title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1812 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Competition-function tradeoffs in ectomycorrhizal fungi link: https://peerj.com/articles/2270 last-modified: 2016-07-27 description: Background. The extent to which ectomycorrhizal fungi mediate primary production, carbon storage, and nutrient remineralization in terrestrial ecosystems depends upon fungal community composition. However, the factors that govern community composition at the root system scale are not well understood. Here, we explore a potential tradeoff between ectomycorrhizal fungal competitive ability and enzymatic function.Methods. We grew Pinus muricata (Bishop Pine) seedlings in association with ectomycorrhizal fungi from three different genera in a fully factorial experimental design. We measured seedling growth responses, ectomycorrhizal abundance, and the root tip activity of five different extracellular enzymes involved in the mobilization of carbon and phosphorus.Results. We found an inverse relationship between competitiveness, quantified based on relative colonization levels, and enzymatic activity. Specifically, Thelephora terrestris, the dominant fungus, had the lowest enzyme activity levels, while Suillus pungens, the least dominant fungus, had the highest.Discussion. Our results identify a tradeoff between competition and function in ectomycorrhizal fungi, perhaps mediated by the competing energetic demands associated with competitive interactions and enzymatic production. These data suggest that mechanisms such as active partner maintenance by host trees may be important to maintaining “high-quality” ectomycorrhizal fungal partners in natural systems. creator: Holly V. Moeller creator: Kabir G. Peay uri: https://doi.org/10.7717/peerj.2270 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Moeller and Peay title: Community shelter use in response to two benthic decapod predators in the Long Island Sound link: https://peerj.com/articles/2265 last-modified: 2016-07-27 description: To investigate community shelter effects of two invasive decapod species, Hemigrapsus sanguineus and Carcinus maenas, in the Long Island Sound (LIS), we deployed artificial shelters in the intertidal and immediate subtidal zones. These consisted of five groups during the summer: a control, a resident H. sanguineus male or female group, and a resident C. maenas male or female group. We quantified utilization of the shelters at 24 h by counting crabs and fish present. We found significant avoidance of H. sanguineus in the field by benthic hermit crabs (Pagurus spp.) and significant avoidance of C. maenas by the seaboard goby (Gobiosoma ginsburgi). The grubby (Myoxocephalus aenaeus) avoided neither treatment, probably since it tends to be a predator of invertebrates. H. sanguineus avoided C. maenas treatments, whereas C. maenas did not avoid any treatment. Seasonal deployments in the subtidal indicated cohabitation of a number of benthic species in the LIS, with peak shelter use corresponding with increased predation and likely reproductive activity in spring and summer for green crabs (C. maenas), hermit crabs (Pagurus spp.), seaboard gobies (G. ginsburgi), and grubbies (Myoxocephalus aenaeus). creator: David M. Hudson creator: Dugan Reagan creator: Joseph F. Crivello uri: https://doi.org/10.7717/peerj.2265 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Hudson et al. title: Dropping behaviour of pea aphid nymphs increases their development time and reduces their reproductive capacity as adults link: https://peerj.com/articles/2236 last-modified: 2016-07-27 description: Background. Many aphid species, including the pea aphid Acyrthosiphon pisum, exhibit a behaviour where they drop or fall from their host plant, a commonly used strategy to avoid predation, parasitism or physical disturbance. We hypothesised that there was a physiological non-consumptive cost due to such dropping behaviour because aphids would expend energy re-establishing themselves on a host plant and also lose feeding time.Methods. We evaluated this non-consumptive cost by determining the development time and reproductive potential of pea aphids that whilst developing as nymphs had regularly dropped to the ground following dislodgment from their host plant. Using a microcosm approach, in a replicated and balanced laboratory experiment, we caused aphid dropping behaviour by tapping the plants on which they were feeding.Results. The results demonstrated that disturbance by dropping behaviour increased nymphal development time and reduced their subsequent reproductive capacity as adults.Discussion. We conclude that dropping behaviour had a strong negative effect on the development of nymphs and their subsequent reproductive capacity. This implies that the physiological cost of such a behaviour choice is substantial, and that such avoidance strategies require a trade-off which reduces the capacity of a population to increase. creator: Barbara Agabiti creator: Roxanne J. Wassenaar creator: Linton Winder uri: https://doi.org/10.7717/peerj.2236 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Agabiti et al. title: Development and characterization of novel microsatellite markers by Next Generation Sequencing for the blue and red shrimp Aristeus antennatus link: https://peerj.com/articles/2200 last-modified: 2016-07-27 description: The blue and red shrimp, Aristeus antennatus, is a commercially important crustacean, in the Mediterranean Sea, which has been listed as a priority species for fishery management. Hypervariable microsatellite markers could be a useful tool to identify genetic stocks among geographically close fishing grounds. Potential microsatellite markers (97) identified from next-generation sequencing of an individual shrimp using a 454 GS Junior Pyrosequencer were tested on a preliminary panel of 15 individuals representing the four worldwide genetic stocks of the species from which 35 polymorphic loci were identified and used to characterize an additional 20 individuals from the Western Mediterranean Sea. In the Western Mediterranean sample, 32 out of 35 were polymorphic loci and the number of alleles per locus ranged from 2 to 14 and expected heterozygosity ranged from 0.050 to 0.968. No linkage disequilibrium was detected, indicating the independence of the loci. These novel microsatellites provide additional tools to address questions relating to genetic diversity, parentage studies and connectivity patterns of A. antennatus populations and help develop effective strategies to ensure long-term sustainability of this resource. creator: Sandra Heras creator: Laia Planella creator: Ilaria Caldarazzo creator: Manuel Vera creator: José-Luis García-Marín creator: Maria Ines Roldán uri: https://doi.org/10.7717/peerj.2200 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Heras et al. title: Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase link: https://peerj.com/articles/2272 last-modified: 2016-07-26 description: The origin and subsequent accumulation of spliceosomal introns are prominent events in the evolution of eukaryotic gene structure. However, the mechanisms underlying intron gain remain unclear because there are few proven cases of recently gained introns. In an RNA-dependent RNA polymerase (RdRp) gene, we found that a tandem duplication occurred after the divergence of potato and its wild relatives among other Solanum plants. The duplicated sequence crosses the intron-exon boundary of the first intron and the second exon. A new intron was detected at this duplicated region, and it includes a small previously exonic segment of the upstream copy of the duplicated sequence and the intronic segment of the downstream copy of the duplicated sequence. The donor site of this new intron was directly obtained from the small previously exonic segment. Most of the splicing signals were inherited directly from the parental intron/exon structure, including a putative branch site, the polypyrimidine tract, the 3′ splicing site, two putative exonic splicing enhancers, and the GC contents differed between the intron and exon. In the widely cited model of intron gain by tandem genomic duplication, the duplication of an AGGT-containing exonic segment provides the GT and AG splicing sites for the new intron. Our results illustrate that the tandem duplication model of intron gain should be diverse in terms of obtaining the proper splicing signals. creator: Ming-Yue Ma creator: Xin-Ran Lan creator: Deng-Ke Niu uri: https://doi.org/10.7717/peerj.2272 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Ma et al. title: Construction and use of a Cupriavidus necator H16 soluble hydrogenase promoter (PSH) fusion to gfp (green fluorescent protein) link: https://peerj.com/articles/2269 last-modified: 2016-07-26 description: Hydrogenases are metalloenzymes that reversibly catalyse the oxidation or production of molecular hydrogen (H2). Amongst a number of promising candidates for application in the oxidation of H2 is a soluble [Ni–Fe] uptake hydrogenase (SH) produced by Cupriavidus necator H16. In the present study, molecular characterisation of the SH operon, responsible for functional SH synthesis, was investigated by developing a green fluorescent protein (GFP) reporter system to characterise PSH promoter activity using several gene cloning approaches. A PSH promoter-gfp fusion was successfully constructed and inducible GFP expression driven by the PSH promoter under de-repressing conditions in heterotrophic growth media was demonstrated in the recombinant C. necator H16 cells. Here we report the first successful fluorescent reporter system to study PSH promoter activity in C. necator H16. The fusion construct allowed for the design of a simple screening assay to evaluate PSH activity. Furthermore, the constructed reporter system can serve as a model to develop a rapid fluorescent based reporter for subsequent small-scale process optimisation experiments for SH expression. creator: Bat-Erdene Jugder creator: Jeffrey Welch creator: Nady Braidy creator: Christopher P. Marquis uri: https://doi.org/10.7717/peerj.2269 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Jugder et al. title: Morphometric comparisons of plant-mimetic juvenile fish associated with plant debris observed in the coastal subtropical waters around Kuchierabu-jima Island, southern Japan link: https://peerj.com/articles/2268 last-modified: 2016-07-26 description: The general morphological shape of plant-resembling fish and plant parts were compared using a geometric morphometrics approach. Three plant-mimetic fish species, Lobotes surinamensis (Lobotidae), Platax orbicularis (Ephippidae) and Canthidermis maculata (Balistidae), were compared during their early developmental stages with accompanying plant debris (i.e., leaves of several taxa) in the coastal subtropical waters around Kuchierabu-jima Island, closely facing the Kuroshio Current. The degree of similarity shared between the plant parts and co-occurring fish species was quantified, however fish remained morphologically distinct from their plant models. Such similarities were corroborated by analysis of covariance and linear discriminant analysis, in which relative body areas of fish were strongly related to plant models. Our results strengthen the paradigm that morphological clues can lead to ecological evidence to allow predictions of behavioural and habitat choice by mimetic fish, according to the degree of similarity shared with their respective models. The resemblance to plant parts detected in the three fish species may provide fitness advantages via convergent evolutionary effects. creator: Alexya Cunha de Queiroz creator: Yoichi Sakai creator: Marcelo Vallinoto creator: Breno Barros uri: https://doi.org/10.7717/peerj.2268 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Queiroz et al. title: Phage on tap–a quick and efficient protocol for the preparation of bacteriophage laboratory stocks link: https://peerj.com/articles/2261 last-modified: 2016-07-26 description: A major limitation with traditional phage preparations is the variability in titer, salts, and bacterial contaminants between successive propagations. Here we introduce the Phage On Tap (PoT) protocol for the quick and efficient preparation of homogenous bacteriophage (phage) stocks. This method produces homogenous, laboratory-scale, high titer (up to 1010–11 PFU·ml−1), endotoxin reduced phage banks that can be used to eliminate the variability between phage propagations and improve the molecular characterizations of phage. The method consists of five major parts, including phage propagation, phage clean up by 0.22 μm filtering and chloroform treatment, phage concentration by ultrafiltration, endotoxin removal, and the preparation and storage of phage banks for continuous laboratory use. From a starting liquid lysate of > 100 mL, the PoT protocol generated a clean, homogenous, laboratory phage bank with a phage recovery efficiency of 85% within just two days. In contrast, the traditional method took upwards of five days to produce a high titer, but lower volume phage stock with a recovery efficiency of only 4%. Phage banks can be further purified for the removal of bacterial endotoxins, reducing endotoxin concentrations by over 3,000-fold while maintaining phage titer. The PoT protocol focused on T-like phages, but is broadly applicable to a variety of phages that can be propagated to sufficient titer, producing homogenous, high titer phage banks that are applicable for molecular and cellular assays. creator: Natasha Bonilla creator: Maria Isabel Rojas creator: Giuliano Netto Flores Cruz creator: Shr-Hau Hung creator: Forest Rohwer creator: Jeremy J. Barr uri: https://doi.org/10.7717/peerj.2261 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Bonilla et al. title: Emotion recognition based on customized smart bracelet with built-in accelerometer link: https://peerj.com/articles/2258 last-modified: 2016-07-26 description: Background: Recently, emotion recognition has become a hot topic in human-computer interaction. If computers could understand human emotions, they could interact better with their users. This paper proposes a novel method to recognize human emotions (neutral, happy, and angry) using a smart bracelet with built-in accelerometer.Methods: In this study, a total of 123 participants were instructed to wear a customized smart bracelet with built-in accelerometer that can track and record their movements. Firstly, participants walked two minutes as normal, which served as walking behaviors in a neutral emotion condition. Participants then watched emotional film clips to elicit emotions (happy and angry). The time interval between watching two clips was more than four hours. After watching film clips, they walked for one minute, which served as walking behaviors in a happy or angry emotion condition. We collected raw data from the bracelet and extracted a few features from raw data. Based on these features, we built classification models for classifying three types of emotions (neutral, happy, and angry).Results and Discussion: For two-category classification, the classification accuracy can reach 91.3% (neutral vs. angry), 88.5% (neutral vs. happy), and 88.5% (happy vs. angry), respectively; while, for the differentiation among three types of emotions (neutral, happy, and angry), the accuracy can reach 81.2%.Conclusions: Using wearable devices, we found it is possible to recognize human emotions (neutral, happy, and angry) with fair accuracy. Results of this study may be useful to improve the performance of human-computer interaction. creator: Zhan Zhang creator: Yufei Song creator: Liqing Cui creator: Xiaoqian Liu creator: Tingshao Zhu uri: https://doi.org/10.7717/peerj.2258 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Zhang et al. title: Flower diversity and bee reproduction in an arid ecosystem link: https://peerj.com/articles/2250 last-modified: 2016-07-26 description: Background: Diverse flower communities are more stable in floral resource production along the flowering season, but the question about how the diversity and stability of resources affect pollinator reproduction remains open. High plant diversity could favor short foraging trips, which in turn would enhance bee fitness. In addition to plant diversity, greater temporal stability of floral resources in diverse communities could favor pollinator fitness because such communities are likely to occupy the phenological space more broadly, increasing floral availability for pollinators throughout the season. In addition, this potential effect of flower diversity on bee reproduction could be stronger for generalist pollinators because they can use a broader floral spectrum. Based on above arguments we predicted that pollinator reproduction would be positively correlated to flower diversity, and to temporal stability in flower production, and that this relationship would be stronger for the most generalized pollinator species.Materials and Methods: Using structural equation models, we evaluated the effect of these variables and other ecological factors on three estimates of bee reproduction (average number of brood cells per nest per site, total number of brood cells per site, and total number of nests per site), and whether such effects were modulated by bee generalization on floral resources.Results: Contrary to our expectations, flower diversity had no effect on bee reproduction, stability in flower production had a weakly negative effect on one of the bee reproductive variables, and the strength of the fitness-diversity relationship was unrelated to bee generalization. In contrast, elevation had a negative effect on bee reproduction, despite the narrow elevation range encompassed by our sites.Discussion: Flower diversity did not affect the reproduction of the solitary bees studied here. This result could stem from the context dependence of the diversity-stability relationship, given that elevation had a positive effect on flower diversity but a negative effect on bee reproduction. Although high temporal stability in flower production is expected to enhance pollinator reproduction, in our study it had a weakly negative—instead of positive—effect on the average number of brood cells per nest. Other environmental factors that vary with elevation could influence bee reproduction. Our study focused on a small group of closely-related bee species, which cautions against generalization of our findings to other groups of pollinators. More studies are clearly needed to assess the extent to which pollinator demography is influenced by the diversity of floral resources. creator: Jimena Dorado creator: Diego P. Vázquez uri: https://doi.org/10.7717/peerj.2250 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Dorado & Vázquez