Abstract In this study, we used a predator-enabled metagenomics strategy to sample the virome of a remote and difficult-to-access densely forested African tropical region. Specifically, we focused our study on the use of army ants of the genus Dorylus that are obligate collective foragers and group predators that attack and overwhelm a broad array of animal prey. Using 209 army ant samples collected from 29 colonies and the virion-associated nucleic acid-based metagenomics approach, we showed that a broad diversity of bacterial, plant, invertebrate and vertebrate viral sequences were accumulated by army ants: including sequences from 157 different viral genera in 56 viral families. This suggests that using predators and scavengers such as army ants to sample broad swathes of tropical forest viromes can shed light on the composition and the structure of viral populations of these complex and inaccessible ecosystems.
The development of radial shakes after felling the tree has been observed on transverse sections of 15 poplar logs.The importance of end splitting is related to the distribution of internal stresses in the stem (growth stress), the angular variations of wood structure (specific gravity and pulp yield), and the transverse mechanical resistance of wood.To investigate growth stresses, longitudinal displacements after stress release were estimated at the periphery of the stem using the single hole method.At least 4 measurements were necessary to estimate the maximum displacement value and the circumferential heterogeneity of the stress field.The position of this maximum was generally found on the upperside of the trees.To examine end splitting, the radial and longitudinal extension of splits were roughly estimated for all visible shakes occurring on cutting sections near stress measurements (breast height).Shakes were also measured for comparison at the felling section of the logs.The dimensions of the longest shake were used as an indicator of the severity of end splitting.A complete map of wood basic specific gravity was made at the breast height level for all trees.This is associated with pulp yield measurements, an increase in density and pulp yield being generally considered as an indicator of gelatinous fibres.Peak values of growth stresses in the stem were associated with a significant increase in pulp yield and specific gravity.The study was completed by a set of experiments on resistance to crack propagation via TR bending specimens.The critical stress intensity factor K IC was calculated.Quantitative measurements of end splitting have proved to be a useful tool for assessing the technological impact of growth stresses in trees; the importance of cracks is clearly related to the maximum value of displacement at stress release.However, crack propagation can also be explained by cell-wall properties and transverse cohesion of green wood.Further research should focus on this second aspect, in order to determine structural properties of importance in crack propagation.growth stresses / end splitting / tension wood / fracture toughness / poplar Résumé — Contraintes de croissance, bois de tension et défauts associés chez le peuplier 1214.Fentes d'abattage, densité du bois et rendement en fibres.L'influence de contraintes internes élevées dans l'arbre, et du comportement mécanique transverse du bois, sur l'importance des fentes d'abattage, a été étudiée chez 15 peupliers 1214 (clone sensible au problème) agés de 30 ans.Pour ces arbres le protocole suivant a été adopté : i) Estimation des déformations résiduelles en 4 points à la périphérie du tronc, à une hauteur de 1,30 m.La position du pic de déformation est généralement estimée par la direction d'inclinaison de l'arbre mesurée sur 6 m. ii) Quantification des fentes sur la section d'abattage et sur une section voisine des points de mesures des déformations : longueur et profondeur maximale estimée des fissures.Les dimensions de la plus grande fente ont été prises comme indicateur de l'importance des fentes.iii) Cartographie de densité : des rondelles prélevées dans la même zone ont été découpées en 24 secteurs angulaires et 4 tranches radiales correspondant à des événements précis (années d'élagage, éclaircie).La présence de bois de tension est évaluée par des zones de densité plus élevée.L'estimation a été complétée par des mesures de rendement en pâte (présence de fibres gélatineuses).La notion de «bois de tension» est dans notre esprit plus mécanique qu'anatomique, et traduit effectivement un changement des propriétés du bois dans les zones plus tendues de l'arbre.iv) Résistance à la propagation de fissure : l'étude a été complétée par des essais de propagation de fissure en mode / réalisés sur des éprouvettes de flexion 3 points en configuration TR (éprouvette SENB, propagation radiale).Cette étude montre qu'une estimation même simplifiée de la fissuration à l'abattage met en évidence l'impact technologique des contraintes de croissance : les arbres pour lesquels des fentes importantes ont été observées présentaient également des pics de contraintes internes.Les cartographies de densité montrent clairement des secteurs de surdensité dans les zones «tendues», parfois limités à la périphérie du tronc, parfois très précoces (près de la moelle).Enfin la fissilité du bois, indicateur de cohésion cellulaire, semble également jouer un rôle dans la variabilité de la fissuration.Ce deuxième aspect devrait être développé ultérieurement.
Abstract Metabarcoding of microbial eukaryotes (collectively known as protists ) has developed tremendously in the last decade, almost uniquely relying on the 18S rRNA gene. As microbial eukaryotes are extremely diverse, many primers and primer pairs have been developed. To cover a relevant and representative fraction of the protist community in a given study system, a wise primer choice is needed as no primer pair can target all protists equally well. As such, a smart primer choice is very difficult even for experts and there are very few on-line resources available to list existing primers. We built a database listing 179 primers and 76 primer pairs that have been used for eukaryotic 18S rRNA metabarcoding. In silico performance of primer pairs was tested against two sequence databases: PR 2 for eukaryotes and a subset of Silva for prokaryotes. This allowed to determine the taxonomic specificity of primer pairs, the location of mismatches as well as amplicon size. We developed a R-based web application that allows to browse the database, visualize the taxonomic distribution of the amplified sequences with the number of mismatches, and to test any user-defined primer set ( https://app.pr2-primers.org ). This tool will provide the basis for guided primer choices that will help a wide range of ecologists to implement protists as part of their investigations.
This paper deals with the specification and search of repeats of biological interest, i.e. repeats that may have a role in genomic structures or functions. Although some particular repeats such as tandem repeats have been well formalized, models developed so far remain of limited expressivity with respect to known forms of repeats in biological sequences. This paper introduces new general and realistic concepts characterizing potentially useful repeats in a sequence: Locality and several refinements around the Maximality concept. Locality is related to the distribution of occurrences of repeated elements and characterizes the way occurrences are clustered in this distribution. The associated notion of neighborhood allows to indirectly exhibit words with a distribution of occurrences that is correlated to a given distribution. Maximality is related to the contextual delimitation of the repeated units. We have extended the usual notion of maximality, working on the inclusion relation between repeats and taking into account larger contexts. Mainly, we introduced a new repeat concept, largest maximal repeats, looking for the existence of a subset of maximal occurrences of a repeated word instead of a global maximization. We propose algorithms checking for local and refined maximal repeats using at the conceptual level a suffix tree data structure. Experiments on natural and artificial data further illustrate various aspects of this new setting. All programs are available on the genouest platform, at http://genouest.org/modulome.
Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2, which has two important novel features: (1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks.
rDNA 18S V9 ASV tables (Swarm) for the Tara Oceans Expedition (2009-2013), including the Tara Polar Circle Expedition (2013) reads were grouped into OTUs using the following swarm-based pipeline: paired-end reads were merged with vsearch’s --fastq_mergepairs command (version 2.15.1, allowing for staggered reads; Rognes et al., 2016), and trimmed with cutadapt (version 3.0; Martin, 2011), keeping only reads containing both forward and reverse primers. After trimming, the expected error per read was estimated with vsearch’s command --fastq_filter and the option --eeout. Each sample was then de-replicated, i.e. strictly identical reads were merged, using vsearch’s command --derep_fulllength, and converted into fasta format. Clustering was performed at the sample level with swarm 3.0 using default parameters (Mahé et al., 2015). Prior to global clustering, individual fasta files (one per sample) were pooled and further dereplicated with vsearch. Files containing per-read expected error values were also dereplicated to retain only the lowest expected error for each unique sequence. Global clustering was performed with swarm (using the fastidious option). Cluster representative sequences were then searched for chimeras with vsearch’s command --uchime_denovo using default parameters (Edgar et al., 2011). Clustering results, expected error values, taxonomic assignments, and chimera detection results were used to build a “raw” occurrence table. Reads without primers, reads shorter than 32 nucleotides and reads with uncalled bases (“N”) were discarded. For a “filtered” occurrence table, non-chimeric sequences, sequences with an expected error per nucleotide below 0.0002, and clusters containing at least 2 reads were retained. Since primer trimming is not perfect, some sequences can still contain primer fragments or be excessively trimmed. These sub- or super-sequences were identified using vsearch and merged with their closest, most abundant perfectly trimmed sequence. Finally, occurrence patterns throughout our sample collection were used to further refine the occurrence table. Clusters that contain sub-clusters with only a single-nucleotide difference but with different ecological patterns (defined here as uncorrelated abundance values in at least 5% of the samples) were turned into distinct clusters (https://github.com/frederic-mahe/fred-metabarcoding-pipeline). On the other hand, clusters with similar sequences that had correlated abundance values in at least 95% of the samples, were merged using a re-implementation of lulu's method (Frøslev et al. 2017; https://github.com/frederic-mahe/mumu).
ABSTRACT Dinophytes are widely distributed in marine- and fresh-waters, but have yet to be conclusively documented in terrestrial environments. Here we evaluated the presence of these protists from an environmental DNA metabarcoding dataset of Neotropical rainforest soils. Using a phylogenetic placement approach with a reference alignment and tree, we showed that the numerous sequencing reads that were assigned to the dinophytes did not associate with taxonomy, environmental preference, nutritional mode, or dormancy. All the dinophytes in the soils are most likely windblown dispersal units of aquatic species, and are not biologically active residents of terrestrial environments.
