PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A new species of Ampharete Malmgren, 1866 (Annelida: Ampharetidae) from Washington and redescription of A. cirrata Webster & Benedict, 1887 and A. labrops Hartman, 1961
items: Identification and characterization of novel SUMO genes in bread wheat
items: Understanding perceived exertion in power-aimed resistance training: the relationship between perceived exertion and muscle fatigue
items: Parasites influence the physiology and personality in a small mammal (Ochotona curzoniae)
items: Biochemical and molecular responses of maize to low and high temperatures in symbiosis with mixed arbuscular mycorrhizal fungi cultures
items: Evaluation of water quality and soil fertility in remediated farmland for protection of wetland ecology by planting different crops
items: Effects of monocropping soil on plant growth and rhizosphere microbial community structure of Salvia miltiorrhiza Bge
items: Effectiveness of respiratory muscle training on pulmonary function recovery in patients with spinal cord injury: a systematic review and meta-analysis
items: Genomics, population dynamics, immune evasion and resistance determinants foster the competence and global dissemination of Klebsiella pneumoniae
items: Structure and diversity of microbial communities in the rhizosphere soil of Trichosanthes kirilowii from different cultivation patterns

A new species of Ampharete Malmgren, 1866 (Annelida: Ampharetidae) from Washington and redescription of A. cirrata Webster & Benedict, 1887 and A. labrops Hartman, 1961
type: item
type: AcademicArticle
description: Ampharete acutifrons (Grube, 1860), originally described from Greenland, has long been considered a widely distributed arctic-boreal species. However, recent morphological re-assessment of the holotype indicates that most previous records of A. acutifrons were misidentifications, and molecular sequence data also suggest that A. acutifrons is a multispecies complex. This study focuses on specimens of the A. acutifrons species complex from Washington, USA, with publicly available cytochrome c oxidase subunit I (COI) sequence data. Specimens from Washington belonging to the Invertebrate Zoology Collection of the Florida Museum of Natural History were examined. Additional specimens were examined for morphological comparison, including type material of A. cirrata Webster & Benedict, 1887, and A. labrops Hartman, 1961. Detailed morphological descriptions of specimens and photographs of the diagnostic characters were made. The molecular analysis includes 37 published COI sequences of Ampharete and Anobothrus species sourced from public databases. Redescriptions of type material of A. cirrata and A. labrops are provided. Ampharete paulayi n. sp. is described as a new species from Washington, USA, based on morphological and COI sequences data. Photographs of living specimens are presented, a hypothesis on the development of buccal tentacles in Ampharete species is proposed, and the use of Methyl green stain is recommended as a standard practice in future descriptions of ampharetids.
format: application/pdf
format: text/html
creator: Yessica Chávez-López
subject: Biodiversity
subject: Evolutionary Studies
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.20457
publisher: PeerJ Inc.
rights: © 2025 Chávez-López
abstract: Ampharete acutifrons (Grube, 1860), originally described from Greenland, has long been considered a widely distributed arctic-boreal species. However, recent morphological re-assessment of the holotype indicates that most previous records of A. acutifrons were misidentifications, and molecular sequence data also suggest that A. acutifrons is a multispecies complex. This study focuses on specimens of the A. acutifrons species complex from Washington, USA, with publicly available cytochrome c oxidase subunit I (COI) sequence data. Specimens from Washington belonging to the Invertebrate Zoology Collection of the Florida Museum of Natural History were examined. Additional specimens were examined for morphological comparison, including type material of A. cirrata Webster & Benedict, 1887, and A. labrops Hartman, 1961. Detailed morphological descriptions of specimens and photographs of the diagnostic characters were made. The molecular analysis includes 37 published COI sequences of Ampharete and Anobothrus species sourced from public databases. Redescriptions of type material of A. cirrata and A. labrops are provided. Ampharete paulayi n. sp. is described as a new species from Washington, USA, based on morphological and COI sequences data. Photographs of living specimens are presented, a hypothesis on the development of buccal tentacles in Ampharete species is proposed, and the use of Methyl green stain is recommended as a standard practice in future descriptions of ampharetids.
bibliographic citation: Chávez-López (2025) A new species of Ampharete Malmgren, 1866 (Annelida: Ampharetidae) from Washington and redescription of A. cirrata Webster & Benedict, 1887 and A. labrops Hartman, 1961. PeerJ 13:e20457 https://doi.org/10.7717/peerj.20457
date submitted: 2025-09-19
date accepted: 2025-10-31
issued: 2025-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chávez-López
  given name: Yessica
doi: 10.7717/peerj.20457
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-28
copyright: © 2025 Chávez-López
attribution name: Chávez-López

Identification and characterization of novel SUMO genes in bread wheat
type: item
type: AcademicArticle
description: The small-ubiquitin-like-modifier (SUMO), composed of approximately 100 amino acid residues, regulates the cellular activity of several proteins by posttranslational modification. Almost all plant species express a family of SUMO isoforms. Nevertheless, the SUMO genes in wheat (TaSUMOs) have not undergone complete characterization, and the roles of TaSUMOs remain unidentified. The study identified four new SUMO genes in wheat, named TaSUMO4-7, in addition to the previously known TaSUMO1-3. These genes are part of the conserved SUMO family, as indicated by phylogenetic analysis. The genes contain the characteristic SUMO-acceptor site motif and the essential C-terminal diglycine motif for processing. Expression analysis showed that TaSUMO4-7 genes are expressed in various wheat tissues. Bioinformatics analysis predicted the biochemical properties and structures of the proteins, which were found to localize in the cytoplasm and nucleus. The study confirms that the new TaSUMO4-7 genes are functional members of the wheat SUMO family and lays the groundwork for further research into their specific roles.
format: application/pdf
format: text/html
creator: Eid I. Ibrahim
creator: Kotb A. Attia
creator: Abdelhalim Ghazy
creator: Itoh Kimiko
creator: Abdullah Al-Doss
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.20432
publisher: PeerJ Inc.
rights: © 2025 Ibrahim et al.
abstract: The small-ubiquitin-like-modifier (SUMO), composed of approximately 100 amino acid residues, regulates the cellular activity of several proteins by posttranslational modification. Almost all plant species express a family of SUMO isoforms. Nevertheless, the SUMO genes in wheat (TaSUMOs) have not undergone complete characterization, and the roles of TaSUMOs remain unidentified. The study identified four new SUMO genes in wheat, named TaSUMO4-7, in addition to the previously known TaSUMO1-3. These genes are part of the conserved SUMO family, as indicated by phylogenetic analysis. The genes contain the characteristic SUMO-acceptor site motif and the essential C-terminal diglycine motif for processing. Expression analysis showed that TaSUMO4-7 genes are expressed in various wheat tissues. Bioinformatics analysis predicted the biochemical properties and structures of the proteins, which were found to localize in the cytoplasm and nucleus. The study confirms that the new TaSUMO4-7 genes are functional members of the wheat SUMO family and lays the groundwork for further research into their specific roles.
bibliographic citation: Ibrahim et al. (2025) Identification and characterization of novel SUMO genes in bread wheat. PeerJ 13:e20432 https://doi.org/10.7717/peerj.20432
date submitted: 2025-02-25
date accepted: 2025-10-30
issued: 2025-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ibrahim
  given name: Eid I.
author list: Agent
  family name: Attia
  given name: Kotb A.
author list: Agent
  family name: Ghazy
  given name: Abdelhalim
author list: Agent
  family name: Kimiko
  given name: Itoh
author list: Agent
  family name: Al-Doss
  given name: Abdullah
doi: 10.7717/peerj.20432
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-28
copyright: ©2025 Ibrahim et al.
attribution name: Ibrahim et al.

Understanding perceived exertion in power-aimed resistance training: the relationship between perceived exertion and muscle fatigue
type: item
type: AcademicArticle
description: Background Perceived exertion is an inevitable outcome of power-oriented resistance training. However, it remains unknown whether perceived exertion is dominated by central or peripheral responses during this type of training. This study examined the effect of neuromuscular responses on the determination of ratings of perceived exertion (RPE) during power bench press (BPress) exercise. Methods Sixteen trained males performed three BPress tasks with varying volumes (low, medium, high) at 65% of their one-repetition maximum. RPE, surface electromyography, and velocity loss were assessed across all conditions. Peak root mean square (RMS) and median frequency (MDF) were calculated from the surface electromyography data. Results Significant effects were observed across experimental conditions for overall RPE, average velocity loss, and average MDF (all p < 0.001), while no significant difference was found in average RMS. As the lifting tasks progressed, significant effects of repetition were observed in all measured variables (all p < 0.001). When comparing conditions, significant differences were found among the three in RPE, velocity loss, and MDF (all p < 0.001), whereas no significant effect of condition was observed in RMS. No significant relationship was found between MDF and velocity loss. Conclusions In power BPress, higher repetitions affected RPE, velocity loss, and MDF, while peak RMS was less responsive. These findings indicate that both athletic performance and RPE are primarily influenced by peripheral fatigue. However, velocity loss should be interpreted with caution as a fatigue marker in this context.
format: application/pdf
format: text/html
creator: Hanye Zhao
creator: Takanori Kurokawa
creator: Masayoshi Tajima
creator: Zijian Liu
creator: Junichi Okada
subject: Kinesiology
subject: Sports Injury
subject: Sports Medicine
description: doi:10.7717/peerj.20426
publisher: PeerJ Inc.
rights: © 2025 Zhao et al.
abstract: Background Perceived exertion is an inevitable outcome of power-oriented resistance training. However, it remains unknown whether perceived exertion is dominated by central or peripheral responses during this type of training. This study examined the effect of neuromuscular responses on the determination of ratings of perceived exertion (RPE) during power bench press (BPress) exercise. Methods Sixteen trained males performed three BPress tasks with varying volumes (low, medium, high) at 65% of their one-repetition maximum. RPE, surface electromyography, and velocity loss were assessed across all conditions. Peak root mean square (RMS) and median frequency (MDF) were calculated from the surface electromyography data. Results Significant effects were observed across experimental conditions for overall RPE, average velocity loss, and average MDF (all p < 0.001), while no significant difference was found in average RMS. As the lifting tasks progressed, significant effects of repetition were observed in all measured variables (all p < 0.001). When comparing conditions, significant differences were found among the three in RPE, velocity loss, and MDF (all p < 0.001), whereas no significant effect of condition was observed in RMS. No significant relationship was found between MDF and velocity loss. Conclusions In power BPress, higher repetitions affected RPE, velocity loss, and MDF, while peak RMS was less responsive. These findings indicate that both athletic performance and RPE are primarily influenced by peripheral fatigue. However, velocity loss should be interpreted with caution as a fatigue marker in this context.
bibliographic citation: Zhao et al. (2025) Understanding perceived exertion in power-aimed resistance training: the relationship between perceived exertion and muscle fatigue. PeerJ 13:e20426 https://doi.org/10.7717/peerj.20426
date submitted: 2025-06-18
date accepted: 2025-10-29
issued: 2025-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Hanye
author list: Agent
  family name: Kurokawa
  given name: Takanori
author list: Agent
  family name: Tajima
  given name: Masayoshi
author list: Agent
  family name: Liu
  given name: Zijian
author list: Agent
  family name: Okada
  given name: Junichi
doi: 10.7717/peerj.20426
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-28
copyright: ©2025 Zhao et al.
attribution name: Zhao et al.

Parasites influence the physiology and personality in a small mammal (Ochotona curzoniae)
type: item
type: AcademicArticle
description: Background Parasites are prevalent in animals and have coexisted with their hosts over long evolutionary periods. However, the link between individual behavioral variations and parasitic infections remains unclear. Plateau pika (Ochotona curzoniae) is a keystone species on the Qinghai-Tibetan Plateau that is commonly infected with Eimeria spp., an intestinal parasite. Methods In this study, 30 adult pikas were assigned to three groups: infected with Eimeria spp. (PA+), administered normal saline (Ctrl), and treated with an anticoccidial drug (PA−). We examined changes in boldness, exploration, and docility, as well as variations in triiodothyronine (T3), thyroxine (T4), resting metabolic rate (RMR), and fecal cortisol (CORT) levels. Results The PA+ group exhibited significantly higher parasite load. Pikas showed increased boldness, exploration, and docility on day 5, when Eimeria spp. numbers were high. The T3 and T4 levels declined as parasite loads increased, whereas the CORT and RMR levels fluctuated at different experimental stages. These results suggest that parasite infection influences host behavior and physiology, providing insights into parasite-host interactions. Conclusion This study provides evidence that Eimeria spp. load modulates the behavior and physiology of plateau pikas. The specific behavioral shifts coinciding with peak infection, coupled with the suppression of thyroid hormones and metabolic responses, reveal a complex and integrated host adaptation strategy. As a keystone species on the Qinghai-Tibet Plateau, the behavior-physiology coupling mechanism in plateau pikas not only provides new evidence for host-parasite coevolution, but also offers critical insights into understanding the stability of regional ecosystems.
format: application/pdf
format: text/html
creator: Rong Wang
creator: Suqin Wang
creator: Jiapeng Qu
subject: Animal Behavior
subject: Ecology
subject: Parasitology
subject: Zoology
description: doi:10.7717/peerj.20420
publisher: PeerJ Inc.
rights: © 2025 Wang et al.
abstract: Background Parasites are prevalent in animals and have coexisted with their hosts over long evolutionary periods. However, the link between individual behavioral variations and parasitic infections remains unclear. Plateau pika (Ochotona curzoniae) is a keystone species on the Qinghai-Tibetan Plateau that is commonly infected with Eimeria spp., an intestinal parasite. Methods In this study, 30 adult pikas were assigned to three groups: infected with Eimeria spp. (PA+), administered normal saline (Ctrl), and treated with an anticoccidial drug (PA−). We examined changes in boldness, exploration, and docility, as well as variations in triiodothyronine (T3), thyroxine (T4), resting metabolic rate (RMR), and fecal cortisol (CORT) levels. Results The PA+ group exhibited significantly higher parasite load. Pikas showed increased boldness, exploration, and docility on day 5, when Eimeria spp. numbers were high. The T3 and T4 levels declined as parasite loads increased, whereas the CORT and RMR levels fluctuated at different experimental stages. These results suggest that parasite infection influences host behavior and physiology, providing insights into parasite-host interactions. Conclusion This study provides evidence that Eimeria spp. load modulates the behavior and physiology of plateau pikas. The specific behavioral shifts coinciding with peak infection, coupled with the suppression of thyroid hormones and metabolic responses, reveal a complex and integrated host adaptation strategy. As a keystone species on the Qinghai-Tibet Plateau, the behavior-physiology coupling mechanism in plateau pikas not only provides new evidence for host-parasite coevolution, but also offers critical insights into understanding the stability of regional ecosystems.
bibliographic citation: Wang et al. (2025) Parasites influence the physiology and personality in a small mammal (Ochotona curzoniae). PeerJ 13:e20420 https://doi.org/10.7717/peerj.20420
date submitted: 2025-09-05
date accepted: 2025-10-29
issued: 2025-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Rong
author list: Agent
  family name: Wang
  given name: Suqin
author list: Agent
  family name: Qu
  given name: Jiapeng
doi: 10.7717/peerj.20420
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-28
copyright: © 2025 Wang et al.
attribution name: Wang et al.

Biochemical and molecular responses of maize to low and high temperatures in symbiosis with mixed arbuscular mycorrhizal fungi cultures
type: item
type: AcademicArticle
description: In this study, changes in mineral element concentrations, physiological parameters, and gene expression of heat shock proteins were investigated in maize plants subjected to mycorrhiza under low and high temperature stress. The application of seven different temperatures (5 °C, 10 °C, 15 °C, 25 °C, 35 °C, 40 °C, and 45 °C) under five different mixed arbuscular mycorrhizal fungi (AMF) culture treatments (M0, M1, M2, M3, and M4) constituted the factors of the experiment. With the application of mycorrhiza, the plant dry weight was found to be the highest at 25 °C, and the M3 group was applied. The highest values in mineral element concentrations were detected at 25 °C in the maize plant, where M4 had N, P, K, Ca, and Fe concentrations; M3 had Cu and Mn concentrations; and M2 had Mg and Zn concentrations. Lipid peroxidation gradually increased with temperature changes in all the applications, and the protective effect of proline was more pronounced at high temperatures than at low temperatures. Antioxidant enzyme activities were altered by applications of mycorrhiza and temperature. For all mycorrhiza applications, the expression of HSP70 and HSP90 reached a maximum at 10 °C, 40 °C, and 45 °C. It has been revealed that low- and high-temperature applications in maize plants cause serious changes in the mycorrhizal symbiosis on the basis of investigated parameters, and these changes occur at different levels depending on the temperature changes and the differences between mixed AMF cultures. However, it can be said that the M3 application has the capacity to facilitate the growth of maize even in conditions of low (−10 °C) and high (45 °C) temperature.
format: application/pdf
format: text/html
creator: Vedia Turudu
creator: Imren Kutlu
creator: Nurdilek Gulmezoglu
subject: Agricultural Science
description: doi:10.7717/peerj.20419
publisher: PeerJ Inc.
rights: © 2025 Turudu et al.
abstract: In this study, changes in mineral element concentrations, physiological parameters, and gene expression of heat shock proteins were investigated in maize plants subjected to mycorrhiza under low and high temperature stress. The application of seven different temperatures (5 °C, 10 °C, 15 °C, 25 °C, 35 °C, 40 °C, and 45 °C) under five different mixed arbuscular mycorrhizal fungi (AMF) culture treatments (M0, M1, M2, M3, and M4) constituted the factors of the experiment. With the application of mycorrhiza, the plant dry weight was found to be the highest at 25 °C, and the M3 group was applied. The highest values in mineral element concentrations were detected at 25 °C in the maize plant, where M4 had N, P, K, Ca, and Fe concentrations; M3 had Cu and Mn concentrations; and M2 had Mg and Zn concentrations. Lipid peroxidation gradually increased with temperature changes in all the applications, and the protective effect of proline was more pronounced at high temperatures than at low temperatures. Antioxidant enzyme activities were altered by applications of mycorrhiza and temperature. For all mycorrhiza applications, the expression of HSP70 and HSP90 reached a maximum at 10 °C, 40 °C, and 45 °C. It has been revealed that low- and high-temperature applications in maize plants cause serious changes in the mycorrhizal symbiosis on the basis of investigated parameters, and these changes occur at different levels depending on the temperature changes and the differences between mixed AMF cultures. However, it can be said that the M3 application has the capacity to facilitate the growth of maize even in conditions of low (−10 °C) and high (45 °C) temperature.
bibliographic citation: Turudu et al. (2025) Biochemical and molecular responses of maize to low and high temperatures in symbiosis with mixed arbuscular mycorrhizal fungi cultures. PeerJ 13:e20419 https://doi.org/10.7717/peerj.20419
date submitted: 2025-07-31
date accepted: 2025-10-28
issued: 2025-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Turudu
  given name: Vedia
author list: Agent
  family name: Kutlu
  given name: Imren
author list: Agent
  family name: Gulmezoglu
  given name: Nurdilek
doi: 10.7717/peerj.20419
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-28
copyright: © 2025 Turudu et al.
attribution name: Turudu et al.

Evaluation of water quality and soil fertility in remediated farmland for protection of wetland ecology by planting different crops
type: item
type: AcademicArticle
description: Enhancements in water quality and soil characteristics of wetlands can improve the ecological environment of the area and enrich its biodiversity. The present study examined the effects of five distinct crops (i.e.: colza oil, mustard, Chinese cabbage, wheat, barley) cultivated in remediation plots, and evaluated their impact on water quality and soil fertility. The water quality within the remediated farmland was categorized as Class III (moderately polluted). The soil exhibited low total nitrogen and organic matter levels (the mean values were respectively 0.032% and 10.84 g/kg), and high readily available phosphorus and potassium concentration (the mean values were respectively 75.71 and 247.64 mg/kg). The soil fertility was comprehensively categorized as Class III (moderately polluted). Subsequently, the different components of bird droppings in the soil were investigated for their potential effects on soil fertility. The present research demonstrated that the remediation of farmland had the potential to enhance the quality of water and soil fertility in wetland. This, in turn, might result in an increased number of migratory birds inhabiting the area.
format: application/pdf
format: text/html
creator: Changqing Liu
creator: Zhongxiang Sun
creator: Hongyang Wang
creator: Tianwen Chen
creator: Lina Deng
creator: Li Zhang
creator: Huixing Liang
creator: Yuxiang Shen
creator: Hongshan Li
creator: Hai Cheng
subject: Plant Science
subject: Soil Science
subject: Aquatic and Marine Chemistry
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.20406
publisher: PeerJ Inc.
rights: © 2025 Liu et al.
abstract: Enhancements in water quality and soil characteristics of wetlands can improve the ecological environment of the area and enrich its biodiversity. The present study examined the effects of five distinct crops (i.e.: colza oil, mustard, Chinese cabbage, wheat, barley) cultivated in remediation plots, and evaluated their impact on water quality and soil fertility. The water quality within the remediated farmland was categorized as Class III (moderately polluted). The soil exhibited low total nitrogen and organic matter levels (the mean values were respectively 0.032% and 10.84 g/kg), and high readily available phosphorus and potassium concentration (the mean values were respectively 75.71 and 247.64 mg/kg). The soil fertility was comprehensively categorized as Class III (moderately polluted). Subsequently, the different components of bird droppings in the soil were investigated for their potential effects on soil fertility. The present research demonstrated that the remediation of farmland had the potential to enhance the quality of water and soil fertility in wetland. This, in turn, might result in an increased number of migratory birds inhabiting the area.
bibliographic citation: Liu et al. (2025) Evaluation of water quality and soil fertility in remediated farmland for protection of wetland ecology by planting different crops. PeerJ 13:e20406 https://doi.org/10.7717/peerj.20406
date submitted: 2025-01-14
date accepted: 2025-10-27
issued: 2025-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Changqing
author list: Agent
  family name: Sun
  given name: Zhongxiang
author list: Agent
  family name: Wang
  given name: Hongyang
author list: Agent
  family name: Chen
  given name: Tianwen
author list: Agent
  family name: Deng
  given name: Lina
author list: Agent
  family name: Zhang
  given name: Li
author list: Agent
  family name: Liang
  given name: Huixing
author list: Agent
  family name: Shen
  given name: Yuxiang
author list: Agent
  family name: Li
  given name: Hongshan
author list: Agent
  family name: Cheng
  given name: Hai
doi: 10.7717/peerj.20406
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-28
copyright: ©2025 Liu et al.
attribution name: Liu et al.

Effects of monocropping soil on plant growth and rhizosphere microbial community structure of Salvia miltiorrhiza Bge
type: item
type: AcademicArticle
description: Salvia miltiorrhiza (Danshen) is a commonly utilized remedy for various blood stasis syndromes, cardiovascular, and cerebrovascular diseases. The practice of continuous cropping presents a notable challenge to the production of high-quality S. miltiorrhiza due to the lack of rotation or soil remediation. Despite this, the precise mechanism, particularly the impact of alterations in the rhizosphere microbial community structure on the development of obstacles related to continuous cropping, remains obscure. The constitution of the rhizosphere microbial community plays a pivotal role in plant growth and has the potential to exacerbate issues associated with continuous cropping. This study aimed to comprehensively compare the impact of continuous vs. non-continuous cropping soils on the growth, physiological and biochemical characteristics, accumulation of active ingredients, and rhizosphere microbial community structure of S. miltiorrhiza seedlings to elucidate the microbial ecological mechanism behind continuous cropping challenges. A pot experiment was executed to assess the effects of continuous cropping on the morphological and physiological parameters of S. miltiorrhiza. High-throughput sequencing technology utilizing the NovaSeq platform was employed to sequence and analyze the V4 region of bacterial 16S rDNA and the ITS1 region of fungi in the rhizosphere. The findings revealed that continuous cropping soil led to a reduction in S. miltiorrhiza biomass, manifesting as wilting and stunted growth, diminished effective leaf area, main root length and diameter, reduced levels of total chlorophyll, carbohydrates, and active ingredients, as well as compromised photosynthesis. In the rhizosphere soil, both the composition and function of the fungal community have undergone significant changes, and the fungal diversity has shown a clear increasing trend; in contrast, the change in bacterial diversity is very slight. In conclusion, continuous cropping soil substantially…
format: application/pdf
format: text/html
creator: Ji Dong Ju
creator: Yuan Meng
creator: Bingqian Zhou
creator: Guohong Yang
creator: Xinyu Fu
creator: Wei Liu
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.20379
publisher: PeerJ Inc.
rights: © 2025 Ju et al.
abstract: Salvia miltiorrhiza (Danshen) is a commonly utilized remedy for various blood stasis syndromes, cardiovascular, and cerebrovascular diseases. The practice of continuous cropping presents a notable challenge to the production of high-quality S. miltiorrhiza due to the lack of rotation or soil remediation. Despite this, the precise mechanism, particularly the impact of alterations in the rhizosphere microbial community structure on the development of obstacles related to continuous cropping, remains obscure. The constitution of the rhizosphere microbial community plays a pivotal role in plant growth and has the potential to exacerbate issues associated with continuous cropping. This study aimed to comprehensively compare the impact of continuous vs. non-continuous cropping soils on the growth, physiological and biochemical characteristics, accumulation of active ingredients, and rhizosphere microbial community structure of S. miltiorrhiza seedlings to elucidate the microbial ecological mechanism behind continuous cropping challenges. A pot experiment was executed to assess the effects of continuous cropping on the morphological and physiological parameters of S. miltiorrhiza. High-throughput sequencing technology utilizing the NovaSeq platform was employed to sequence and analyze the V4 region of bacterial 16S rDNA and the ITS1 region of fungi in the rhizosphere. The findings revealed that continuous cropping soil led to a reduction in S. miltiorrhiza biomass, manifesting as wilting and stunted growth, diminished effective leaf area, main root length and diameter, reduced levels of total chlorophyll, carbohydrates, and active ingredients, as well as compromised photosynthesis. In the rhizosphere soil, both the composition and function of the fungal community have undergone significant changes, and the fungal diversity has shown a clear increasing trend; in contrast, the change in bacterial diversity is very slight. In conclusion, continuous cropping soil substantially…
bibliographic citation: Ju et al. (2025) Effects of monocropping soil on plant growth and rhizosphere microbial community structure of Salvia miltiorrhiza Bge. PeerJ 13:e20379 https://doi.org/10.7717/peerj.20379
date submitted: 2025-04-29
date accepted: 2025-10-21
issued: 2025-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ju
  given name: Ji Dong
author list: Agent
  family name: Meng
  given name: Yuan
author list: Agent
  family name: Zhou
  given name: Bingqian
author list: Agent
  family name: Yang
  given name: Guohong
author list: Agent
  family name: Fu
  given name: Xinyu
author list: Agent
  family name: Liu
  given name: Wei
doi: 10.7717/peerj.20379
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-28
copyright: © 2025 Ju et al.
attribution name: Ju et al.

Effectiveness of respiratory muscle training on pulmonary function recovery in patients with spinal cord injury: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Objective This study conducted a thorough review and meta-analysis to examine how respiratory muscle training (RMT) affects lung function recovery in individuals with spinal cord injury (SCI). Methods We conducted a systematic review of Randomized Controlled Trials (RCTs) examining the effects of RMT on lung function in patients with SCI. The search included databases such as PubMed, Embase, The Cochrane Library, Scopus, and Web of Science up to October 2025. The experimental group received RMT as the main intervention, while the control group received either no treatment, a placebo, or conventional rehabilitation. Outcome measures included Forced Expiratory Volume in the first second (FEV1), Forced Vital Capacity (FVC), Maximum Inspiratory Pressure (MIP), Maximum Expiratory Pressure (MEP), Peak Expiratory Flow (PEF), Minute Ventilation Volume (MVV), Total Lung Capacity (TLC), Inspiratory Capacity (IC), and Vital Capacity (VC). Two reviewers independently screened, extracted data, and assessed bias. Meta-analysis was conducted using RevMan 5.3 software, and the quality of included studies was evaluated using the Cochrane bias risk assessment tool and the Physical Therapy Evidence Database scale. The reporting of this study followed the PRISMA guidelines and was registered with PROSPERO (ID: CRD42024627736). Results In this meta-analysis, 25 RCTs were included, comprising a total of 679 patients. The meta-analysis showed that compared with conventional rehabilitation, respiratory muscle training significantly improved FEV1 (p < 0.0001), FVC (p = 0.0001), MIP (p < 0.00001), MEP (p = 0.0004), PEF (p < 0.00001), MVV (p < 0.0001), TLC (p = 0.05), VC (p = 0.04), and their differences were statistically significant. However, IC (p = 0.40) was not statistically significant. Subgroup analyses showed that resistive training and surface electromyography biofeedback training were effective for improving FEV1 and FVC, while threshold training significantly improved MVV. Conclusi…
format: application/pdf
format: text/html
creator: Shuqi Yao
creator: Haozhe Guo
creator: Fuhai Ma
creator: Aiping Chi
subject: Kinesiology
subject: Rehabilitation
subject: Sports Medicine
description: doi:10.7717/peerj.20373
publisher: PeerJ Inc.
rights: © 2025 Yao et al.
abstract: Objective This study conducted a thorough review and meta-analysis to examine how respiratory muscle training (RMT) affects lung function recovery in individuals with spinal cord injury (SCI). Methods We conducted a systematic review of Randomized Controlled Trials (RCTs) examining the effects of RMT on lung function in patients with SCI. The search included databases such as PubMed, Embase, The Cochrane Library, Scopus, and Web of Science up to October 2025. The experimental group received RMT as the main intervention, while the control group received either no treatment, a placebo, or conventional rehabilitation. Outcome measures included Forced Expiratory Volume in the first second (FEV1), Forced Vital Capacity (FVC), Maximum Inspiratory Pressure (MIP), Maximum Expiratory Pressure (MEP), Peak Expiratory Flow (PEF), Minute Ventilation Volume (MVV), Total Lung Capacity (TLC), Inspiratory Capacity (IC), and Vital Capacity (VC). Two reviewers independently screened, extracted data, and assessed bias. Meta-analysis was conducted using RevMan 5.3 software, and the quality of included studies was evaluated using the Cochrane bias risk assessment tool and the Physical Therapy Evidence Database scale. The reporting of this study followed the PRISMA guidelines and was registered with PROSPERO (ID: CRD42024627736). Results In this meta-analysis, 25 RCTs were included, comprising a total of 679 patients. The meta-analysis showed that compared with conventional rehabilitation, respiratory muscle training significantly improved FEV1 (p < 0.0001), FVC (p = 0.0001), MIP (p < 0.00001), MEP (p = 0.0004), PEF (p < 0.00001), MVV (p < 0.0001), TLC (p = 0.05), VC (p = 0.04), and their differences were statistically significant. However, IC (p = 0.40) was not statistically significant. Subgroup analyses showed that resistive training and surface electromyography biofeedback training were effective for improving FEV1 and FVC, while threshold training significantly improved MVV. Conclusi…
bibliographic citation: Yao et al. (2025) Effectiveness of respiratory muscle training on pulmonary function recovery in patients with spinal cord injury: a systematic review and meta-analysis. PeerJ 13:e20373 https://doi.org/10.7717/peerj.20373
date submitted: 2025-06-20
date accepted: 2025-10-20
issued: 2025-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yao
  given name: Shuqi
author list: Agent
  family name: Guo
  given name: Haozhe
author list: Agent
  family name: Ma
  given name: Fuhai
author list: Agent
  family name: Chi
  given name: Aiping
doi: 10.7717/peerj.20373
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-28
copyright: ©2025 Yao et al.
attribution name: Yao et al.

Genomics, population dynamics, immune evasion and resistance determinants foster the competence and global dissemination of Klebsiella pneumoniae
type: item
type: AcademicArticle
description: Background According to the World Health Organization (WHO), Klebsiella pneumoniae is a critical public health concern and an established ESKAPE (E. faecium, S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa, and Enterobacter spp.) pathogen. Mounting incidence of MDR K. pneumoniae is worrisome across the globe. K. pneumoniae is an established ubiquitous pathogen and associated with various infections in a wide range of hosts. Methods The peer reviewed findings with given problem statements were thoroughly studied through literature review technique. Multiple antibiotic-resistance genes and virulence genes across various Klebsiella species were studied to explore their evolutionary dynamics and genetic diversity. Results Population dynamics revealed that the clonal group (CG) 258 and CG 14 are considered as global disseminated clones. The genome size (5.7 Mbps) of K. pneumoniae is reported to be larger than the other Enterobacteriaceae which allows K. pneumoniae to survive in diverse geographical niches. It has adequate resistome and virulence machinery to evade the host immune system and establish the infection. Due to the emergence of resistant variants K. pneumoniae needs appropriate alternative control measures. Conclusion The current review described the characteristics features of K. pneumoniae which are the key players in making this organism a credential pathogen. Additionally, it would be instructive and underpin the molecular insights that may aid in restraining this pathogen.
format: application/pdf
format: text/html
creator: Bilal Aslam
creator: Sulaiman F. Aljasir
subject: Microbiology
subject: Molecular Biology
subject: Epidemiology
subject: Infectious Diseases
description: doi:10.7717/peerj.20296
publisher: PeerJ Inc.
rights: © 2025 Aslam and Aljasir
abstract: Background According to the World Health Organization (WHO), Klebsiella pneumoniae is a critical public health concern and an established ESKAPE (E. faecium, S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa, and Enterobacter spp.) pathogen. Mounting incidence of MDR K. pneumoniae is worrisome across the globe. K. pneumoniae is an established ubiquitous pathogen and associated with various infections in a wide range of hosts. Methods The peer reviewed findings with given problem statements were thoroughly studied through literature review technique. Multiple antibiotic-resistance genes and virulence genes across various Klebsiella species were studied to explore their evolutionary dynamics and genetic diversity. Results Population dynamics revealed that the clonal group (CG) 258 and CG 14 are considered as global disseminated clones. The genome size (5.7 Mbps) of K. pneumoniae is reported to be larger than the other Enterobacteriaceae which allows K. pneumoniae to survive in diverse geographical niches. It has adequate resistome and virulence machinery to evade the host immune system and establish the infection. Due to the emergence of resistant variants K. pneumoniae needs appropriate alternative control measures. Conclusion The current review described the characteristics features of K. pneumoniae which are the key players in making this organism a credential pathogen. Additionally, it would be instructive and underpin the molecular insights that may aid in restraining this pathogen.
bibliographic citation: Aslam et al. (2025) Genomics, population dynamics, immune evasion and resistance determinants foster the competence and global dissemination of Klebsiella pneumoniae. PeerJ 13:e20296 https://doi.org/10.7717/peerj.20296
date submitted: 2025-04-25
date accepted: 2025-10-06
issued: 2025-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aslam
  given name: Bilal
author list: Agent
  family name: Aljasir
  given name: Sulaiman F.
doi: 10.7717/peerj.20296
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-28
copyright: © 2025 Aslam and Aljasir
attribution name: Aslam and Aljasir

Structure and diversity of microbial communities in the rhizosphere soil of Trichosanthes kirilowii from different cultivation patterns
type: item
type: AcademicArticle
description: Background To analyze the effects of different cultivation patterns on the structure and diversity of the microbial community in the rhizosphere soil of Trichosanthes kirilowii (T. kirilowii) arms to establish reasonable and effective strategies to mitigate the continuous cropping barriers and promote the high-quality cultivation of T. kirilowii. Methods Three distinct cultivation patterns were investigated: open-field cultivation (TM1), film-mulched cultivation (TM2), and soybean intercropping cultivation (TM3). High-throughput sequencing and bioinformatic analyses were employed to evaluate the rhizosphere microbiome, and redundancy analysis was utilized to investigate the relationship between the microbial communities and soil nutrient indicators. Results TM2 and TM3 increased soil bacterial community diversity, reduced fungal community diversity, elevated the relative abundance of beneficial bacterial genera, and reduced the abundance of detrimental fungal genera in the rhizosphere soil. The relative abundance of Pseudarthrobacter, unclassified_Steroidobacteraceae, and Nocardioides in TM2 and TM3 was markedly higher than in TM1. Conversely, the relative abundance of Fusarium, Rhizoctonia, Ceratobasidium, and Plectosphaerella in TM2 and TM3 was significantly reduced compared to TM1. The contents of available potassium (AK), total nitrogen (TN), total phosphorus (TP), and pH in the rhizosphere soil of TM2 and TM3 were significantly higher than those in TM1. The distribution of soil bacterial genera was significantly influenced by the contents of TN and AK, while the distribution of soil fungal genera was significantly or extremely significantly impacted by the contents of TP, total potassium (TK), soil organic matter (SOM), and pH. The content of AK was extremely significantly positively correlated with the relative abundance of Nocardioides, whereas the content of TK showed an extremely negative correlation with the relative abundance of Ceratobasidium. Similarly,…
format: application/pdf
format: text/html
creator: Lei Zheng
creator: Huadong Wang
creator: Zhiqiang Zhang
creator: Jiulin Gu
creator: Yao Yin
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.20459
publisher: PeerJ Inc.
rights: © 2025 Zheng et al.
abstract: Background To analyze the effects of different cultivation patterns on the structure and diversity of the microbial community in the rhizosphere soil of Trichosanthes kirilowii (T. kirilowii) arms to establish reasonable and effective strategies to mitigate the continuous cropping barriers and promote the high-quality cultivation of T. kirilowii. Methods Three distinct cultivation patterns were investigated: open-field cultivation (TM1), film-mulched cultivation (TM2), and soybean intercropping cultivation (TM3). High-throughput sequencing and bioinformatic analyses were employed to evaluate the rhizosphere microbiome, and redundancy analysis was utilized to investigate the relationship between the microbial communities and soil nutrient indicators. Results TM2 and TM3 increased soil bacterial community diversity, reduced fungal community diversity, elevated the relative abundance of beneficial bacterial genera, and reduced the abundance of detrimental fungal genera in the rhizosphere soil. The relative abundance of Pseudarthrobacter, unclassified_Steroidobacteraceae, and Nocardioides in TM2 and TM3 was markedly higher than in TM1. Conversely, the relative abundance of Fusarium, Rhizoctonia, Ceratobasidium, and Plectosphaerella in TM2 and TM3 was significantly reduced compared to TM1. The contents of available potassium (AK), total nitrogen (TN), total phosphorus (TP), and pH in the rhizosphere soil of TM2 and TM3 were significantly higher than those in TM1. The distribution of soil bacterial genera was significantly influenced by the contents of TN and AK, while the distribution of soil fungal genera was significantly or extremely significantly impacted by the contents of TP, total potassium (TK), soil organic matter (SOM), and pH. The content of AK was extremely significantly positively correlated with the relative abundance of Nocardioides, whereas the content of TK showed an extremely negative correlation with the relative abundance of Ceratobasidium. Similarly,…
bibliographic citation: Zheng et al. (2025) Structure and diversity of microbial communities in the rhizosphere soil of Trichosanthes kirilowii from different cultivation patterns. PeerJ 13:e20459 https://doi.org/10.7717/peerj.20459
date submitted: 2025-09-24
date accepted: 2025-11-03
issued: 2025-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zheng
  given name: Lei
author list: Agent
  family name: Wang
  given name: Huadong
author list: Agent
  family name: Zhang
  given name: Zhiqiang
author list: Agent
  family name: Gu
  given name: Jiulin
author list: Agent
  family name: Yin
  given name: Yao
doi: 10.7717/peerj.20459
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-27
copyright: © 2025 Zheng et al.
attribution name: Zheng et al.

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