Microbial community genomics in the ocean

• Published in: Nature reviews. Microbiology Vol. 3; no. 6; pp. 459 - 469
• Main Author: DeLong, Edward F.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.06.2005; Nature Publishing Group
• Subjects: Archaea; Artificial chromosomes; Bacteria; Bacteria - classification; Bacteria - genetics; Base Sequence; Biomedical and Life Sciences; Cloning; Cloning, Molecular; Community structure; Cultivation; DNA, Bacterial - chemistry; DNA, Bacterial - genetics; Ecology; Ecosystem; Genes; Genomes; Genomics; Infectious Diseases; Life Sciences; Marine; Medical Microbiology; Microbial activity; Microbiology; Microorganisms; Nucleic Acid Conformation; Parasitology; Protista; review-article; Ribosomal RNA; Seawater - microbiology; Virology; United States > US; Massachusetts; AN, Sargasso Sea
• ISSN: 1740-1526; 1740-1534
• DOI: 10.1038/nrmicro1158

Key Points Over the past 20 years, molecular approaches, such as ribosomal RNA gene-sequence comparisons, have revolutionized our understanding of microbial diversity and ecology. Similarly, advances in genome sequencing technologies are now beginning to have a major impact on microbial ecology and the environmental sciences, particularly ocean science. Several whole genome sequences for marine microorganisms have been completed and many more marine bacterial, archaeal and protistan genome sequencing projects are underway. In addition to 'simple' genome sequencing, new genomic approaches to analyse natural microbial assemblages have been, and continue to be, developed. These new approaches, which are referred to by various names, including environmental genomics and metagenomics (the subject of this Focus issue), focus on cultivation-independent genomic survey strategies, such as the construction of large-insert bacterial artificial chromosome and fosmid libraries for large DNA inserts and the use of whole-genome shotgun sequencing for small DNA inserts. Three main case studies are discussed in detail: the discovery of bacterial proteorhodopsin using a phylogenetically anchored chromosome walking strategy; the shotgun sequence analysis of the microbial community in the Sargasso Sea; and the reconstruction of methane oxidation pathways in deep-sea archaea by shotgun sequencing of methanotroph-enriched fractions. In the future, comparative community genomic approaches will hopefully begin to yield important, detailed information on microbial distribution, population structure and dynamics in various different environments. Marine microbial communities were among the first microbial communities to be studied using cultivation-independent genomic approaches. Ocean-going genomic studies are now providing a more comprehensive description of the organisms and processes that shape microbial community structure, function and dynamics in the sea. Through the lens of microbial community genomics, a more comprehensive view of uncultivated microbial species, gene and biochemical pathway distributions, and naturally occurring genomic variability is being brought into sharper focus. Besides providing new perspectives on oceanic microbial communities, these new studies are now poised to reveal the fundamental principles that drive microbial ecological and evolutionary processes.