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Applied and Environmental Microbiology, August 2009, p. 5345-5355, Vol. 75, No. 16
0099-2240/09/$08.00+0     doi:10.1128/AEM.00473-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Comparative Metagenomic Analysis of a Microbial Community Residing at a Depth of 4,000 Meters at Station ALOHA in the North Pacific Subtropical Gyre ^,

Konstantinos T. Konstantinidis,^1, Jennifer Braff,¹ David M. Karl,² and Edward F. DeLong^1*

Department of Civil and Environmental Engineering and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts,¹ University of Hawaii, Honolulu, Hawaii²

Received 25 February 2009/ Accepted 9 June 2009

The deep sea (water depth of >2,000 m) represents the largest biome on Earth. Yet relatively little is known about its microbial community's structure, function, and adaptation to the cold and deep biosphere. To provide further genomic insights into deep-sea planktonic microbes, we sequenced a total of 200 Mbp of a random whole-genome shotgun (WGS) library from a microbial community residing at a depth of 4,000 m at Station ALOHA in the Pacific Ocean and compared it to other available WGS sequence data from surface and deep waters. Our analyses indicated that the deep-sea lifestyle is likely facilitated by a collection of very subtle adaptations, as opposed to dramatic alterations of gene content or structure. These adaptations appear to include higher metabolic versatility and genomic plasticity to cope with the sparse and sporadic energy resources available, a preference for hydrophobic and smaller-volume amino acids in protein sequences, unique proteins not found in surface-dwelling species, and adaptations at the gene expression level. The deep-sea community is also characterized by a larger average genome size and a higher content of "selfish" genetic elements, such as transposases and prophages, whose propagation is apparently favored by more relaxed purifying (negative) selection in deeper waters.

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* Corresponding author. Mailing address: Dept. of Civil and Environmental Engineering & Division of Biological Engineering, Massachusetts Institute of Technology, 48-427 MIT, 15 Vassar St., Cambridge, MA 02139. Phone: (617) 253-5271. Fax: (617) 253-2679. E-mail: delong{at}mit.edu

Published ahead of print on 19 June 2009.

Supplemental material for this article may be found at http://aem.asm.org/.

Present address: School of Civil and Environmental Engineering and School of Biology, Georgia Institute of Technology, Atlanta, GA.

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Applied and Environmental Microbiology, August 2009, p. 5345-5355, Vol. 75, No. 16
0099-2240/09/$08.00+0     doi:10.1128/AEM.00473-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

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