Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units' ecological profiles

DNA metabarcoding has been introduced as a revolutionary way to identify organisms and monitor ecosystems. However, the potential of this approach for biomonitoring remains partially unfulfilled because a significant part of the sampled DNA cannot be affiliated to species due to incomplete reference libraries. Thus, biotic indices, which are based on the estimated abundances of species in a community and their ecological profiles, can be inaccurate. We propose to compute biotic indices using phylogenetic imputation of operational taxonomic units (OTUs') ecological profiles (OTU-PITI approach). First, OTUs sequences are inserted within a reference phylogeny. Second, OTUs' ecological profiles are estimated on the basis of their phylogenetic relationships with reference species whose ecology is known. Based on these ecological profiles, biotic indices can be computed using all available OTUs. Using freshwater diatoms as a case study, we show that short DNA barcodes can be placed accurately within a phylogeny and their ecological preferences estimated with a satisfactory level of precision. In the light of these results, we tested the approach with a data set of 139 environmental samples of benthic river diatoms for which the same biotic index (specific sensitivity index) was calculated using (a) traditional microscopy, (b) OTUs with taxonomic assignment approach, (c) OTUs with phylogenetic estimation of ecological profiles (OTU-PITI) and (d) OTU with taxonomic assignment completed by the phylogenetic approach (OTU-PITI) for unclassified OTUs. Using traditional microscopy as a reference, we found that the combination of the OTUs' taxonomic assignment completed by the phylogenetic method performed satisfactorily and substantially better than the other methods tested

Flight distance of mosquitoes (Culicidae): A metadata analysis to support the management of barrier zones around rewetted and newly constructed wetlands

Society responds to changes in climate and land use via mitigation measures, including rainwater retention and storage in rewetted and newly constructed wetlands. Humans living close to these wetlands express concerns about future mosquito nuisance situations, and request the necessary distance between human occupation and wetlands to avoid such problems. Wetland managers need to know the distance required, as well as the type of management needed for such buffer or barrier zones. Here we performed an extensive literature survey to collect quantitative information on mosquito flight distance and the relevant environmental conditions. Mosquitoes have an average maximum flight distance of between 50 m and 50 km, depending on the species. Long-distance or migratory flights are strongly related to species ecological preferences and physiology, are survived by few specimens, and do not relate to nuisance situations. Nuisance-related or non-oriented flights are also species-specific and cover much shorter distances-between 25 m and 6 km for the 23 species analyzed. Based on these results, we made regression-based estimations of the percentages of the population that cross certain distances. A 90% reduction in breeding site population density would require minimal distances of 56 m for Anopheles saperoi and 8.6 km for Anopheles sinensis, and much greater distances for Aedes vexans, Culex quinquefasciatus, and Culiseta morsitans. Little useful information was available regarding the environmental conditions under which non-oriented flights took place. Qualitatively, the review showed that flight capacity was influenced by landscape structure, meteorological conditions (temperature, humidity, and illumination), and species physiology (energy available for flight). Overall, our findings suggest that predictions regarding the construction of barrier zones around breeding sites can be made based on mosquito and host density and human nuisance perception, and that barrier zone usefulness strongly depends on the mosquito species involved. Additional quantitative research is needed to better document the non-oriented dispersal patterns of the mosquitoes that populate rewetted and newly constructed wetlands, and the effects of vegetation types in barrier zones on mosquito densities. (C) 2013 Elsevier GmbH. All rights reserved

Stekende insecten Griendtsveen : situatie 2015

Naar aanleiding van het advies van de Tijdelijke Adviescommissie LIFE+ Mariapeel om een onderzoek naar de muggenoverlast te verrichten is door de gemeente Horst aan de Maas gezamenlijk met de provincie Limburg een onderzoeksopdracht aan Alterra – Wageningen UR verstrekt. Alterra is gevraagd om de muggenoverlast te monitoren en daarmee de nulsituatie vast te stellen, de mate van overlast aan te geven en te adviseren over de effecten van voorgenomen maatregelen op de overlast

Zandsuppletie in de Leuvenumse beek: monitoring van de fysische en biologische effecten 2014-2015

In 2014-2105 zijn de fysische en biologische korte-termijn-effecten van het herhaaldelijk suppleren van zand op een drietal locaties in de Leuvenumse beek onderzocht. Er is gekeken naar de mate van ophoging en verspoeling van het ingebrachte zand, de interactie tussen het zand en houtpakketten, de consequenties van depositie van organisch materiaal als gevolg van verstuwing van de beek en tenslotte naar de effecten op de macrofauna

Resultaten monitoring stekende insecten nabij het Wisselse Veen en Landgoed Tongeren

De belangrijkste vragen van Het Geldersch Landschap en Landgoed Tongeren zijn: 1. Welke stekende insecten (steekmuggen (Culicidae) en knutten (Ceratopogonidae)) veroorzaken momenteel overlast en waar komen die vandaan? 2. Zo ja, met welke aanvullende maatregelen kan deze overlast voorkomen worden? Het doel van deze notitie is: Het vaststellen van de aard (soortgroepen) en oorzaken van de overlast veroorzakende stekende insecten en klustervliegen in en rondom het gebied Wisselse Veen en Landgoed Tongeren

The significance of refuge heterogeneity for lowland stream caddisfly larvae to escape from drift

The process of macroinvertebrate drift in freshwater lowland streams is characterized by dislodgement, drift distance and subsequent return to the bottom. Refuges are important to all drift phases, since they may help larvae to avoid dislodgement and to escape from drift, even more so if the refuge structure is complex and heterogeneous. The aim of the present study was therefore to determine the influence of refuge heterogeneity on the ability of caddisfly larvae to return to the bottom from drift and to avoid secondary dislodgement. To this purpose a series of indoor flume experiments were undertaken, testing six Limnephilidae (Trichoptera) species, that occur on a gradient from lotic to lentic environments. Bed morphology (plain, refuges with or without leaf patches) and flow velocity (low (0.1 m/s), intermediate (0.3 m/s) and high (0.5 m/s) were manipulated. We showed that all species were favoured by refuges and that especially for species on the lentic end of the gradient (L. lunatus, L. rhombicus and A. nervosa), the ability to escape from drift and to avoid secondary dislodgement was increased. Moreover, we showed that all species spent more time in refuges than in open channel parts and more time in heterogeneous refuges (leaf patches) than in bare refuges, the latter being especially the case for larvae of the lotic species. For lentic species, not well adapted to high flow velocity, refuges are thus crucial to escape from drift, while for the lotic species, better adapted to high flow velocity, the structure of the refuge becomes increasingly important. It is concluded that refuges may play a crucial role in restoring and maintaining biodiversity in widened, channelized and flashy lowland streams.</p