Aquatic macroinvertebrates are widely used as indicators for water quality assessment around the world. Modern strategies for environmental assessment implement molecular analysis to delimitate species of aquatic macroinvertebrates. Delimitation methods have been established to determine boundaries between species units using sequencing data from DNA barcodes and serve as the first exploratory tools for taxonomic revisions. This is useful in regions such as the neotropics where aquatic macroinvertebrate habitats are threatened by human interference and DNA databases remain under-studied. We asked whether the biodiversity of aquatic macroinvertebrates in a stream in Nicaragua, within the Central American Dry Corridor, could be characterized with biological indices and DNA barcoding. In this study, we combined regional biological indices (BMWP-CR, IBF-SV-2010) along with distance-based (ASAP, BIN) and tree-based (GMYC, bPTP) delimitation methods, as well as nucleotide BLAST in public barcode databases. We collected samples from the upper, middle, and low reaches of the Petaquilla river. The three sites presented excellent water quality with the BMWP-CR index, but evidence of high organic pollution was found in the middle reach with the IBF-SV-2010 index. We report a total of 219 COI sequences successfully generated from 18 families and 8 orders. Operational taxonomic units (OTUs) designation ranged from 69–73 using the four methods, with a congruency of 92% for barcode assignation. Nucleotide BLAST identified 14 species (27.4% of barcodes) and 33 genera (39.3% of barcodes) from query sequences in GenBank and BOLD systems databases. This small number of identified OTUs may be explained by the paucity of molecular data from the Neotropical region. Our study provides valuable information about the characterization of macroinvertebrate families that are important biological indicators for the assessment of water quality in Nicaragua. The application of molecular approaches will allow the study of local diversity and further improve the application of molecular techniques for biomonitoring.

Collection of samples was done using a multi-habitat approach with a 500 µm mesh D-frame dip net. DNA was extracted using the DNeasy Blood & Tissue kit (Qiagen, CA, USA). Extraction was done using the 658-bp fragment of the COI region with Folmer et al. primers. Sequencing was completed using a SeqStudio genetic analyzer (SeqStudio, Thermofisher, MA, USA). 

Sanger sequencing and fragment analysis software (e.g., MEGA, FinchTV, SeqA, etc.).