Animals, protists and bacteria share marine biogeographic patterns

Abstract

Over millennia, ecological and evolutionary mechanisms have shaped macroecological distributions across the tree of life. Research describing patterns of regional and global biogeography has traditionally focussed on the study of conspicuous species. Consequently, there is limited understanding of cross-phyla biogeographic structuring, and an escalating need to understand the macroecology of both microscopic and macroscopic organisms. Here we used environmental DNA (eDNA) metabarcoding to explore the biodiversity of marine metazoans, micro-eukaryotes and prokaryotes along an extensive and highly heterogeneous coastline. Our results showed remarkably consistent biogeographic structure across the kingdoms of life, which were underpinned by environmental and anthropogenic influence. Additionally, metazoan communities displayed biographic patterns that suggest regional biotic homogenisation of conspicuous species. Against the backdrop of global pervasive anthropogenic environmental change, our work highlights the importance of considering multiple domains of life to understand the maintenance and drivers of marine biodiversity across broad taxonomic, ecological and geographical scales..

How does eDNA decay affect metabarcoding experiments?

“…Forward and reserve reads were visually examined to evaluate the decrease in sequence quality over the read length. Based on these observations forward reads were truncated to 250 bp and reverse reads to 180 bp, these values are typical for eDNA metabarcoding data generated from seawater (Holman et al, 2021). Sequences were retained if they had a per sequence expected error of less than 1.…”

How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs?

“…Despite decades of sampling efforts, biodiversity monitoring still covers only a small fraction of global ecosystems and is particularly challenging in isolated and remote regions across the oceans (Collen et al ., 2009; Webb, Vanden Berghe and O’Dor, 2010; Dornelas et al ., 2018; Letessier et al ., 2019). An emerging tool for rapid biodiversity assessment is environmental DNA (eDNA) metabarcoding (Stat et al ., 2017;Eble et al ., 2020), which is proving to be particularly effective for marine environments (Juhel et al ., 2020; Boulanger et al ., 2021; Holman et al ., 2021). eDNA-based methods rely on the detection of DNA fragments from various sources including faeces, shed skin cells, organelles, or extruded waste of animals, which become suspended in the water (Dejean et al ., 2012; Collins et al ., 2018; Harrison, Sunday and Rogers, 2019).…”

“…eDNA-based methods rely on the detection of DNA fragments from various sources including faeces, shed skin cells, organelles, or extruded waste of animals, which become suspended in the water (Dejean et al ., 2012; Collins et al ., 2018; Harrison, Sunday and Rogers, 2019). Using filtered water and molecular analyses, eDNA metabarcoding can estimate biodiversity across kingdoms at different taxonomic levels without isolating any target organisms (Valentini et al ., 2016; Holman et al ., 2021), and even without exhaustive genetic reference databases (Flynn et al ., 2015; Juhel et al ., 2020; Marques et al ., 2020, 2021). Overall, eDNA metabarcoding has the potential to overcome some limitations of common sampling methods by targeting complete species assemblages, detecting rare (Rees et al ., 2014), elusive (Boussarie et al ., 2018) or non-indigenous species (Ficetola et al ., 2008; Holman et al ., 2019) and is harmless to organisms and less time-consuming (Bohmann et al ., 2014; Smart et al ., 2016).…”

Metabarcoding Reveals High Diversity of Benthic Foraminifera Driven by Atlantification of Coastal Svalbard

“…However, morphological identification is timeconsuming and expertise-demanding, making it costly and unpractical, particularly for largescale surveys. Recently, the metabarcoding of environmental DNA (eDNA) samples have provided new insights into biodiversity and ecological distribution of numerous taxonomic groups and offer an alternative to the traditional morphology-based approach [28][29][30] .…”

“…Metabarcoding consists in high-throughput sequencing of short DNA barcodes that include enough information for species identification to get a comprehensive inventory of all organisms present in a given sample, e.g., foraminiferal sequences derived from the 37f hypervariable region of the 18S small subunit (SSU) rRNA gene 31,32 . To better understand large-scale patterns of biodiversity and distribution in various groups, this method is increasingly being employed, particularly in marine environments 22,29,33,34 . While numerous foraminiferal metabarcoding studies were conducted in various coastal areas [35][36][37][38] , and the deep-sea 22,[39][40][41] ; the application of eDNA metabarcoding to monitor foraminiferal diversity in the Arctic was limited to a few paleogenomic studies using foraminifera as proxies in palaeoceanographic reconstructions [42][43][44] .…”