National Oceanic and
Atmospheric Administration
United States Department of Commerce

Metagenomic Fluctuations of Zooplankton and Ichthyoplankton Communities in the Salish Sea: Association with Water Chemistry

Metagenomic Fluctuations of Zooplankton and Ichthyoplankton Communities in the Salish Sea: Association with Water Chemistry

How do zooplankton and ichthyoplankton community compositions, species diversities, and their relative abundances differ with water chemistry and environmental conditions across the Salish Sea over time and space? We're answering this fundamental question by investigating taxonomic and metagenomic variance across regions, seasons, and years of contrasting water chemistry. Our project aim is to achieve a new understanding of the dynamic responses by zooplankton and ichthyoplankton communities to physical and chemical changes using state-of-the-art high-throughput metagenomic assays. Zooplankton and ichthyoplankton communities are some of the most vulnerable to ocean acidification (OA) - and other chemical and environmental perturbations, including hypoxia (H) and warming - and comprise the prey items for larger pelagic and benthic invertebrates, fishes, and marine mammals. Zooplankton and ichthyoplankton are unevenly distributed across coastal ecosystems, with their numbers, composition, and survival being highly sensitive and responsive to environmental conditions. Moreover, the organisms that make up these planktonic communities interact together, accentuating or dampening the effects of environmental stressors on each other. The novel metagenomic approach to be applied here will allow us for the first time to understand biological interactions and responses to OA and hypoxia (together, termed "OAH") at the species and community levels.

New metagenomic/bioinformatic technology will allow us to evaluate the relationships between community-level biological diversity and physical and chemical ocean parameters, in order to understand possible responses to OAH and other perturbations, such as warming and hypoxia. To evaluate key community responses, special focus will be placed on ichthyoplankton, crab larvae, copepods, and mollusks (including pteropods and bivalve veliger larvae), which laboratory studies have indicated are sensitive to OA. Many of these taxa are very difficult to distinguish and identify to species, and most can only be identified to higher taxonomic levels in their early life history stages (e.g., as eggs and larvae). Yet, different species are not interchangeable, often respond differentially to OAH and other stressors, and are present at different times and different places in the planktonic communities. In other words, these are dynamic communities upon which larger organisms depend on for food, which are critical to our ecosystem services and seafood resources.

Sampling eDNA water

Plankton net and eDNA water sampling for the new analyses is occurring during ongoing WOAC (Washington Ocean Acidification Center) cruises. Microscopic identification of the zooplankton using traditional morphological characters is conducted in Dr. Keister's lab at the University of Washington. In the G3 (Genetics and Genomics Group) Laboratory headed by Dr. Stepien at NOAA PMEL, we are applying metagenomic high-throughput assays to analyze suites of nuclear and mitochondrial gene markers. These assays aim to simultaneously identify zooplankton and ichthyoplankton communities to species levels (which is impossible using traditional morphology) and estimate their relative representation (calibrated to biomass and numbers) using internal standards and advanced custom bioinformatics.

This metagenomic technology will help advance scientific ability to rapidly assess responses of biological communities to environmental conditions. Moreover, the approach is powerful, data-rich, and inexpensive, and produces data that are readily integrated into existing modeling efforts. This methodology will pave the way towards a new understanding of America's ocean resources, elucidating their relationship to physical and biological oceanographic factors.