Update on the changing NEON microbial data

There have been many changes in NEON's microbial data products, as were detailed in an earlier Data Notification. This is an update on the status of NEON microbe data.

For the metagenomics data products (soil: DP1.10107.001, benthic: DP1.20279.001, and surface water: DP1.20281.001), starting with the 2022 collections, metagenomic DNA sequencing has now moved to the much larger capacity Illumina NovaSeq sequencing platform. The first of the 2022 samples will be released as Provisional data during Summer 2024 (rather than March 2024 as originally estimated). For the 2023 and 2024 collections, the Joint Genome Institute (JGI) will run the sequencing and the National Microbiome Data Collaborative (NMDC) will coordinate the data analysis. Processing of the first of the 2023 samples has begun and will begin to be available by the end of Summer 2024 (rather than May 2024 as originally estimated). These data will be available on the NEON Data Portal, the NMDC Data Portal, and the JGI Integrated Microbial Genomes & Microbiomes (IMG) websites.

The marker gene data products (soil: DP1.10108.001, benthic: DP1.20280.001, surface water: DP1.20282.001) have also gone through major changes, as detailed previously. Amplicon sequencing of the 2020 and 2021 samples has now been completed (both ITS and 16S) and is available (as Provisional data) on the NEON Data Portal. Sequencing of the 2022 samples is underway and will be released as Provisional Data as they become available. Sequencing of the 2023 samples is on track to begin in July and should be completed by Fall 2024.

The microbe community composition data products (soil: DP1.10081.001, benthic: DP1.20086.001, and surface water: DP1.20141.001), are undergoing major modifications, primarily to the data analysis pipeline. The new pipeline is still being finalized and then all NEON samples collected from 2014 through 2023 are planned to be processed through the new pipeline by the end of 2024, and available as part of the 2025 Data Release.