Amaia Iribar

Using metabarcoding to reveal and quantify plant-pollinator interactions

Given the ongoing decline of both pollinators and plants, it is crucial to implement effective methods to describe complex pollination networks across time and space in a comprehensive and high-throughput way. Here we tested if metabarcoding may circumvent the limits of conventional methodologies in detecting and quantifying plant-pollinator interactions. Metabarcoding experiments on pollen DNA mixtures described a positive relationship between the amounts of DNA from focal species and the number of trnL and ITS1 sequences yielded. The study of pollen loads of insects captured in plant communities revealed that as compared to the observation of visits, metabarcoding revealed 2.5 times more plant species involved in plant-pollinator interactions. We further observed a tight positive relationship between the pollen-carrying capacities of insect taxa and the number of trnL and ITS1 sequences. The number of visits received per plant species also positively correlated to the number of their ITS1 and trnL sequences in insect pollen loads. By revealing interactions hard to observe otherwise, metabarcoding significantly enlarges the spatiotemporal observation window of pollination interactions. By providing new qualitative and quantitative information, metabarcoding holds great promise for investigating diverse facets of interactions and will provide a new perception of pollination networks as a whole.

Shotgun assembly of the complete mitochondrial genome of the neotropical cracker butterfly Hamadryas epinome.

Abstract The complete mitochondrial genome of the cracker butterfly Hamadryas epinome (C. Felder and R. Felder, 1867) (Lepidoptera: Nymphalidae: Biblidinae) has been sequenced using a genome-skimming approach on an Illumina Hiseq 2000 platform. The mitochondrial genome of H. epinome was determined to be 15,207 bp long and presents an organization similar to other Ditrysia mitogenomes. A non-coding poly-AT region of uncertain length is present at position 6180.

Abundance, activity and structure of denitrifier communities in phototrophic river biofilms (River Garonne, France)

Phototrophic river biofilms are microbial assemblages involved in in-stream processes. For a better understanding of N-cycling, the denitrifier community abundance, activity and structure were monitored in natural biofilm assemblages, in two sites exhibiting contrasting nutrient concentrations during a 1-year period. The denitrifier abundance, estimated by quantification of the nirS, nirK and nosZ genes, correlated to biofilm biomass and total bacterial counts. Site-related differences in denitrification activity were observed and the rates were significantly correlated with the nosZ gene copy numbers and biofilm biomass. The denitrifier community structure, assessed by PCR-DGGE of nosZ, differed between sites with only minor differences between sampling occasions, and correlated with the total bacterial community structure. Altogether, these findings suggest that nutrient loading, especially nitrogen, affect both denitrifier community structure and activity.

Stronger seasonal adjustment in leaf turgor loss point in lianas than trees in an Amazonian forest

Pan-tropically, liana density increases with decreasing rainfall and increasing seasonality. This pattern has led to the hypothesis that lianas display a growth advantage over trees under dry conditions. However, the physiological mechanisms underpinning this hypothesis remain elusive. A key trait influencing leaf and plant drought tolerance is the leaf water potential at turgor loss point (πtlp). πtlp adjusts under drier conditions and this contributes to improved leaf drought tolerance. For co-occurring Amazonian tree (n = 247) and liana (n = 57) individuals measured during the dry and the wet seasons, lianas showed a stronger osmotic adjustment than trees. Liana leaves were less drought-tolerant than trees in the wet season, but reached similar drought tolerances during the dry season. Stronger osmotic adjustment in lianas would contribute to turgor maintenance, a critical prerequisite for carbon uptake and growth, and to the success of lianas relative to trees in growth under drier conditions.

Cracking the Code: Examination of Species Delimitations among Hamadryas Butterflies with DNA Barcodes Suggests Caribbean Cracker is Hamadryas februa Hübner (Nymphalidae: Biblidinae)

ABSTRACT. Hamadryas februa Hübner and close relatives H. amphichloe Boisduval, H. glauconome Bates and H. julitta Fruhstorfer are a homogeneous group of taxa loosely defined as different species mainly by a combination of wing color characters. Here we explored the utility of the mtDNA COI barcode region in delimiting these taxa and examined its overall performance to identify species of Hamadryas. We compiled all the barcode sequences available for 16 of the 20 species in the genus, and added new sequences from 34 samples for 8 species from Peru and Ecuador. The complete data set includes 260 individuals. After filtering out identical sequences, a parsimony analysis of 142 individuals with unique haplotypes found that almost all the samples grouped according to their traditional species identification. The exceptions were samples of H. amphichloe diasia Fruhstorfer from the Dominican Republic and H. amphichloe ferox Staudinger from Colombia, which grouped with samples of H. februa. The barcodes of widespread species or polytypic species such as H. laodamia Cramer, H. arinome Lucas and H. februa grouped according to the geographic limits of their subspecies, but this was not the case for H. amphichloe, H. feronia Linnaeus, H. amphinome Linnaeus and H. guatemalena Bates. Our results suggest that of the three subspecies of H. amphichloe included here, only H. amphichloe amphichloe Boisduval, originally described from Ecuador, should be considered a distinct species, and that H. amphichloe diasia and H. amphichloe ferox do not belong to that lineage, but instead are part of H. februa. Furthermore we found extensive intraspecific sequence variation that overlapped with interspecific genetic distances of closely related species. We offer some general comments on species delimitation by tree-based and distance-based approaches. In conclusion, our dataset shows that the majority of the species Hamadryas included here can be distinguished by their barcode sequence (11 of 16 or about half of the species in the genus). However, the geographical coverage of our dataset is somewhat limited. Broader sampling of widespread species and the comprehensive inclusion of samples from closely related species will determine the utility of the barcode with more confidence.

Soil community assembly varies across body sizes in a tropical forest

The relative influence of deterministic niche-based (i.e. abiotic conditions, biotic interactions) and stochastic-distance dependent neutral processes (i.e. demography, dispersal) in shaping communities has been extensively studied for various organisms, but is far less explored jointly across the tree of life, in particular in soil environments. Here, using a thorough DNA-based census of the whole soil biota in a large tropical forest plot, we show that soil aluminium, topography, and plant species identity are all important drivers of soil richness and community composition. Body size emerges as an important feature of the comparative ecology of the different taxa at the studied spatial scale, with microorganisms being more importantly controlled by environmental factors, while soil mesofauna rather display random spatial distribution. We infer that niche-based processes contribute differently to community assembly across trophic levels due to spatial scaling. Body size could hence help better quantifying important properties of multitrophic assemblages.

Unlocking biodiversity and conservation studies in high‐diversity environments using environmental DNA (eDNA): A test with Guianese freshwater fishes

Determining the species compositions of local assemblages is a prerequisite to understanding how anthropogenic disturbances affect biodiversity. However, biodiversity measurements often remain incomplete due to the limited efficiency of sampling methods. This is particularly true in freshwater tropical environments that host rich fish assemblages, for which assessments are uncertain and often rely on destructive methods. Developing an efficient and nondestructive method to assess biodiversity in tropical freshwaters is highly important. In this study, we tested the efficiency of environmental DNA (eDNA) metabarcoding to assess the fish diversity of 39 Guianese sites. We compared the diversity and composition of assemblages obtained using traditional and metabarcoding methods. More than 7,000 individual fish belonging to 203 Guianese fish species were collected by traditional sampling methods, and ~17 million reads were produced by metabarcoding, among which ~8 million reads were assigned to 148 fish taxonomic units, including 132 fish species. The two methods detected a similar number of species at each site, but the species identities partially matched. The assemblage compositions from the different drainage basins were better discriminated using metabarcoding, revealing that while traditional methods provide a more complete but spatially limited inventory of fish assemblages, metabarcoding provides a more partial but spatially extensive inventory. eDNA metabarcoding can therefore be used for rapid and large-scale biodiversity assessments, while at a local scale, the two approaches are complementary and enable an understanding of realistic fish biodiversity.