Michelle J. Jungbluth | Geology Reports

USGS2024

The MIEM guidelines: Minimum information for reporting of environmental metabarcoding data

Environmental DNA ( eDNA ) and RNA ( eRNA ) metabarcoding has become a popular tool for assessing biodiversity from environmental samples, but inconsistent documentation of methods, data and metadata makes results difficult to reproduce and synthesise. A working group of scientists have collaborated to produce a set of minimum reporting guidelines for the constituent steps of metabarcoding workflows, from the physical layout of laboratories through to data archiving. We emphasise how reporting the suite of data and metadata should adhere to findable, accessible, interoperable and reproducible ( FAIR ) data standards, thereby providing context for evaluating and understanding study results. An overview of the documentation considerations for each workflow step is presented and then summarised in a checklist that can accompany a published study or report. Ensuring workflows are transparent and documented is critical to reproducible research and should allow for more efficient uptake of metabarcoding data into management decision-making.

Metabarcoding and Metagenomics↗

USGS2020

Production of the copepod Pseudodiaptomus forbesi is not enhanced by ingestion of the diatom Aulacoseira granulata during a bloom

In 2016, a massive bloom of the chain-forming diatom Aulacoseira granulata occurred in the upper San Francisco Estuary, California, with chlorophyll concentrations up to 75 μg Chl L −1 . In this study, quantitative PCR was used to investigate consumption of the bloom organism by the numerically dominant zooplankter Pseudodiaptomus forbesi (Copepoda: Calanoida) and to estimate the contribution of the bloom to egg production. Copepods were collected on four transects during May and June 2016; egg production rates were somewhat elevated above previous rates measured in the estuary. Ingestion of A. granulata was highest on the first sampling day, just after the peak of the bloom, ranging from 175 to 945 cells copepod −1 day −1 . One month later ingestion rates dropped to 0–130 cells copepod −1 day −1 , despite continued dominance of A. granulata in the plankton. Ingestion of A. granulata provided from 0 to 21% (median 1%) of the estimated daily carbon required for growth and reproduction of P. forbesi . Although the copepods probably obtained nutrition from a microbial food web stimulated by the bloom, monitoring data showed little demographic response to this bloom. Thus, a massive diatom bloom in an unproductive estuary provided only a minor stimulus through an abundant consumer to the pelagic food web.

California↗