DNA-based assessment of environmental degradation in an unknown fauna: the freshwater macroinvertebrates of the Indo-Burmese hotspot.
New methods are required for biomonitoring of poorly known tropical ecosystems, but biological assessments of environmental status are limited by insufficient information on taxonomy, composition and ecology of local communities. The current work applies DNA-based assessment to establish the impact of various types of anthropogenic disturbances on the freshwater macroinvertebrates in an understudied biodiversity hotspot in South Asia, an area that attracts increasing attention for the loss of aquatic ecosystems. We sampled 16 river systems in the Chittagong Hill Tracts region of Bangladesh and characterised habitat intactness based on a set of 14 environmental parameters associated with habitat quality and human activities. Whole-community metabarcoding was used to investigate the distribution of hypothetical species-level clusters (Operational Taxonomic Units, OTUs) across sites of different impacts. We found >900 DNA clusters of insects, decapods and molluscs, dominated by Diptera, which revealed significant variation (p < 0.001) in richness across sites. The presumed sensitive Ephemeroptera-Plecoptera-Trichoptera (EPT) represented 15.6% of total OTU richness. The type and strength of anthropogenic stressors varied greatly across streams but did not affect total OTU diversity. In contrast, EPT richness decreased by ~50% in response to habitat degradation. Partial-network analysis revealed 26 OTUs that may serve as potential indicators for either good or poor ecological status. Overall, our results document high diversity, local endemicity and pronounced responses to disturbance in these largely unexplored but threatened habitats. Synthesis and applications. The proposed methodology combines local habitat surveys across sites of various degrees of disturbance with species-level metabarcoding, as a model for biological evaluation of water bodies in poorly known and inaccessible places across the world. Implemented here for the Indo-Burmese hotspot, the approach will have great value for applied conservation management as a step towards building a biomonitoring system in this region where currently little is known about the taxonomy, diversity and endemicity in both intact and disturbed ecosystems.