Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage
Autor: | Andrew G. Hadd, Corey Garrigues, Mojgan Amjadi, Oded Béjà, Rachel Villacorta, Linh Nguyen, Robert A. Feldman, Marcelino T. Suzuki, Edward F. DeLong, Eugene V. Koonin, L. Aravind, Stevan B. Jovanovich |
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Rok vydání: | 2000 |
Předmět: |
DNA
Bacterial Chromosomes Artificial Bacterial Molecular Sequence Data Biology DNA Ribosomal Polymerase Chain Reaction Microbiology Genome RNA Ribosomal 16S Sequence Homology Nucleic Acid Environmental Microbiology Seawater ORFS Gene Phylogeny Ecology Evolution Behavior and Systematics Genetics Genomic Library Bacterial artificial chromosome Bacteria Phylogenetic tree Genetic Variation Ribosomal RNA Archaea Electrophoresis Gel Pulsed-Field genomic DNA Phylogenetic diversity Evolutionary biology |
Zdroj: | Environmental Microbiology. 2:516-529 |
ISSN: | 1462-2920 1462-2912 |
Popis: | Cultivation-independent surveys of ribosomal RNA genes have revealed the existence of novel microbial lineages, many with no known cultivated representatives. Ribosomal RNA-based analyses, however, often do not provide significant information beyond phylogenetic affiliation. Analysis of large genome fragments recovered directly from microbial communities represents one promising approach for characterizing uncultivated microbial species better. To assess further the utility of this approach, we constructed large-insert bacterial artificial chromosome (BAC) libraries from the genomic DNA of planktonic marine microbial assemblages. The BAC libraries we prepared had average insert sizes of ≈ 80 kb, with maximal insert sizes > 150 kb. A rapid screening method assessing the phylogenetic diversity and representation in the library was developed and applied. In general, representation in the libraries agreed well with previous culture-independent surveys based on polymerase chain reaction (PCR)-amplified rRNA fragments. A significant fraction of the genome fragments in the BAC libraries originated from as yet uncultivated microbial species, thought to be abundant and widely distributed in the marine environment. One entire BAC insert, derived from an uncultivated, surface-dwelling euryarchaeote, was sequenced completely. The planktonic euryarchaeal genome fragment contained some typical archaeal genes, as well as unique open reading frames (ORFs) suggesting novel function. In total, our results verify the utility of BAC libraries for providing access to the genomes of as yet uncultivated microbial species. Further analysis of these BAC libraries has the potential to provide significant insight into the genomic potential and ecological roles of many indigenous microbial species, cultivated or not. |
Databáze: | OpenAIRE |
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