1 / 1

Genomic DNA extraction

16S rRNA sequences identified as within the Class Pseudomonadales (2002 data) Colors indicate what location and type of sample from which the sequences were obtained Bamboo coral from Murray Seamount Black coral from Murray Seamount Bamboo coral Isidella from Warwick Seamount

paige
Télécharger la présentation

Genomic DNA extraction

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. 16S rRNA sequences identified as within the Class Pseudomonadales (2002 data) • Colors indicate what location and type of sample from which the sequences were obtained • Bamboo coral from Murray Seamount • Black coral from Murray Seamount • Bamboo coral Isidella from Warwick Seamount • Water collected at Murray Seamount • Caribbean coral (Rohwer et al., 2002) • Closest BLASTN match in Genbank • Biofilm from rock at Murray Seamount • Bamboo coral from Chirikof Seamount AY513646.1|Psychrobacter.alimentarius F282 CGO 1 F238 CGO 1 F227 CGO 1 F103 CGO 1RC AB016058.1|Psychrobacter.pacificensis AA29 BRR 1RC F213 CGO 1RC AB002657| 16S Mariana trench mud AJ619070.1|Beer bottling plant biofilm L01575.1|Thyasira.flexuosa AA04 CGO 1RC A196 NIS 1 AA53 BRR 1 AA33 BRR 1 AA61 BRR 1 AF384206|Ectothiorhodospira.sp AJ404972|Alcalilimnicola.halodurans A092 NIS 1RC A182 NIS 1 A021 NIS 1RC AA31 NIS 1 L10949.1|Marine.aggregate gi 19851156 gb gi 19851165 gb gi 19851177 gb gi 19851169 gb AF321239|Pseudomonas.sp. F104 CGO 1 PFU492830|Pseudomonas.fulgida AF388206|Pseudomonas.sp AF131104.Pseudomonas.putida.MT PSEIAM13|Pseudomonas.fragi ABE308319|Azotobacter.beijerin AA77 NIS 1RC AB125367.1|Pseudomonas.pachastrellae AA92 NIS 1 AJ609270.1|Marinobacter.sedimentalis DA30 CGO 1 DA16 CGO 1 DA42 CGO 1 DA55 CGO 1 DA72 CGO 1 DA79 CGO 1RC Specific to Coral DA22 CGO 1RC DA38 CGO 1 DA49 CGO 1 DA37 CGO 1 DA50 CGO 1 F019 CGO 1RC F180 CGO 1 F046 CGO 1RC F044 CGO 1 F078 CGO 1 F030 CGO 1RC F184 CGO 1 F124 CGO 1RC AY386337.1|Marine.oligotrophic.water AA05 NIS 1RC AB015519.1|deep sea sediments DA73 CGO 1 U70693.1|Continental shelf Cape hateras AF001650.1|Continental shelf off Oregon CA36 CGO 1 Acknowledgements We thank the Captain and crew of the R/V Atlantis, as well as members of the Alvin group, for all their help during both the 2002 and 2004 expeditions. Special thanks to Randy Keller, Brad Stevens, Tom Shirley, Tom Guilderson, Amy Baco-Taylor, and Peter Etnoyer for taking us on board. Thanks also to WHOI and NOAA’s Ocean Explorer program (especially Catalina Martinez) for supporting our participation. gi 19851209 gb gi 19851368 gb gi 19851219 gb F145 CGO 1 gi 19851230 gb gi 19851179 gb gi 19851409 gb AA62 NIS 1 AA87 BRR 1 15282445.Aquifex.aeolicus.VF5 10 In Search of Bacterial Communities Inhabiting Deep-Sea Corals on Gulf of Alaska Seamounts Kevin Penn and Naomi Ward, TIGR Seamounts visited during the 2004 expedition to the Gulf of Alaska Bamboo coral observed during Alvin dive 4035. We know that bacterial populations are associated with these corals, but their function (parasitic, or beneficial to the coral) remains unclear. Bamboo coral specimen successfully transferred to the surface in Alvin’s basket Life as we know it can be divided into three broad groups, the Eucarya, Archaea, and Bacteria. The only group visible to us with the naked eye is the Eucarya, containing animals, plants, and fungi. The Bacteria and Archaea are single-celled microbes and are only visible with use of a microscope. However, despite their small size, they have important roles in many spheres, and interactions with many larger organisms. These interactions can be either detrimental or beneficial to the eukaryote host. Collection of bamboo coral specimen using Alvin’s manipulators Laboratory Methods Bacteria in sample P. aeruginosa ATTCGATCCG... B. cereus M. luteus Collection of exopolysaccharide (mucus) produced by bamboo coral. Coral mucus may protect the coral from desiccation, predators, and disease. Sequence individual cloned genes, compare sequence to database, and identify original bacteria We know that the mucus contains many different species of bacteria. The mucus presumably provides shelter and nutrition to the bacteria, but is not yet known whether the bacteria provide a benefit to their coral host. Separate mixture of 16S rDNAs by cloning into plasmid vector and transformation of host cells Genomic DNA extraction B. subtilis PCR amplification of 16S rDNA P. stutzeri We use 16S rDNA cloning and sequencing to determine community composition, without the need to cultivate bacteria in the lab. This approach has been shown to recover bacterial diversity much more extensively than cultivation-based methods. 16S rDNA sequences can be used to draw a family tree of relationships between different bacteria. These data suggest that different coral species harbor specific groups of bacteria. What is TIGR? TIGR (The Institute for Genomic Research) is a private, not-for-profit research institute located in Rockville, Maryland. TIGR principally conducts large-scale genome sequencing projects; sequencing targets include many microbial species, but also plant, animal, and fungal organisms. The DNA sequence data obtained from these projects is used to derive genome-based insights into the biology of the target organism. TIGR has been participating in research cruises aboard R/V Atlantis, at the invitation of WHOI and NOAA OE, since 2002.

More Related