Environmental DNA in a global biodiversity hotspot: Lessons from coral reef fish diversity across the Indonesian archipelago

Indonesia is the heart of the Coral Triangle, the world’s most diverse
marine ecosystem. Preserving the biological and economic value of this
marine biodiversity requires efficient and economical ecosystem
monitoring, yet our understanding of marine biodiversity in this region
remains limited. Towards this end, this study uses environmental DNA
(eDNA) to survey fish communities across a well-documented biodiversity
gradient in Indonesia. A total of  6,608,693 sequence reads of
MiFish 12S rRNA from 39 sites spanning 7 regions of Indonesia revealed
1,099 fish Amplified Sequence Variants (ASVs), 80.4% of which could be
identified to species through the inclusion of new reference sequences
from Mo’orea BIOCODE. Patterns of regional fish diversity inferred from
eDNA broadly conformed to expectations, with the highest fish biodiversity
in Raja Ampat and lowest in Western Indonesia. Similarly, zeta diversity
analysis showed greater community turnover in higher diversity reefs of
Eastern Indonesia, and greater community similarity in low diversity
regions of Western Indonesia. However, several results highlight
challenges for eDNA in megadiverse ecosystems. Despite a two-fold
difference in fish diversity between Eastern and Western Indonesia, mean
ASVs recovered per one-liter seawater was relatively similar across 7
regions of Indonesia. Moreover, although ASV recovery from individual
seawater samples saturated, ASV recovery did not saturate at the site or
region level, indicating that sampling/sequencing efforts employed in
lower diversity temperate marine ecosystems are insufficient for
biodiversity hotspots like the Coral Triangle. Despite these limitations,
36.3% to 84.1% (mean 57.1%) of fish species detected by eDNA at 8 sites
within Raja Ampat were not observed during intensive visual surveys. Taxa
missed include pelagic (tuna, jacks, scads, mackerels), nocturnal
(soldierfish, lanternfish), and crevice dwelling species (eels, blennies,
gobies) that are difficult to document in visual surveys. These results
demonstrate the added value of eDNA in biodiversity hotspots like the
Coral Triangle and the need for further research to understand how best to
sample eDNA in high diversity regions like the Coral Triangle to deliver
on the promise of eDNA as a tool to monitor marine biodiversity
effectively and efficiently.