Environmental DNA (eDNA) metabarcoding has lagged in parasite biodiversity assessments. We implemented this method to examine parasite diversity in sediment and water from 4 physically connected aquatic habitats in coastal South Carolina, USA, as part of a ParasiteBlitz in April 2023. Sediment was collected using a syringe corer, and water was sampled using active filtration and passive collection. Five amplicon libraries, using primers targeting portions of the mitochondrial COI of platyhelminths and 18S ribosomal RNA genes of nematodes, myxozoans, microsporidians, and protists, successfully yielded parasite sequences. Out of >5.8 million sequences, we identified >1,000 parasite amplicon sequence variants (ASVs) corresponding to ~600 parasite operational taxonomic units, from 6 parasite groups. Most diversity was observed among the microsporidians, whose assay demonstrated the highest fidelity. Actively-filtered water samples captured ASVs of all 6 groups, whereas sediment captured only 4, despite yielding 3× as many ASVs. Low DNA yields from passive water samples resulted in fewer, but some unique, ASVs representing 3 parasite groups. The most efficient sampling method varied with respect to parasite group across habitats, and the parasite communities from each habitat were distinct regardless of sampling method. We detected ASVs of 9 named species, 4 of which may represent introductions to the US. The abundance of our results demonstrates the effectiveness and efficiency of eDNA metabarcoding for assessing parasite diversity during short, intensive surveys, and highlights the critical need for more comprehensive sequence databases and the development of primers for those parasite taxa that elude detection using eDNA methods.
Located in
Library
/
RBINS Staff Publications 2025
Background: The identification of free-living marine nematodes is difficult because of the paucity of easily scorable diagnostic morphological characters. Consequently, molecular identification tools could solve this problem. Unfortunately, hitherto most of these tools relied on 18S rDNA and 28S rDNA sequences, which often lack sufficient resolution at the species level. In contrast, only a few mitochondrial COI data are available for free-living marine nematodes. Therefore, we investigate the amplification and sequencing success of two partitions of the COI gene, the M1-M6 barcoding region and the I3-M11 partition. Methodology: Both partitions were analysed in 41 nematode species from a wide phylogenetic range. The taxon specific primers for the I3-M11 partition outperformed the universal M1-M6 primers in terms of amplification success (87.8\% vs. 65.8\%, respectively) and produced a higher number of bidirectional COI sequences (65.8\% vs 39.0\%, respectively). A threshold value of 5\% K2P genetic divergence marked a clear DNA barcoding gap separating intra-and interspecific distances: 99.3\% of all interspecific comparisons were 〉0.05, while 99.5\% of all intraspecific comparisons were 〈0.05 K2P distance. Conclusion: The I3-M11 partition reliably identifies a wide range of marine nematodes, and our data show the need for a strict scrutiny of the obtained sequences, since contamination, nuclear pseudogenes and endosymbionts may confuse nematode species identification by COI sequences.
Located in
Library
/
No RBINS Staff publications
