A practical limitation to many metabarcoding initiatives is that sampling methods tend to collect many non-target taxa, which become “amplicon noise” that can saturate Next Generation Sequencing results and lead to both financial and resource inefficiencies. An available molecular tool that can significantly decrease these non-target amplicons and decrease the need for pre-DNA-extraction sorting of bycatch is the design of PCR primers tailored to the taxa under investigation. We assessed whether the D2 extension segment of the 28S ribosomal operon can limit this shortcoming within the context of mosquito (Culicidae) monitoring. We designed PCR primers that are fully conserved across mosquitos and exclude from amplification most other taxa likely to be collected with current sampling apparatuses. We show that, given enough sequencing depth, D2 is an effective marker for the detection of mosquito sequences within mock genomic DNA pools. As few as 3,050 quality-filtered Illumina reads were able to recover all 17 species in a bulk pool containing as little as 0.2% of constituent DNA from single taxa. We also mixed these mosquito DNA pools with high concentrations of non-Culicidae bycatch DNA and show that the component mosquito species are generally still recoverable and faithful to their original relative frequencies. Finally, we show that there is little loss of fidelity in abundance parameters when pools from degraded DNA samples were sequenced using the D2 primers.

Mansonia (Diptera: Culicidae) are known to cause discomfort to the local populations of Amazon. Considering the fact that the effective control of these mosquitoes can only be obtained by understanding their ecology and behavior, entomological monitoring becomes essential. In view of this, mosquitoes of the genus Mansonia were collected by human landing catches (HLC) from 2015 to 2019, in four locations of Porto Velho, Rondônia, Brazil. The collections were performed inside and outside the homes, once in every four months, uninterrupted for 24 hr. Human bite indices/hour was used to analyze the hourly activity of the species for different seasons and environment (indoor and outdoor). Moreover, nonparametric Mann–Whitney tests were conducted to indicate if there were differences between exophagic and endophagic behavior. The seasonality of Mansonia species was also analyzed. Overall, 96,766 specimens were collected over five years of sampling. Mansonia titillans (Walker) was found to be the most abundant species (76.9%). The highest percentage of mosquitoes was collected in February (48.4%), followed by October (39.6%) and June (12.0%). The biting activity of the two most abundant species showed peak host seeking activity/behavior during twilight and night, more perceptible in the outdoor environment (peridomiciliary). In general, seasonality showed a tendency towards a reduction in the abundance of Mansonia in the years after 2015. Our results will be essential in the formulation of effective control methodology for Mansonia in the studied area.

The rapid and economical monitoring of mosquitos is imperative to understanding the dynamics of both disease vectors and nuisance species. In light of technological advances in mosquito sampling and DNA sequencing, health agencies can now utilize the full potential of metabarcoding pipelines for rapid and standardizable surveillance. Here, we describe mosquito spatial and temporal variation, with particular focus on Mansonia Blanchard species, in the Madeira (Rondônia State) and the Ribeira (São Paulo) watersheds, Brazil using metabarcoding of the D2 rDNA marker. Sampling and molecular pipelines were used to evaluate the taxonomic contribution of mosquitos in pools of culicids collected en masse from macrophyte-roots (immatures) and from Mosquito Magnet traps and protected human landings (adults). Results for adult captures are comparable to morphological diagnoses and clarify previously unknown temporal and spatial species turnover. Metabarcoding of immature stages also confirmed the extent of the geographical distribution of some species and each taxon’s association with macrophyte species. Given the benefits of metabarcoding, such as taxonomic acuity, high throughput processing, and objectivity, we suggest such techniques should be more fully incorporated into culicid monitoring schemes. The metabarcoding protocol described herein paired with standardized field sampling schemes, when used by mosquito monitoring professionals, offers substantial improvements in terms of practicality, speed and cost.