title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1218
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: The influence of ecological infrastructures adjacent to crops on their carabid assemblages in intensive agroecosystems
link: https://peerj.com/articles/8094
last-modified: 2020-01-10
description: BackgroundConserving biodiversity and enhancing ecosystem services of interest in intensive agroecosystems is a major challenge. Perennial ecological infrastructures (EIs), such as hedges and grassy strips, and annual EI under Agri-Environment Schemes appear to be good candidates to promote both. Our study focused on carabids, an indicator group responding both at the species and functional trait level to disturbances and supporting pest control and weed seed consumption services.MethodsWe compared carabid assemblages at the species and functional traits levels, sampled via pitfall trapping, in three types of EIs (hedges, grassy strips and annual flower strips) and crops. We also tested via GLMs the effect of (1) the type of EI at the crops’ border and (2) the distance from the crops’ border (two meters or 30 meters) on carabid assemblages of crops. Tested variables comprised: activity-density, species richness, functional dispersion metrics (FDis) and proportions of carabids by functional categories (Diet: generalist predators/specialist predators/seed-eaters; Size: small/medium/large/very large; Breeding period: spring/autumn).Results and DiscussionCarabid assemblages on the Principal Coordinate Analysis split in two groups: crops and EIs. Assemblages from all sampled EIs were dominated by mobile generalist predator species from open-land, reproducing in spring. Assemblages of hedges were poor in activity-density and species richness, contrarily to grassy and annual flower strips. Differences in carabid assemblages in crops were mainly driven by the presence of hedges. The presence of hedges diminished the Community Weighted Mean size of carabids in crops, due to an increased proportion of small (<5 mm) individuals, while distance from crops’ border favoured large (between 10–15 mm) carabids. Moreover, even if they were attracted by EIs, granivorous carabid species were rare in crops. Our results underlie the importance of local heterogeneity when adapting crops’ borders to enhance carabid diversity and question the relevance of hedge implantation in intensive agrolandscapes, disconnected from any coherent ecological network. Moreover, this study emphasizes the difficulty to modify functional assemblages of crops for purposes of ecosystem services development, especially for weed seed consumption, as well as the role of distance from the crops’ border in the shaping of crop carabid assemblages.
creator: Emilie Pecheur
creator: Julien Piqueray
creator: Arnaud Monty
creator: Marc Dufrêne
creator: Grégory Mahy
uri: https://doi.org/10.7717/peerj.8094
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Pecheur et al.

title: Haplopelma hainanum venom induces inflammatory skin lesions
link: https://peerj.com/articles/8264
last-modified: 2020-01-10
description: The Haplopelma hainanum is a species of theraphosid spider from China. Its large size and charming appearance make this species a popular pet. According to a previous study, theraphosid spider bites can induce pain, erythema, and edema in humans and can present more severely in domestic animals. The pathological consequences of envenomation by H. hainanum remain unclear. In this study, we investigated the effects and mechanisms of H. hainanum envenomation in mice. We showed that the venom induced slight swelling, intense inflammatory response, and increased the microvascular density in mice skin. Moreover, we found that 50 µg/ml of the spider’s venom induced IL-1β expression in both HaCaT cells and fibroblast cells, but repressed CXCL10 expression in fibroblasts. The venom significantly induced cell senescence and repressed cell proliferation and migration in both HaCaT cells and fibroblast cells. Finally, we examined the expression of Nav channel in HaCaT and fibroblast cells and found that H. hainanum venom effectively inhibited Na+ currents in HaCaT cells. Our study calls for further investigation of the pathological consequences and potential mechanisms of H. hainanum envenomation. This information might assist in the development of suitable therapy.
creator: Zhili Deng
creator: Yaling Wang
creator: Wei Shi
creator: Lei Zhou
creator: San Xu
creator: Ji Li
creator: Yiya Zhang
uri: https://doi.org/10.7717/peerj.8264
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Deng et al.

title: Identifying model violations under the multispecies coalescent model using P2C2M.SNAPP
link: https://peerj.com/articles/8271
last-modified: 2020-01-10
description: Phylogenetic estimation under the multispecies coalescent model (MSCM) assumes all incongruence among loci is caused by incomplete lineage sorting. Therefore, applying the MSCM to datasets that contain incongruence that is caused by other processes, such as gene flow, can lead to biased phylogeny estimates. To identify possible bias when using the MSCM, we present P2C2M.SNAPP. P2C2M.SNAPP is an R package that identifies model violations using posterior predictive simulation. P2C2M.SNAPP uses the posterior distribution of species trees output by the software package SNAPP to simulate posterior predictive datasets under the MSCM, and then uses summary statistics to compare either the empirical data or the posterior distribution to the posterior predictive distribution to identify model violations. In simulation testing, P2C2M.SNAPP correctly classified up to 83% of datasets (depending on the summary statistic used) as to whether or not they violated the MSCM model. P2C2M.SNAPP represents a user-friendly way for researchers to perform posterior predictive model checks when using the popular SNAPP phylogenetic estimation program. It is freely available as an R package, along with additional program details and tutorials.
creator: Drew J. Duckett
creator: Tara A. Pelletier
creator: Bryan C. Carstens
uri: https://doi.org/10.7717/peerj.8271
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Duckett et al.

title: Morphological variation of leaf traits in the Ternstroemia lineata species complex (Ericales: Penthaphylacaceae) in response to geographic and climatic variation
link: https://peerj.com/articles/8307
last-modified: 2020-01-10
description: Variation in leaf morphology is correlated with environmental variables, such as precipitation, temperature and soil composition. Several studies have pointed out that individual plasticity can largely explain the foliar phenotypic differences observed in populations due to climatic change and have suggested that the environment plays an important role in the evolution of plant species by selecting for phenotypic variation. Thus, the study of foliar morphology in plant populations can help us identify the environmental factors that have potentially influenced the process of species diversification. In this study, we analyzed morphological variation in the leaf traits of the Ternstroemia lineata species complex (Penthaphylacaceae) and its relation to climatic variables across the species distribution area to identify the patterns of morphological differentiation within this species complex. Based on the collected leaves of 270 individuals from 32 populations, we analyzed nine foliar traits using spatial interpolation models and multivariate statistics. A principal component analysis identified three main morphological traits (leaf length and two leaf shape variables) that were used to generate interpolated surface maps to detect discrete areas delimited by zones of rapid change in the values of the morphological traits. We identified a mosaic coarse-grain pattern of geographical distribution in the variation of foliar traits. According to the interpolation maps, we could define nine morphological groups and their geographic distributions. Longer leaves, spatulate leaves and the largest foliar area were located in sites with lower precipitation and higher seasonality of precipitation following a northwest–southeast direction and following significant latitudinal and longitudinal gradients. According to the phenogram of the relationships of the nine morphological groups based on morphological similarity, the putative species and subspecies of the T. lineata species complex did not show a clear pattern of differentiation. In this study, we found a complex pattern of differentiation with some isolated populations and some other contiguous populations differentiated by different traits. Further genetic and systematic studies are needed to clarify the evolutionary relationships in this species complex.
creator: Othón Alcántara-Ayala
creator: Ken Oyama
creator: César A. Ríos-Muñoz
creator: Gerardo Rivas
creator: Santiago Ramirez-Barahona
creator: Isolda Luna-Vega
uri: https://doi.org/10.7717/peerj.8307
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Alcántara-Ayala et al.

title: 16S rRNA metagenomic analysis of the bacterial community associated with turf grass seeds from low moisture and high moisture climates
link: https://peerj.com/articles/8417
last-modified: 2020-01-10
description: Turfgrass investigators have observed that plantings of grass seeds produced in moist climates produce seedling stands that show greater stand evenness with reduced disease compared to those grown from seeds produced in dry climates. Grass seeds carry microbes on their surfaces that become endophytic in seedlings and promote seedling growth. We hypothesize that incomplete development of the microbiome associated with the surface of seeds produced in dry climates reduces the performance of seeds. Little is known about the influence of moisture on the structure of this microbial community. We conducted metagenomic analysis of the bacterial communities associated with seeds of three turf species (Festuca rubra, Lolium arundinacea, and Lolium perenne) from low moisture (LM) and high moisture (HM) climates. The bacterial communities were characterized by Illumina high-throughput sequencing of 16S rRNA V3–V4 regions. We performed seed germination tests and analyzed the correlations between the abundance of different bacterial groups and seed germination at different taxonomy ranks. Climate appeared to structure the bacterial communities associated with seeds. LM seeds vectored mainly Proteobacteria (89%). HM seeds vectored a denser and more diverse bacterial community that included Proteobacteria (50%) and Bacteroides (39%). At the genus level, Pedobacter (20%), Sphingomonas (13%), Massilia (12%), Pantoea (12%) and Pseudomonas (11%) were the major genera in the bacterial communities regardless of climate conditions. Massilia, Pantoea and Pseudomonas dominated LM seeds, while Pedobacter and Sphingomonas dominated HM seeds. The species of turf seeds did not appear to influence bacterial community composition. The seeds of the three turf species showed a core microbiome consisting of 27 genera from phyla Actinobacteria, Bacteroidetes, Patescibacteria and Proteobacteria. Differences in seed-vectored microbes, in terms of diversity and density between high and LM climates, may result from effects of moisture level on the colonization of microbes and the development of microbe community on seed surface tissues (adherent paleas and lemmas). The greater diversity and density of seed vectored microbes in HM climates may benefit seedlings by helping them tolerate stress and fight disease organisms, but this dense microbial community may also compete with seedlings for nutrients, slowing or modulating seed germination and seedling growth.
creator: Qiang Chen
creator: William A. Meyer
creator: Qiuwei Zhang
creator: James F. White
uri: https://doi.org/10.7717/peerj.8417
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Chen et al.

title: Effects of plant growth-promoting rhizobacteria on co-inoculation with Bradyrhizobium in soybean crop: a meta-analysis of studies from 1987 to 2018
link: https://peerj.com/articles/7905
last-modified: 2020-01-09
description: BackgroundThe co-inoculation of soybean with Bradyrhizobium and other plant growth-promoting rhizobacteria (PGPR) is considered a promising technology. However, there has been little quantitative analysis of the effects of this technique on yield variables. In this context, the present study aiming to provide a quantification of the effects of the co-inoculation of Bradyrhizobium and PGPR on the soybean crop using a meta-analysis approach.MethodsA total of 42 published articles were examined, all of which considered the effects of co-inoculation of PGPR and Bradyrhizobium on the number of nodules, nodule biomass, root biomass, shoot biomass, shoot nitrogen content, and grain yield of soybean. We also determined whether the genus of the PGPR used as co-inoculant, as well as the experimental conditions, altered the effect size of the PGPR.ResultsThe co-inoculation technology resulted in a significant increase in nodule number (11.40%), nodule biomass (6.47%), root biomass (12.84%), and shoot biomass (6.53%). Despite these positive results, no significant increase was observed in shoot nitrogen content and grain yield. The response of the co-inoculation varied according to the PGPR genus used as co-inoculant, as well as with the experimental conditions. In general, the genera Azospirillum, Bacillus, and Pseudomonas were more effective than Serratia. Overall, the observed increments were more pronounced under pot than that of field conditions. Collectively, this study summarize that co-inoculation improves plant development and increases nodulation, which may be important in overcoming nutritional limitations and potential stresses during the plant growth cycle, even though significant increases in grain yield have not been evidenced by this data meta-analysis.
creator: Douglas M. Zeffa
creator: Lucas H. Fantin
creator: Alessandra Koltun
creator: André L.M. de Oliveira
creator: Maria P.B.A. Nunes
creator: Marcelo G. Canteri
creator: Leandro S.A. Gonçalves
uri: https://doi.org/10.7717/peerj.7905
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Zeffa et al.

title: Genetic structure of Australian glass shrimp, Paratya australiensis, in relation to altitude
link: https://peerj.com/articles/8139
last-modified: 2020-01-09
description: Paratya australiensis Kemp (Decapoda: Atyidae) is a widely distributed freshwater shrimp in eastern Australia. The species has been considered as an important stream organism for studying genetics, dispersal, biology, behaviour and evolution in atyids and is a major food source for stream dwelling fishes. Paratya australiensis is a cryptic species complex consisting of nine highly divergent mitochondrial DNA lineages. Previous studies in southeast Queensland showed that “lineage 4” favours upstream sites at higher altitudes, with cooler water temperatures. This study aims to identify putative selection and population structure between high elevation and low elevation populations of this lineage at relatively small spatial scales. Sample localities were selected from three streams: Booloumba Creek, Broken Bridge Creek and Obi Obi Creek in the Conondale Range, southeast Queensland. Six sample localities, consisting of 142 individuals in total were sequenced using double digest Restriction Site Associated DNA-sequencing (ddRAD-seq) technique. Among the 142 individuals, 131 individuals shared 213 loci. Outlier analysis on 213 loci showed that 27 loci were putatively under selection between high elevation and low elevation populations. Outlier analysis on individual streams was also done to test for parallel patterns of adaptation, but there was no evidence of a parallel pattern. Population structure was observed using both the 27 outliers and 186 neutral loci and revealed similar population structure in both cases. Therefore, we cannot differentiate between selection and drift here. The highest genetic differentiation was observed between high elevation and low elevation populations of Booloumba Creek, with small levels of differentiation in the other two streams.
creator: Sharmeen Rahman
creator: Daniel Schmidt
creator: Jane M. Hughes
uri: https://doi.org/10.7717/peerj.8139
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Rahman et al.

title: Dendritic complexity change in the triple transgenic mouse model of Alzheimer’s disease
link: https://peerj.com/articles/8178
last-modified: 2020-01-09
description: Alzheimer’s disease (AD) is an irreversible, neurodegenerative disease that is characterized by memory impairment and executive dysfunction. However, the change of fine structure of neuronal morphology remains unclear in the AD model mouse. In this study, high-resolution mouse brain sectional images were scanned by Micro-Optical Sectioning Tomography (MOST) technology and reconstructed three-dimensionally to obtain the pyramidal neurons. The method of Sholl analysis was performed to analyze the neurons in the brains of 6- and 12-month-old AD mice. The results showed that dendritic complexity was not affected in the entorhinal cortex between 6-month-old mice and 12-month-old mice. The dendritic complexity had increased in the primary motor cortex and CA1 region of hippocampus of 12- month-old mice compared with 6-month-old mice. On the contrary, dendritic complexity in the prefrontal cortex was decreased significantly between 6-month-old and 12-month-old mice. To our knowledge, this is the first study to provide high-resolution brain images of triple transgenic AD mice for statistically analyzing neuronal dendrite complexity by MOST technology to reveal the morphological changes of neurons during AD progression.
creator: Yu Zhang
creator: Zhenlong Xiao
creator: Zhijun He
creator: Junyu Chen
creator: Xin Wang
creator: Liang Jiang
uri: https://doi.org/10.7717/peerj.8178
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Zhang et al.

title: Spraying 6-BA could alleviate the harmful impacts of waterlogging on dry matter accumulation and grain yield of wheat
link: https://peerj.com/articles/8193
last-modified: 2020-01-09
description: BackgroundThe middle and lower reaches of the Yangtze River plain produce the second highest amount of wheat in China; however, waterlogging is an important environmental factor that substantially affects the yield production of wheat (Triticum aestivum L.) in this region.MethodsIn this study, seven treatments were implemented, including no waterlogging and exogenous 6-benzylaminopurine (6-BA) as a control (CK); waterlogging at booting (BW), anthesis (AW) and 15 days after anthesis (DAA, FW); and spraying 6-BA before waterlogging at booting (BW-6BA), anthesis (AW-6BA) and 15 DAA (FW-6BA), to determine the ability of 6-BA to alleviate the harmful impact of waterlogging on aboveground biomass production and grain yield. The widely cultivated wheat cultivar “Zhengmai 9023” was used.ResultsThe results showed that more than 190.0 mm of rainfall, which accounted for approximately 45.0% of the precipitation over the whole wheat growing season, was distributed after the booting stage (April and May). In all waterlogged treatments, the photosynthetic rate, aboveground biomass and grain yield decreased, but the differences between the CK and the FW treatment were not significant. The grain yield decreased by 18.38%, 41.79% and 5.67% in the BW, AW and FW treatments, respectively. Spraying 6-BA before waterlogging enhanced the root activities after anthesis and then decreased the malondialdehyde concentrations of the flag leaves and the third leaf, increased the photosynthetic rate of the flag leaves and enhanced aboveground biomass and grain yield. Among the increments between the treatments, the increments between the BW and BW-6BA treatments were the largest, but between the FW and FW-6BA were smallest. In comparison to the other waterlogging treatments, the grain yields from the FW and FW-6BA treatments were significantly higher because of the higher kernel numbers per spike. The results indicated that waterlogging after the booting stage restrained the dry matter production of winter wheat, but spraying 6-BA before waterlogging slowed the plant senescence rate and reduced grain yield loss.
creator: Xiaoyan Wang
creator: Daoming Liu
creator: Mingmei Wei
creator: Jianguo Man
uri: https://doi.org/10.7717/peerj.8193
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Wang et al.

title: Elucidating physiological and biochemical alterations in giant duckweed (Spirodela polyrhiza L. Schleiden) under diethyl phthalate stress: insights into antioxidant defence system
link: https://peerj.com/articles/8267
last-modified: 2020-01-09
description: BackgroundThe emollient properties of phthalates have led to their extensive production and intense use in plastic products. Owing to their weak covalent bonding with the plastic polymers, phthalates enter into the environment during their manufacturing, processing, disposal, consequently found their way directly into water sources, soil, and sediments.MethodsThe present study envisaged the toxic effects of diethyl phthalate (DEP) on physiological and biochemical attributes of Spirodela polyrhiza, when exposed to various concentrations of DEP (0, 10, 20, 40, 80, 100, 200, and 400 ppm) for short term exposure period of seven days.ResultsPlants of S. polyrhiza accumulated significant amount of DEP (112 mg kg−1 fw) when exposed to various concentrations of DEP for seven days. Results depicted that DEP toxicity significantly (p ≤ 0.05) affected growth parameters and pigments in treated S. polyrhiza as compared to control. Further, high doses of DEP (400 ppm) caused significant decrement in carbohydrate (86%), protein (76%) and elevation in MDA content (42%). Meanwhile, DEP altered the activities of antioxidant enzymes (SOD, CAT, APX, GPX and GR) along with the induction of enhanced levels of proline, electrolyte leakage and phenolic content. Scanning electron microscopic and confocal studies also confirmed oxidative stress in plants under DEP stress.ConclusionsPresent findings will help understand the accumulation, tolerance, and detoxification mechanisms of DEP by S. polyrhiza to counteract the effects of reactive oxygen species (ROS), along with the evaluation of environmental threat for aquatic plants in aquatic ecosystems.
creator: Ritika Sharma
creator: Rajinder Kaur
uri: https://doi.org/10.7717/peerj.8267
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Sharma and Kaur