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Abstract. Eastern boundary upwelling systems (EBUS) contribute a disproportionatefraction of the global fish catch relative to their size and are especiallysusceptible to global environmental change. Here we present the evolution ofcommunities over 50 d in an in situ mesocosm 6 km offshore of Callao, Peru, andin the nearby unenclosed coastal Pacific Ocean. The communities weremonitored using multi-marker environmental DNA (eDNA) metabarcoding and flowcytometry. DNA extracted from weekly water samples were subjected toamplicon sequencing for four genetic loci: (1) the V1–V2 region of the 16SrRNA gene for photosynthetic eukaryotes (via their chloroplasts) andbacteria; (2) the V9 region of the 18S rRNA gene for exploration ofeukaryotes but targeting phytoplankton; (3) cytochrome oxidase I (COI) forexploration of eukaryotic taxa but targeting invertebrates; and (4) the 12SrRNA gene, targeting vertebrates. The multi-marker approach showed adivergence of communities (from microbes to fish) between the mesocosm andthe unenclosed ocean. Together with the environmental information, thegenetic data furthered our mechanistic understanding of the processes thatare shaping EBUS communities in a changing ocean. The unenclosed oceanexperienced significant variability over the course of the 50 d experiment,with temporal shifts in community composition, but remained dominated byorganisms that are characteristic of high-nutrient upwelling conditions(e.g., diatoms, copepods, anchovies). A large directional change was found inthe mesocosm community. The mesocosm community that developed wascharacteristic of upwelling regions when upwelling relaxes and watersstratify (e.g., dinoflagellates, nanoflagellates). The selection ofdinoflagellates under the salinity-driven experimentally stratifiedconditions in the mesocosm, as well as the warm conditions brought about bythe coastal El Niño, may be an indication of how EBUS will respond underthe global environmental changes (i.e., increases in surface temperature andfreshwater input, leading to increased stratification) forecast by the IPCC. 

Biodiversity is changing at an accelerating rate at both local and regional scales. Beta diversity, which quantifies species turnover between these two scales, is emerging as a key driver of ecosystem function that can inform spatial conservation. Yet measuring biodiversity remains a major challenge, especially in aquatic ecosystems. Decoding environmental DNA (eDNA) left behind by organisms offers the possibility of detecting species sans direct observation, a Rosetta Stone for biodiversity. While eDNA has proven useful to illuminate diversity in aquatic ecosystems, its utility for measuring beta diversity over spatial scales small enough to be relevant to conservation purposes is poorly known. Here we tested how eDNA performs relative to underwater visual census (UVC) to evaluate beta diversity of marine communities. We paired UVC with 12S eDNA metabarcoding and used a spatially structured hierarchical sampling design to assess key spatial metrics of fish communities on temperate rocky reefs in southern California. eDNA provided a more-detailed picture of the main sources of spatial variation in both taxonomic richness and community turnover, which primarily arose due to strong species filtering within and among rocky reefs. As expected, eDNA detected more taxa at the regional scale (69 vs. 38) which accumulated quickly with space and plateaued at only ~ 11 samples. Conversely, the discovery rate of new taxa was slower with no sign of saturation for UVC. Based on historical records in the region (2000–2018) we found that 6.9 times more UVC samples would be required to detect 50 taxa compared to eDNA. Our results show that eDNA metabarcoding can outperform diver counts to capture the spatial patterns in biodiversity at fine scales with less field effort and more power than traditional methods, supporting the notion that eDNA is a critical scientific tool for detecting biodiversity changes in aquatic ecosystems.

 

Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities.

 

ABSTRACT Auxotrophy, or an organism's requirement for an exogenous source of an organic molecule, is widespread throughout species and ecosystems. Auxotrophy can result in obligate interactions between organisms, influencing ecosystem structure and community composition. We explore how auxotrophy-induced interactions between aquatic microorganisms affect microbial community structure and stability. While some studies have documented auxotrophy in aquatic microorganisms, these studies are not widespread, and we therefore do not know the full extent of auxotrophic interactions in aquatic environments. Current theoretical and experimental work suggests that auxotrophy links microbial community members through a complex web of metabolic dependencies. We discuss the proposed ways in which auxotrophy may enhance or undermine the stability of aquatic microbial communities, highlighting areas where our limited understanding of these interactions prevents us from being able to predict the ecological implications of auxotrophy. Finally, we examine an example of auxotrophy in harmful algal blooms to place this often theoretical discussion in a field context where auxotrophy may have implications for the development and robustness of algal bloom communities. We seek to draw attention to the relationship between auxotrophy and community stability in an effort to encourage further field and theoretical work that explores the underlying principles of microbial interactions.