Blood parasites infecting the Hoatzin (Opisthocomus hoazin), a unique neotropical folivorous bird
The Hoatzin (Opisthocomus hoazin) is the only extant member of the order Opisthocomiformes. This unique South American bird lives in the riparian lowland vegetation characteristic of the Amazon and Orinoco basins. Hoatzins nest in communal social units close to water bodies; they are strictly folivores being the only bird with pregastric fermentation in the crop. Because of the complex logistics involved in capturing this bird, there is a knowledge gap on its parasites. This study documents two distant lineages of haemosporidian parasites (Plasmodium spp.) in a juvenile and two adults sampled in the Cojedes state, Venezuela. Although negative by microscopy, the parasite identification was possible by using molecular methods. We estimated the phylogenetic relationships on the parasite cytochrome b (cytb, 480 bp) gene and the mitochondrial DNA. We found one of the parasites lineages in two individuals (nestling and adult), and the corresponding fragment of cytb was identical to a one found in Wood Stork (Mycteria americana) from Brazil. The other lineage, found in an adult, has an identity of 469 out of 478 bp (98%) with Plasmodium sp. GAL-2012 (isolate THAMB08) from Brazil. Although a morphological description of these parasites was not possible, this is the first molecular study focusing on Hoatzin haemosporidian parasites and the first documentation of Plasmodium infections in the Hoatzin from Venezuela. Furthermore, we reported microfilaria in two adults as well as hematological parameters for six individuals. Information on hematological parameters could contribute to establishing the necessary baseline to detect underlying conditions, such as infections, in this bird species.
Pacheco et al. (2019) Blood parasites infecting the Hoatzin (Opisthocomus hoazin), a unique neotropical folivorous bird. PeerJ 7:e6361 https://doi.org/10.7717/peerj.6361
Molecular and morphological congruence of three new cryptic Neopetrosia spp. in the Caribbean
Neopetrosia proxima (Porifera: Demospongiae: Haplosclerida) is described as a morphologically variable sponge common on shallow reefs of the Caribbean. However, the range of morphological and reproductive variation within putative N. proxima led us to hypothesize that such variability may be indicative of cryptic species rather than plasticity. Using DNA sequences and morphological characters we confirmed the presence of three previously undescribed species of Neopetrosia. Morphological differences of each new congener were best resolved by partial gene sequences of the mitochondrial cytochrome oxidase subunit 1 over nuclear ones (18S rRNA and 28S rRNA). Several new characters for Neopetrosia were revealed by each new species. For example, N. dendrocrevacea sp. nov. and N. cristata sp. nov. showed the presence of grooves on the surface of the sponge body that converge at the oscula, and a more disorganized skeleton than previously defined for the genus. N. sigmafera sp. nov. adds the (1) presence of sigma microscleres, (2) significantly wider/longer oxeas (>200 μm), and (3) the presence of parenchymella larvae. Sampling of conspecifics throughout several locations in the Caribbean revealed larger spicules in habitats closer to the continental shelf than those in remote island locations. Our study highlights the importance of integrating molecular and morphological systematics for the discrimination of new Neopetrosia spp. despite belonging to one of several polyphyletic groups (families, genera) within the current definition of the order Haplosclerida.
Vicente et al. (2019) Molecular and morphological congruence of three new cryptic Neopetrosia spp. in the Caribbean. PeerJ 7:e6371 https://doi.org/10.7717/peerj.6371
Disentangling the effect of host-genotype and environment on the microbiome of the coral Acropora tenuis
Genotype-specific contributions to the environmental tolerance and disease susceptibility of corals are widely accepted. Yet our understanding of how host genotype influences the composition and stability of the coral microbiome subjected to environmental fluctuations is limited. To gain insight into the community dynamics and environmental stability of microbiomes associated with distinct coral genotypes, we assessed the microbial community associated with Acropora tenuis under single and cumulative pressure experiments. Experimental treatments comprised either a single pulse of reduced salinity (minimum of 28 psu) or exposure to the cumulative pressures of reduced salinity (minimum of 28 psu), elevated seawater temperature (+2 °C), elevated pCO2 (900 ppm), and the presence of macroalgae. Analysis of 16S rRNA gene amplicon sequence data revealed that A. tenuis microbiomes were highly host-genotype specific and maintained high compositional stability irrespective of experimental treatment. On average, 48% of the A. tenuis microbiome was dominated by Endozoicomonas. Amplicon sequence variants (ASVs) belonging to this genus were significantly different between host individuals. Although no signs of stress were evident in the coral holobiont and the vast majority of ASVs remained stable across treatments, a microbial indicator approach identified 26 ASVs belonging to Vibrionaceae, Rhodobacteraceae, Hahellaceae, Planctomycetes, Phylobacteriaceae, Flavobacteriaceae, and Cryomorphaceae that were significantly enriched in corals exposed to single and cumulative stressors. While several recent studies have highlighted the efficacy of microbial indicators as sensitive markers for environmental disturbance, the high host-genotype specificity of coral microbiomes may limit their utility and we therefore recommend meticulous control of host-genotype effects in coral microbiome research.
Glasl et al. (2019) Disentangling the effect of host-genotype and environment on the microbiome of the coral Acropora tenuis. PeerJ 7:e6377 https://doi.org/10.7717/peerj.6377
Motor expertise modulates unconscious rather than conscious executive control
Background Executive control, the ability to regulate the execution of a goal-directed task, is an important element in an athlete’s skill set. Although previous studies have shown that executive control in athletes is better than that in non-athletes, those studies were mainly confined to conscious executive control. Many recent studies have suggested that executive control can be triggered by the presentation of visual stimuli without participant’s conscious awareness. However, few studies have examined unconscious executive control in sports. Thus, the present study investigated whether, similar to conscious executive control, unconscious executive control in table tennis athletes is superior to that in non-athletes. Methods In total, 42 age-matched undergraduate students were recruited for this study; 22 nonathletic students lacking practical athletic experience comprised one group, and 20 table tennis athletes with many years of training in this sport comprised a second group. Each participant first completed an unconscious response priming task, the unconscious processing of visual-spatial information, and then completed a conscious version of this same response priming task. Results Table tennis athletes showed a significant response priming effect, whereas non-athletes did not, when participants were unable to consciously perceive the visual-spatial priming stimuli. In addition, the number of years the table tennis athletes had trained in this sport (a measure of their motor expertise) was positively correlated with the strength of the unconscious response priming effect. However, both table tennis athletes and non-athletes showed a response priming effect when the primes were unmasked and the participants were able to consciously perceive the visual-spatial priming stimuli. Conclusion Our results suggest that motor expertise modulates unconscious, rather than conscious, executive control and that motor expertise is positively correlated with unconscious executive control in table tennis athletes.
Meng et al. (2019) Motor expertise modulates unconscious rather than conscious executive control. PeerJ 7:e6387 https://doi.org/10.7717/peerj.6387
Fruit availability for migratory birds: a GIS approach
Bird migration is a widely studied phenomenon, however many factors that influence migratory flows remain unknown or poorly understood. Food availability en route is particularly important for many species and can affect their migration success, pattern and timing but this relationship has not been addressed at a wide scale due to the lack of spatial models of food availability on the terrain. This work presents a GIS-database approach that combines spatial and non-spatial ecological information in order to map fruit availability from vegetation over time in the SE Alps, an important node of European migratory routes. We created a unique database that contains information on the presence and periods of fructification of 52 wild plants carrying berries and a series of original cartographic themes. The presence and coverage of the plant species was modelled with the geo-statistical method of the Gaussian Kernel, which was validated against the ground truth of field sampling data with a correct classification power above 80% in most cases. The highest fruit availability in the study area during September and October co-occurs with the peak of captures of berry eating birds. The maps created and distributed along this work can be useful to address more detailed studies about stopover sites as well as the spatial ecology of other fruit eating animals.
Spatial and Geographic Information Science
Tattoni et al. (2019) Fruit availability for migratory birds: a GIS approach. PeerJ 7:e6394 https://doi.org/10.7717/peerj.6394
Evaluation of DESS as a storage medium for microbial community analysis
Microbial ecology research requires sampling strategies that accurately represent the microbial community under study. These communities must typically be transported from the collection location to the laboratory and then stored until they can be processed. However, there is a lack of consensus on how best to preserve microbial communities during transport and storage. Here, we evaluated dimethyl sulfoxide, ethylenediamine tetraacetic acid, saturated salt (DESS) solution as a broadly applicable preservative for microbial ecology experiments. We stored fungus gardens grown by the ant Trachymyrmex septentrionalis in DESS, 15% glycerol, and phosphate buffered saline (PBS) to test their impact on the fungus garden microbial community. Variation in microbial community structure due to differences in preservative type was minimal when compared to variation between ant colonies. Additionally, DESS preserved the structure of a defined mock community more faithfully than either 15% glycerol or PBS. DESS is inexpensive, easy to transport, and effective in preserving microbial community structure. We therefore conclude that DESS is a valuable preservative for use in microbial ecology research.
Lee et al. (2019) Evaluation of DESS as a storage medium for microbial community analysis. PeerJ 7:e6414 https://doi.org/10.7717/peerj.6414
LiBiNorm: an htseq-count analogue with improved normalisation of Smart-seq2 data and library preparation diagnostics
Protocols for preparing RNA sequencing (RNA-seq) libraries, most prominently “Smart-seq” variations, introduce global biases that can have a significant impact on the quantification of gene expression levels. This global bias can lead to drastic over- or under-representation of RNA in non-linear length-dependent fashion due to enzymatic reactions during cDNA production. It is currently not corrected by any RNA-seq software, which mostly focus on local bias in coverage along RNAs. This paper describes LiBiNorm, a simple command line program that mimics the popular htseq-count software and allows diagnostics, quantification, and global bias removal. LiBiNorm outputs gene expression data that has been normalized to correct for global bias introduced by the Smart-seq2 protocol. In addition, it produces data and several plots that allow insights into the experimental history underlying library preparation. The LiBiNorm package includes an R script that allows visualization of the main results. LiBiNorm is the first software application to correct for the global bias that is introduced by the Smart-seq2 protocol. It is freely downloadable at http://www2.warwick.ac.uk/fac/sci/lifesci/research/libinorm.
Dyer et al. (2019) LiBiNorm: an htseq-count analogue with improved normalisation of Smart-seq2 data and library preparation diagnostics. PeerJ 7:e6222 https://doi.org/10.7717/peerj.6222
Methods of body temperature assessment in Conolophus subcristatus, Conolophus pallidus (Galápagos land iguanas), and Amblyrhynchus cristatus X C. subcristatus hybrid
Since cardiovascular, respiratory, and metabolic systems of reptiles are affected by temperature, accurate measurements are of great importance in both captive husbandry and research. Ectothermic animals generally have core body temperatures close to ambient temperature but can differ from the immediate environment if they are using sunlight to thermoregulate. Many zoological facilities and exotic pet caregivers have begun using infrared temperature guns to assess ambient temperatures of reptile enclosures but there are currently few studies assessing the efficacy of these devices for measuring the body temperatures of reptiles. Conolophus subcristatus, Conolophus pallidus (Galápagos land iguanas), and Amblyrhynchus cristatus X C. subcristatus hybrid are robust land iguanas endemic to the Galápagos archipelago. By comparing the infrared body temperature measurements of land iguanas against virtual simultaneous collection of cloacal temperatures obtained using a thermocouple thermometer, we sought to assess the efficacy of this non-invasive method. We found that internal body temperature can be predicted with a high level of accuracy from three external body temperature sites, providing a good non-invasive method that avoids the capture of animals.
Valle et al. (2019) Methods of body temperature assessment in Conolophus subcristatus, Conolophus pallidus (Galápagos land iguanas), and Amblyrhynchus cristatus X C. subcristatus hybrid. PeerJ 7:e6291 https://doi.org/10.7717/peerj.6291
Effects of particle size on physicochemical and functional properties of superfine black kidney bean (Phaseolus vulgaris L.) powder
Black kidney bean (Phaseolus vulgaris L.) powder (BKBP) with particle sizes of 250–180, 180–125, 125–75, 75–38, and <38 μm was prepared by using coarse and eccentric vibratory milling, respectively. Physicochemical properties, cholesterol adsorption, and antioxidant activities of powders were investigated. Size and scanning electron microscopy analyses showed that particle size of BKBP could be effectively decreased after the superfine grinding treatment, and the specific surface area was increased. Flow properties, hydration properties, thermal stability, and cholesterol adsorption efficiency significantly improved with the reducing of particle size. The superfine powder with sizes of 75–38 or <38 μm exhibited higher antioxidant activity via 2,2-diphenyl-1-picryhydrazyl, hydroxyl radical-scavenging, and ferrous ion-chelating assays. The results indicated that the BKBP with a size of <38 μm could serve as a better potential biological resource for food additives, and could be applied for the development of low-cholesterol products.
Sun et al. (2019) Effects of particle size on physicochemical and functional properties of superfine black kidney bean (Phaseolus vulgaris L.) powder. PeerJ 7:e6369 https://doi.org/10.7717/peerj.6369
Density dependent attributes of fish aggregative behaviour
Grouping behaviour, as fascinating as it is unclear, has lately drawn the attention of numerous researchers. While most of the authors focused their work on a mechanistic approach to the matter of schooling, this study explores the issue from a population point of view. Present camera observation study on the fish community carried out in the epipelagic habitat of a European temperate reservoir in the Czech Republic explored the relationship between density and aggregative features of predominantly cyprinid fish stock. Results demonstrated that schooling behaviour is triggered by the ‘critical density’ of fish in the habitat. School size as well as counts of schools and proportion of schooling individuals increased with the density of fish. Counts of clusters (observed units in time, including singletons, pairs and schools) and cluster size, on the other hand, showed a slowing tendency to increase. The slower increase implies the tendency of fish for not being frequent but rather to create larger groups. Altogether, our findings suggest that fish density is a triggering factor in the formation of large fish schools. As the tendency of cyprinid species for school formation could be an evolutional advantage responsible for dominance in later succession phases of water bodies, we suggest that more in situ studies should be encouraged for the proper understanding of the ecological interactions that drive the structure of aquatic ecosystems and for ensuring unbiased assessment.
Holubová et al. (2019) Density dependent attributes of fish aggregative behaviour. PeerJ 7:e6378 https://doi.org/10.7717/peerj.6378