Environmental DNA reveals seasonal shifts and potential interactions in a marine community

Anni Djurhuus,Ryan P Kelly,Frank E Muller-Karger,Mya Breitbart,Katherine Hubbard,Kathleen J Pitz,Hilary A Starks,Collin J Closek,Kristine R Walz,Reiko P Michisaki,Enrique Montes,Daniel Otis,Francisco P Chavez,Emily Olesin,Alexandria B Boehm,Elizabeth A Andruszkiewicz

doi:10.1038/s41467-019-14105-1

Abstract

Environmental DNA (eDNA) analysis allows the simultaneous examination of organisms across multiple trophic levels and domains of life, providing critical information about the complex biotic interactions related to ecosystem change. Here we used multilocus amplicon sequencing of eDNA to survey biodiversity from an eighteen-month (2015–2016) time-series of seawater samples from Monterey Bay, California. The resulting dataset encompasses 663 taxonomic groups (at Family or higher taxonomic rank) ranging from microorganisms to mammals. We inferred changes in the composition of communities, revealing putative interactions among taxa and identifying correlations between these communities and environmental properties over time. Community network analysis provided evidence of expected predator-prey relationships, trophic linkages, and seasonal shifts across all domains of life. We conclude that eDNA-based analyses can provide detailed information about marine ecosystem dynamics and identify sensitive biological indicators that can suggest ecosystem changes and inform conservation strategies.

Highlights

Environmental DNA analysis allows the simultaneous examination of organisms across multiple trophic levels and domains of life, providing critical information about the complex biotic interactions related to ecosystem change
Environmental variables were measured in situ or from seawater samples at all sampling time points. Environmental DNA (eDNA) was concentrated from seawater on membrane filters
When a taxon was detected with multiple genetic loci, we averaged these indices to create an ensemble index for that taxon

Summary

Introduction

Environmental DNA (eDNA) analysis allows the simultaneous examination of organisms across multiple trophic levels and domains of life, providing critical information about the complex biotic interactions related to ecosystem change. Examination of eDNA genetic sequences has emerged as a method to infer co-occurrence patterns of organisms within an ecosystem, across all domains of life simultaneously[5,8,9], this is not common practice yet[7] These methods have been used to provide essential information about the spatial distribution and temporal variability in single-celled organisms spanning large areas in the world’s oceans[2,4,10,11,12,13]. We analyse a time-series of eDNA metabarcoding data to assess changes in the proportional abundance of taxa in a marine setting, and to analyse linkages of organisms ranging from microorganisms to mammals This coordinated survey of entire biotic communities using high-throughput sequencing of multiple conserved genetic markers from eDNA elucidated relationships between community dynamics and environmental properties. We found that groups of co-occurring organisms spanning different trophic levels were directly correlated to changes in environmental parameters, providing insights into the underlying response of whole communities to the environment and highlighting cooccurrences and potential trophic interactions

Methods

Results

Conclusion