Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1

Jimmy H Saw^*¹^,10 , Bruce W Mountain^*² , Lu Feng^*³^,4^,5 , Marina V Omelchenko^*⁶ , Shaobin Hou^*⁷ , Jennifer A Saito¹ , Matthew B Stott² , Dan Li³^,4^,5 , Guang Zhao³^,4^,5 , Junli Wu³^,4^,5 , Michael Y Galperin⁶ , Eugene V Koonin⁶ , Kira S Makarova⁶ , Yuri I Wolf⁶ , Daniel J Rigden⁸ , Peter F Dunfield⁹ , Lei Wang³^,4^,5 and Maqsudul Alam¹^,7

¹Department of Microbiology, University of Hawai'i, 2538 The Mall, Honolulu, HI 96822, USA

²GNS Science, Extremophile Research Group, 3352 Taupo, New Zealand

³TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China

⁴Tianjin Research Center for Functional Genomics and Biochip, Tianjin 300457, PR China

⁵Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin 300457, PR China

⁶National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA

⁷Advance Studies in Genomics, Proteomics and Bioinformatics, College of Natural Sciences, University of Hawai'i, Honolulu, HI 96822, USA

⁸School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK

⁹Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada

¹⁰Current address: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA

author email corresponding author email* Contributed equally

Genome Biology 2008, 9:R161doi:10.1186/gb-2008-9-11-r161


Published:	17 November 2008

Subject areas: Evolution, Genetics, Microbiology and parasitology

Abstract

Background

Gram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and in processed foods such as gelatin and milk powder. Anoxybacillus flavithermus is a facultatively anaerobic bacterium found in super-saturated silica solutions and in opaline silica sinter. The ability of A. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, which might be similar to the biomineralization processes that occurred at the dawn of life.

Results

We report here the complete genome sequence of A. flavithermus strain WK1, isolated from the waste water drain at the Wairakei geothermal power station in New Zealand. It consists of a single chromosome of 2,846,746 base pairs and is predicted to encode 2,863 proteins. In silico genome analysis identified several enzymes that could be involved in silica adaptation and biofilm formation, and their predicted functions were experimentally validated in vitro. Proteomic analysis confirmed the regulation of biofilm-related proteins and crucial enzymes for the synthesis of long-chain polyamines as constituents of silica nanospheres.

Conclusions

Microbial fossils preserved in silica and silica sinters are excellent objects for studying ancient life, a new paleobiological frontier. An integrated analysis of the A. flavithermus genome and proteome provides the first glimpse of metabolic adaptation during silicification and sinter formation. Comparative genome analysis suggests an extensive gene loss in the Anoxybacillus/Geobacillus branch after its divergence from other bacilli.