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