Microbial composition at phylum level and at genus level along the Shangqiu Section of the Old Course of the Yellow River

Public Description: This project focuses on characterizing microbial communities in Shangqiu Section of the Old Course of the Yellow River, a region with ecological and practical significance in agricultural irrigation, tourism, and flood prevention. Despite its importance, microbial community composition in this specific stretch remains underexplored. The study targets microbial sequencing analysis of soil, sediment, and water samples collected from 6 sites: A: Fanzhuang Village, B: Xinwen Village, C:Linqi Reservoir, D:Forest Park, E: Tianmu Lake, F: Liuyang Village. Sampling protocols included triplicate collections of 1 water sample, 1 sediment sample, and 3 soil samples per site. For soil, 3 sampling points were established at 10 m , 50 m, and 100 m from the riverbank.<br>Sequencing Methods: Microbial DNA was extracted using the EZNA Soil DNA Kit and EZNA Water DNA Kit. The V3V4 hypervariable region of the 16S rRNA gene was amplified with primers 338F 5'ACTCCTACGGGAGGCAGCAG3' and 806R 5'GGACTACHVGGGTWTCTAAT3', followed by paired-end sequencing on the Illumina MiSeq platform. Raw reads were quality-filtered, merged, and clustered into Operational Taxonomic Units at 97% similarity using Uparse software. Taxonomic annotation was performed against the Silva: Release 138, RDP: Release 11.5, and Greengene: Release 135 databases via RDP Classifier: confidence threshold: 0.7.<br>Relevance: This sequencing data elucidates microbial community structures in the study area, aiding in identifying taxa involved in environmental processes such as metal cycling. It supports ecological risk assessment and enhances understanding of microbial-mediated bioremediation potential, contributing to the sustainable management of the Old Course of the Yellow River.

数据集公开说明：本项目聚焦黄河故道商丘段的微生物群落特征解析。该区域在农业灌溉、旅游及防洪领域兼具生态价值与实用意义，尽管其重要性突出，但这一特定河段的微生物群落组成尚未得到充分探索。本研究针对6个采样点采集的土壤、沉积物及水样开展微生物测序分析，采样点分别为：A：范庄村，B：新文村，C：林七水库，D：森林公园，E：天目湖，F：浏阳村。每个采样点的采样方案为：采集3份平行水样、3份平行沉积物样以及3份土样；其中土样分别设置在距河岸10米、50米及100米处的采样点位。
测序方法：采用EZNA土壤DNA提取试剂盒（EZNA Soil DNA Kit）与EZNA水体DNA提取试剂盒（EZNA Water DNA Kit）提取微生物总DNA。以引物338F（5'-ACTCCTACGGGAGGCAGCAG-3'）与806R（5'-GGACTACHVGGGTWTCTAAT-3'）扩增16S rRNA基因的V3-V4高变区，随后在Illumina MiSeq测序平台上进行双端测序。对原始下机读数进行质量过滤与序列拼接后，使用Uparse软件按照97%的相似性阈值聚类为操作分类单元（Operational Taxonomic Units，OTU）。采用RDP分类器（RDP Classifier），以0.7的置信度阈值，分别对照Silva数据库Release 138、RDP数据库Release 11.5及Greengene数据库Release 135完成物种分类注释。
研究意义：本测序数据阐明了研究区域内的微生物群落结构，有助于识别参与金属循环等环境过程的微生物类群；可为生态风险评估提供科学支撑，加深对微生物介导的生物修复潜力的认知，进而为黄河故道的可持续管理提供理论依据。