loading page

Taxonomic diversity assessment across the tree of life from extracellular environmental DNA in aquatic ecosystems
  • Shivakumara Manu,
  • Govindhaswamy Umapathy
Shivakumara Manu
Centre for Cellular and Molecular Biology CSIR

Corresponding Author:smanu@ccmb.res.in

Author Profile
Govindhaswamy Umapathy
Centre for Cellular and Molecular Biology CSIR

Corresponding Author:guma@ccmb.res.in

Author Profile

Abstract

Global biodiversity is declining at an alarming pace due to anthropogenic factors. It is
imperative to monitor the health of ecosystems through biodiversity assessments. But
existing biodiversity assessment approaches are not scalable to assess the complete
diversity of all the life forms in large ecosystems. We hypothesized that the extracellular
environmental DNA (eDNA) released by natural cell lysis of biological matter in aquatic
ecosystems is a repertoire of genetic material from all the inhabiting organisms and
deep sequencing of extracellular eDNA could enable the detection of taxa across the
tree of life. We developed a lysis-free and PCR-free workflow to directly enrich and
sequence extracellular eDNA from environmental water samples and demonstrate its
utility for taxonomic diversity assessment across the tree of life in a large biodiverse
model aquatic ecosystem (Ramsar wetland: Chilika lagoon). Using incidence-based
asymptotic richness analysis, we estimated that Chilika harbors about 1071 families
across the tree of life comprising approximately 799 families of Eukaryotes, 230 families
of Bacteria, 27 families of Archaea, and 13 families of DNA Viruses. We also quantified
the compositional changes in the relative abundance of families across the tree of life
and detected a higher temporal variation (46%) across the seasons than the spatial
variation (37%) across the lagoon. With the increasing genomic resources and
decreasing sequencing costs, we envision the wide adoption of extracellular eDNA-
based taxonomic diversity assessment across the tree of life to track the future
biodiversity loss and aid the conservation, restoration, and management efforts in the
Anthropocene.