Idiomarina loihiensis

From MicrobeWiki, the student-edited microbiology resource

A Microbial Biorealm page on the genus Idiomarina loihiensis

Classification

Higher order taxa

Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Idiomarinaceae; Idiomarina

Species

NCBI: Taxonomy

Idiomarina loihiensis

Description and significance

Describe the appearance, habitat, etc. of the organism, and why it is important enough to have its genome sequenced. Describe how and where it was isolated. Include a picture or two (with sources) if you can find them.

Idiomarina loihiensis is a rod shaped, Gram-negative aerobic cell driven through a single polar or subpolar flagellum. It was first throughly studied during a survey of bacterial diversity along deep sea hydrothermal vents located 35 kilometers off the coast of Hawaii. The volcanically active Lo'ihi Seamount is the home of Idiomarina loihiensis and several other metabolically active bacteria (2). The harsh conditions of the Lo'ihi Seamount, including high pressure and temperature (vents at 163º C), led to the early belief that these areas would be dominated by Archaea. However, further studies have indicated that it is Bacteria, instead that have dominated these vent microbial populations (2). Idiomarina loihiensis was one of the first bacterias cultivated and studied from these vents.

The bacteria was first collected in several dives during 1999 into Pele's Pit in the Lo'ihi Seamount. They were cultivated in marine agar or broth to be isolated and incubated at 30º C. The cells were determined to typically be 0.35µm wide and 0.7-1.8µm in length with optimum growth temperatures between 4-46º C. Comparison of the 16S rRNA genes with other bacteria revealed its similarity to I. abyssalis. However, the cultivated Idiomarina loihiensis were not similar to any other bacteria along the hydrothermal vents of the Lo'ihi Seamount. The strain cultivated, L2-TR, demonstrated the highest optimum growth salinity (7.5-10.0%) and growth temperatures relative to other species within its genus (2).

Genome structure

Complete Genome Sequence of Idiomarina loihiensis3

Describe the size and content of the genome. How many chromosomes? Circular or linear? Other interesting features? What is known about its sequence? Does it have any plasmids? Are they important to the organism's lifestyle?

The genome of Idiomarina loihiensis is a circular chromosome comprised of 2,839,318 base pairs. It was fully sequenced through bacterial artificial chromosome (BAC) clone and whole-genome shotgun libraries (WGSL) and determined to have a G+C content of 47.04%. The genome contains 4 rRNA operons , encodes 2,640 proteins, and 56 tRNAs genes. Based on comparisons to other γ-proteobacteria, I. loihiensis's genome revealed a distinct excess of amino acid transport and degradation enzymes rather than of sugar transport systems and sugar metabolism (3). This indicates that I. loihiensis gains its energy and carbon sources through amino acid catabolism and not sugar fermentation. I. loihiensis has a cluster of 32 genes that specifically encode for exopolysaccharides (EPS)to create necessary biofilms for their growth and survival within the hydrothermal environment (3).

Complete Genome Sequence of Idiomarina loihiensis3

Cell structure and metabolism

Describe any interesting features and/or cell structures; how it gains energy; what important molecules it produces.

Ecology

Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.

Application to Biotechnology

Does this organism produce any useful compounds or enzymes? What are they and how are they used?

Current Research

Enter summaries of the most recent research here--at least three required

References

1) Collyn, F., Roten, C., and Guy, L. "Solving ambiguities in contig assembly of Idiomarina loihiensis L2TR chromosome by in silico analyses." FEMS Microbiology Letters. 2007. Volume 271. p. 187-192.

2) Donachie, S., Hou, S., Gregory, T., et al. "Idiomarina loihiensis sp. nov., a halophilic γ-proteobacterium from the Lo'ihi submarine volcano, Hawai'i." International Journal of Systematic and Evolutionary Microbiology. Volume 53. p. 1873-1879.

3) Hou, S., Saw, J., Lee,K., et al. "Genome sequence of the deep-sea γ-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy". Proceedings of the National Academy of Sciences of the United States of America. 2004. Volume 101.

4) Guezennec, J. "Deep-sea hydrothermal vents: A new source of innovative bacterial exopolysaccharides of biotechnological interest?" Journal of Industrial Microbiology & Biotechnology. 2008. Volume 29. p. 204-208.

5) Nichols, C.A., Guezennec, J., and Bowman, J.P. "Bacterial Exopolysaccharides from Extreme Marine Environments with Special Consideration of the Southern Ocean, Sea Ice, and Deep-Sea Hydrothermal Vents: A Review." Marine Biotechnology. 2005. Volume 7. p. 253-271.

6) Shibata, S., Alam, M., and Aizawa, S. "Flagellar Filaments of the Deep-Sea Bacteria Idiomarina loihiensis Belong to a Family Different from those of Salmonella tymphimurium." Journal of Molecular Biology. 2005. Volume 352. p 510-516.

7) Xu, Y., Glandsdorff, N., and Labedan, B. "Bioinformatic analysis of an unusual gene-enzyme relationship in the arginine biosynthetic pathway among marine gamma proteobacteria: implications concerning the formation of N-acetylated intermediates in prokaryotes." BMC Genomics. 2006. Volume 7.



Edited by student of Rachel Larsen