Environmental Genome Shotgun Sequencing of the Sargasso Sea

@article{Venter2004EnvironmentalGS,
  title={Environmental Genome Shotgun Sequencing of the Sargasso Sea},
  author={J. Craig Venter and Karin A. Remington and John F. Heidelberg and Aaron L. Halpern and Douglas B. Rusch and Jonathan A. Eisen and Dongying Wu and Ian T. Paulsen and Karen E. Nelson and William Nelson and Derrick E. Fouts and Samuel Levy and Anthony H. Knap and Michael W. Lomas and Kenneth H. Nealson and Owen White and Jeremy D. Peterson and Jeff Hoffman and Rachel J Parsons and Holly Baden-Tillson and Cynthia Pfannkoch and Y H Rogers and Hamilton O. Smith},
  journal={Science},
  year={2004},
  volume={304},
  pages={66 - 74}
}
We have applied “whole-genome shotgun sequencing” to microbial populations collected en masse on tangential flow and impact filters from seawater samples collected from the Sargasso Sea near Bermuda. A total of 1.045 billion base pairs of nonredundant sequence was generated, annotated, and analyzed to elucidate the gene content, diversity, and relative abundance of the organisms within these environmental samples. These data are estimated to derive from at least 1800 genomic species based on… Expand
Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities
TLDR
The aim of this review is to introduce the bioinformatics community to this emerging field by surveying existing techniques and promising new approaches for several of the most interesting of these computational problems. Expand
Microbial diversity characterization of seawater in a pilot study using Oxford Nanopore Technologies long-read sequencing
TLDR
The utility of Oxford Nanopore Technologies (ONT) sequencing to characterize microbial diversity in seawater from multiple locations is evaluated and k-mer analysis reveals that a large part of the data represents species of which close relatives have not yet been deposited to the database. Expand
etagenome Analysis using Megan
TLDR
A new software called MEGAN (Meta Genome ANalyzer) is introduced that generates species profiles from large-scale random shotgun sequencing data by assigning reads to taxa of the NCBI taxonomy using a straight-forward assignment algorithm. Expand
METAGENOME ANALYSIS USING MEGAN
In metagenomics, the goal is to analyze the genomic content of a sample of organisms collected from a common habitat. One approach is to apply large-scale random shotgun sequencing techniques toExpand
Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage
TLDR
Bacteria in the 16S rRNA clade SAR86 are among the most abundant uncultivated constituents of microbial assemblages in the surface ocean for which little genomic information is currently available, and their genomes contain an expanded capacity for the degradation of lipids and carbohydrates acquired using a wealth of tonB-dependent outer membrane receptors. Expand
Environmental shotgun sequencing
Shotgun sequencing of microbial communities is a promising means for delving into community function and interactions, population structure and dynamics, and bypassing the cultivation bottleneck inExpand
The trajectory of microbial single-cell sequencing
TLDR
This review highlights newly added leaves and branches in the genomic tree of bacterial and archaeal life and illustrates the unique and exciting advantages that single-cell genomics offers over metagenomics, both now and in the near future. Expand
Prediction of effective genome size in metagenomic samples
We introduce a novel computational approach to predict effective genome size (EGS; a measure that includes multiple plasmid copies, inserted sequences, and associated phages and viruses) from shortExpand
Molecular Phylogeny of Arctic Microbes Using Metagenomic Approach
TLDR
Metagenomic approach to the characterization of uncultured and mixed bacterial consortium has been used in this study for a few arctic micro-organisms, most of these arctic bacteria were Bacillus species as these were isolated from a single spot. Expand
Miraculous catch of iron–sulfur protein sequences in the Sargasso Sea
TLDR
Iron–sulfur proteins, which are ancient, diverse and ubiquitous, have been implemented here to further probe the sequence diversity of the Sargasso Sea database (SSDB). Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 77 REFERENCES
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. Expand
Proteorhodopsin genes are distributed among divergent marine bacterial taxa
TLDR
Comparisons of PR-bearing genomic fragments recovered directly from planktonic bacteria inhabiting the California coast, the central Pacific Ocean, and waters offshore the Antarctica Peninsula indicate that PR genes are distributed among a variety of divergent marine bacterial taxa, including both α- and γ-proteobacteria. Expand
The genome of a motile marine Synechococcus
TLDR
The genome of WH8102 seems to have been greatly influenced by horizontal gene transfer, partially through phages, and is more of a generalist than two related marine cyanobacteria. Expand
Cyanobacterial community structure as seen from RNA polymerase gene sequence analysis
  • B. Palenik
  • Medicine, Biology
  • Applied and environmental microbiology
  • 1994
TLDR
The approach described here can be used as a general method for examining cyanobacterial diversity, while an oligotrophic ocean ecosystem such as the Sargasso Sea may be an ideal model for examining diversity in relation to environmental parameters. Expand
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. Expand
Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon
TLDR
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. Expand
Genomic analysis of uncultured marine viral communities
TLDR
Diversity of the viral communities was extremely high, and the results showed that it would be possible to sequence the entire genome of an uncultured marine viral community. Expand
Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation
TLDR
The genomes of two Prochlorococcus strains that span the largest evolutionary distance within the Pro chlorococcus lineage are compared and reveal dynamic genomes that are constantly changing in response to myriad selection pressures. Expand
Proteorhodopsin phototrophy in the ocean
TLDR
It is reported that photoactive proteorhodopsin is present in oceanic surface waters and evidence is provided of an extensive family of globally distributed proteorodopsin variants that seem to be spectrally tuned to different habitats—absorbing light at different wavelengths in accordance with light available in the environment. Expand
Estimating prokaryotic diversity and its limits
TLDR
It is evident that local and global prokaryotic diversity can be understood through species abundance curves and purely experimental approaches to solving this conundrum will be fruitless. Expand
...
1
2
3
4
5
...