Metagenomic/metatranscriptomic analysis within an ocean acidification
Metagenomics and metatranscriptomics of marine plankton under conditions of ocean acidification
The dissolution of anthropogenic CO2 from the atmosphere into the oceans will decrease surface pH by 0.3 units over the next 100 years (IPCC 2007); the phenomenon is referred to as ocean acidification (OA). There are concerns that OA will affect marine microorganisms, with significant impacts on marine biogeochemical cycling. To investigate the impact of this on marine microorganisms, a mesocosm experiment was set-up in a Norwegian Fjord in May 2006.   Six bags containing 11,000 L of sea water were suspended in a Coastal Fjord.  CO2 was bubbled through three of these bags to simulate ocean acidification conditions in the year 2100. The other three bags were bubbled with air. A phytoplankton bloom was induced in all six bags and phytoplankton, bacterioplankton and physiochemical characteristics were measured and analyzed over a 18 day period. Water samples from the peak of the phytoplankton bloom were isolated and used to follow the decline of the phytoplankton bloom. Nucleic acid extractions were performed to analyse bacterial diversity and functionality using 454 metagenomics and 454 metatranscriptomics.   Sequencing the metatranscriptome can provide information about the response of organisms to varying environmental conditions. A methodology for obtaining random whole-community mRNA from a complex microbial assemblage using pyrosequencing was used. The metatranscriptome had, with minimum contamination by ribosomal RNA, significant coverage of abundant transcripts, and included significantly more potentially novel proteins than in the metagenome.    Four 454 metatranscriptomic datasets and four 454 metagenomic datasets have been produced. These were derived from 4 samples: Day 1, High CO2 Bag and Day 1, Present Day Bag, refer to the metatranscriptomes from the peak of the bloom; Day 2, High CO2 Bag and Day 2, Present Day Bag, refer to the metatranscriptomes following the decline of the bloom. High CO2 refers to the ocean acidification mesocosm and Present Day refers to the control mesocosm.      <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=&db=Nucleotide&cmd=search&term=EU012135:EU012221[accn]">EU012135-EU012221</a> , <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=&db=Nucleotide&cmd=search&term=EU421954:EU421957[accn]">EU421954-EU421957</a> , <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=&db=Nucleotide&cmd=search&term=EU410956[accn]">EU410956</a> , <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=&db=Nucleotide&cmd=search&term=EU476008[accn]">EU476008</a>  , and <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=&db=Nucleotide&cmd=search&term=EU819141:EU819142[accn]">EU819141-EU819142</a>  are genomic sequences derived from this study.   454 sequence data is available from the Short Read Archive (SRA): <a href="ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead/SRA000266  ">SRA000266</a>.   454-metatranscriptomic data is available from the Gene Expression Omnibus (GEO): <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10119  ">GSE10119</a>.