Department of Microbiology, University of Georgia, Athens, GA 30602, USA.
College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
Microbiome. 2014 May 15;2:17. doi: 10.1186/2049-2618-2-17. eCollection 2014.
The Amazon River is by far the world's largest in terms of volume and area, generating a fluvial export that accounts for about a fifth of riverine input into the world's oceans. Marine microbial communities of the Western Tropical North Atlantic Ocean are strongly affected by the terrestrial materials carried by the Amazon plume, including dissolved (DOC) and particulate organic carbon (POC) and inorganic nutrients, with impacts on primary productivity and carbon sequestration.
We inventoried genes and transcripts at six stations in the Amazon River plume during June 2010. At each station, internal standard-spiked metagenomes, non-selective metatranscriptomes, and poly(A)-selective metatranscriptomes were obtained in duplicate for two discrete size fractions (0.2 to 2.0 μm and 2.0 to 156 μm) using 150 × 150 paired-end Illumina sequencing. Following quality control, the dataset contained 360 million reads of approximately 200 bp average size from Bacteria, Archaea, Eukarya, and viruses. Bacterial metagenomes and metatranscriptomes were dominated by Synechococcus, Prochlorococcus, SAR11, SAR116, and SAR86, with high contributions from SAR324 and Verrucomicrobia at some stations. Diatoms, green picophytoplankton, dinoflagellates, haptophytes, and copepods dominated the eukaryotic genes and transcripts. Gene expression ratios differed by station, size fraction, and microbial group, with transcription levels varying over three orders of magnitude across taxa and environments.
This first comprehensive inventory of microbial genes and transcripts, benchmarked with internal standards for full quantitation, is generating novel insights into biogeochemical processes of the Amazon plume and improving prediction of climate change impacts on the marine biosphere.
就体积和面积而言，亚马逊河是目前世界上最大的河流，其河流出口量约占世界海洋河流输入量的五分之一。西热带北大西洋海洋的海洋微生物群落受到亚马逊羽流携带的陆地物质的强烈影响，包括溶解（DOC）和颗粒有机碳（POC）以及无机养分，这对初级生产力和碳封存有影响。
我们在 2010 年 6 月对亚马逊河羽流的六个站点进行了基因和转录本的清查。在每个站点，我们使用 150×150 配对末端 Illumina 测序，从两个离散的大小分数（0.2 至 2.0 μm 和 2.0 至 156 μm）中获得了内部标准加标宏基因组、非选择性宏转录组和 poly(A)-选择性宏转录组的重复样本。经过质量控制，该数据集包含了大约 3.6 亿个平均大小为 200 bp 的来自细菌、古菌、真核生物和病毒的读取。细菌宏基因组和宏转录组主要由聚球藻、原绿球藻、SAR11、SAR116 和 SAR86 主导，在一些站点中，SAR324 和疣微菌门的贡献很高。硅藻、绿色微微型浮游植物、甲藻、甲藻和桡足类动物主导了真核生物基因和转录本。基因表达比率因站点、大小分数和微生物群而异，转录水平在不同分类群和环境中变化了三个数量级。
这是首次对微生物基因和转录本进行全面清查，通过内部标准进行全面定量，为亚马逊羽流的生物地球化学过程提供了新的见解，并提高了对海洋生物群落受气候变化影响的预测能力。
