Characterization of microbial diversity and functionality in Arctic and sub-Arctic sediments - Annual report 2009

Annual report VISTA 2009

Project title: Characterization of microbial diversity and functionality in Arctic and sub-Arctic seafloor sediments influenced by natural hydrocarbon seepage

Project director:                                                                 Rike, Anne Gunn, NGI

Post-doc/ scholar:                                                                             Håvelsrud, Othilde Elise

Project duration:                                                                01.05.2007 – 30.04.2010

Technical contact person in Statoil:                              Kotlar, Hans Kristian

Division head:                                                                    Mostad, Helle Brit

Project number:                                                                 6151

Objectives: The main objective of the study is to identify microbial genetic markers that characterize microbial communities associated with deep seafloor sediments influenced by hydrocarbon seepage.

Sub-objectives in 2009: To development of pipelines for taxonomic and functional analysis of datasets generated by 454 GS-FLX high throughput sequencing of metagenomic DNA extracts. Processing and alignment of the datasets to various databases for analysis and interpretation of microbial diversity at various taxonomic ranks as well as in-depth analysis of taxa with putative functionalities related to hydrocarbon seepage have been emphasized.

Furture work: Two Californian sediment seep samples taken from different depths (A: 0-4cm bsf and B: 10-15cm bsf) have been sequenced and are currently being analysed. These samples will provide knowledge of the biodiversity and metabolic capacity at different sediment depths. DNA from five samples collected in a pockmark area of the Troll-field, a sample from a proposed seep site in Mozambique and two negative control samples from the Oslo fjord are in line to be sequenced at the ultra high troughput sequencing platform at CEES, University of Oslo. A new analytical protocol recently taken into use at CEES will be used for generation of longer reads (about 500 bp). Comparative analysis of the metagenomes from these samples will provide microbial signatures typically for hydrocarbon seep influenced sediments. Further development of workflows and pipeline refinements for more effective taxonomic and functional analysis of the metagenome datasets will be emphasised.

Status: At present a sediment sample from the Håkon Mosby mud volcano (HMMV) has been sequenced and analysed. A manuscript on this work will be submitted shortly. Analysis of this sample in the Metagenome Analyser program (MEGAN) shows high microbial diversity. The bacterial reads, dominated by Proteobacteria, were assigned to 26 different phyla. Euryarchaeota dominated the archaeal reads, but reads were also assigned to Crenarchaeota, Thaumarchaeota, Korarchaeota and Nanoarchaeota. The results of the functional diversity analysis, based on MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) and KAAS (KEGG automatic annotation server), show that it is possible, even with short reads (220 bp), to reconstruct the metabolic capacity of the microbial consortium (Bacteria and Archaea) in the sample. The diversity and metabolic capacity of the two Californian seep samples have been explored in MEGAN and KAAS. Considerable higher representation of Archaea was observed in the deepest sample (1.4 % at 0-4 cm versus 14.4 % at 10-15 cm). In both samples Proteobacteria and Euryarchaeota was the predominant phyla.

The project is about one year after schedule. The reason for this is that traditional microbial phylogeny analysis (PCR amplification of 16S rDNA, cloning and Sanger sequencing) was used for diversity analysis the first project year. When the GS-FLX technology was established at CEES, Department of Biology, University of Oslo in 2007/2008 is was decided to take this new technology into use, because it is faster and most primer-bias problems are avoided. In addition the huge amount of data generated gives us a broader insight into the microbial diversity and functionality as well as the possibility for in-depth analysis of the microbial signatures of seep influenced sediments. The project has applied Vista for one year extension.

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