PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The role of solar radiation and tidal emersion on oxidative stress and glutathione synthesis in mussels exposed to air
items: The effect of FMT and vitamin C on immunity-related genes in antibiotic-induced dysbiosis in mice
items: Higher serum β2-microglobulin is a predictive biomarker for cognitive impairment in spinal cord injury
items: Estimating the impact of environmental management on strawberry yield using publicly available agricultural data in South Korea
items: Necked strawberries are especially susceptible to cracking
items: Zinc solubilizing bacteria and their potential as bioinoculant for growth promotion of green soybean (Glycine max L. Merr.)
items: Precipitation extremes observed over and around the Taklimakan Desert, China
items: CPJSdraw: analysis and visualization of junction sites of chloroplast genomes
items: Regenerative plantlets with improved agronomic characteristics caused by anther culture of tetraploid potato (Solanum tuberosum L.)
items: Factors shaping the gut microbiome of five species of lizards from different habitats

The role of solar radiation and tidal emersion on oxidative stress and glutathione synthesis in mussels exposed to air
type: item
type: AcademicArticle
description: Preparation for oxidative stress (POS) is a widespread adaptive response to harsh environmental conditions, whose hallmark is the upregulation of antioxidants. In contrast to controlled laboratory settings, animals are exposed to multiple abiotic stressors under natural field conditions. Still, the interplay between different environmental factors in modulating redox metabolism in natural settings remains largely unexplored. Here, we aim to shed light on this topic by assessing changes in redox metabolism in the mussel Brachidontes solisianus naturally exposed to a tidal cycle. We compared the redox biochemical response of mussels under six different natural conditions in the field along two consecutive days. These conditions differ in terms of chronology, immersion/emersion, and solar radiation, but not in terms of temperature. Animals were collected after being exposed to air early morning (7:30), immersed during late morning and afternoon (8:45–15:30), and then exposed to air again late afternoon towards evening (17:45–21:25), in two days. Whole body homogenates were used to measure the activity of antioxidant (catalase, glutathione transferase and glutathione reductase) and metabolic (glucose 6-phosphate dehydrogenase, malate dehydrogenase, isocitrate dehydrogenase and pyruvate kinase) enzymes, reduced (GSH) and disulfide (GSSG) glutathione levels, and oxidative stress markers (protein carbonyl and thiobarbituric acid reactive substances). Air and water temperature remained stable between 22.5 °C and 26 °C during both days. Global solar radiation (GSR) greatly differed between days, with a cumulative GSR of 15,381 kJ/m2 for day 1 and 5,489 kJ/m2 for day 2, whose peaks were 2,240 kJ/m2/h at 14:00 on day 1 and 952 kJ/m2/h at 12:00 on day 2. Compared with animals underwater, emersion during early morning did not elicit any alteration in redox biomarkers in both days. Air exposure for 4 h in the late afternoon towards evening caused oxidative damage to proteins and …
format: application/pdf
format: text/html
creator: Daniel C. Moreira
creator: Marcus Aurélio da Costa Tavares Sabino
creator: Marina Minari
creator: Felipe Torres Brasil Kuzniewski
creator: Ronaldo Angelini
creator: Marcelo Hermes-Lima
subject: Biochemistry
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.15345
publisher: PeerJ Inc.
rights: © 2023 Moreira et al.
abstract: Preparation for oxidative stress (POS) is a widespread adaptive response to harsh environmental conditions, whose hallmark is the upregulation of antioxidants. In contrast to controlled laboratory settings, animals are exposed to multiple abiotic stressors under natural field conditions. Still, the interplay between different environmental factors in modulating redox metabolism in natural settings remains largely unexplored. Here, we aim to shed light on this topic by assessing changes in redox metabolism in the mussel Brachidontes solisianus naturally exposed to a tidal cycle. We compared the redox biochemical response of mussels under six different natural conditions in the field along two consecutive days. These conditions differ in terms of chronology, immersion/emersion, and solar radiation, but not in terms of temperature. Animals were collected after being exposed to air early morning (7:30), immersed during late morning and afternoon (8:45–15:30), and then exposed to air again late afternoon towards evening (17:45–21:25), in two days. Whole body homogenates were used to measure the activity of antioxidant (catalase, glutathione transferase and glutathione reductase) and metabolic (glucose 6-phosphate dehydrogenase, malate dehydrogenase, isocitrate dehydrogenase and pyruvate kinase) enzymes, reduced (GSH) and disulfide (GSSG) glutathione levels, and oxidative stress markers (protein carbonyl and thiobarbituric acid reactive substances). Air and water temperature remained stable between 22.5 °C and 26 °C during both days. Global solar radiation (GSR) greatly differed between days, with a cumulative GSR of 15,381 kJ/m2 for day 1 and 5,489 kJ/m2 for day 2, whose peaks were 2,240 kJ/m2/h at 14:00 on day 1 and 952 kJ/m2/h at 12:00 on day 2. Compared with animals underwater, emersion during early morning did not elicit any alteration in redox biomarkers in both days. Air exposure for 4 h in the late afternoon towards evening caused oxidative damage to proteins and …
bibliographic citation: Moreira et al. (2023) The role of solar radiation and tidal emersion on oxidative stress and glutathione synthesis in mussels exposed to air. PeerJ 11:e15345 https://doi.org/10.7717/peerj.15345
date submitted: 2022-12-20
date accepted: 2023-04-12
issued: 2023-05-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moreira
  given name: Daniel C.
author list: Agent
  family name: Aurélio da Costa Tavares Sabino
  given name: Marcus
author list: Agent
  family name: Minari
  given name: Marina
author list: Agent
  family name: Torres Brasil Kuzniewski
  given name: Felipe
author list: Agent
  family name: Angelini
  given name: Ronaldo
author list: Agent
  family name: Hermes-Lima
  given name: Marcelo
doi: 10.7717/peerj.15345
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-11
copyright: ©2023 Moreira et al.
attribution name: Moreira et al.

The effect of FMT and vitamin C on immunity-related genes in antibiotic-induced dysbiosis in mice
type: item
type: AcademicArticle
description: Antibiotics are double-edged swords. Although antibiotics are used to inhibit pathogenic bacteria, they also run the risk of destroying some of the healthy bacteria in our bodies. We examined the effect of penicillin on the organism through a microarray dataset, after which 12 genes related to immuno-inflammatory pathways were selected by reading the literature and validated using neomycin and ampicillin. The expression of genes was measured using qRT-PCR. Several genes were significantly overexpressed in antibiotic-treated mice, including CD74 and SAA2 in intestinal tissues that remained extremely expressed after natural recovery. Moreover, transplantation of fecal microbiota from healthy mice to antibiotic-treated mice was made, where GZMB, CD3G, H2-AA, PSMB9, CD74, and SAA1 were greatly expressed; however, SAA2 was downregulated and normal expression was restored, and in liver tissue, SAA1, SAA2, SAA3 were extremely expressed. After the addition of vitamin C, which has positive effects in several aspects, to the fecal microbiota transplantation, in the intestinal tissues, the genes that were highly expressed after the fecal microbiota transplantation effectively reduced their expression, and the unaffected genes remained normally expressed, but the CD74 gene remained highly expressed. In liver tissues, normally expressed genes were not affected, but the expression of SAA1 was reduced and the expression of SAA3 was increased. In other words, fecal microbiota transplantation did not necessarily bring about a positive effect of gene expression restoration, but the addition of vitamin C effectively reduced the effects of fecal microbiota transplantation and regulated the balance of the immune system.
format: application/pdf
format: text/html
creator: Xiaorong Huang
creator: Yv Zhang
creator: Junsong Huang
creator: Wenli Gao
creator: Xie Yongfang
creator: Chuisheng Zeng
creator: Chao Gao
subject: Bioinformatics
subject: Molecular Biology
subject: Toxicology
description: doi:10.7717/peerj.15356
publisher: PeerJ Inc.
rights: © 2023 Huang et al.
abstract: Antibiotics are double-edged swords. Although antibiotics are used to inhibit pathogenic bacteria, they also run the risk of destroying some of the healthy bacteria in our bodies. We examined the effect of penicillin on the organism through a microarray dataset, after which 12 genes related to immuno-inflammatory pathways were selected by reading the literature and validated using neomycin and ampicillin. The expression of genes was measured using qRT-PCR. Several genes were significantly overexpressed in antibiotic-treated mice, including CD74 and SAA2 in intestinal tissues that remained extremely expressed after natural recovery. Moreover, transplantation of fecal microbiota from healthy mice to antibiotic-treated mice was made, where GZMB, CD3G, H2-AA, PSMB9, CD74, and SAA1 were greatly expressed; however, SAA2 was downregulated and normal expression was restored, and in liver tissue, SAA1, SAA2, SAA3 were extremely expressed. After the addition of vitamin C, which has positive effects in several aspects, to the fecal microbiota transplantation, in the intestinal tissues, the genes that were highly expressed after the fecal microbiota transplantation effectively reduced their expression, and the unaffected genes remained normally expressed, but the CD74 gene remained highly expressed. In liver tissues, normally expressed genes were not affected, but the expression of SAA1 was reduced and the expression of SAA3 was increased. In other words, fecal microbiota transplantation did not necessarily bring about a positive effect of gene expression restoration, but the addition of vitamin C effectively reduced the effects of fecal microbiota transplantation and regulated the balance of the immune system.
bibliographic citation: Huang et al. (2023) The effect of FMT and vitamin C on immunity-related genes in antibiotic-induced dysbiosis in mice. PeerJ 11:e15356 https://doi.org/10.7717/peerj.15356
date submitted: 2022-10-11
date accepted: 2023-04-14
issued: 2023-05-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Xiaorong
author list: Agent
  family name: Zhang
  given name: Yv
author list: Agent
  family name: Huang
  given name: Junsong
author list: Agent
  family name: Gao
  given name: Wenli
author list: Agent
  family name: Yongfang
  given name: Xie
author list: Agent
  family name: Zeng
  given name: Chuisheng
author list: Agent
  family name: Gao
  given name: Chao
doi: 10.7717/peerj.15356
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-11
copyright: ©2023 Huang et al.
attribution name: Huang et al.

Higher serum β2-microglobulin is a predictive biomarker for cognitive impairment in spinal cord injury
type: item
type: AcademicArticle
description: Objective Recent studies have suggested that high levels of β2-microglobulin are linked to cognitive deterioration; however, it is unclear how this connects to spinal cord injury (SCI). This study sought to determine whether there was any association between cognitive decline and serum β2-microglobulin levels in patients with SCI. Methods A total of 96 patients with SCI and 56 healthy volunteers were enrolled as study participants. At the time of enrollment, specific baseline data including age, gender, triglycerides (TG), low-density lipoprotein (LDL), systolic blood pressure (SBP), diastolic blood pressure (DBP), fasting blood glucose (FBG), smoking, and alcohol use were recorded. Each participant was assessed by a qualified physician using the Montreal cognitive assessment (MoCA) scale. Serum β2-microglobulin levels were measured using an enzyme-linked immunosorbent assay (ELISA) reagent for β2-microglobulin. Results A total of 152 participants were enrolled, with 56 in the control group and 96 in the SCI group. There were no significant baseline data differences between the two groups (p > 0.05). The control group had a MoCA score of 27.4 ± 1.1 and the SCI group had a score of 24.3 ± 1.5, with the difference being significant (p < 0.05). The serum ELISA results revealed that the levels of β2-microglobulin in the SCI group were considerably higher (p < 0.05) than those in the control group (2.08 ± 0.17 g/mL compared to 1.57 ± 0.11 g/mL). The serum β2-microglobulin level was used to categorize the patients with SCI into four groups. As serum β2-microglobulin levels increased, the MoCA score reduced (p < 0.05). After adjustment of baseline data, further regression analysis showed that serum β2-microglobulin level remained an independent risk factor for post-SCI cognitive impairment. Conclusions Patients with SCI had higher serum levels of β2-microglobulin, which may be a biomarker for cognitive decline following SCI.
format: application/pdf
format: text/html
creator: Zhonghao Cui
creator: Shuai Wang
creator: Yanke Hao
creator: Yuanzhen Chen
subject: Cognitive Disorders
subject: Hematology
subject: Immunology
subject: Neurology
description: doi:10.7717/peerj.15372
publisher: PeerJ Inc.
rights: © 2023 Cui et al.
abstract: Objective Recent studies have suggested that high levels of β2-microglobulin are linked to cognitive deterioration; however, it is unclear how this connects to spinal cord injury (SCI). This study sought to determine whether there was any association between cognitive decline and serum β2-microglobulin levels in patients with SCI. Methods A total of 96 patients with SCI and 56 healthy volunteers were enrolled as study participants. At the time of enrollment, specific baseline data including age, gender, triglycerides (TG), low-density lipoprotein (LDL), systolic blood pressure (SBP), diastolic blood pressure (DBP), fasting blood glucose (FBG), smoking, and alcohol use were recorded. Each participant was assessed by a qualified physician using the Montreal cognitive assessment (MoCA) scale. Serum β2-microglobulin levels were measured using an enzyme-linked immunosorbent assay (ELISA) reagent for β2-microglobulin. Results A total of 152 participants were enrolled, with 56 in the control group and 96 in the SCI group. There were no significant baseline data differences between the two groups (p > 0.05). The control group had a MoCA score of 27.4 ± 1.1 and the SCI group had a score of 24.3 ± 1.5, with the difference being significant (p < 0.05). The serum ELISA results revealed that the levels of β2-microglobulin in the SCI group were considerably higher (p < 0.05) than those in the control group (2.08 ± 0.17 g/mL compared to 1.57 ± 0.11 g/mL). The serum β2-microglobulin level was used to categorize the patients with SCI into four groups. As serum β2-microglobulin levels increased, the MoCA score reduced (p < 0.05). After adjustment of baseline data, further regression analysis showed that serum β2-microglobulin level remained an independent risk factor for post-SCI cognitive impairment. Conclusions Patients with SCI had higher serum levels of β2-microglobulin, which may be a biomarker for cognitive decline following SCI.
bibliographic citation: Cui et al. (2023) Higher serum β2-microglobulin is a predictive biomarker for cognitive impairment in spinal cord injury. PeerJ 11:e15372 https://doi.org/10.7717/peerj.15372
date submitted: 2023-02-28
date accepted: 2023-04-18
issued: 2023-05-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cui
  given name: Zhonghao
author list: Agent
  family name: Wang
  given name: Shuai
author list: Agent
  family name: Hao
  given name: Yanke
author list: Agent
  family name: Chen
  given name: Yuanzhen
doi: 10.7717/peerj.15372
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-11
copyright: © 2023 Cui et al.
attribution name: Cui et al.

Estimating the impact of environmental management on strawberry yield using publicly available agricultural data in South Korea
type: item
type: AcademicArticle
description: Advanced information and communication technologies (ICTs) have made data collection more efficient for agricultural studies. Using publicly available database in South Korea, we estimated the relationship between the management of air temperature and relative humidity and the strawberry yield during two harvest seasons. Longitudinal data of multiple greenhouses were merged and processed, and mixed-effects models were applied to account both observed and unobserved factors across the greenhouses. The averages of air temperature and relative humidity inside each greenhouse do not take volatility of the time-varying variables into consideration, so we assessed the management of each greenhouse by the percent of time that air temperature between 15 °C and 20 °C (denoted as T%) and the percent of time that relative humidity between 0% and 50% (denoted by H%). The statistical models estimated that the strawberry yield decreases with respect to the number of days since harvest began and the rate of decrease is slower when T% and H% are higher. This study used large-scale multilocation data to provide the practical suggestion that air temperature and relative humidity should be maintained within the optimal ranges to mitigate the loss of strawberry yield especially at the later phase of a harvest season.
format: application/pdf
format: text/html
creator: Steven Kim
creator: Jung Su Jo
creator: Vicky Luk
creator: Sung Kyeom Kim
creator: Dong Sub Kim
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.15390
publisher: PeerJ Inc.
rights: © 2023 Kim et al.
abstract: Advanced information and communication technologies (ICTs) have made data collection more efficient for agricultural studies. Using publicly available database in South Korea, we estimated the relationship between the management of air temperature and relative humidity and the strawberry yield during two harvest seasons. Longitudinal data of multiple greenhouses were merged and processed, and mixed-effects models were applied to account both observed and unobserved factors across the greenhouses. The averages of air temperature and relative humidity inside each greenhouse do not take volatility of the time-varying variables into consideration, so we assessed the management of each greenhouse by the percent of time that air temperature between 15 °C and 20 °C (denoted as T%) and the percent of time that relative humidity between 0% and 50% (denoted by H%). The statistical models estimated that the strawberry yield decreases with respect to the number of days since harvest began and the rate of decrease is slower when T% and H% are higher. This study used large-scale multilocation data to provide the practical suggestion that air temperature and relative humidity should be maintained within the optimal ranges to mitigate the loss of strawberry yield especially at the later phase of a harvest season.
bibliographic citation: Kim et al. (2023) Estimating the impact of environmental management on strawberry yield using publicly available agricultural data in South Korea. PeerJ 11:e15390 https://doi.org/10.7717/peerj.15390
date submitted: 2023-02-09
date accepted: 2023-04-19
issued: 2023-05-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kim
  given name: Steven
author list: Agent
  family name: Jo
  given name: Jung Su
author list: Agent
  family name: Luk
  given name: Vicky
author list: Agent
  family name: Kim
  given name: Sung Kyeom
author list: Agent
  family name: Kim
  given name: Dong Sub
doi: 10.7717/peerj.15390
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-11
copyright: © 2023 Kim et al.
attribution name: Kim et al.

Necked strawberries are especially susceptible to cracking
type: item
type: AcademicArticle
description: Fruit cracking is a commercially important disorder that reduces both quantity and quality of strawberries (Fragaria × ananassa Duch.). The objective was to identify the physiological mechanism of cracking and the factors affecting cracking. Cracking is more common in necked than in normal-shaped fruit. Most macroscopic cracks (‘macrocracks’) occur in the seedless neck. Large fruit is more cracking susceptible than medium size or small fruit. Macrocrack orientation is predominantly latitudinal in the proximal region of the neck and longitudinal in the mid and distal regions of the neck. The neck region of necked fruit has a thicker cuticle than the body of necked or normal-shaped fruit. The vascular bundles in the neck (seedless) are orientated longitudinally, while those in the body (with seeds) are both longitudinal and radial. Epidermal cells in the neck region are elongated longitudinally, with those in the proximal region of the neck being more elongated than those in the mid or distal regions of the neck. Cuticular microcracking was more severe in necked fruit than in normal-shaped fruit. The orientations of the microcracks matched those of the macrocracks, i.e., latitudinal in the proximal neck and longitudinal in the mid and distal neck regions. Following artificial incisions (blade), gaping was significantly more pronounced in necked than in normal-shaped fruit. Incubation of fruit in deionized water induced macrocracks in about 75% of fruit. Necked fruit cracked more than normal-shaped fruit. Most macrocracks were oriented latitudinally in the proximal neck and longitudinally in the distal neck regions. The results indicate cracking results from excessive growth strains which are further increased by surface water uptake.
format: application/pdf
format: text/html
creator: Grecia Hurtado
creator: Moritz Knoche
subject: Agricultural Science
subject: Food Science and Technology
subject: Plant Science
description: doi:10.7717/peerj.15402
publisher: PeerJ Inc.
rights: © 2023 Hurtado and Knoche
abstract: Fruit cracking is a commercially important disorder that reduces both quantity and quality of strawberries (Fragaria × ananassa Duch.). The objective was to identify the physiological mechanism of cracking and the factors affecting cracking. Cracking is more common in necked than in normal-shaped fruit. Most macroscopic cracks (‘macrocracks’) occur in the seedless neck. Large fruit is more cracking susceptible than medium size or small fruit. Macrocrack orientation is predominantly latitudinal in the proximal region of the neck and longitudinal in the mid and distal regions of the neck. The neck region of necked fruit has a thicker cuticle than the body of necked or normal-shaped fruit. The vascular bundles in the neck (seedless) are orientated longitudinally, while those in the body (with seeds) are both longitudinal and radial. Epidermal cells in the neck region are elongated longitudinally, with those in the proximal region of the neck being more elongated than those in the mid or distal regions of the neck. Cuticular microcracking was more severe in necked fruit than in normal-shaped fruit. The orientations of the microcracks matched those of the macrocracks, i.e., latitudinal in the proximal neck and longitudinal in the mid and distal neck regions. Following artificial incisions (blade), gaping was significantly more pronounced in necked than in normal-shaped fruit. Incubation of fruit in deionized water induced macrocracks in about 75% of fruit. Necked fruit cracked more than normal-shaped fruit. Most macrocracks were oriented latitudinally in the proximal neck and longitudinally in the distal neck regions. The results indicate cracking results from excessive growth strains which are further increased by surface water uptake.
bibliographic citation: Hurtado et al. (2023) Necked strawberries are especially susceptible to cracking. PeerJ 11:e15402 https://doi.org/10.7717/peerj.15402
date submitted: 2023-01-30
date accepted: 2023-04-20
issued: 2023-05-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hurtado
  given name: Grecia
author list: Agent
  family name: Knoche
  given name: Moritz
doi: 10.7717/peerj.15402
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-11
copyright: © 2023 Hurtado and Knoche
attribution name: Hurtado and Knoche

Zinc solubilizing bacteria and their potential as bioinoculant for growth promotion of green soybean (Glycine max L. Merr.)
type: item
type: AcademicArticle
description: Zinc-solubilizing rhizobacteria can convert insoluble zinc to an accessible form and increase Zn bioavailability in soil, which help mitigate Zn deficiency in crops. In this work, 121 bacterial isolates were isolated from the rhizosphere soils of peanuts, sweet potatoes, and cassava, and their capability to solubilize Zn was evaluated using Bunt and Rovira’s agar containing 0.1% ZnO and ZnCO3. Among these isolates, six showed high Zn solubilization efficiencies ranging from 1.32 to 2.84 and 1.93 to 2.27 on the medium supplemented with 0.1% ZnO and ZnCO3, respectively. In a quantitative analysis of soluble Zn in liquid medium supplemented with 0.1% ZnO, the isolate KAH109 showed the maximum soluble zinc concentration of 62.89 mg L−1. Among the six isolates, the isolate KAH109 also produced the most indole-3-acetic acid (IAA) at 33.44 mg L−1, whereas the isolate KEX505 also produced IAA at 17.24 mg L−1 along with showing zinc and potassium solubilization activity. These strains were identified as Priestia megaterium KAH109 and Priestia aryabhattai KEX505 based on 16S rDNA sequence analysis. In a greenhouse experiment conducted in Nakhon Pathom, Thailand the ability of P. megaterium KAH109 and P. aryabhattai KEX505 to stimulate the growth and production of green soybeans was examined. The results revealed that inoculation with P. megaterium KAH109 and P. aryabhattai KEX505 considerably increased plant dry weight by 26.96% and 8.79%, respectively, and the number of grains per plant by 48.97% and 35.29% when compared to those of the uninoculated control. According to these results, both strains can be considered as a potential zinc solubilizing bioinoculant to promote the growth and production yield of green soybeans.
format: application/pdf
format: text/html
creator: Moltira Srithaworn
creator: Jieb Jaroenthanyakorn
creator: Janpen Tangjitjaroenkun
creator: Chanwit Suriyachadkun
creator: Orawan Chunhachart
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.15128
publisher: PeerJ Inc.
rights: © 2023 Srithaworn et al.
abstract: Zinc-solubilizing rhizobacteria can convert insoluble zinc to an accessible form and increase Zn bioavailability in soil, which help mitigate Zn deficiency in crops. In this work, 121 bacterial isolates were isolated from the rhizosphere soils of peanuts, sweet potatoes, and cassava, and their capability to solubilize Zn was evaluated using Bunt and Rovira’s agar containing 0.1% ZnO and ZnCO3. Among these isolates, six showed high Zn solubilization efficiencies ranging from 1.32 to 2.84 and 1.93 to 2.27 on the medium supplemented with 0.1% ZnO and ZnCO3, respectively. In a quantitative analysis of soluble Zn in liquid medium supplemented with 0.1% ZnO, the isolate KAH109 showed the maximum soluble zinc concentration of 62.89 mg L−1. Among the six isolates, the isolate KAH109 also produced the most indole-3-acetic acid (IAA) at 33.44 mg L−1, whereas the isolate KEX505 also produced IAA at 17.24 mg L−1 along with showing zinc and potassium solubilization activity. These strains were identified as Priestia megaterium KAH109 and Priestia aryabhattai KEX505 based on 16S rDNA sequence analysis. In a greenhouse experiment conducted in Nakhon Pathom, Thailand the ability of P. megaterium KAH109 and P. aryabhattai KEX505 to stimulate the growth and production of green soybeans was examined. The results revealed that inoculation with P. megaterium KAH109 and P. aryabhattai KEX505 considerably increased plant dry weight by 26.96% and 8.79%, respectively, and the number of grains per plant by 48.97% and 35.29% when compared to those of the uninoculated control. According to these results, both strains can be considered as a potential zinc solubilizing bioinoculant to promote the growth and production yield of green soybeans.
bibliographic citation: Srithaworn et al. (2023) Zinc solubilizing bacteria and their potential as bioinoculant for growth promotion of green soybean (Glycine max L. Merr.). PeerJ 11:e15128 https://doi.org/10.7717/peerj.15128
date submitted: 2022-09-15
date accepted: 2023-03-04
issued: 2023-05-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Srithaworn
  given name: Moltira
author list: Agent
  family name: Jaroenthanyakorn
  given name: Jieb
author list: Agent
  family name: Tangjitjaroenkun
  given name: Janpen
author list: Agent
  family name: Suriyachadkun
  given name: Chanwit
author list: Agent
  family name: Chunhachart
  given name: Orawan
doi: 10.7717/peerj.15128
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-10
copyright: ©2023 Srithaworn et al.
attribution name: Srithaworn et al.

Precipitation extremes observed over and around the Taklimakan Desert, China
type: item
type: AcademicArticle
description: The Taklimakan Desert (TD) is the largest desert in China located in the Tarim Basin (TB) in China’s arid region. This study is a review of the change in precipitation and its extremes since 1961 and the high-impact extreme precipitation events in 2012–2021, particularly in 2021, with a focus on the TD along with the surrounding oases and mountainous regions.The TB has experienced significantly warmer and wetter trends since 1961, and extreme rainfall has increased significantly in the TD and its surrounding areas during the 2000s. In the TB, the year 2021 was identified as the 4th warmest for 1961–2021, and was remembered for unprecedented extreme events. Three high-impact extreme events that occurred in 2021 are highlighted, including extreme heavy rainfall over Hetian in mid-June. The earliest extreme rainfall event occurred over North Bazhou in early spring, and the strongest heavy snowfall over Baicheng in April. In addition, we also discussed the underlying physical mechanisms of extreme events over the TB and proposed novel perspectives and unresolved questions on the sciences of heavy rainfall in arid regions. Our results provide a reference for the physical mechanism, attribution, and high-resolution modeling of extreme events.
format: application/pdf
format: text/html
creator: Moyan Li
creator: Junqiang Yao
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.15256
publisher: PeerJ Inc.
rights: © 2023 Li and Yao
abstract: The Taklimakan Desert (TD) is the largest desert in China located in the Tarim Basin (TB) in China’s arid region. This study is a review of the change in precipitation and its extremes since 1961 and the high-impact extreme precipitation events in 2012–2021, particularly in 2021, with a focus on the TD along with the surrounding oases and mountainous regions.The TB has experienced significantly warmer and wetter trends since 1961, and extreme rainfall has increased significantly in the TD and its surrounding areas during the 2000s. In the TB, the year 2021 was identified as the 4th warmest for 1961–2021, and was remembered for unprecedented extreme events. Three high-impact extreme events that occurred in 2021 are highlighted, including extreme heavy rainfall over Hetian in mid-June. The earliest extreme rainfall event occurred over North Bazhou in early spring, and the strongest heavy snowfall over Baicheng in April. In addition, we also discussed the underlying physical mechanisms of extreme events over the TB and proposed novel perspectives and unresolved questions on the sciences of heavy rainfall in arid regions. Our results provide a reference for the physical mechanism, attribution, and high-resolution modeling of extreme events.
bibliographic citation: Li et al. (2023) Precipitation extremes observed over and around the Taklimakan Desert, China. PeerJ 11:e15256 https://doi.org/10.7717/peerj.15256
date submitted: 2022-11-17
date accepted: 2023-03-28
issued: 2023-05-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Li
  given name: Moyan
author list: Agent
  family name: Yao
  given name: Junqiang
doi: 10.7717/peerj.15256
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-10
copyright: ©2023 Li and Yao
attribution name: Li and Yao

CPJSdraw: analysis and visualization of junction sites of chloroplast genomes
type: item
type: AcademicArticle
description: Background Chloroplast genomes are usually circular molecules, and most of them are tetrad structures with two inverted repeat (IR) regions, a large single-copy region, and a small single-copy region. IR contraction and expansion are among the genetic diversities during the evolution of plant chloroplast genomes. The only previously released tool for the visualization of junction sites of the regions does not consider the diversity of the starting point of genomes, which leads to incorrect results or even no results for the examination of IR contraction and expansion. Results In this work, a new tool named CPJSdraw was developed for visualizing the junction sites of chloroplast genomes. CPJSdraw can format the starting point of the irregular linearized genome, correct the junction sites of IR and single-copy regions, display the tetrad structure, visualize the junction sites of any number (≥1) of chloroplast genomes, show the transcription direction of genes adjacent to junction sites, and indicate the IR expansion or contraction of chloroplast genomes. Conclusions CPJSdraw is a software that is universal and reliable in analysis and visualization of IR expansion or contraction of chloroplast genomes. CPJSdraw has more accurate analysis and more complete functions when compared with previously released tool. CPJSdraw as a perl package and tested data are available at http://dx.doi.org/10.5281/zenodo.7669480 for English users. In addition, an online version with a Chinese interface is available at http://cloud.genepioneer.com:9929/#/tool/alltool/detail/335.
format: application/pdf
format: text/html
creator: Huie Li
creator: Qiqiang Guo
creator: Lei Xu
creator: Haidong Gao
creator: Lei Liu
creator: Xiangyang Zhou
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.15326
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Background Chloroplast genomes are usually circular molecules, and most of them are tetrad structures with two inverted repeat (IR) regions, a large single-copy region, and a small single-copy region. IR contraction and expansion are among the genetic diversities during the evolution of plant chloroplast genomes. The only previously released tool for the visualization of junction sites of the regions does not consider the diversity of the starting point of genomes, which leads to incorrect results or even no results for the examination of IR contraction and expansion. Results In this work, a new tool named CPJSdraw was developed for visualizing the junction sites of chloroplast genomes. CPJSdraw can format the starting point of the irregular linearized genome, correct the junction sites of IR and single-copy regions, display the tetrad structure, visualize the junction sites of any number (≥1) of chloroplast genomes, show the transcription direction of genes adjacent to junction sites, and indicate the IR expansion or contraction of chloroplast genomes. Conclusions CPJSdraw is a software that is universal and reliable in analysis and visualization of IR expansion or contraction of chloroplast genomes. CPJSdraw has more accurate analysis and more complete functions when compared with previously released tool. CPJSdraw as a perl package and tested data are available at http://dx.doi.org/10.5281/zenodo.7669480 for English users. In addition, an online version with a Chinese interface is available at http://cloud.genepioneer.com:9929/#/tool/alltool/detail/335.
bibliographic citation: Li et al. (2023) CPJSdraw: analysis and visualization of junction sites of chloroplast genomes. PeerJ 11:e15326 https://doi.org/10.7717/peerj.15326
date submitted: 2023-01-12
date accepted: 2023-04-10
issued: 2023-05-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Huie
author list: Agent
  family name: Guo
  given name: Qiqiang
author list: Agent
  family name: Xu
  given name: Lei
author list: Agent
  family name: Gao
  given name: Haidong
author list: Agent
  family name: Liu
  given name: Lei
author list: Agent
  family name: Zhou
  given name: Xiangyang
doi: 10.7717/peerj.15326
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-10
copyright: ©2023 Li et al.
attribution name: Li et al.

Regenerative plantlets with improved agronomic characteristics caused by anther culture of tetraploid potato (Solanum tuberosum L.)
type: item
type: AcademicArticle
description: Objective As the primary means of plant-induced haploid, anther culture is of great significance in quickly obtaining pure lines and significantly shortening the potato breeding cycle. Nevertheless, the methods of anther culture of tetraploid potato were still not well established. Methods In this study, 16 potato cultivars (lines) were used for anther culture in vitro. The corresponding relation between the different development stages of microspores and the external morphology of buds was investigated. A highly-efficient anther culture system of tetraploid potatoes was established. Results It was shown in the results that the combined use of 0.5 mg/L 1-Naphthylacetic acid (NAA), 1.0 mg/L 2,4-Dichlorophenoxyacetic acid (2,4-D), and 1.0 mg/L Kinetin (KT) was the ideal choice of hormone pairing for anther callus. Ten of the 16 potato cultivars examined could be induced callus with their respective anthers, and the induction rate ranged from 4.44% to 22.67% using this hormone combination. According to the outcome from the orthogonal design experiments of four kinds of appendages, we found that the medium with sucrose (40 g/L), AgNO3 (30 mg/L), activated carbon (3 g/L), potato extract (200 g/L) had a promotive induction effect on the anther callus. In contrast, adding 1 mg/L Zeatin (ZT) effectively facilitated callus differentiation. Conclusion Finally, 201 anther culture plantlets were differentiated from 10 potato cultivars. Among these, Qingshu 168 and Ningshu 15 had higher efficiency than anther culture. After identification by flow cytometry and fluorescence in situ hybridization, 10 haploid plantlets (5%), 177 tetraploids (88%), and 14 octoploids (7%) were obtained. Some premium anther-cultured plantlets were further selected by morphological and agronomic comparison. Our findings provide important guidance for potato ploidy breeding.
format: application/pdf
format: text/html
creator: Li Zhang
creator: Feng-jie Nie
creator: Lei Gong
creator: Xiao-yan Gan
creator: Guo-hui Zhang
creator: Xuan Liu
creator: Wen-jing Yang
creator: Lei Shi
creator: Yu-chao Chen
creator: Rui-xia Xie
creator: Zhi-qian Guo
creator: Yuxia Song
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.14984
publisher: PeerJ Inc.
rights: © 2023 Zhang et al.
abstract: Objective As the primary means of plant-induced haploid, anther culture is of great significance in quickly obtaining pure lines and significantly shortening the potato breeding cycle. Nevertheless, the methods of anther culture of tetraploid potato were still not well established. Methods In this study, 16 potato cultivars (lines) were used for anther culture in vitro. The corresponding relation between the different development stages of microspores and the external morphology of buds was investigated. A highly-efficient anther culture system of tetraploid potatoes was established. Results It was shown in the results that the combined use of 0.5 mg/L 1-Naphthylacetic acid (NAA), 1.0 mg/L 2,4-Dichlorophenoxyacetic acid (2,4-D), and 1.0 mg/L Kinetin (KT) was the ideal choice of hormone pairing for anther callus. Ten of the 16 potato cultivars examined could be induced callus with their respective anthers, and the induction rate ranged from 4.44% to 22.67% using this hormone combination. According to the outcome from the orthogonal design experiments of four kinds of appendages, we found that the medium with sucrose (40 g/L), AgNO3 (30 mg/L), activated carbon (3 g/L), potato extract (200 g/L) had a promotive induction effect on the anther callus. In contrast, adding 1 mg/L Zeatin (ZT) effectively facilitated callus differentiation. Conclusion Finally, 201 anther culture plantlets were differentiated from 10 potato cultivars. Among these, Qingshu 168 and Ningshu 15 had higher efficiency than anther culture. After identification by flow cytometry and fluorescence in situ hybridization, 10 haploid plantlets (5%), 177 tetraploids (88%), and 14 octoploids (7%) were obtained. Some premium anther-cultured plantlets were further selected by morphological and agronomic comparison. Our findings provide important guidance for potato ploidy breeding.
bibliographic citation: Zhang et al. (2023) Regenerative plantlets with improved agronomic characteristics caused by anther culture of tetraploid potato (Solanum tuberosum L.). PeerJ 11:e14984 https://doi.org/10.7717/peerj.14984
date submitted: 2022-08-31
date accepted: 2023-02-10
issued: 2023-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Li
author list: Agent
  family name: Nie
  given name: Feng-jie
author list: Agent
  family name: Gong
  given name: Lei
author list: Agent
  family name: Gan
  given name: Xiao-yan
author list: Agent
  family name: Zhang
  given name: Guo-hui
author list: Agent
  family name: Liu
  given name: Xuan
author list: Agent
  family name: Yang
  given name: Wen-jing
author list: Agent
  family name: Shi
  given name: Lei
author list: Agent
  family name: Chen
  given name: Yu-chao
author list: Agent
  family name: Xie
  given name: Rui-xia
author list: Agent
  family name: Guo
  given name: Zhi-qian
author list: Agent
  family name: Song
  given name: Yuxia
doi: 10.7717/peerj.14984
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-09
copyright: ©2023 Zhang et al.
attribution name: Zhang et al.

Factors shaping the gut microbiome of five species of lizards from different habitats
type: item
type: AcademicArticle
description: Background Host-gut microbiota interactions are complex and can have a profound impact on the ecology and evolution of both counterparts. Several host traits such as systematics, diet and social behavior, and external factors such as prey availability and local environment are known to influence the composition and diversity of the gut microbiota. Methods In this study, we investigate the influence of systematics, sex, host size, and locality/habitat on gut microbiota diversity in five lizard species from two different sites in Portugal: Podarcis bocagei and Podarcis lusitanicus, living in syntopy in a rural area in northern Portugal (Moledo); the invasive Podarcis siculus and the native Podarcis virescens, living in sympatry in an urbanized environment (Lisbon); and the invasive Teira dugesii also living in an urban area (Lisbon). We also infer the potential microbial transmission occurring between species living in sympatry and syntopy. To achieve these goals, we use a metabarcoding approach to characterize the bacterial communities from the cloaca of lizards, sequencing the V4 region of the 16S rRNA. Results Habitat/locality was an important factor explaining differences in gut bacterial composition and structure, with species from urbanized environments having higher bacterial diversity. Host systematics (i.e., species) influenced gut bacterial community structure only in lizards from the urbanized environment. We also detected a significant positive correlation between lizard size and gut bacterial alpha-diversity in the invasive species P. siculus, which could be due to its higher exploratory behavior. Moreover, estimates of bacterial transmission indicate that P. siculus may have acquired a high proportion of local microbiota after its introduction. These findings confirm that a diverse array of host and environmental factors can influence lizards’ gut microbiota.
format: application/pdf
format: text/html
creator: Diana S. Vasconcelos
creator: D. James Harris
creator: Isabel Damas-Moreira
creator: Ana Pereira
creator: Raquel Xavier
subject: Ecology
subject: Microbiology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.15146
publisher: PeerJ Inc.
rights: © 2023 Vasconcelos et al.
abstract: Background Host-gut microbiota interactions are complex and can have a profound impact on the ecology and evolution of both counterparts. Several host traits such as systematics, diet and social behavior, and external factors such as prey availability and local environment are known to influence the composition and diversity of the gut microbiota. Methods In this study, we investigate the influence of systematics, sex, host size, and locality/habitat on gut microbiota diversity in five lizard species from two different sites in Portugal: Podarcis bocagei and Podarcis lusitanicus, living in syntopy in a rural area in northern Portugal (Moledo); the invasive Podarcis siculus and the native Podarcis virescens, living in sympatry in an urbanized environment (Lisbon); and the invasive Teira dugesii also living in an urban area (Lisbon). We also infer the potential microbial transmission occurring between species living in sympatry and syntopy. To achieve these goals, we use a metabarcoding approach to characterize the bacterial communities from the cloaca of lizards, sequencing the V4 region of the 16S rRNA. Results Habitat/locality was an important factor explaining differences in gut bacterial composition and structure, with species from urbanized environments having higher bacterial diversity. Host systematics (i.e., species) influenced gut bacterial community structure only in lizards from the urbanized environment. We also detected a significant positive correlation between lizard size and gut bacterial alpha-diversity in the invasive species P. siculus, which could be due to its higher exploratory behavior. Moreover, estimates of bacterial transmission indicate that P. siculus may have acquired a high proportion of local microbiota after its introduction. These findings confirm that a diverse array of host and environmental factors can influence lizards’ gut microbiota.
bibliographic citation: Vasconcelos et al. (2023) Factors shaping the gut microbiome of five species of lizards from different habitats. PeerJ 11:e15146 https://doi.org/10.7717/peerj.15146
date submitted: 2022-11-07
date accepted: 2023-03-09
issued: 2023-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vasconcelos
  given name: Diana S.
author list: Agent
  family name: Harris
  given name: D. James
author list: Agent
  family name: Damas-Moreira
  given name: Isabel
author list: Agent
  family name: Pereira
  given name: Ana
author list: Agent
  family name: Xavier
  given name: Raquel
doi: 10.7717/peerj.15146
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-09
copyright: ©2023 Vasconcelos et al.
attribution name: Vasconcelos et al.

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