Microeukaryote metabolism across the western North Atlantic Ocean revealed through autonomous underwater profiling

Abstract

Protists (microeukaryotes) are key contributors to marine carbon cycling, influencing the transfer of energy to higher trophic levels and the vertical movement of carbon to the ocean interior. Their physiology, ecology, and interactions with the chemical environment are still poorly understood in offshore ecosystems, and especially in the deep ocean. Using the Autonomous Underwater Vehicle (AUV)Clio, the microbial community along a 1,050 km transect in the western North Atlantic Ocean was surveyed at 10-200 m vertical depth increments to capture metabolic microeukaryote signatures spanning a gradient of oligotrophic, continental margin, and productive coastal ecosystems. Plankton biomass was collected along the surface of this transect and across depth features, and taxonomy and metabolic function were examined using a paired metatranscriptomic and metaproteomic approach. A shift in the microeukaryote community composition was observed from the euphotic zone through the mesopelagic and into the bathypelagic ocean. A diverse surface assemblage consisting of haptophytes, stramenopiles, dinoflagellates and ciliates was represented in both the transcript and protein fractions, with foraminifera, radiolaria, picozoa, and discoba proteins enriched at >200 m depth, and fungal proteins emerging in waters >3,000 m depth. In the broad microeukaryote community, nitrogen stress biomarkers were found in productive coastal sites, with phosphorus stress biomarkers in offshore waters where Saharan dust input is thought to supply iron and nitrogen. This multi-omics dataset broadens our understanding of how microeukaryotic taxa and their functional processes are structured along environmental gradients of temperature, light, macronutrients, and trace metals.

Results from a Multi-Laboratory Ocean Metaproteomic Intercomparison: Effects of LC-MS Acquisition and Data Analysis Procedures

“…Samples for the informatic component were collected by the autonomous underwater vehicle Clio. The vehicle and its sampling characteristics were used as previously described (Breier et al, 2020;Cohen et al, 2023). Specifically, samples Ocean-8 and Ocean-11 were also collected from the BATS station on R/V Atlantic Explorer expedition identifier AE1913 (also described as BATS validation track BV55 32.75834 o N 65.7374 o W).…”

Rhizaria in the oligotrophic ocean exhibit clear temporal and vertical variability

“…𝑚 −2 respectively. All UVP data processing was done using the EcotaxaTools package in R (Barth 2023).…”

“…DNA metabarcoding studies have revealed insights into the distributional patterns (Biard et al, 2017; Blanco-Bercial et al, 2022; Decelle et al, 2013; Llopis Monferrer et al, 2022; Mars Brisbin et al, 2020; Sogawa et al, 2022), ecological relationships (Decelle et al, 2012; Nakamura et al, 2023), and contribution to biogeochemical fluxes (Guidi et al, 2016; Gutierrez-Rodriguez et al, 2019). Transcriptomic and proteomic approaches also have been used to quantify Rhizaria contribution to community metabolism (Cohen et al, 2023). Yet, despite the excellent taxonomic resolution provided by molecular approaches, they do not provide a truly quantitative metric for estimating Rhizaria abundance or biomass.…”