PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The influence of ecological infrastructures adjacent to crops on their carabid assemblages in intensive agroecosystems
items: Haplopelma hainanum venom induces inflammatory skin lesions
items: Identifying model violations under the multispecies coalescent model using P2C2M.SNAPP
items: Morphological variation of leaf traits in the Ternstroemia lineata species complex (Ericales: Penthaphylacaceae) in response to geographic and climatic variation
items: 16S rRNA metagenomic analysis of the bacterial community associated with turf grass seeds from low moisture and high moisture climates
items: Effects of plant growth-promoting rhizobacteria on co-inoculation with Bradyrhizobium in soybean crop: a meta-analysis of studies from 1987 to 2018
items: Genetic structure of Australian glass shrimp, Paratya australiensis, in relation to altitude
items: Dendritic complexity change in the triple transgenic mouse model of Alzheimer’s disease
items: Spraying 6-BA could alleviate the harmful impacts of waterlogging on dry matter accumulation and grain yield of wheat
items: Elucidating physiological and biochemical alterations in giant duckweed (Spirodela polyrhiza L. Schleiden) under diethyl phthalate stress: insights into antioxidant defence system

The influence of ecological infrastructures adjacent to crops on their carabid assemblages in intensive agroecosystems
type: item
type: AcademicArticle
description: Background Conserving 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. Methods We 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 Discussion Carabid 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 cr…
format: application/pdf
format: text/html
creator: Emilie Pecheur
creator: Julien Piqueray
creator: Arnaud Monty
creator: Marc Dufrêne
creator: Grégory Mahy
subject: Agricultural Science
subject: Biodiversity
subject: Conservation Biology
subject: Coupled Natural and Human Systems
description: doi:10.7717/peerj.8094
publisher: PeerJ Inc.
rights: © 2020 Pecheur et al.
abstract: Background Conserving 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. Methods We 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 Discussion Carabid 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 cr…
bibliographic citation: Pecheur et al. (2020) The influence of ecological infrastructures adjacent to crops on their carabid assemblages in intensive agroecosystems. PeerJ 8:e8094 https://doi.org/10.7717/peerj.8094
date submitted: 2018-10-31
date accepted: 2019-10-24
issued: 2020-01-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pecheur
  given name: Emilie
author list: Agent
  family name: Piqueray
  given name: Julien
author list: Agent
  family name: Monty
  given name: Arnaud
author list: Agent
  family name: Dufrêne
  given name: Marc
author list: Agent
  family name: Mahy
  given name: Grégory
doi: 10.7717/peerj.8094
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-10
copyright: ©2020 Pecheur et al.
attribution name: Pecheur et al.

Haplopelma hainanum venom induces inflammatory skin lesions
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Zhili Deng
creator: Yaling Wang
creator: Wei Shi
creator: Lei Zhou
creator: San Xu
creator: Ji Li
creator: Yiya Zhang
subject: Toxicology
subject: Dermatology
description: doi:10.7717/peerj.8264
publisher: PeerJ Inc.
rights: © 2020 Deng et al.
abstract: 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.
bibliographic citation: Deng et al. (2020) Haplopelma hainanum venom induces inflammatory skin lesions. PeerJ 8:e8264 https://doi.org/10.7717/peerj.8264
date submitted: 2019-07-16
date accepted: 2019-11-21
issued: 2020-01-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Deng
  given name: Zhili
author list: Agent
  family name: Wang
  given name: Yaling
author list: Agent
  family name: Shi
  given name: Wei
author list: Agent
  family name: Zhou
  given name: Lei
author list: Agent
  family name: Xu
  given name: San
author list: Agent
  family name: Li
  given name: Ji
author list: Agent
  family name: Zhang
  given name: Yiya
doi: 10.7717/peerj.8264
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-10
copyright: ©2020 Deng et al.
attribution name: Deng et al.

Identifying model violations under the multispecies coalescent model using P2C2M.SNAPP
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Drew J. Duckett
creator: Tara A. Pelletier
creator: Bryan C. Carstens
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genetics
description: doi:10.7717/peerj.8271
publisher: PeerJ Inc.
rights: © 2020 Duckett et al.
abstract: 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.
bibliographic citation: Duckett et al. (2020) Identifying model violations under the multispecies coalescent model using P2C2M.SNAPP. PeerJ 8:e8271 https://doi.org/10.7717/peerj.8271
date submitted: 2019-06-27
date accepted: 2019-11-22
issued: 2020-01-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Duckett
  given name: Drew J.
author list: Agent
  family name: Pelletier
  given name: Tara A.
author list: Agent
  family name: Carstens
  given name: Bryan C.
doi: 10.7717/peerj.8271
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-10
copyright: © 2020 Duckett et al.
attribution name: Duckett et al.

Morphological variation of leaf traits in the Ternstroemia lineata species complex (Ericales: Penthaphylacaceae) in response to geographic and climatic variation
type: item
type: AcademicArticle
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 com…
format: application/pdf
format: text/html
creator: Othón Alcántara-Ayala
creator: Ken Oyama
creator: César A. Ríos-Muñoz
creator: Gerardo Rivas
creator: Santiago Ramirez-Barahona
creator: Isolda Luna-Vega
subject: Biogeography
subject: Ecology
subject: Plant Science
subject: Taxonomy
subject: Population Biology
description: doi:10.7717/peerj.8307
publisher: PeerJ Inc.
rights: © 2020 Alcántara-Ayala et al.
abstract: 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 com…
bibliographic citation: Alcántara-Ayala et al. (2020) Morphological variation of leaf traits in the Ternstroemia lineata species complex (Ericales: Penthaphylacaceae) in response to geographic and climatic variation. PeerJ 8:e8307 https://doi.org/10.7717/peerj.8307
date submitted: 2019-03-30
date accepted: 2019-11-27
issued: 2020-01-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alcántara-Ayala
  given name: Othón
author list: Agent
  family name: Oyama
  given name: Ken
author list: Agent
  family name: Ríos-Muñoz
  given name: César A.
author list: Agent
  family name: Rivas
  given name: Gerardo
author list: Agent
  family name: Ramirez-Barahona
  given name: Santiago
author list: Agent
  family name: Luna-Vega
  given name: Isolda
doi: 10.7717/peerj.8307
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-10
copyright: ©2020 Alcántara-Ayala et al.
attribution name: Alcántara-Ayala et al.

16S rRNA metagenomic analysis of the bacterial community associated with turf grass seeds from low moisture and high moisture climates
type: item
type: AcademicArticle
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…
format: application/pdf
format: text/html
creator: Qiang Chen
creator: William A. Meyer
creator: Qiuwei Zhang
creator: James F. White
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.8417
publisher: PeerJ Inc.
rights: © 2020 Chen et al.
abstract: 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…
bibliographic citation: Chen et al. (2020) 16S rRNA metagenomic analysis of the bacterial community associated with turf grass seeds from low moisture and high moisture climates. PeerJ 8:e8417 https://doi.org/10.7717/peerj.8417
date submitted: 2019-08-29
date accepted: 2019-12-16
issued: 2020-01-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Qiang
author list: Agent
  family name: Meyer
  given name: William A.
author list: Agent
  family name: Zhang
  given name: Qiuwei
author list: Agent
  family name: White
  given name: James F.
doi: 10.7717/peerj.8417
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-10
copyright: © 2020 Chen et al.
attribution name: Chen et al.

Effects of plant growth-promoting rhizobacteria on co-inoculation with Bradyrhizobium in soybean crop: a meta-analysis of studies from 1987 to 2018
type: item
type: AcademicArticle
description: Background The 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. Methods A 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. Results The 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.
format: application/pdf
format: text/html
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
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.7905
publisher: PeerJ Inc.
rights: © 2020 Zeffa et al.
abstract: Background The 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. Methods A 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. Results The 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.
bibliographic citation: Zeffa et al. (2020) Effects of plant growth-promoting rhizobacteria on co-inoculation with Bradyrhizobium in soybean crop: a meta-analysis of studies from 1987 to 2018. PeerJ 8:e7905 https://doi.org/10.7717/peerj.7905
date submitted: 2019-06-10
date accepted: 2019-09-16
issued: 2020-01-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zeffa
  given name: Douglas M.
author list: Agent
  family name: Fantin
  given name: Lucas H.
author list: Agent
  family name: Koltun
  given name: Alessandra
author list: Agent
  family name: de Oliveira
  given name: André L.M.
author list: Agent
  family name: Nunes
  given name: Maria P.B.A.
author list: Agent
  family name: Canteri
  given name: Marcelo G.
author list: Agent
  family name: Gonçalves
  given name: Leandro S.A.
doi: 10.7717/peerj.7905
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-09
copyright: ©2020 Zeffa et al.
attribution name: Zeffa et al.

Genetic structure of Australian glass shrimp, Paratya australiensis, in relation to altitude
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Sharmeen Rahman
creator: Daniel Schmidt
creator: Jane M. Hughes
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Genomics
subject: Molecular Biology
subject: Freshwater Biology
description: doi:10.7717/peerj.8139
publisher: PeerJ Inc.
rights: © 2020 Rahman et al.
abstract: 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.
bibliographic citation: Rahman et al. (2020) Genetic structure of Australian glass shrimp, Paratya australiensis, in relation to altitude. PeerJ 8:e8139 https://doi.org/10.7717/peerj.8139
date submitted: 2018-10-26
date accepted: 2019-11-01
issued: 2020-01-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rahman
  given name: Sharmeen
author list: Agent
  family name: Schmidt
  given name: Daniel
author list: Agent
  family name: Hughes
  given name: Jane M.
doi: 10.7717/peerj.8139
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-09
copyright: ©2020 Rahman et al.
attribution name: Rahman et al.

Dendritic complexity change in the triple transgenic mouse model of Alzheimer’s disease
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Yu Zhang
creator: Zhenlong Xiao
creator: Zhijun He
creator: Junyu Chen
creator: Xin Wang
creator: Liang Jiang
subject: Bioinformatics
subject: Computational Biology
subject: Neuroscience
subject: Geriatrics
subject: Neurology
description: doi:10.7717/peerj.8178
publisher: PeerJ Inc.
rights: © 2020 Zhang et al.
abstract: 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.
bibliographic citation: Zhang et al. (2020) Dendritic complexity change in the triple transgenic mouse model of Alzheimer’s disease. PeerJ 8:e8178 https://doi.org/10.7717/peerj.8178
date submitted: 2019-05-10
date accepted: 2019-11-08
issued: 2020-01-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yu
author list: Agent
  family name: Xiao
  given name: Zhenlong
author list: Agent
  family name: He
  given name: Zhijun
author list: Agent
  family name: Chen
  given name: Junyu
author list: Agent
  family name: Wang
  given name: Xin
author list: Agent
  family name: Jiang
  given name: Liang
doi: 10.7717/peerj.8178
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-09
copyright: ©2020 Zhang et al.
attribution name: Zhang et al.

Spraying 6-BA could alleviate the harmful impacts of waterlogging on dry matter accumulation and grain yield of wheat
type: item
type: AcademicArticle
description: Background The 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. Methods In 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. Results The 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 prod…
format: application/pdf
format: text/html
creator: Xiaoyan Wang
creator: Daoming Liu
creator: Mingmei Wei
creator: Jianguo Man
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.8193
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Background The 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. Methods In 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. Results The 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 prod…
bibliographic citation: Wang et al. (2020) Spraying 6-BA could alleviate the harmful impacts of waterlogging on dry matter accumulation and grain yield of wheat. PeerJ 8:e8193 https://doi.org/10.7717/peerj.8193
date submitted: 2019-03-12
date accepted: 2019-11-11
issued: 2020-01-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Xiaoyan
author list: Agent
  family name: Liu
  given name: Daoming
author list: Agent
  family name: Wei
  given name: Mingmei
author list: Agent
  family name: Man
  given name: Jianguo
doi: 10.7717/peerj.8193
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-09
copyright: © 2020 Wang et al.
attribution name: Wang et al.

Elucidating physiological and biochemical alterations in giant duckweed (Spirodela polyrhiza L. Schleiden) under diethyl phthalate stress: insights into antioxidant defence system
type: item
type: AcademicArticle
description: Background The 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. Methods The 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. Results Plants 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. Conclusions Present 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.
format: application/pdf
format: text/html
creator: Ritika Sharma
creator: Rajinder Kaur
subject: Ecology
subject: Plant Science
subject: Ecotoxicology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.8267
publisher: PeerJ Inc.
rights: © 2020 Sharma and Kaur
abstract: Background The 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. Methods The 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. Results Plants 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. Conclusions Present 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.
bibliographic citation: Sharma et al. (2020) Elucidating physiological and biochemical alterations in giant duckweed (Spirodela polyrhiza L. Schleiden) under diethyl phthalate stress: insights into antioxidant defence system. PeerJ 8:e8267 https://doi.org/10.7717/peerj.8267
date submitted: 2019-05-31
date accepted: 2019-11-22
issued: 2020-01-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sharma
  given name: Ritika
author list: Agent
  family name: Kaur
  given name: Rajinder
doi: 10.7717/peerj.8267
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-09
copyright: ©2020 Sharma and Kaur
attribution name: Sharma and Kaur

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359