Salt Marsh Sediment PIE-LTER Massachusetts Raw sequence reads

Subtidal sediment was sampled along two salt marsh creeks, from freshwater head to saline outlet, at Plum Island Ecosystems Long Term Ecological Research site (PIE-LTER) north of Boston. Greenwood Creek has had the Ipswich, MA sewage outfall at its head for more than 60 years. Egypt Creek also has a freshwater head but no sewage input. Sediment sampling was conducted in triplicate at each of 6 locations along each creek, along the salinity gradient. Extracted DNA was used for shotgun metagenomic and amplicon sequencing of microbial communities, to assess effects of (1) the salinity gradient along both creeks, and (2) the long-term exposure to sewage inputs to Greenwood Creek. Shotgun metagenomic sequencing was conducted on samples from only 5 sites along each creek; the most saline site was excluded for both creeks given limitations on numbers of samples per Illumina HiSeq lane. Bacterial v4v5 amplicon sequencing was conducted on all 36 samples (Illumina MiSeq). Research was conducted as part of the NSF IGERT training program "Reverse Ecology: Computational Integration of Genomes, Organisms, and Environments," PI David Rand at Brown University (Providence, RI) and the Marine Biological Laboratory (Woods Hole, MA).

本数据集的沉积物样本采集于波士顿以北的普拉姆岛生态系统长期生态学研究站点（Plum Island Ecosystems Long Term Ecological Research site, PIE-LTER），沿两条盐沼潮沟从淡水源头至咸水出口处开展潮下带沉积物采样。格林伍德潮沟（Greenwood Creek）的源头六十余年来始终接纳马萨诸塞州伊普斯维奇的污水排放；埃及潮沟（Egypt Creek）同样拥有淡水源头，但未接收任何污水输入。沿每条潮沟的盐度梯度设置6个采样点位，每个点位采集三份平行沉积物样本。提取的沉积物DNA被用于微生物群落的鸟枪宏基因组（shotgun metagenomic）与扩增子（amplicon）测序，以评估两项效应：一是两条潮沟沿线的盐度梯度对微生物群落的影响，二是格林伍德潮沟长期暴露于污水输入所产生的生态效应。受限于Illumina HiSeq测序泳道的样本承载量，两条潮沟的最高盐度点位均被排除，因此每条潮沟仅选取5个点位的样本进行鸟枪宏基因组测序。所有36份样本均通过Illumina MiSeq平台完成了细菌v4-v5区扩增子测序。本研究作为美国国家科学基金会研究生教育跨学科培训计划（NSF IGERT）“反向生态学：基因组、生物与环境的计算整合”项目的一部分开展，项目负责人为布朗大学（罗德岛州普罗维登斯）与海洋生物实验室（马萨诸塞州伍兹霍尔）的戴维·兰德（David Rand）教授。