Environmental Genome Shotgun Sequencing of the Sargasso Sea

Venter, J. Craig; Remington, Karin; Heidelberg, John F.; Halpern, Aaron L.; Rusch, Doug; Eisen, Jonathan A.; Wu, Dongying; Paulsen, Ian T.; Nelson, Karen E.; Nelson, William; Fouts, Derrick E.; Lévy, Samuel; Knap, Anthony H.; Lomas, Michael W.; Nealson, K.; White, Owen; Peterson, Jeremy; Hoffman, Jeff; Parsons, Rachel; Baden-Tillson, Holly; Pfannkoch, Cynthia; Rogers, Yu Hui; Smith, Hamilton O.

doi:10.1126/science.1093857

Cited by 3,772 publications

(3,252 citation statements)

References 35 publications

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“…1 online), which ensures a high dosage of alkane hydroxylation genes. A search for alkB genes in sequenced marine organisms and the only marine metagenomic database available 19 revealed that only a comparatively small number of bacteria harbor alkB homologs and even fewer have multiple copies ( Supplementary Fig. 4 and Supplementary Table 1 online).…”

Section: Genomic Islands and Mobile Genetic Elementsmentioning

confidence: 99%

Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis

et al. 2006

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Alcanivorax borkumensis is a cosmopolitan marine bacterium that uses oil hydrocarbons as its exclusive source of carbon and energy. Although barely detectable in unpolluted environments, A. borkumensis becomes the dominant microbe in oil-polluted waters. A. borkumensis SK2 has a streamlined genome with a paucity of mobile genetic elements and energy generation–related genes, but with a plethora of genes accounting for its wide hydrocarbon substrate range and efficient oil-degradation capabilities. The genome further specifies systems for scavenging of nutrients, particularly organic and inorganic nitrogen and oligo-elements, biofilm formation at the oil-water interface, biosurfactant production and niche-specific stress responses. The unique combination of these features provides A. borkumensis SK2 with a competitive edge in oil-polluted environments. This genome sequence provides the basis for the future design of strategies to mitigate the ecological damage caused by oil spills. Supplementary information The online version of this article (doi:10.1038/nbt1232) contains supplementary material, which is available to authorized users.

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Section: Genomic Islands and Mobile Genetic Elementsmentioning

confidence: 99%

Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis

et al. 2006

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“…These examples represent the first steps towards engineering an entire biological system from the ground up. Massive sequencing efforts exploring the biodiversity of culturable organisms as well as metagenomes, such as the Sargasso Sea project [77], have generated a wealth of genetic information. These endeavors are providing novel biosynthetic pathway infor-mation that can be used to design optimized systems for every fuel category.…”

Section: Box 2 Microbial Sources Of Other Petrochemical Commoditiesmentioning

confidence: 99%

Biofuel alternatives to ethanol: pumping the microbial well

Fortman

Chhabra

Mukhopadhyay

et al. 2008

Trends in Biotechnology

338

209

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“…While eDNA has commonly been used to assess microbial diversity and abundance (Venter et al . 2004; Rusch et al . 2007), only recently has the technique been used to survey higher eukaryotes including fishes (Thomsen et al .…”

Section: Introductionmentioning

confidence: 99%

Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA

et al. 2015

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Preserving biodiversity is a global challenge requiring data on species’ distribution and abundance over large geographic and temporal scales. However, traditional methods to survey mobile species’ distribution and abundance in marine environments are often inefficient, environmentally destructive, or resource‐intensive. Metabarcoding of environmental DNA (eDNA) offers a new means to assess biodiversity and on much larger scales, but adoption of this approach for surveying whole animal communities in large, dynamic aquatic systems has been slowed by significant unknowns surrounding error rates of detection and relevant spatial resolution of eDNA surveys. Here, we report the results of a 2.5 km eDNA transect surveying the vertebrate fauna present along a gradation of diverse marine habitats associated with a kelp forest ecosystem. Using PCR primers that target the mitochondrial 12S rRNA gene of marine fishes and mammals, we generated eDNA sequence data and compared it to simultaneous visual dive surveys. We find spatial concordance between individual species’ eDNA and visual survey trends, and that eDNA is able to distinguish vertebrate community assemblages from habitats separated by as little as ~60 m. eDNA reliably detected vertebrates with low false‐negative error rates (1/12 taxa) when compared to the surveys, and revealed cryptic species known to occupy the habitats but overlooked by visual methods. This study also presents an explicit accounting of false negatives and positives in metabarcoding data, which illustrate the influence of gene marker selection, replication, contamination, biases impacting eDNA count data and ecology of target species on eDNA detection rates in an open ecosystem.

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Environmental Genome Shotgun Sequencing of the Sargasso Sea

Cited by 3,772 publications

References 35 publications

Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis

Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis

Biofuel alternatives to ethanol: pumping the microbial well

Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA

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