species is the ability to use ethanol and a variety of secondary alcohols as electron donors for methanogenesis, a feature that may contribute to their role in biomethanation processes.The complete genome sequence will allow greater insight into the metabolic pathways involved in this uncommon metabolism.The genome sequence of M. marisnigri, in combination with that of Methanocorpusculum labreanum, will give the first insights into the genomes of the Methanomicrobiales.Having these two genomes will allow comparative studies to see what genes constitute a signature for this grouping compared to other Archaea, thus providing insight into their evolution as a taxonomic group.

9. Methanohalobium evestigatum is an autotrophic, extremely halophilic methanogen from the order Methanosarcinales.It was isolated from a microbial mat community in Crimea, Russia, where it forms a syntrophic association with a halophilic bacterium that breaks down betaine to trimethylamine (Zhilina and Zavarzin, 1990).It grows at neutral pH with a temperature optimum of 40-50˚C.It is surprisingly restricted in its methanogenic substrates, with good growth only on trimethylamine and weak growth on mono- and dimethylamine (Zhilina and Zavarzin, 1987; 1990).While other methanogens have been found to grow at moderate salinities, this is the only methanogen classified as an extreme Halophile.

10. Staphylothermus marinus F1 is a hyperthermophile isolated from geothermally heated marine sediments in Italy and from a black smoker on the East Pacific Rise.It grows as clusters of up to 100 cells at low nutrient concentrations, but at higher nutrient levels it grows as single cells or clusters of up to five cells (Fiala et al., 1986).When S. marinus is grown with high concentrations of yeast extract giant cells with diameters of up to 15 mm are formed.Growth requires elemental sulfur and a complex nutrient source.S. marinus is a member of the Desulfurococcales order of Crenarchaeota.This order also includes Aeropyrum pernix for which the complete genome sequence is known.Both of these organisms require complex nutrient sources, but while A. pernix requires oxygen for growth S. marinus is a strict anaerobe. The genome of S. marinus will allow comparative studies of the Desulfurococcales to be initiated.

11. Thermofilum pendens Hrk5 is a thermophile and mild acidophile isolated from a solfataric hot spring in Iceland (Zillig et al., 1983).It has a long filamentous structure, with a length of up to 100 mm.Like several other Archaea, it appears to respire with sulfur and utilize peptides as an energy source.One of the unusual things about T. pendens is its mode of reproduction.It does not appear to form a septum in the middle of the cell.Instead "golf club" shaped organisms are found with a spherical enlargement at one end of the cell, and these likely detach to become new cells (Zillig et al., 1983).Another interesting thing about this organism is that it is almost always found associated with another member of the Thermoproteales, Thermoproteus tenax.Growth of T. pendens in the absence of T. tenax requires an unknown lipid growth factor from T. tenax to be present (Zillig et al., 1983).Perhaps the most interesting characteristic of T. pendens for genome sequencing is that it is the most deeply branching culturable member of the Crenarchaeota, thus it provides more phylogenetic breadth to the sequencing of this group.Currently there are only four Crenarchaeal genomes sequenced.The T. pendens genome can be compared with the genome of Pyrobaculum aerophilum to identify genes shared between the Thermoproteales order of the Crenarchaeota.