title: Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes.
abstract: BACKGROUND
  The extremely halophilic archaea are present worldwide in saline environments and have important biotechnological applications. Ten complete genomes of haloarchaea are now available, providing an opportunity for comparative analysis.
  
  
  RESULTS
  We report here the comparative analysis of five newly sequenced haloarchaeal genomes with five previously published ones. Whole genome trees based on protein sequences provide strong support for deep relationships between the ten organisms. Using a soft clustering approach, we identified 887 protein clusters present in all halophiles. Of these core clusters, 112 are not found in any other archaea and therefore constitute the haloarchaeal signature. Four of the halophiles were isolated from water, and four were isolated from soil or sediment. Although there are few habitat-specific clusters, the soil/sediment halophiles tend to have greater capacity for polysaccharide degradation, siderophore synthesis, and cell wall modification. Halorhabdus utahensis and Haloterrigena turkmenica encode over forty glycosyl hydrolases each, and may be capable of breaking down naturally occurring complex carbohydrates. H. utahensis is specialized for growth on carbohydrates and has few amino acid degradation pathways. It uses the non-oxidative pentose phosphate pathway instead of the oxidative pathway, giving it more flexibility in the metabolism of pentoses.
  
  
  CONCLUSIONS
  These new genomes expand our understanding of haloarchaeal catabolic pathways, providing a basis for further experimental analysis, especially with regard to carbohydrate metabolism. Halophilic glycosyl hydrolases for use in biofuel production are more likely to be found in halophiles isolated from soil or sediment.
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America. IJAnderson@lbl.gov
authors.forename: Iain
authors.initials: I
authors.lastname: Anderson
authors.forename: Carmen
authors.initials: C
authors.lastname: Scheuner
authors.forename: Markus
authors.initials: M
authors.lastname: Göker
authors.forename: Kostas
authors.initials: K
authors.lastname: Mavromatis
authors.forename: Sean D
authors.initials: SD
authors.lastname: Hooper
authors.forename: Iris
authors.initials: I
authors.lastname: Porat
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Klenk
authors.forename: Natalia
authors.initials: N
authors.lastname: Ivanova
authors.forename: Nikos
authors.initials: N
authors.lastname: Kyrpides
mesh_terms: D019843:Archaeal Proteins / Q000235:genetics / Q000378:metabolism; D001622:Betaine / Q000378:metabolism; D044822:Biodiversity; D016000:Cluster Analysis; D005690:Galactose / Q000378:metabolism; D014644:Genetic Variation; D020745:Genome, Archaeal / Q000235:genetics*; D019015:Geologic Sediments / Q000382:microbiology; D005965:Glucuronates / Q000378:metabolism; D005990:Glycerol / Q000378:metabolism; D006216:Halobacteriaceae / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D010802:Phylogeny; D011422:Propionates / Q000378:metabolism; D012988:Soil Microbiology; D013045:Species Specificity; D014871:Water Microbiology; D014994:Xylose / Q000378:metabolism
chemical_list: D019843:Archaeal Proteins; D005965:Glucuronates; D011422:Propionates; D001622:Betaine; D014994:Xylose; D005990:Glycerol; D005690:Galactose