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Thevenin, J. - M., Rossi, V., Ducamp, M., Doare, F., Condina, V., & Lachenaud, P. (2012). Numerous clones resistant to Phytophthora palmivora in the “Guiana” genetic group of Theobroma cacao L. PLoS ONE, 7(7), e40915.
Abstract: Cocoa black pod rot, a disease caused by Stramenopiles of the genus Phytophthora, and particularly by the pan-tropical species P. palmivora, causes serious production losses worldwide. In order to reduce the impact of these pests and diseases, preference is given to genetic control using resistant varieties and, to that end, breeders seek sources of resistance in wild cocoa trees. For instance, surveys of spontaneous cocoa trees in French Guiana between 1985 and 1995 led to the collection of abundant plant material forming a particular genetic group (the “Guiana” group). Following numerous one-off studies demonstrating the merits of this group as a source of resistance to Phytophthora, this article presents the results of a comprehensive study assessing the resistance of 186 “Guiana” clones in relation to the Guianan strain (GY 27) of P. palmivora. This study, undertaken in French Guiana, using an efficient methodology (ten series of tests and a statistical test adapted to the ordinal nature of the data) confirmed that the “Guiana” genetic group does indeed constitute an important source of resistance to P. palmivora, though with some variations depending on the demes of origin. Numerous clones (59) proved to be as resistant as the SCAVINA 6 resistance control, whilst nine were statistically more resistant. The “Resistant” and “Moderately Resistant” Guianan clones totalled 108 (58% of the total tested). Some of the clones more resistant than SCAVINA 6 could be incorporated into numerous cocoa breeding programmes, particularly those that also display other notable qualities. The same applies for numerous other clones equivalent to SCAVINA 6, especially the “elite”' clones GU 134-B, GU 139-A and GU 285-A. © 2012 Thevenin et al.
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Hibert, F., Taberlet, P., Chave, J., Scotti-Saintagne, C., Sabatier, D., & Richard-Hansen, C. (2013). Unveiling the Diet of Elusive Rainforest Herbivores in Next Generation Sequencing Era? The Tapir as a Case Study. PLoS ONE, 8(4), e60799.
Abstract: Characterizing the trophic relationships between large herbivores and the outstanding plant diversity in rainforest is a major challenge because of their elusiveness. This is crucial to understand the role of these herbivores in the functioning of the rainforest ecosystems. We tested a non-invasive approach based on the high-throughput sequencing of environmental samples using small plant plastid sequences (the trnL P6 loop) and ribosomal ITS1 primers, referred to as DNA metabarcoding, to investigate the diet of the largest neotropical herbivore, the lowland tapir. Sequencing was performed on plant DNA extracted from tapir faeces collected at the Nouragues station, a protected area of French Guiana. In spite of a limited sampling, our approach reliably provided information about the lowland tapir's diet at this site. Indeed, 95.1% and 74.4% of the plant families and genera identified thanks to the trnL P6 loop, respectively, matched with taxa already known to be consumed by tapirs. With this approach we were able to show that two families and eight new genera are also consumed by the lowland tapir. The taxonomic resolution of this method is limited to the plant family and genera. Complementary barcodes, such as a small portion of ITS1, can be used to efficiently narrow identifications down to the species in some problematic families. We will discuss the remaining limitations of this approach and how useful it is at this stage to unravel the diet of elusive rainforest herbivores and better understand their role as engineers of the ecosystem. © 2013 Hibert et al.
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Mortier, F., Rossi, V., Guillot, G., Gourlet-Fleury, S., & Picard, N. (2013). Population dynamics of species-rich ecosystems: The mixture of matrix population models approach. Methods Ecol. Evol., 4(4), 316–326.
Abstract: Matrix population models are widely used to predict population dynamics, but when applied to species-rich ecosystems with many rare species, the small population sample sizes hinder a good fit of species-specific models. This issue can be overcome by assigning species to groups to increase the size of the calibration data sets. However, the species classification is often disconnected from the matrix modelling and from the estimation of matrix parameters, thus bringing species groups that may not be optimal with respect to the predicted community dynamics. We proposed here a method that jointly classified species into groups and fit the matrix models in an integrated way. The model was a special case of mixture with unknown number of components and was cast in a Bayesian framework. An MCMC algorithm was developed to infer the unknown parameters: the number of groups, the group of each species and the dynamics parameters. We applied the method to simulated data and showed that the algorithm efficiently recovered the model parameters. We applied the method to a data set from a tropical rain forest in French Guiana. The mixture matrix model classified tree species into well-differentiated groups with clear ecological interpretations. It also accurately predicted the forest dynamics over the 16-year observation period. Our model and algorithm can straightforwardly be adapted to any type of matrix model, using the life cycle diagram. It can be used as an unsupervised classification technique to group species with similar population dynamics. © 2012 The Authors. Methods in Ecology and Evolution © 2012 British Ecological Society.
Keywords: Bayesian; Clustering; Mixture models; Population dynamics; Reversible jump Markov chain Monte Carlo; Species-rich ecosystems; Tropical rain forests
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Touchard, A., Brust, A., Cardoso, F. C., Chin, Y. K. - Y., Herzig, V., Jin, A. - H., et al. (2016). Isolation and characterization of a structurally unique β-hairpin venom peptide from the predatory ant Anochetus emarginatus. Biochimica et Biophysica Acta – General Subjects, 1860(11), 2553–2562.
Abstract: Background Most ant venoms consist predominantly of small linear peptides, although some contain disulfide-linked peptides as minor components. However, in striking contrast to other ant species, some Anochetus venoms are composed primarily of disulfide-rich peptides. In this study, we investigated the venom of the ant Anochetus emarginatus with the aim of exploring these novel disulfide-rich peptides. Methods The venom peptidome was initially investigated using a combination of reversed-phase HPLC and mass spectrometry, then the amino acid sequences of the major peptides were determined using a combination of Edman degradation and de novo MS/MS sequencing. We focused on one of these peptides, U1-PONTX-Ae1a (Ae1a), because of its novel sequence, which we predicted would form a novel 3D fold. Ae1a was chemically synthesized using Fmoc chemistry and its 3D structure was elucidated using NMR spectroscopy. The peptide was then tested for insecticidal activity and its effect on a range of human ion channels. Results Seven peptides named poneritoxins (PONTXs) were isolated and sequenced. The three-dimensional structure of synthetic Ae1a revealed a novel, compact scaffold in which a C-terminal β-hairpin is connected to the N-terminal region via two disulfide bonds. Synthetic Ae1a reversibly paralyzed blowflies and inhibited human L-type voltage-gated calcium channels (CaV1). Conclusions Poneritoxins from Anochetus emarginatus venom are a novel class of toxins that are structurally unique among animal venoms. General significance This study demonstrates that Anochetus ant venoms are a rich source of novel ion channel modulating peptides, some of which might be useful leads for the development of biopesticides. © 2016
Keywords: Anochetus; Ant venom; Disulfide-rich peptides; L-type calcium channels; Neurotoxin; Poneritoxins; U1-PONTX-Ae1a
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Aili, S. R., Touchard, A., Koh, J. M. S., Dejean, A., Orivel, J., Padula, M. P., et al. (2016). Comparisons of Protein and Peptide Complexity in Poneroid and Formicoid Ant Venoms. Journal of Proteome Research, 15(9), 3039–3054.
Abstract: Animal venom peptides are currently being developed as novel drugs and bioinsecticides. Because ants use venoms for defense and predation, venomous ants represent an untapped source of potential bioactive toxins. This study compared the protein and peptide components of the poneroid ants Neoponera commutata, Neoponera apicalis, and Odontomachus hastatus and the formicoid ants Ectatomma tuberculatum, Ectatomma brunneum, and Myrmecia gulosa. 1D and 2D PAGE revealed venom proteins in the mass range <10 to >250 kDa. NanoLC-ESI-QTOF MS/MS analysis of tryptic peptides revealed the presence of common venom proteins and also many undescribed proteins. RP-HPLC separation followed by MALDI-TOF MS of the venom peptides also revealed considerable heterogeneity. It was found that the venoms contained between 144 and 1032 peptides with 5-95% of peptides in the ranges 1-4 and 1-8 kDa for poneroid and formicoid ants, respectively. By employing the reducing MALDI matrix 1,5-diaminonapthalene, up to 28 disulfide-bonded peptides were also identified in each of the venoms. In particular, the mass range of peptides from poneroid ants is lower than peptides from other venoms, indicating possible novel structures and pharmacologies. These results indicate that ant venoms represent an enormous, untapped source of novel therapeutic and bioinsecticide leads. © 2016 American Chemical Society.
Keywords: ant venom; Hymenoptera; Lc-Maldi-Tof Ms; mass spectrometry; nanoLC-ESI-QTOF MS/MS; peptidome; proteomic analysis; toxin
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Gibson, J. C., Larabee, F. J., Touchard, A., Orivel, J., & Suarez, A. V. (2018). Mandible strike kinematics of the trap-jaw ant genus Anochetus Mayr (Hymenoptera: Formicidae). Journal of Zoology, 306(2), 119–128.
Abstract: High-speed power-amplification mechanisms are common throughout the animal kingdom. In ants, power-amplified trap-jaw mandibles have evolved independently at least four times, including once in the subfamily Ponerinae which contains the sister genera Odontomachus and Anochetus. In Odontomachus, mandible strikes have been relatively well described and can occur in <0.15 ms and reach speeds of over 60 m s−1. In contrast, the kinematics of mandible strikes have not been examined in Anochetus, whose species are smaller and morphologically distinct from Odontomachus. In this study, we describe the mandible strike kinematics of four species of Anochetus representative of the morphological, phylogenetic, and size diversity present within the genus. We also compare their strikes to two representative species of Odontomachus. We found that two species, Anochetus targionii and Anochetus paripungens, have mandible strikes that overall closely resemble those found in Odontomachus, reaching a mean maximum rotational velocity and acceleration of around 3.7 × 104 rad s−1 and 8.5 × 108 rad s−2, respectively. This performance is consistent with predictions based on body size scaling relationships described for Odontomachus. In contrast, Anochetus horridus and Anochetus emarginatus have slower strikes relative to the other species of Anochetus and Odontomachus, reaching mean maximum rotational velocity and acceleration of around 1.3 × 104 rad s−1 and 2 × 108 rad s−2, respectively. This variation in strike performance among species of Anochetus likely reflects differences in evolutionary history, physiology, and natural history among species. © 2018 The Zoological Society of London
Keywords: catapult mechanism; comparative biomechanics; Formicidae; functional morphology; kinematics; mandible strike; power amplification
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Michalet, S., Rohr, J., Warshan, D., Bardon, C., Roggy, J. - C., Domenach, A. - M., et al. (2013). Phytochemical analysis of mature tree root exudates in situ and their role in shaping soil microbial communities in relation to tree N-acquisition strategy. Plant Physiol. Biochem., 72, 169–177.
Abstract: Eperua falcata (Aublet), a late-successional species in tropical rainforest and one of the most abundant tree in French Guiana, has developed an original strategy concerning N-acquisition by largely preferring nitrate, rather than ammonium (H. Schimann, S. Ponton, S. Hättenschwiler, B. Ferry, R. Lensi, A.M. Domenach, J.C. Roggy, Differing nitrogen use strategies of two tropical rainforest tree species in French Guiana: evidence from 15N natural abundance and microbial activities, Soil Biol. Biochem. 40 (2008) 487-494). Given the preference of this species for nitrate, we hypothesized that root exudates would promote nitrate availability by (a) enhancing nitrate production by stimulating ammonium oxidation or (b) minimizing nitrate losses by inhibiting denitrification.Root exudates were collected in situ in monospecific planted plots. The phytochemical analysis of these exudates and of several of their corresponding root extracts was achieved using UHPLC/DAD/ESI-QTOF and allowed the identification of diverse secondary metabolites belonging to the flavonoid family.Our results show that (i) the distinct exudation patterns observed are related to distinct root morphologies, and this was associated with a shift in the root flavonoid content, (ii) a root extract representative of the diverse compounds detected in roots showed a significant and selective metabolic inhibition of isolated denitrifiers invitro, and (iii) in soil plots the abundance of nirK-type denitrifiers was negatively affected in rhizosphere soil compared to bulk. Altogether this led us to formulate hypothesis concerning the ecological role of the identified compounds in relation to N-acquisition strategy of this species. © 2013 Elsevier Masson SAS.
Keywords: Chemical ecology; Denitrification; Eperua falcata; Metabolic profiling; Mycorrhizae; Plant-microbes interactions; Root exudates
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Rifflet, A., Gavalda, S., Téné, N., Orivel, J., Leprince, J., Guilhaudis, L., et al. (2012). Identification and characterization of a novel antimicrobial peptide from the venom of the ant Tetramorium bicarinatum. Peptides, 38(2), 363–370.
Abstract: A novel antimicrobial peptide, named Bicarinalin, has been isolated from the venom of the ant Tetramorium bicarinatum. Its amino acid sequence has been determined by de novo sequencing using mass spectrometry and by Edman degradation. Bicarinalin contained 20 amino acid residues and was C-terminally amidated as the majority of antimicrobial peptides isolated to date from insect venoms. Interestingly, this peptide had a linear structure and exhibited no meaningful similarity with any known peptides. Antibacterial activities against Staphylococcus aureus and S. xylosus strains were evaluated using a synthetic replicate. Bicarinalin had a potent and broad antibacterial activity of the same magnitude as Melittin and other hymenopteran antimicrobial peptides such as Pilosulin or Defensin. Moreover, this antimicrobial peptide has a weak hemolytic activity compared to Melittin on erythrocytes, suggesting potential for development into an anti-infective agent for use against emerging antibiotic-resistant pathogens. © 2012 Elsevier Inc.
Keywords: Amp; Ant venom; Antibacterial peptide; Bicarinalin; Esi-Ms/Ms; Staphylococcus; Tetramorium bicarinatum
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Rodrigues, A. M. S., Stien, D., Eparvier, V., Espindola, L. S., Beauchene, J., Amusant, N., et al. (2012). The wood preservative potential of long-lasting Amazonian wood extracts. International Biodeterioration and Biodegradation, 75, 146–149.
Abstract: Investigations were carried out on the efficacy of extracts from seven Amazonian woods (Bagassa guianensis, Manilkara huberi, Sextonia rubra, Vouacapoua americana, Andira surinamensis, Handroanthus serratifolius, and Qualea rosea) with varying natural durability to reduce soft-rot degradation in a 6-wk soil-bed test. Six of the wood extracts had shown efficacy against soft-rot fungi. In particular, the preservation efficacies of B. guianensis, H. serratifolius, and S. rubra extracts were highly significant up to retention levels of 23, 25, and 12 kg m-3, respectively. Three extracts (A. surinamensis, H. serratifolius, and Q. rosea) were then tested against Gloeophyllum trabeum (brown rot) and Trametes versicolor (white rot), in an agar-block test. H. serratifolius wood extract was very efficient at protecting P. sylvestris samples at 5.1 kg m-3 against the brown rot. This extract could be used as a basis for new wood protectant formulations. © 2012 Elsevier Ltd.
Keywords: Durable wood extracts; Handroanthus serratifolius; Rotting fungi; Wood preservation
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Rockwell, C. A., Kainer, K. A., d'Oliveira, M. V. N., Staudhammer, C. L., & Baraloto, C. (2014). Logging in bamboo-dominated forests in southwestern Amazonia: Caveats and opportunities for smallholder forest management. For. Ecol. Manage., 315, 202–210.
Abstract: Guadua sarcocarpa and Guadua weberbaueri (Poaceae: Bambuseae) have a negative influence on tree regeneration and recruitment in bamboo-dominated forests of southwestern Amazonia. The lack of advanced regeneration and sparse canopy in this forest type present a considerable challenge for developing sustainable timber management plans. We conducted field studies in the Porto Dias Agroextractive Settlement Project in Acre, Brazil to assess influences of logging in bamboo-dominated forest sites. Taxonomic composition, stand structure, aboveground biomass, commercial timber volume, and commercial tree seedling and bamboo culm density were compared between five logged vs. unlogged sites in different landholdings, using modified 0.5. ha Gentry plots. No differences in taxonomic composition, aboveground biomass, adult and juvenile stem density, or woody seedling and bamboo culm density were detected between paired logged and unlogged sites. Commercial timber volume, however, was reduced by almost two-thirds in logged plots, suggesting that long-term timber management goals in this forest type are compromised since so few future crop trees remained onsite. Our findings indicate that in order to maximize local management objectives, community forest managers must approach logging in bamboo-dominated forests with caution. We suggest an integration of non-timber forest product extraction with low harvest intensity and low-impact logging, tending of natural regeneration, and diversification of commercial species. © 2014 Elsevier B.V.
Keywords: Bamboo; Community forest management; Guadua; Logging; Timber management; Tropical forest
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