Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage.

@article{Bj2000ConstructionAA,
  title={Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage.},
  author={Oded B{\'e}j{\`a} and M. T. Suzuki and Eugene V. Koonin and L. Aravind and Andrew G. Hadd and L P Nguyen and Roosevelt Garc{\'i}a Villacorta and Motahareh Ala Amjadi and Christel Garrigues and Stevan B. Jovanovich and Robert Alan Feldman and Edward F. Delong},
  journal={Environmental microbiology},
  year={2000},
  volume={2 5},
  pages={
          516-29
        }
}
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… 

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References

SHOWING 1-10 OF 59 REFERENCES

Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample

The hypothesis that many of the most abundant bacterioplankton species are not readily culturable by standard methods is supported but also shows that heterotrophic bacteriopLankton that are culturable on media with high organic contents include many strains for which SSU rDNA sequences are not available in sequence databases.

Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing

The data confirm the earlier conclusion that a majority of planktonic bacteria are new species previously unrecognized by bacteriologists.

Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon

The results indicate that genomic analysis of large DNA fragments retrieved from mixed microbial assemblages can provide useful perspective on the physiological potential of abundant but as yet uncultivated prokaryotes.

Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing

The phylogenetic diversity of an oligotrophic marine picoplankton community was examined by analyzing the sequences of cloned ribosomal genes, and sequences obtained from two phylogenetic groups of organisms that are not closely related to any known rRNA sequences from cultivated organisms.

Screening of a Fosmid Library of Marine Environmental Genomic DNA Fragments Reveals Four Clones Related to Members of the OrderPlanctomycetales

ABSTRACT A fosmid library with inserts containing approximately 40 kb of marine bacterial DNA (J. L. Stein, T. L. Marsh, K. Y. Wu, H. Shizuya, and E. F. DeLong, J. Bacteriol. 178:591–599, 1996)

Phylogenetic diversity of aggregate‐attached vs. free‐living marine bacterial assemblages

The data indicate that specific bacterial populations, different from those which predominate in free-living bacterioplankton, develop on marine phytodetrital aggregates.

Genetic diversity in Sargasso Sea bacterioplankton

The phylogenetically analysed clone libraries of eubacterial 16S ribosomal RNA genes amplified from natural populations of Sargasso Sea picoplankton indicate the presence of a novel microbial group, the SAR 11 cluster, which appears to be a significant component of this oligotrophic bacterioplankton community.

Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria

It is concluded that some of the genetic diversity within the SAR11 gene cluster represents macroevolutionary divergence correlated with niche specialization and the utility for marine microbial ecology of oligonucleotide probes based on gene sequences amplified from natural populations is demonstrated.

Toward functional genomics in bacteria: analysis of gene expression in Escherichia coli from a bacterial artificial chromosome library of Bacillus cereus.

The application of the bacterial artificial chromosome (BAC) vector to prokaryotic biology as a powerful approach to address the need for molecular tools for analysis of a wide diversity of microorganisms is reported.

Stable-isotope probing as a tool in microbial ecology

Stable-isotope probing offers a powerful new technique for identifying microorganisms that are actively involved in specific metabolic processes under conditions which approach those occurring in situ.
...