The uncultured microbial majority.

@article{Rapp2003TheUM,
  title={The uncultured microbial majority.},
  author={Michael S. Rapp{\'e} and Stephen J. Giovannoni},
  journal={Annual review of microbiology},
  year={2003},
  volume={57},
  pages={
          369-94
        }
}
Since the delineation of 12 bacterial phyla by comparative phylogenetic analyses of 16S ribosomal RNA in 1987 knowledge of microbial diversity has expanded dramatically owing to the sequencing of ribosomal RNA genes cloned from environmental DNA. Currently, only 26 of the approximately 52 identifiable major lineages, or phyla, within the domain Bacteria have cultivated representatives. Evidence from field studies indicates that many of the uncultivated phyla are found in diverse habitats, and… 

Figures from this paper

Metagenomics: genomic analysis of microbial communities.
TLDR
Progress toward understanding the biology of uncultured Bacteria, Archaea, and viruses through metagenomic analyses is described.
Global patterns in bacterial diversity
TLDR
This work reports the most comprehensive analysis of the environmental distribution of bacteria to date, based on 21,752 16S rRNA sequences compiled from 111 studies of diverse physical environments, and finds that sediments are more phylogenetically diverse than any other environment type.
Novel bacterial lineages in the uncultured candidate division SR1
TLDR
Phylogenetic analyses indicated that SR1 members associated with animal hosts clustered separately from those collected at the environmental sites, and 18 operational taxonomic units that were used in combination with SR1 reference sequences to build an SR1 phylogenetic tree were identified.
Cultivating the uncultivated: a community genomics perspective.
Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla
TLDR
Deep sequenced microbial communities from acetate-stimulated aquifer sediment are deeply sequenced to recover the complete and essentially complete genomes of single representatives of the candidate phyla SR1, WWE3, TM7, and OD1, revealing metabolic capabilities on the basis of gene content.
Assessment of Microbial Phylogenetic Diversity Based on Environmental Nucleic Acids
“It is a Golden Age for the discovery of new organisms and for achieving a better understanding of the global ecosystem, which is, after all, based upon the microbial world” (Hugenholtz and Pace
Diversity, ecology and evolution of Archaea
TLDR
How genomes belonging to uncultured groups from the environment elucidate the metabolic capabilities of the Archaea and their ecological roles are discussed, while also expanding the view of the tree of life and of eukaryogenesis.
Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes
TLDR
The results suggest that the capacity to produce extracellular enzymes varies at relatively fine-scale phylogenetic resolution, consistent with other traits that require a small number of genes and provides insight into the relationship between taxonomy and traits that may be useful for predicting ecological function.
Molecular Approach to Study Soil Bacterial Diversity
TLDR
This chapter aims to summarize the molecular techniques, which offer insight into phylogenetic and functional diversity of microbial assemblages along with the advantages and pitfalls of commonly used molecular methods.
...
...

References

SHOWING 1-10 OF 155 REFERENCES
A molecular view of microbial diversity and the biosphere.
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,
Expanding the Known Diversity and Environmental Distribution of an Uncultured Phylogenetic Division of Bacteria
TLDR
The extent of phylogenetic divergence in this candidate division was found to be among the largest of any known bacterial division, indicating that organisms representing the WS6 phylogenetic division offer a broad diversity of undiscovered biochemical and metabolic novelty.
Cultivation of the ubiquitous SAR11 marine bacterioplankton clade
TLDR
The isolation of representatives of the SAR11 clade is reported, which indicates that diverse uncultivated microbial taxa dominate most natural ecosystems, which has prompted widespread efforts to elucidate the geochemical activities of these organisms without the benefit of cultures for study.
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.
Exploring prokaryotic diversity in the genomic era
Our understanding of prokaryote biology from study of pure cultures and genome sequencing has been limited by a pronounced sampling bias towards four bacterial phyla - Proteobacteria, Firmicutes,
Cultivating the uncultured
TLDR
This technique combines encapsulation of cells in gel micro droplets for massively parallel microbial cultivation under low nutrient flux conditions, followed by flow cytometry to detect microdroplets containing microcolonies to enhance understanding of microbial physiology and metabolic adaptation and will provide new sources of microbial metabolites.
Bacterial diversity in a soil sample from a subtropical Australian environment as determined by 16S rDNA analysis
TLDR
Comparison of partial 16S rDNA sequences with published sequences revealed that few sequences originated from streptomycetes, and the majority of sequences belonged to members of the alpha subclass of Proteobacteria.
Novel major archaebacterial group from marine plankton
TLDR
16S rRNA sequences obtained from Pacific Ocean bacterioplankton samples collected from depths of 100 m and 500 m are reported and it is suggested that these sequences are from a previously undescribed archaebacterial group that may have diverged from the ancestors of characterized organisms very early in evolution.
Widespread Archaea and novel Bacteria from the deep sea as shown by 16S rRNA gene sequences
TLDR
The deep sea contains numerous novel and widespread major prokaryotic lineages, and it appears that the previously unknown archaeal and bacterial groups may be the most abundant organisms on Earth.
Assignment of hitherto unidentified 16S rDNA species to a main line of descent within the domain Bacteria
Phylogenetic analysis of the almost complete 16S rDNA sequence of the fimbriate prosthecate bacterium Verrucomicrobium spinosum confirms the unique phylogenetic position of this organism, as
...
...