Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes.

Niyaz Ahmed,Iain Anderson,Markus Göker,Iris Porat,Nikos Kyrpides,Kostas Mavromatis,Hans-Peter Klenk,Natalia Ivanova,Sean D Hooper,Carmen Scheuner

doi:10.1371/journal.pone.0020237

Abstract

BackgroundThe 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.Methodology/Principal FindingsWe 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.ConclusionsThese 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.

Highlights

Halophilic glycosyl hydrolases for use in biofuel production are more likely to be found in halophiles isolated from soil or sediment
The organisms in the euryarchaeal order Halobacteriales are generally extreme halophiles requiring at least 1.5 M salt and growing optimally at 3.5–4.5 M salt [1], some have recently been found to grow at lower salt concentrations [2,3]
Phylogenetic inference The Maximum likelihood (ML) phylogeny inferred from the concatenated gene alignments is shown in Figure 1 together with ML and maximum parsimony (MP) bootstrap support values

Summary

Introduction

The organisms in the euryarchaeal order Halobacteriales are generally extreme halophiles requiring at least 1.5 M salt and growing optimally at 3.5–4.5 M salt [1], some have recently been found to grow at lower salt concentrations [2,3]. The haloarchaea are found in the water and sediment of salt lakes and salterns, and in saline soils. Their mechanism of adaptation to high salinity involves the accumulation of molar concentrations of KCl in the cytoplasm and the production of proteins with a higher number of negative charges than in other organisms. The haloarchaea are heterotrophs, growing with amino acids and/or carbohydrates as carbon and energy sources. They are either aerobic or facultatively anaerobic using various electron acceptors [1]. Glycerol is a important nutrient for haloarchaea as it is produced by eukaryotic algae in high-salt environments [6]. Ten complete genomes of haloarchaea are available, providing an opportunity for comparative analysis

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Conclusion