Community structure and metabolism through reconstruction of microbial genomes from the environment

@article{Tyson2004CommunitySA,
  title={Community structure and metabolism through reconstruction of microbial genomes from the environment},
  author={Gene W. Tyson and Jarrod Chapman and P. Bernt Hugenholtz and Eric E. Allen and Rachna J. Ram and Paul Richardson and Victor V. Solovyev and Edward M. Rubin and Daniel S. Rokhsar and Jillian F. Banfield},
  journal={Nature},
  year={2004},
  volume={428},
  pages={37-43}
}
Microbial communities are vital in the functioning of all ecosystems; however, most microorganisms are uncultivated, and their roles in natural systems are unclear. Here, using random shotgun sequencing of DNA from a natural acidophilic biofilm, we report reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II, and partial recovery of three other genomes. This was possible because the biofilm was dominated by a small number of species populations and the… 
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References

SHOWING 1-10 OF 45 REFERENCES
Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage.
TLDR
The results verify the utility of BAC libraries for providing access to the genomes of as yet uncultivated microbial species and investigate the genomic potential and ecological roles of many indigenous microbial species, cultivated or not.
Cloning the Soil Metagenome: a Strategy for Accessing the Genetic and Functional Diversity of Uncultured Microorganisms
TLDR
Phylogenetic analysis of 16S rRNA gene sequences recovered from one of the libraries indicates that the BAC libraries contain DNA from a wide diversity of microbial phyla, including sequences from diverse taxa such as the low-G+C, gram-positive Acidobacterium,Cytophagales, and Proteobacteria.
Complete genome sequences of cellular life forms: glimpses of theoretical evolutionary genomics.
TLDR
A comparison of the protein sequences encoded in these genes with those of the proteins encoded in the complete yeast genome suggests that the last common ancestor of all extant life might have had an RNA genome.
Phylogenetic identification and in situ detection of individual microbial cells without cultivation.
TLDR
Phylogenetic analysis of the retrieved rRNA sequence of an uncultured microorganism reveals its closest culturable relatives and may, together with information on the physicochemical conditions of its natural habitat, facilitate more directed cultivation attempts.
A molecular view of microbial diversity and the biosphere.
  • N. Pace
  • Biology, Medicine
    Science
  • 1997
Over three decades of molecular-phylogenetic studies, researchers have compiled an increasingly robust map of evolutionary diversification showing that the main diversity of life is microbial,
Comparative Genomic Analysis of Archaeal Genotypic Variants in a Single Population and in Two Different Oceanic Provinces
TLDR
The data suggest that considerable functional diversity may exist within single populations of coexisting microbial strains, even those with identical 16S rRNA sequences, and that genomic approaches can provide high-resolution information relevant to microbial population genetics, ecology, and evolution.
Gene function analysis in environmental isolates: The nif regulon of the strict iron oxidizing bacterium Leptospirillum ferrooxidans
  • V. Parro, M. Moreno-Paz
  • Biology, Medicine
    Proceedings of the National Academy of Sciences of the United States of America
  • 2003
TLDR
The results show that shotgun DNA microarrays are very powerful tools to accomplish gene expression studies with environmental bacteria whose genome sequence is still unknown, avoiding the time and effort necessary for whole genome sequencing projects.
Capturing whole-genome characteristics in short sequences using a naïve Bayesian classifier.
TLDR
A naïve Bayesian classifier was developed and sequences as short as 400 bases could be correctly classified with an accuracy of 85% and it was found that this classification methodology could be a valuable tool in biodiversity studies.
The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum
TLDR
The interest in protein folding and degradation led us to seek a more complete representation of the proteins involved in these pathways by determining the genome sequence of the organism, and here the 1,564,905-base-pair genome is sequenced in just 7,855 sequencing reactions by using a new strategy.
Phylogeny of Microorganisms Populating a Thick, Subaerial, Predominantly Lithotrophic Biofilm at an Extreme Acid Mine Drainage Site
TLDR
Microenvironments of low redox potential possibly exist in the predominantly oxidizing environments of the slime, and this results expand the knowledge of the biodiversity of acid mine drainage environments and extend the understanding of the ecology of extremely acidic systems.
...
1
2
3
4
5
...