Metagenomic and metatranscriptomic inventories of the lower Amazon River, May 2011 Public Deposited

http://ir.library.oregonstate.edu/concern/articles/c247dt971

This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by BioMed Central. The published article can be found at:  http://microbiomejournal.biomedcentral.com/

Supporting Information: Sequences from this May 2011 Amazon Continuum study are available from NCBI under accession numbers SRP039390 (metagenomes) and SRP037995 (metatranscriptomes). The NCBI sequences are fastq files from which internal standard sequences (metagenomes and metatranscriptomes) and rRNA sequences (metatranscriptomes only) have been removed prior to deposition. Metadata accompanying the omics datasets are provided in Additional file 2. ANACONDAS and ROCA project data are also available at the BCO-DMO data repository ( http://www.bco-dmo.org/project/2097).

Additional Files are available online at:  http://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-015-0099-0#Sec7

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  • Background: The Amazon River runs nearly 6500 km across the South American continent before emptying into the western tropical North Atlantic Ocean. In terms of both volume and watershed area, it is the world’s largest riverine system, affecting elemental cycling on a global scale. Results: A quantitative inventory of genes and transcripts benchmarked with internal standards was obtained at five stations in the lower Amazon River during May 2011. At each station, metagenomes and metatranscriptomes were obtained in duplicate for two microbial size fractions (free-living, 0.2 to 2.0 μm; particle-associated, 2.0 to 297 μm) using 150 × 150 paired-end Illumina sequencing. Forty eight sample datasets were obtained, averaging 15 × 10⁶ potential protein-encoding reads each (730 × 10⁶ total). Prokaryotic metagenomes and metatranscriptomes were dominated by members of the phyla Actinobacteria, Planctomycetes, Betaproteobacteria, Verrucomicrobia, Nitrospirae, and Acidobacteria. The actinobacterium SCGC AAA027-L06 reference genome recruited the greatest number of reads overall, with this single bin contributing an average of 50 billion genes and 500 million transcripts per liter of river water. Several dominant taxa were unevenly distributed between the free-living and particle-associated size fractions, such as a particle-associated bias for reads binning to planctomycete Schlesneria paludicola and a free-living bias for actinobacterium SCGC AAA027-L06. Gene expression ratios (transcripts to gene copy ratio) increased downstream from Óbidos to Macapá and Belém, indicating higher per cell activity of Amazon River bacteria and archaea as river water approached the ocean. Conclusion: This inventory of riverine microbial genes and transcripts, benchmarked with internal standards for full quantitation, provides an unparalleled window into microbial taxa and functions in the globally important Amazon River ecosystem.
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  • Satinsky, B. M., Fortunato, C. S., Doherty, M., Smith, C. B., Sharma, S., Ward, N. D., ... & Crump, B. C. (2015). Metagenomic and metatranscriptomic inventories of the lower Amazon River, May 2011. Microbiome, 3, UNSP 39. doi:10.1186/s40168-015-0099-0
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  • description.provenance : Approved for entry into archive by Patricia Black(patricia.black@oregonstate.edu) on 2015-11-18T16:48:16Z (GMT) No. of bitstreams: 2 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) Crump ByronCEOASMetagenomicMetatranscriptomicInventories.pdf: 1089965 bytes, checksum: 498c4e0e2861594e32a9d2e0249785a1 (MD5)
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