Malaria vector species in Amazonian Peru co-occur in larval habitats but have distinct larval microbial communities

In Amazonian Peru, the primary malaria vector, Nyssorhynchus darlingi (formerly Anopheles darlingi), is difficult to target using standard vector control methods because it mainly feeds and rests outdoors. Larval source management could be a useful supplementary intervention, but to determine its feasibility, more detailed studies on the larval ecology of Ny. darlingi are essential. We conducted a multi-level study of the larval ecology of Anophelinae mosquitoes in the peri-Iquitos region of Amazonian Peru, examining the environmental characteristics of the larval habitats of four species, comparing the larval microbiota among species and habitats, and placing Ny. darlingi larval habitats in the context of spatial heterogeneity in human malaria transmission. We collected Ny. darlingi, Nyssorhynchus rangeli (formerly Anopheles rangeli), Nyssorhynchus triannulatus s.l. (formerly Anopheles triannulatus s.l.), and Nyssorhynchus sp. nr. konderi (formerly Anopheles sp. nr. konderi) from natural and artificial water bodies throughout the rainy and dry seasons. We found that, consistent with previous studies in this region and in Brazil, the presence of Ny. darlingi was significantly associated with water bodies in landscapes with more recent deforestation and lower light intensity. Nyssorhynchus darlingi presence was also significantly associated with a lower vegetation index, other Anophelinae species, and emergent vegetation. Though they were collected in the same water bodies, the microbial communities of Ny. darlingi larvae were distinct from those of Ny. rangeli and Ny. triannulatus s.l., providing evidence either for a species-specific larval microbiome or for segregation of these species in distinct microhabitats within each water body. We demonstrated that houses with more reported malaria cases were located closer to Ny. darlingi larval habitats; thus, targeted control of these sites could help ameliorate malaria risk. The co-occurrence of Ny. darlingi larvae in water bodies with other putative malaria vectors increases the potential impact of larval source management in this region. Author summary The standard methods used to combat mosquitoes that transmit malaria, long-lasting insecticide treated nets and indoor residual spraying, target mosquitoes that bite people indoors and rest indoors after biting. In Amazonian Peru, the major malaria vector, Nyssorhynchus darlingi (formerly Anopheles darlingi), is known to bite and rest mostly outdoors and to feed on animals as well as humans. Therefore, additional methods are needed to control this species, such as targeting immature mosquitoes in water bodies using chemical or biological larvicides or environmental modification. To determine whether this is feasible, more ecological information about Ny. darlingi larval habitats in this region is needed. In this study, we found that Ny. darlingi were more likely to be collected from water bodies in more deforested areas, and in the presence of other species of mosquitoes that transmit malaria. We characterized the bacteria detected in three species of mosquito larvae, and found that the species of mosquito, and not the water body, determined which bacteria were identified. As we found that houses with more malaria cases were located closer to Ny. darlingi larval habitats, management of larval habitats may be an effective method to reduce the risk of malaria in this region.