title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1152 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Phyllosphere bacterial assembly in citrus crop under conventional and ecological management link: https://peerj.com/articles/9152 last-modified: 2020-06-02 description: Divergences between agricultural management can result in different types of biological interactions between plants and microorganisms, which may affect food quality and productivity. Conventional practices are well-established in the agroindustry as very efficient and lucrative; however, the increasing demand for sustainable alternatives has turned attention towards agroecological approaches. Here we intend to explore microbial dynamics according to the agricultural management used, based on the composition and structure of these bacterial communities on the most environmentally exposed habitat, the phyllosphere. Leaf samples were collected from a Citrus crop (cultivated Orange) in Mogi-Guaçu (SP, Brazil), where either conventional or ecological management systems were properly applied in two different areas. NGS sequencing analysis and quantitative PCR allowed us to comprehend the phyllosphere behavior and µ-XRF (micro X-ray fluorescence) could provide an insight on agrochemical persistence on foliar tissues. Our results demonstrate that there is considerable variation in the phyllosphere community due to the management practices used in the citrus orchard, and it was possible to quantify most of this variation. Equally, high copper concentrations may have influenced bacterial abundance, having a relevant impact on the differences observed. Moreover, we highlight the intricate relationship microorganisms have with crop production, and presumably with crop yield as well. creator: Carolinne R. Carvalho creator: Armando CF Dias creator: Sérgio K. Homma creator: Elke JBN Cardoso uri: https://doi.org/10.7717/peerj.9152 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Carvalho et al. title: Limpet disturbance effects on barnacle recruitment are related to recruitment intensity but not recruit size link: https://peerj.com/articles/9190 last-modified: 2020-06-02 description: Intertidal limpets are important grazers along rocky coastlines worldwide that not only control algae but also influence invertebrates such as common barnacles. For instance, grazing limpets ingest settling barnacle cyprid larvae (hereafter cyprids) and push cyprids and barnacle recruits off the substrate. Such limpet disturbance effects (LDEs) can limit barnacle recruitment, a key demographic variable affecting barnacle population establishment and persistence. In this study, we examined limpet (Lottia cassis) disturbance to barnacle (Chthamalus dalli, Balanus glandula) recruitment on the Pacific coast of Hokkaido, Japan, as information on limpet-barnacle interactions from this region is missing. We investigated, for the first time, whether barnacle size and recruitment intensity influence LDEs on barnacle recruitment. Small barnacles may be less susceptible to LDEs than larger barnacles, because small size may reduce the propbability of limpet disturbance. Moreover, recruitment intensity can influence LDEs, as high recruitment can compensate for LDEs on barnacle recruitment density. In Hokkaido, C. dalli cyprids are smaller than B. glandula cyprids, and C. dalli recruitment is higher than B. glandula recruitment. Thus, we hypothesized that LDEs on C. dalli recruitment would be weaker than those on B. glandula recruitment. To test our hypothesis, we conducted a field experiment during which we manipulated limpet presence/absence on the interior surfaces of ring-shaped cages. After four weeks, we measured barnacle recruitment and recruit size on the interior surfaces of the cages and found negative LDEs on C. dalli and B. glandula recruitment and recruit size. As hypothesized, the LDEs on C. dalli recruitment were weaker than the LDEs on B. glandula recruitment. Additionally, C. dalli recruits were smaller than B. glandula recruits. However, the LDEs on C. dalli recruit size were as strong as the LDEs on B. glandula recruit size, indicating that the smaller C. dalli recruits are not less susceptible to LDEs than B. glandula recruits. Since C. dalli recruitment was higher than B. glandula recruitment, we propose that the higher C. dalli recruitment compensated for the LDEs on C. dalli recruitment. Our findings indicate that the detected differences in LDEs on barnacle recruitment are related to barnacle recruitment intensity but not recruit size. creator: Julius A. Ellrich creator: Takefumi Yorisue creator: Kyosuke Momota uri: https://doi.org/10.7717/peerj.9190 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ellrich et al. title: Repurposing a traditional Japanese method of pest control for wintering pine moths, Komo-trap, for use against summer and winter populations of fall webworms link: https://peerj.com/articles/9244 last-modified: 2020-06-02 description: BackgroundThe fall webworm, Hyphantria cunea Drury (Lepidoptera: Erebidae), is a widespread invasive species. It is native to North America, ranging from southern Canada to northern Mexico. During and after the 1940s, this pest was accidentally introduced in many parts of Europe and Asia. It has now spread to more than 30 countries. The larvae feed on leaves of a wide range of tree species, including ones used as street trees in cities, causing an increase in urban management cost. Although several pest management methods have been employed, pest damage continues especially in newly invaded areas. In this study, we examined the effect and cost-effectiveness of the komo-trap, traditionally used in Japan to reduce the population of larvae of the pine moth Dendrolimus spectabilis Butler (Lepidoptera: Lasiocampidae). This trap, which is safe for people and ecosystems, has not yet been applied to trap the fall webworm.MethodsIn two seasons of 2017, we set komo-traps on street trees in Hakodate City, Japan. We counted the numbers of captured fall webworms compared with controls. We also monitored other species to evaluate any nontarget effects of the trap.ResultsOne komo, the material cost of which is about 1.10 USD, captured 43.8 fall webworms on average in summer and 27.2 in the fall. The values were significantly larger than those of the controls, which were 0.07 in summer and 0.14 in winter. Bycatch of other species was minimal in summer, whereas in the fall one komo, on average, caught 10.7 woodlice Porcellio sp. or spp. (Isopoda: Porcellionidae).DiscussionThe komo-trap is effective in capturing fall webworm. The cost performance of the trap is very favorable, and the nontarget effects can be reduced by using the trap in summer only. The komo-trap would complement other control methods such as tree pruning. Because its cost is low, we recommend that the komo-trap be introduced as a larger-scale trial. creator: Osamu K. Mikami creator: Misaki Takamatsu creator: Rika Yarita uri: https://doi.org/10.7717/peerj.9244 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Mikami et al. title: The severity of mobile phone addiction and its relationship with quality of life in Chinese university students link: https://peerj.com/articles/8859 last-modified: 2020-06-01 description: ObjectiveThis study examined the severity of mobile phone addiction and its relationship with quality of life (QOL) in Chinese university students.MethodsA total of 2,312 university students from Macao, Hong Kong and mainland China participated in this cross-sectional study. The Mobile Phone Addiction Scale (MPAS), and the World Health Organization Quality of Life-Brief version (WHOQOL-BREF) rating instruments were used to assess the severity of mobile phone addiction and QOL, respectively.ResultsCompared to students in mainland China, those in Macao and Hong Kong were more likely to have excessive mobile phone use. Multiple linear regression revealed that high academic pressure and poor academic performance were positively associated, while male gender, greater interest in academic major and long sleep duration were negatively associated with the severity of mobile phone addiction. Students addicted to mobile phone use had significantly lower scores across all QOL domains.ConclusionDue to the adverse impact of excessive mobile phone use on QOL, public education and effective preventive measures should be developed for Chinese university students. creator: Lu Li creator: Grace K.I. Lok creator: Song Li Mei creator: Xi Ling Cui creator: Lin Li creator: Chee H. Ng creator: Gabor S. Ungvari creator: Juan Zhang creator: Feng Rong An creator: Yu Tao Xiang uri: https://doi.org/10.7717/peerj.8859 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Li et al. title: Prognostic value of KRAS mutation status in colorectal cancer patients: a population-based competing risk analysis link: https://peerj.com/articles/9149 last-modified: 2020-06-01 description: BackgroundTo use competing analyses to estimate the prognostic value of KRAS mutation status in colorectal cancer (CRC) patients and to build nomogram for CRC patients who had KRAS testing.MethodThe cohort was selected from the Surveillance, Epidemiology, and End Results database. Cumulative incidence function model and multivariate Fine-Gray regression for proportional hazards modeling of the subdistribution hazard (SH) model were used to estimate the prognosis. An SH model based nomogram was built after a variable selection process. The validation of the nomogram was conducted by discrimination and calibration with 1,000 bootstraps.ResultsWe included 8,983 CRC patients who had KRAS testing. SH model found that KRAS mutant patients had worse CSS than KRAS wild type patients in overall cohort (HR = 1.10 (95% CI [1.04–1.17]), p < 0.05), and in subgroups that comprised stage III CRC (HR = 1.28 (95% CI [1.09–1.49]), p < 0.05) and stage IV CRC (HR = 1.14 (95% CI [1.06–1.23]), p < 0.05), left side colon cancer (HR = 1.28 (95% CI [1.15–1.42]), p < 0.05) and rectal cancer (HR = 1.23 (95% CI [1.07–1.43]), p < 0.05). We built the SH model based nomogram, which showed good accuracy by internal validation of discrimination and calibration. Calibration curves represented good agreement between the nomogram predicted CRC caused death and actual observed CRC caused death. The time dependent area under the curve of receiver operating characteristic curves (AUC) was over 0.75 for the nomogram.ConclusionThis is the first population based competing risk study on the association between KRAS mutation status and the CRC prognosis. The mutation of KRAS indicated a poor prognosis of CRC patients. The current competing risk nomogram would help physicians to predict cancer specific death of CRC patients who had KRAS testing. creator: Dongjun Dai creator: Yanmei Wang creator: Liyuan Zhu creator: Hongchuan Jin creator: Xian Wang uri: https://doi.org/10.7717/peerj.9149 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Dai et al. title: Developments in marine invertebrate primary culture reveal novel cell morphologies in the model bivalve Crassostrea gigas link: https://peerj.com/articles/9180 last-modified: 2020-06-01 description: Cell culture provides useful model systems used in a wide range of biological applications, but its utility in marine invertebrates is limited due to the lack of immortalised cell lines. Primary cell and tissue cultures are typically used but remain poorly characterised for oysters, which can cause issues with experimental consistency and reproducibility. Improvements to methods of repeatable isolation, culture, and characterisation of oyster cells and tissues are required to help address these issues. In the current study, systematic improvements have been developed to facilitate the culture of primary cells from adult Pacific oyster tissues and identify novel cell morphologies that have not been reported previously. Cultures analysed by light microscopy, qPCR, and live cell imaging demonstrated maintenance of live, metabolically active Pacific oyster cells for several weeks post-explant. Interestingly, whole hearts dissected from adult oysters were found to continue contracting rhythmically up to 8 weeks after being transferred to a tissue culture system. Mantle tissue explants were also actively moving in the culture system. These improvements in primary cell culture of bivalves may be beneficial for research in ecotoxicology, virology, immunology, and genetic resistance to disease. creator: Robert W.A. Potts creator: Alejandro P. Gutierrez creator: Yennifer Cortés-Araya creator: Ross D. Houston creator: Tim P. Bean uri: https://doi.org/10.7717/peerj.9180 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Potts et al. title: Woodlice change the habitat use of spiders in a different food chain link: https://peerj.com/articles/9184 last-modified: 2020-06-01 description: BackgroundIn old field systems, the common woodlouse may have an indirect effect on a nursery web spider. Woodlice and nursery web spiders feed in different food chains, yet previous work demonstrated that the presence of woodlice is correlated with higher predation success by nursery web spiders upon their grasshopper prey. This finding suggested a new hypothesis which links two seemingly disparate food chains: when woodlice are present, the spider predator or the grasshopper prey changes their location in the vegetative canopy in a way that increases their spatial overlap and therefore predation rate. However, warming temperatures may complicate this phenomenon. The spider cannot tolerate thermal stress, meaning warming temperatures may cause the spider to move downwards in the vegetative canopy or otherwise alter its response to woodlice. Therefore, we would expect warming and woodlice presence to have an interactive effect on predation rate.MethodsWe conducted behavioral experiments in 2015, 2017, and 2018 to track habitat domains—the use of the vegetative canopy space by grasshoppers and spiders—in experimental cages. Then, we used three models of spider movement to try to explain the response of spiders to woodlice: expected net energy gain, signal detection theory, and individual-based modelling.ResultsHabitat domain observations revealed that spiders shift upward in the canopy when woodlice are present, but the corresponding effect on grasshopper prey survival was variable over the different years of study. Under warming conditions, spiders remained lower in the canopy regardless of the presence of woodlice, suggesting that thermal stress is more important than the effect of woodlice. Our modelling results suggest that spiders do not need to move away from woodlice to maximize net energy gain (expected net energy gain and signal detection theory models). Instead spider behavior is consistent with the null hypothesis that they move away from unsuccessful encounters with woodlice (individual-based simulation). We conclude that mapping how predator behavior changes across biotic (e.g. woodlouse presence) and abiotic conditions (e.g. temperature) may be critical to anticipate changes in ecosystem dynamics. creator: Stefanie M. Guiliano creator: Cerina M. Karr creator: Nathalie R. Sommer creator: Robert W. Buchkowski uri: https://doi.org/10.7717/peerj.9184 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Guiliano et al. title: The prediction of swim start performance based on squat jump force-time characteristics link: https://peerj.com/articles/9208 last-modified: 2020-06-01 description: BackgroundDepending on the stroke and distances of the events, swim starts have been estimated to account for 0.8% to 26.1% of the overall race time, with the latter representing the percentage in a 50 m sprint front crawl event (Cossor & Mason, 2001). However, it is still somewhat unclear what are the key physiological characteristics underpinning swim start performance. The primary aim of this study was to develop a multiple regression model to determine key lower body force-time predictors using the squat jump for swim start performance as assessed by time to 5 m and 15 m in national and international level swimmers. A secondary aim was to determine if any differences exist between males and females in jump performance predictors for swim start performance.MethodsA total of 38 males (age 21 ±  3.1 years, height 1.83 ±  0.08 m, body mass 76.7 ±  10.2 kg) and 34 females (age 20.1 ±  3.2 years, height 1.73 ±  0.06 m, body mass 64.8 ±  8.4 kg) who had competed at either an elite (n = 31) or national level (n = 41) participated in this study. All tests were performed on the same day, with participants performing three bodyweight squat jumps on a force platform, followed by three swim starts using their main swimming stroke. Swim start performance was quantified via time to 5 m and 15 m using an instrumented starting block.ResultsStepwise multiple linear regression with quadratic fitting identified concentric impulse and concentric impulse2 as statistically significant predictors for time to 5 m (R2 = 0.659) in males. With time to 15 m, concentric impulse, age and concentric impulse2 were statistically significant predictors for males (R2 = 0.807). A minimum concentric impulse of 200–230 N.s appears required for faster times to 5 m and 15 m, with any additional impulse production not being associated with a reduction in swim start times for most male swimmers. Concentric impulse, Reactive strength index modified and concentric mean power were identified as statistically significant predictors for female swimmers to time to 5 m (R2 = 0.689). Variables that were statistically significant predictors of time to 15 m in females were concentric impulse, body mass, concentric rate of power development and Reactive strength index modified (R2 = 0.841).DiscussionThe results of this study highlight the importance of lower body power and strength for swim start performance, although being able to produce greater than 200 or 230 N.s concentric impulse in squat jump did not necessarily increase swim start performance over 5 m and 15 m, respectively. Swimmers who can already generate greater levels of concentric impulse may benefit more from improving their rate of force development and/or technical aspects of the swim start performance. The sex-related differences in key force-time predictors suggest that male and female swimmers may require individualised strength and conditioning programs and regular monitoring of performance. creator: Shiqi Thng creator: Simon Pearson creator: Evelyne Rathbone creator: Justin W.L. Keogh uri: https://doi.org/10.7717/peerj.9208 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Thng et al. title: New insights into the giant mustelids (Mammalia, Carnivora, Mustelidae) from Langebaanweg fossil site (West Coast Fossil Park, South Africa, early Pliocene) link: https://peerj.com/articles/9221 last-modified: 2020-06-01 description: Giant mustelids are a paraphyletic group of mustelids found in the Neogene of Eurasia, Africa and North America. Most are known largely from dental remains, with their postcranial skeleton mostly unknown. Here, we describe new craniodental and postcranial remains of the large lutrine Sivaonyx hendeyi and the leopard-size gulonine Plesiogulo aff. monspessulanus from the early Pliocene site Langebaanweg, South Africa. The new material of the endemic S. hendeyi, includes upper incisors and premolars, and fragmentary humerus, ulna and a complete astragalus. Its postcrania shares more traits with the living Aonyx capensis than the late Miocene Sivaonyx beyi from Chad. Sivaonyx hendeyi could therefore be tentatively interpreted as a relatively more aquatic taxon than the Chadian species, comparable to A. capensis. The new specimens of Plesiogulo comprise two edentulous maxillae, including one of a juvenile individual with incomplete decidual dentition, and a fragmentary forelimb of an adult individual. The new dental measurements point to this form being amongst the largest specimens of the genus. Both P3-4 differs from the very large species Plesiogulo botori from late Miocene of Kenya and Ethiopia. This confirms the existence of two distinct large species of Plesiogulo in Africa during the Mio/Pliocene, P. botori in the Late Miocene of Eastern Africa (6.1–5.5 Ma) and Plesiogulo aff. monspessulanus at the beginning of the Pliocene in southern Africa (5.2 Ma). Lastly, we report for the first time the presence of both Sivaonyx and Plesiogulo in MPPM and LQSM at Langebaanweg, suggesting that the differences observed from the locality may be produced by sedimentation or sampling biases instead of temporal replacement within the carnivoran guild. creator: Alberto Valenciano creator: Romala Govender uri: https://doi.org/10.7717/peerj.9221 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Valenciano and Govender title: The transferability of microsatellite loci from a homoploid to a polyploid hybrid complex: an example from fine-leaved Festuca species (Poaceae) link: https://peerj.com/articles/9227 last-modified: 2020-06-01 description: BackgroundMicrosatellite loci, or single sequence repeats (SSR), are widely used as powerful markers in population genetics. They represent an attractive tool for studying plants such as grasses, whose evolution is driven by hybridisation and polyploidization. However, the development of microsatellite markers has been challenging and time-consuming, especially for non-model organisms lacking available genome-wide sequence data. One straightforward and low-cost approach is to transfer the SSR loci developed for one species, or complex, to another closely-related one. This work evaluates the transferability of microsatellite loci from homoploid to allopolyploid complexes of fine-leaved Festuca species and to assess their use in two new species. The studied complex (F. amethystina—F. tatrae) is a useful model for research on the local adaptability of grasses with different ploidy levels. Since both species can be considered as rare or threatened (F. tatrae—as a mountain and narrow endemic species and F. amethystina—a mountain species with relict lowland populations), any tool enabling studies on genetic diversity and population genetics, such as SSR markers, could also be very useful in a conservation context.MethodsThe ploidy level within populations was estimated using flow cytometry. One diploid and one tetraploid population of F. amethystina and a diploid population of F. tatrae were chosen to test the transferability of SSR loci. Because our work describes the transfer of SSR nuclear markers designed originally for F. gautieri, a phylogenetic tree was prepared based on the ITS marker to assess the genetic distance between the studied complexes. The PCR products were separated on a high-resolution agarose gel, intended for SSR marker analysis. Appropriate solutions for the allotetraploid population and whole mixed-ploidy complex were implemented.ResultsFlow cytometry confirmed earlier data regarding DNA content in the investigated species and cytotypes. The phylogenetic ITS tree indicated a small genetic distance between F. gautieri complexes and the studied species. Ten microsatellite markers were successfully transferred. All markers were polymorphic. In total, 163 different alleles were scored from the 10 SSR loci. PCoA of accessions revealed well-separated groups corresponding to studied populations. Over 60% of the total variance is explained by differentiation within populations and one third among them.ConclusionsThe transferred markers are valid tools for the study of population genetics and inheritance relationships within cytotypes and species and between them. The presented markers can be used to study inbreeding depression in the Festuca species, and variations in the degrees of genetic diversity between different cytotypes in mountain and lowland areas. Our findings can also be applied to study conservation strategies for ensuring biodiversity at the genetic level in polyploid complexes. creator: Przemysław P. Tomczyk creator: Marcin Kiedrzyński creator: Iwona Jedrzejczyk creator: Monika Rewers creator: Pawel Wasowicz uri: https://doi.org/10.7717/peerj.9227 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tomczyk et al.