Metagenomes and Metagenome-Assembled Genomes from Tidal Lagoons at a New York City Waterfront Park

We report the sequencing and analysis of 15 shotgun metagenomes from tidal lagoons and bay water at Bush Terminal Pier Park in Brooklyn, NY from July to September 2024. This waterfront park, developed on a former brownfield, is subject to storm- and sea level rise-related flooding, is a social and environmental amenity for area residents, and, in combination with efforts to rezone nearby industrial areas for mixed-use development, is impacted by the contested forces of gentrification. In addition to sports fields, there are a series of short nature trails through a small, wooded area, and walking paths near our focal lagoons. These lagoons have been used for community events (e.g., a community boating event in summer 2024) and we frequently encountered members of the public using these spaces. Notably, this park is an active site of ecological research and restoration. The Billion Oyster Project, a community organization building artificial oyster reefs across the New York Harbor, has an active community-maintained oyster reef in the innermost of our focal lagoons and preliminary plans to build another nearby. Details: "bin_coverage_coverm.tsv": CoverM output for each bin across metagenomic samples "cog_counts.rda": Counts of individual COGs per MAG annotated by eggnogmapper "high_quality_bins.txt": List of high-quality bins "hq.taxonomy.gtdbtk.bac120.summary.tsv": Taxonomy of high quality bins from gtdbtk "hq_bins.tar.gz": Fasta sequences of high-quality bins "microreef_gRodon_out.rda": gRodon predictions for bins "microreef_gRodon_scaffolds.rda": gRodon predictions for metagenomes "quality_report.tsv": CheckM2 wuality report "sylph_profiles.tar.gz": Sylph profiles for each metagenome "S1_table_mag_info.csv": Summary information for each bin "sylph_analysis.R": Code to analyze sylph output "gRodon_analysis.R": Code to analyze gRodon output "checkv_hq_viral.fa": Fasta of high-quality viral MAGs "checkv_hq_viral.tsv": CheckV output for high-quality viral MAGs "checkv_hq_virsorter2.tsv": VirSorter2 output for high-quality viral MAGs "bush_terminal_proximal_stations_NYC_Harbor_Water_Quality_20250728.csv" metadata from nearby NYC water quality monitoring stations during the study period本研究报道了2024年7月至9月期间，采集自纽约州布鲁克林布什码头码头公园（Bush Terminal Pier Park）潮汐潟湖与海湾水体的15条鸟枪宏基因组（shotgun metagenome）的测序与分析结果。该滨水公园建于昔日棕地（brownfield）之上，易受风暴与海平面上升引发的洪涝灾害影响，是周边居民的社会与环境公共设施；同时其附近工业区正被重新规划为混合用途开发区，因此也受到了存在争议的绅士化（gentrification）力量的影响。园区内除运动场外，还设有串联小片林区的多条短途自然步道，以及紧邻研究聚焦潟湖的人行路径。这些潟湖曾承办各类社区活动（例如2024年夏季的社区划船活动），研究团队在此期间也常偶遇使用该区域的公众。值得注意的是，该园区同时是生态研究与修复工程的活跃开展地。"十亿牡蛎计划"（Billion Oyster Project）是一家在纽约港全域搭建人工牡蛎礁的社区组织，其已在本次研究聚焦的最内侧潟湖设立了由社区维护的活性牡蛎礁，并计划在附近搭建第二座此类礁体。 本次研究附带的数据文件详情如下： "bin_coverage_coverm.tsv": 各宏基因组样本中各分箱（bin）的CoverM输出结果 "cog_counts.rda": 经eggnogmapper注释的宏基因组组装基因组（metagenome-assembled genome, MAG）的单个直系同源簇（Cluster of Orthologous Groups, COG）计数 "high_quality_bins.txt": 高质量分箱列表 "hq.taxonomy.gtdbtk.bac120.summary.tsv": 基于GTDB-Tk的bac120数据库的高质量分箱分类学注释结果汇总表 "hq_bins.tar.gz": 高质量分箱的FASTA序列文件 "microreef_gRodon_out.rda": 针对宏基因组组装基因组的gRodon预测结果文件 "microreef_gRodon_scaffolds.rda": 针对宏基因组测序片段的gRodon预测结果文件 "quality_report.tsv": CheckM2质量评估报告 "sylph_profiles.tar.gz": 各宏基因组样本的Sylph分析特征文件 "S1_table_mag_info.csv": 各宏基因组组装基因组的汇总信息表 "sylph_analysis.R": Sylph输出结果的分析代码脚本 "gRodon_analysis.R": gRodon输出结果的分析代码脚本 "checkv_hq_viral.fa": 高质量病毒宏基因组组装基因组的FASTA序列文件 "checkv_hq_viral.tsv": 高质量病毒宏基因组组装基因组的CheckV注释结果文件 "checkv_hq_virsorter2.tsv": 高质量病毒宏基因组组装基因组的VirSorter2注释结果文件 "bush_terminal_proximal_stations_NYC_Harbor_Water_Quality_20250728.csv": 研究周期内纽约港附近水质监测站的元数据文件