PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The conservation value of freshwater habitats for frog communities of lowland fynbos
items: Association between free thyroxine levels and clinical phenotype in first-episode psychosis: a prospective observational study
items: Influence of SPIO labelling on the function of BMSCs in chemokine receptors expression and chemotaxis
items: Functional responses of male and female European green crabs suggest potential sex-specific impacts of invasion
items: Antimicrobial susceptibility and integrons detection among extended-spectrum β-lactamase producing Enterobacteriaceae isolates in patients with urinary tract infection
items: Unraveling the functional genes present in rhizosphere microbiomes of Solanum lycopersicum
items: Uncertainty in projections of future lake thermal dynamics is differentially driven by lake and global climate models
items: The complete mitochondrial genomes of four lagriine species (Coleoptera, Tenebrionidae) and phylogenetic relationships within Tenebrionidae
items: Macrophyte communities as bioindicator of stormwater pollution in rivers: a quantitative analysis
items: New seed coating containing Trichoderma viride with anti-pathogenic properties

The conservation value of freshwater habitats for frog communities of lowland fynbos
type: item
type: AcademicArticle
description: Amphibians are more threatened than any other vertebrate class, yet evidence for many threats is missing. The Cape lowland fynbos (endemic scrub biome) is threatened by habitat loss, and natural temporary freshwater habitats are removed in favour of permanent impoundments. In this study, we determine amphibian assemblages across different freshwater habitat types with special attention to the presence of invasive fish. We find that anuran communities differ primarily by habitat type, with permanent water habitats having more widespread taxa, while temporary water bodies have more range restricted taxa. Invasive fish are found to have a significant impact on frogs with toads most tolerant of their presence. Temporary freshwater habitats are a conservation priority in the area, and their amphibian assemblages represent endemic taxa that are intolerant of invasive fish. Conservation of a biodiverse amphibian assemblage in lowland fynbos areas will rely on the creation of temporary freshwater habitats, rather than a northern hemisphere pond based solution.
format: application/pdf
format: text/html
creator: Naas Terblanche
creator: John Measey
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.15516
publisher: PeerJ Inc.
rights: © 2023 Terblanche and Measey
abstract: Amphibians are more threatened than any other vertebrate class, yet evidence for many threats is missing. The Cape lowland fynbos (endemic scrub biome) is threatened by habitat loss, and natural temporary freshwater habitats are removed in favour of permanent impoundments. In this study, we determine amphibian assemblages across different freshwater habitat types with special attention to the presence of invasive fish. We find that anuran communities differ primarily by habitat type, with permanent water habitats having more widespread taxa, while temporary water bodies have more range restricted taxa. Invasive fish are found to have a significant impact on frogs with toads most tolerant of their presence. Temporary freshwater habitats are a conservation priority in the area, and their amphibian assemblages represent endemic taxa that are intolerant of invasive fish. Conservation of a biodiverse amphibian assemblage in lowland fynbos areas will rely on the creation of temporary freshwater habitats, rather than a northern hemisphere pond based solution.
bibliographic citation: Terblanche et al. (2023) The conservation value of freshwater habitats for frog communities of lowland fynbos. PeerJ 11:e15516 https://doi.org/10.7717/peerj.15516
date submitted: 2022-11-17
date accepted: 2023-05-15
issued: 2023-06-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Terblanche
  given name: Naas
author list: Agent
  family name: Measey
  given name: John
doi: 10.7717/peerj.15516
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-05
copyright: © 2023 Terblanche and Measey
attribution name: Terblanche and Measey

Association between free thyroxine levels and clinical phenotype in first-episode psychosis: a prospective observational study
type: item
type: AcademicArticle
description: Aim To determine whether thyroid hormone levels are associated with a specific clinical phenotype in patients with first-episode psychosis (FEP). Methods Ninety-eight inpatients experiencing FEP and with less than 6 weeks of antipsychotic treatment were included in the study and were followed up for one year. Baseline psychiatric evaluation included assessment of prodromal symptoms, positive and negative symptoms, depressive symptoms, stressful life events and cycloid psychosis criteria. Thyroid function (thyroid-stimulating hormone (TSH) and free thyroxin (FT4)) was determined at admission. Partial correlation analysis was conducted to analyse the correlation between levels of TSH/FT4 and symptoms. Logistic regression was performed to explore the association between psychopathological symptoms, 12-month diagnoses and thyroid hormones while adjusting for covariates. Results Patients with prodromal symptomatology showed lower baseline FT4 levels (OR = 0.06; p = 0.018). The duration of untreated psychosis (DUP) was inversely associated with FT4 concentrations (r = − 0.243; p = 0.039). FEP patients with sudden onset of psychotic symptoms (criteria B, cycloid psychosis) showed higher FT4 levels at admission (OR = 10.49; p = 0.040). Patients diagnosed with affective psychotic disorders (BD or MDD) at the 12-month follow-up showed higher FT4 levels at admission than patients diagnosed with nonaffective psychosis (schizophrenia, schizoaffective) (OR = 8.57; p = 0.042). Conclusions Our study suggests that higher free-thyroxine levels are associated with a specific clinical phenotype of FEP patients (fewer prodromal symptoms, shorter DUP duration and sudden onset of psychosis) and with affective psychosis diagnoses at the 12-month follow-up.
format: application/pdf
format: text/html
creator: Eloi Gine-Serven
creator: Maria Martinez-Ramirez
creator: Ester Boix-Quintana
creator: Eva Davi-Loscos
creator: Nicolau Guanyabens
creator: Virginia Casado
creator: Desiree Muriana
creator: Cristina Torres-Rivas
creator: M.J. Cuesta
creator: Javier Labad
subject: Psychiatry and Psychology
subject: Mental Health
description: doi:10.7717/peerj.15347
publisher: PeerJ Inc.
rights: © 2023 Gine-Serven et al.
abstract: Aim To determine whether thyroid hormone levels are associated with a specific clinical phenotype in patients with first-episode psychosis (FEP). Methods Ninety-eight inpatients experiencing FEP and with less than 6 weeks of antipsychotic treatment were included in the study and were followed up for one year. Baseline psychiatric evaluation included assessment of prodromal symptoms, positive and negative symptoms, depressive symptoms, stressful life events and cycloid psychosis criteria. Thyroid function (thyroid-stimulating hormone (TSH) and free thyroxin (FT4)) was determined at admission. Partial correlation analysis was conducted to analyse the correlation between levels of TSH/FT4 and symptoms. Logistic regression was performed to explore the association between psychopathological symptoms, 12-month diagnoses and thyroid hormones while adjusting for covariates. Results Patients with prodromal symptomatology showed lower baseline FT4 levels (OR = 0.06; p = 0.018). The duration of untreated psychosis (DUP) was inversely associated with FT4 concentrations (r = − 0.243; p = 0.039). FEP patients with sudden onset of psychotic symptoms (criteria B, cycloid psychosis) showed higher FT4 levels at admission (OR = 10.49; p = 0.040). Patients diagnosed with affective psychotic disorders (BD or MDD) at the 12-month follow-up showed higher FT4 levels at admission than patients diagnosed with nonaffective psychosis (schizophrenia, schizoaffective) (OR = 8.57; p = 0.042). Conclusions Our study suggests that higher free-thyroxine levels are associated with a specific clinical phenotype of FEP patients (fewer prodromal symptoms, shorter DUP duration and sudden onset of psychosis) and with affective psychosis diagnoses at the 12-month follow-up.
bibliographic citation: Gine-Serven et al. (2023) Association between free thyroxine levels and clinical phenotype in first-episode psychosis: a prospective observational study. PeerJ 11:e15347 https://doi.org/10.7717/peerj.15347
date submitted: 2022-12-23
date accepted: 2023-04-13
issued: 2023-06-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gine-Serven
  given name: Eloi
author list: Agent
  family name: Martinez-Ramirez
  given name: Maria
author list: Agent
  family name: Boix-Quintana
  given name: Ester
author list: Agent
  family name: Davi-Loscos
  given name: Eva
author list: Agent
  family name: Guanyabens
  given name: Nicolau
author list: Agent
  family name: Casado
  given name: Virginia
author list: Agent
  family name: Muriana
  given name: Desiree
author list: Agent
  family name: Torres-Rivas
  given name: Cristina
author list: Agent
  family name: Cuesta
  given name: M.J.
author list: Agent
  family name: Labad
  given name: Javier
doi: 10.7717/peerj.15347
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-02
copyright: ©2023 Gine-Serven et al.
attribution name: Gine-Serven et al.

Influence of SPIO labelling on the function of BMSCs in chemokine receptors expression and chemotaxis
type: item
type: AcademicArticle
description: Bone marrow-derived mesenchymal stem cells (BMSCs) are increasingly being used in bone marrow transplantation (BMT) to enable homing of the allogeneic hematopoietic stem cells and suppress acute graft versus host disease (aGVHD). The aim of this study was to optimize the labelling of BMSCs with superparamagnetic iron oxide particles (SPIOs), and evaluate the impact of the SPIOs on the biological characteristics, gene expression profile and chemotaxis function of the BMSCs. The viability and proliferation rates of the SPIO-labeled BMSCs were analyzed by trypan blue staining and CCK-8 assay respectively, and the chemotaxis function was evaluated by the transwell assay. The expression levels of chemokine receptors were measured by RT-PCR and flow cytometry. The SPIOs had no effect on the viability of the BMSCs regardless of the labelling concentration and culture duration. The labelling rate of the cells was higher when cultured for 48 h with the SPIOs. Furthermore, cells labeled with 25 µg/ml SPIOs for 48 h had the highest proliferation rates, along with increased expression of chemokine receptor genes and proteins. However, there was no significant difference between the chemotaxis function of the labeled and unlabeled BMSCs. To summarize, labelling BMSCs with 25 µg/ml SPIOs for 48h did not affect their biological characteristics and chemotaxis function, which can be of significance for in vivo applications.
format: application/pdf
format: text/html
creator: Yuanchun Liu
creator: Wanyi Huang
creator: Huiyang Wang
creator: Wei Lu
creator: Jiayu Guo
creator: Li Yu
creator: Lina Wang
subject: Biotechnology
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.15388
publisher: PeerJ Inc.
rights: © 2023 Liu et al.
abstract: Bone marrow-derived mesenchymal stem cells (BMSCs) are increasingly being used in bone marrow transplantation (BMT) to enable homing of the allogeneic hematopoietic stem cells and suppress acute graft versus host disease (aGVHD). The aim of this study was to optimize the labelling of BMSCs with superparamagnetic iron oxide particles (SPIOs), and evaluate the impact of the SPIOs on the biological characteristics, gene expression profile and chemotaxis function of the BMSCs. The viability and proliferation rates of the SPIO-labeled BMSCs were analyzed by trypan blue staining and CCK-8 assay respectively, and the chemotaxis function was evaluated by the transwell assay. The expression levels of chemokine receptors were measured by RT-PCR and flow cytometry. The SPIOs had no effect on the viability of the BMSCs regardless of the labelling concentration and culture duration. The labelling rate of the cells was higher when cultured for 48 h with the SPIOs. Furthermore, cells labeled with 25 µg/ml SPIOs for 48 h had the highest proliferation rates, along with increased expression of chemokine receptor genes and proteins. However, there was no significant difference between the chemotaxis function of the labeled and unlabeled BMSCs. To summarize, labelling BMSCs with 25 µg/ml SPIOs for 48h did not affect their biological characteristics and chemotaxis function, which can be of significance for in vivo applications.
bibliographic citation: Liu et al. (2023) Influence of SPIO labelling on the function of BMSCs in chemokine receptors expression and chemotaxis. PeerJ 11:e15388 https://doi.org/10.7717/peerj.15388
date submitted: 2022-10-10
date accepted: 2023-04-19
issued: 2023-06-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Yuanchun
author list: Agent
  family name: Huang
  given name: Wanyi
author list: Agent
  family name: Wang
  given name: Huiyang
author list: Agent
  family name: Lu
  given name: Wei
author list: Agent
  family name: Guo
  given name: Jiayu
author list: Agent
  family name: Yu
  given name: Li
author list: Agent
  family name: Wang
  given name: Lina
doi: 10.7717/peerj.15388
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-02
copyright: ©2023 Liu et al.
attribution name: Liu et al.

Functional responses of male and female European green crabs suggest potential sex-specific impacts of invasion
type: item
type: AcademicArticle
description: Predicting the impacts of predatory invasive species is important for prioritising conservation interventions. Functional response experiments, which examine consumption by predators in relation to prey density, are a useful way to assess the potential strength of novel predator-prey relationships. However, such experiments are often conducted without consideration of sex or only with males to reduce invasion risk. Here, we compared the functional responses of male and female European green crabs (Carcinus maenas), a global invader, feeding on varnish clams (Nuttallia obscurata) to test whether the two sexes have similar potential for impact. We also examined potential correlates of predation behaviour by measuring sex-specific movement and prey choice. Both sexes displayed a Type II hyperbolic functional response, which can destabilise prey populations at low prey densities. However, males and females exhibited some differences in foraging behaviour. Female green crabs had slightly lower attack rates, which were not linked to sex differences in movement, and slightly longer handling times, which were not linked to sex differences in prey choice. These small, non-significant differences nevertheless translated into significantly greater functional response ratios, which are used to predict the ecological impact of invasive species, for males than females. There was no difference in the proportion of clams consumed between males and females with similar crusher claw heights, but females have smaller crusher claws on average, hence they consumed a smaller proportion of clams. Repeated surveys of four populations of European green crabs established in British Columbia, Canada, showed that sex ratio is highly variable. Taken together, these results and population-level modelling suggest that trying to evaluate the potential impact of European green crabs on clam populations by sampling only males could result in overestimation, even in populations that have male-biased …
format: application/pdf
format: text/html
creator: Kiara R. Kattler
creator: Elizabeth M. Oishi
creator: Em G. Lim
creator: Hannah V. Watkins
creator: Isabelle M. Côté
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.15424
publisher: PeerJ Inc.
rights: © 2023 Kattler et al.
abstract: Predicting the impacts of predatory invasive species is important for prioritising conservation interventions. Functional response experiments, which examine consumption by predators in relation to prey density, are a useful way to assess the potential strength of novel predator-prey relationships. However, such experiments are often conducted without consideration of sex or only with males to reduce invasion risk. Here, we compared the functional responses of male and female European green crabs (Carcinus maenas), a global invader, feeding on varnish clams (Nuttallia obscurata) to test whether the two sexes have similar potential for impact. We also examined potential correlates of predation behaviour by measuring sex-specific movement and prey choice. Both sexes displayed a Type II hyperbolic functional response, which can destabilise prey populations at low prey densities. However, males and females exhibited some differences in foraging behaviour. Female green crabs had slightly lower attack rates, which were not linked to sex differences in movement, and slightly longer handling times, which were not linked to sex differences in prey choice. These small, non-significant differences nevertheless translated into significantly greater functional response ratios, which are used to predict the ecological impact of invasive species, for males than females. There was no difference in the proportion of clams consumed between males and females with similar crusher claw heights, but females have smaller crusher claws on average, hence they consumed a smaller proportion of clams. Repeated surveys of four populations of European green crabs established in British Columbia, Canada, showed that sex ratio is highly variable. Taken together, these results and population-level modelling suggest that trying to evaluate the potential impact of European green crabs on clam populations by sampling only males could result in overestimation, even in populations that have male-biased …
bibliographic citation: Kattler et al. (2023) Functional responses of male and female European green crabs suggest potential sex-specific impacts of invasion. PeerJ 11:e15424 https://doi.org/10.7717/peerj.15424
date submitted: 2023-01-16
date accepted: 2023-04-25
issued: 2023-06-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kattler
  given name: Kiara R.
author list: Agent
  family name: Oishi
  given name: Elizabeth M.
author list: Agent
  family name: Lim
  given name: Em G.
author list: Agent
  family name: Watkins
  given name: Hannah V.
author list: Agent
  family name: Côté
  given name: Isabelle M.
doi: 10.7717/peerj.15424
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-02
copyright: ©2023 Kattler et al.
attribution name: Kattler et al.

Antimicrobial susceptibility and integrons detection among extended-spectrum β-lactamase producing Enterobacteriaceae isolates in patients with urinary tract infection
type: item
type: AcademicArticle
description: Background Integrons are bacterial mobile genetic components responsible for mediating the antibiotic resistance process by carrying and spreading antimicrobial resistance genes among bacteria through horizontal gene transfer. Objectives This cross-sectional hospital-based study aimed to find the prevalence of antibiotic resistance patterns and to detect integrons classes (I, II, and III) among bacterial isolates in patients with urinary tract infections (UTI) in Sulaimani, Iraq. Patients and Methods Mid-stream urine samples (no. = 400) were collected from patients with UTI at three different Hospitals from Sulaimani, Iraq, between September 2021 to January 2022. Urine samples were cultured on various agar media, and grown bacteria were isolated. Antibiotic susceptibility test (AST) and an extended-spectrum β-lactamase (ESBL) screen were done for isolated bacteria. Then, integrons classes were screened using conventional PCR with gene sequencing and uploaded to the National Center for Biotechnology Information (NCBI). Results The frequency rate of Enterobacteriaceae was 67.03% among positive urine cultures. E. coli (no. = 86) and Klebsiella pneumoniae (no. = 32) isolates were identified. The most sensitive antibiotics were the carbapenem group (85.3%) and nitrofurantoin (NFN) (64.2%), while the most resistant antibiotics were nalidixic acid (NA) and 3rd generation cephalosporin. The occurrence rate of ESBL was 56.6% with a predominance of class I integron (54.2%), then class II (15.8%) and no positive record for class III integron were observed. Conclusion Most bacterial isolates from patients with UTI produced class I and II integrons genes with favourable ESBL properties.
format: application/pdf
format: text/html
creator: Karzan Taha Abubaker
creator: Khanda Abdulateef Anwar
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.15429
publisher: PeerJ Inc.
rights: © 2023 Abubaker and Anwar
abstract: Background Integrons are bacterial mobile genetic components responsible for mediating the antibiotic resistance process by carrying and spreading antimicrobial resistance genes among bacteria through horizontal gene transfer. Objectives This cross-sectional hospital-based study aimed to find the prevalence of antibiotic resistance patterns and to detect integrons classes (I, II, and III) among bacterial isolates in patients with urinary tract infections (UTI) in Sulaimani, Iraq. Patients and Methods Mid-stream urine samples (no. = 400) were collected from patients with UTI at three different Hospitals from Sulaimani, Iraq, between September 2021 to January 2022. Urine samples were cultured on various agar media, and grown bacteria were isolated. Antibiotic susceptibility test (AST) and an extended-spectrum β-lactamase (ESBL) screen were done for isolated bacteria. Then, integrons classes were screened using conventional PCR with gene sequencing and uploaded to the National Center for Biotechnology Information (NCBI). Results The frequency rate of Enterobacteriaceae was 67.03% among positive urine cultures. E. coli (no. = 86) and Klebsiella pneumoniae (no. = 32) isolates were identified. The most sensitive antibiotics were the carbapenem group (85.3%) and nitrofurantoin (NFN) (64.2%), while the most resistant antibiotics were nalidixic acid (NA) and 3rd generation cephalosporin. The occurrence rate of ESBL was 56.6% with a predominance of class I integron (54.2%), then class II (15.8%) and no positive record for class III integron were observed. Conclusion Most bacterial isolates from patients with UTI produced class I and II integrons genes with favourable ESBL properties.
bibliographic citation: Abubaker et al. (2023) Antimicrobial susceptibility and integrons detection among extended-spectrum β-lactamase producing Enterobacteriaceae isolates in patients with urinary tract infection. PeerJ 11:e15429 https://doi.org/10.7717/peerj.15429
date submitted: 2023-02-03
date accepted: 2023-04-26
issued: 2023-06-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abubaker
  given name: Karzan Taha
author list: Agent
  family name: Anwar
  given name: Khanda Abdulateef
doi: 10.7717/peerj.15429
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-02
copyright: © 2023 Abubaker and Anwar
attribution name: Abubaker and Anwar

Unraveling the functional genes present in rhizosphere microbiomes of Solanum lycopersicum
type: item
type: AcademicArticle
description: The microbiomes living in the rhizosphere soil of the tomato plant contribute immensely to the state of health of the tomato plant alongside improving sustainable agriculture. With the aid of shotgun metagenomics sequencing, we characterized the putative functional genes (plant-growth-promoting and disease-resistant genes) produced by the microbial communities dwelling in the rhizosphere soil of healthy and powdery mildew-diseased tomato plants. The results identified twenty-one (21) plant growth promotion (PGP) genes in the microbiomes inhabiting the healthy rhizosphere (HR) which are more predomiant as compared to diseased rhizosphere (DR) that has nine (9) genes and four (4) genes in bulk soil (BR). Likewise, we identified some disease-resistant genes which include nucleotide binding genes and antimicrobial genes. Our study revealed fifteen (15) genes in HR which made it greater in comparison to DR that has three (3) genes and three (3) genes in bulk soil. Further studies should be conducted by isolating these microorganisms and introduce them to field experiments for cultivation of tomatoes.
format: application/pdf
format: text/html
creator: Afeez Adesina Adedayo
creator: Ayomide Emmanuel Fadiji
creator: Olubukola Oluranti Babalola
subject: Agricultural Science
subject: Genomics
subject: Microbiology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.15432
publisher: PeerJ Inc.
rights: © 2023 Adedayo et al.
abstract: The microbiomes living in the rhizosphere soil of the tomato plant contribute immensely to the state of health of the tomato plant alongside improving sustainable agriculture. With the aid of shotgun metagenomics sequencing, we characterized the putative functional genes (plant-growth-promoting and disease-resistant genes) produced by the microbial communities dwelling in the rhizosphere soil of healthy and powdery mildew-diseased tomato plants. The results identified twenty-one (21) plant growth promotion (PGP) genes in the microbiomes inhabiting the healthy rhizosphere (HR) which are more predomiant as compared to diseased rhizosphere (DR) that has nine (9) genes and four (4) genes in bulk soil (BR). Likewise, we identified some disease-resistant genes which include nucleotide binding genes and antimicrobial genes. Our study revealed fifteen (15) genes in HR which made it greater in comparison to DR that has three (3) genes and three (3) genes in bulk soil. Further studies should be conducted by isolating these microorganisms and introduce them to field experiments for cultivation of tomatoes.
bibliographic citation: Adedayo et al. (2023) Unraveling the functional genes present in rhizosphere microbiomes of Solanum lycopersicum. PeerJ 11:e15432 https://doi.org/10.7717/peerj.15432
date submitted: 2023-02-16
date accepted: 2023-04-26
issued: 2023-06-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Adedayo
  given name: Afeez Adesina
author list: Agent
  family name: Fadiji
  given name: Ayomide Emmanuel
author list: Agent
  family name: Babalola
  given name: Olubukola Oluranti
doi: 10.7717/peerj.15432
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-02
copyright: © 2023 Adedayo et al.
attribution name: Adedayo et al.

Uncertainty in projections of future lake thermal dynamics is differentially driven by lake and global climate models
type: item
type: AcademicArticle
description: Freshwater ecosystems provide vital services, yet are facing increasing risks from global change. In particular, lake thermal dynamics have been altered around the world as a result of climate change, necessitating a predictive understanding of how climate will continue to alter lakes in the future as well as the associated uncertainty in these predictions. Numerous sources of uncertainty affect projections of future lake conditions but few are quantified, limiting the use of lake modeling projections as management tools. To quantify and evaluate the effects of two potentially important sources of uncertainty, lake model selection uncertainty and climate model selection uncertainty, we developed ensemble projections of lake thermal dynamics for a dimictic lake in New Hampshire, USA (Lake Sunapee). Our ensemble projections used four different climate models as inputs to five vertical one-dimensional (1-D) hydrodynamic lake models under three different climate change scenarios to simulate thermal metrics from 2006 to 2099. We found that almost all the lake thermal metrics modeled (surface water temperature, bottom water temperature, Schmidt stability, stratification duration, and ice cover, but not thermocline depth) are projected to change over the next century. Importantly, we found that the dominant source of uncertainty varied among the thermal metrics, as thermal metrics associated with the surface waters (surface water temperature, total ice duration) were driven primarily by climate model selection uncertainty, while metrics associated with deeper depths (bottom water temperature, stratification duration) were dominated by lake model selection uncertainty. Consequently, our results indicate that researchers generating projections of lake bottom water metrics should prioritize including multiple lake models for best capturing projection uncertainty, while those focusing on lake surface metrics should prioritize including multiple climate models. Overall, our ens…
format: application/pdf
format: text/html
creator: Jacob H. Wynne
creator: Whitney Woelmer
creator: Tadhg N. Moore
creator: R. Quinn Thomas
creator: Kathleen C. Weathers
creator: Cayelan C. Carey
subject: Computational Biology
subject: Ecosystem Science
subject: Climate Change Biology
subject: Freshwater Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.15445
publisher: PeerJ Inc.
rights: © 2023 Wynne et al.
abstract: Freshwater ecosystems provide vital services, yet are facing increasing risks from global change. In particular, lake thermal dynamics have been altered around the world as a result of climate change, necessitating a predictive understanding of how climate will continue to alter lakes in the future as well as the associated uncertainty in these predictions. Numerous sources of uncertainty affect projections of future lake conditions but few are quantified, limiting the use of lake modeling projections as management tools. To quantify and evaluate the effects of two potentially important sources of uncertainty, lake model selection uncertainty and climate model selection uncertainty, we developed ensemble projections of lake thermal dynamics for a dimictic lake in New Hampshire, USA (Lake Sunapee). Our ensemble projections used four different climate models as inputs to five vertical one-dimensional (1-D) hydrodynamic lake models under three different climate change scenarios to simulate thermal metrics from 2006 to 2099. We found that almost all the lake thermal metrics modeled (surface water temperature, bottom water temperature, Schmidt stability, stratification duration, and ice cover, but not thermocline depth) are projected to change over the next century. Importantly, we found that the dominant source of uncertainty varied among the thermal metrics, as thermal metrics associated with the surface waters (surface water temperature, total ice duration) were driven primarily by climate model selection uncertainty, while metrics associated with deeper depths (bottom water temperature, stratification duration) were dominated by lake model selection uncertainty. Consequently, our results indicate that researchers generating projections of lake bottom water metrics should prioritize including multiple lake models for best capturing projection uncertainty, while those focusing on lake surface metrics should prioritize including multiple climate models. Overall, our ens…
bibliographic citation: Wynne et al. (2023) Uncertainty in projections of future lake thermal dynamics is differentially driven by lake and global climate models. PeerJ 11:e15445 https://doi.org/10.7717/peerj.15445
date submitted: 2022-12-02
date accepted: 2023-05-01
issued: 2023-06-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wynne
  given name: Jacob H.
author list: Agent
  family name: Woelmer
  given name: Whitney
author list: Agent
  family name: Moore
  given name: Tadhg N.
author list: Agent
  family name: Thomas
  given name: R. Quinn
author list: Agent
  family name: Weathers
  given name: Kathleen C.
author list: Agent
  family name: Carey
  given name: Cayelan C.
doi: 10.7717/peerj.15445
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-02
copyright: ©2023 Wynne et al.
attribution name: Wynne et al.

The complete mitochondrial genomes of four lagriine species (Coleoptera, Tenebrionidae) and phylogenetic relationships within Tenebrionidae
type: item
type: AcademicArticle
description: It is common to use whole mitochondrial genomes to analyze phylogenetic relationships among insects. In this study, seven mitogenomes of Tenebrionidae are newly sequenced and annotated. Among them, four species (Cerogira janthinipennis (Fairmaire, 1886), Luprops yunnanus (Fairmaire, 1887), Anaedus unidentasus Wang & Ren, 2007, and Spinolyprops cribricollis Schawaller, 2012) represent the subfamily Lagriinae. In this subfamily, the mitogenomes of the tribes Goniaderini (A. unidentasus) and Lupropini (L. yunnanus and S. cribricollis) were first reported; they were found to be 15,328–16,437 bp in length and encode 37 typical mitochondrial genes (13 PCGs, 2 rRNAs, 22 tRNAs, and a single noncoding control region). Most protein-coding genes in these mitogenomes have typical ATN start codons and TAR or an incomplete stop codon T–. In these four lagriine species, F, L2, I, and N are the most frequently used amino acids. In the 13 PCGs, the gene atp8 (Pi = 0.978) was the most diverse nucleotide, while cox1 was the most conserved gene with the lowest value (Pi = 0.211). The phylogenetic results suggest that Pimelinae, Lagriinae, Blaptinae, Stenochiinae, and Alleculinae are monophyletic, Diaperinae is paraphyletic, and Tenebrioninae appears polyphyletic. In Lagriinae, the tribe Lupropini appears paraphyletic because Spinolyprops is clustered with Anaedus in Goniaderini. These mitogenomic data provide important molecular data for the phylogeny of Tenebrionidae.
format: application/pdf
format: text/html
creator: Zhonghua Wei
creator: Aimin Shi
subject: Entomology
subject: Genomics
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.15483
publisher: PeerJ Inc.
rights: © 2023 Wei and Shi
abstract: It is common to use whole mitochondrial genomes to analyze phylogenetic relationships among insects. In this study, seven mitogenomes of Tenebrionidae are newly sequenced and annotated. Among them, four species (Cerogira janthinipennis (Fairmaire, 1886), Luprops yunnanus (Fairmaire, 1887), Anaedus unidentasus Wang & Ren, 2007, and Spinolyprops cribricollis Schawaller, 2012) represent the subfamily Lagriinae. In this subfamily, the mitogenomes of the tribes Goniaderini (A. unidentasus) and Lupropini (L. yunnanus and S. cribricollis) were first reported; they were found to be 15,328–16,437 bp in length and encode 37 typical mitochondrial genes (13 PCGs, 2 rRNAs, 22 tRNAs, and a single noncoding control region). Most protein-coding genes in these mitogenomes have typical ATN start codons and TAR or an incomplete stop codon T–. In these four lagriine species, F, L2, I, and N are the most frequently used amino acids. In the 13 PCGs, the gene atp8 (Pi = 0.978) was the most diverse nucleotide, while cox1 was the most conserved gene with the lowest value (Pi = 0.211). The phylogenetic results suggest that Pimelinae, Lagriinae, Blaptinae, Stenochiinae, and Alleculinae are monophyletic, Diaperinae is paraphyletic, and Tenebrioninae appears polyphyletic. In Lagriinae, the tribe Lupropini appears paraphyletic because Spinolyprops is clustered with Anaedus in Goniaderini. These mitogenomic data provide important molecular data for the phylogeny of Tenebrionidae.
bibliographic citation: Wei et al. (2023) The complete mitochondrial genomes of four lagriine species (Coleoptera, Tenebrionidae) and phylogenetic relationships within Tenebrionidae. PeerJ 11:e15483 https://doi.org/10.7717/peerj.15483
date submitted: 2022-10-13
date accepted: 2023-05-09
issued: 2023-06-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Wei
  given name: Zhonghua
author list: Agent
  family name: Shi
  given name: Aimin
doi: 10.7717/peerj.15483
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-02
copyright: © 2023 Wei and Shi
attribution name: Wei and Shi

Macrophyte communities as bioindicator of stormwater pollution in rivers: a quantitative analysis
type: item
type: AcademicArticle
description: Macrophytes are one of the important indicators used in assessing the anthropic impact on aquatic ecosystems. The structure of macrophyte communities of two rivers were compared by species composition, dominant species and projective cover using statistical methods. It is shown that the influence of storm runoff on these rivers is manifested in the form of a change in the dominant species composition. Based on the statistical analysis carried out, it can be argued that, despite the peculiarities of the flora composition of each of the rivers, the influence of storm runoffs largely neutralizes this specificity, determining the situation in local areas immediately below the runoff. In the area of the effluent discharge the dominance of individual species and an increase in the area overgrown with macrophytes was observed. In the area of stormwater discharge on the Psel River, species were usually present: Nuphar lutea, Ceratophyllum demersum, Myriophyllum spicatum and on the Bystrica River—Glyceria maxima, Sagitaria sagittiformis, Stuckenia pectinata and Potamogeton crispus. The use of the NMDS method has been found to provide good insight into the structural rearrangements in macrophyte communities affected by runoff from stormwater systems.
format: application/pdf
format: text/html
creator: Roman Babko
creator: Tetiana Diachenko
creator: Jacek Zaburko
creator: Yaroslav Danko
creator: Tatiana Kuzmina
creator: Joanna Szulżyk-Cieplak
creator: Joanna Czarnota
creator: Grzegorz Łagód
subject: Ecology
subject: Plant Science
subject: Freshwater Biology
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.15248
publisher: PeerJ Inc.
rights: © 2023 Babko et al.
abstract: Macrophytes are one of the important indicators used in assessing the anthropic impact on aquatic ecosystems. The structure of macrophyte communities of two rivers were compared by species composition, dominant species and projective cover using statistical methods. It is shown that the influence of storm runoff on these rivers is manifested in the form of a change in the dominant species composition. Based on the statistical analysis carried out, it can be argued that, despite the peculiarities of the flora composition of each of the rivers, the influence of storm runoffs largely neutralizes this specificity, determining the situation in local areas immediately below the runoff. In the area of the effluent discharge the dominance of individual species and an increase in the area overgrown with macrophytes was observed. In the area of stormwater discharge on the Psel River, species were usually present: Nuphar lutea, Ceratophyllum demersum, Myriophyllum spicatum and on the Bystrica River—Glyceria maxima, Sagitaria sagittiformis, Stuckenia pectinata and Potamogeton crispus. The use of the NMDS method has been found to provide good insight into the structural rearrangements in macrophyte communities affected by runoff from stormwater systems.
bibliographic citation: Babko et al. (2023) Macrophyte communities as bioindicator of stormwater pollution in rivers: a quantitative analysis. PeerJ 11:e15248 https://doi.org/10.7717/peerj.15248
date submitted: 2022-01-03
date accepted: 2023-03-28
issued: 2023-06-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Babko
  given name: Roman
author list: Agent
  family name: Diachenko
  given name: Tetiana
author list: Agent
  family name: Zaburko
  given name: Jacek
author list: Agent
  family name: Danko
  given name: Yaroslav
author list: Agent
  family name: Kuzmina
  given name: Tatiana
author list: Agent
  family name: Szulżyk-Cieplak
  given name: Joanna
author list: Agent
  family name: Czarnota
  given name: Joanna
author list: Agent
  family name: Łagód
  given name: Grzegorz
doi: 10.7717/peerj.15248
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-01
copyright: ©2023 Babko et al.
attribution name: Babko et al.

New seed coating containing Trichoderma viride with anti-pathogenic properties
type: item
type: AcademicArticle
description: Background To ensure food security in the face of climate change and the growing world population, multi-pronged measures should be taken. One promising approach uses plant growth-promoting fungi (PGPF), such as Trichoderma, to reduce the usage of agrochemicals and increase plant yield, stress tolerance, and nutritional value. However, large-scale applications of PGPF have been hampered by several constraints, and, consequently, usage on a large scale is still limited. Seed coating, a process that consists of covering seeds with low quantities of exogenous materials, is gaining attention as an efficient and feasible delivery system for PGPF. Methods We have designed a new seed coating composed of chitin, methylcellulose, and Trichoderma viride spores and assessed its effect on canola (Brassica napus L.) growth and development. For this purpose, we analyzed the antifungal activity of T. viride against common canola pathogenic fungi (Botrytis cinerea, Fusarium culmorum, and Colletotrichum sp.). Moreover, the effect of seed coating on germination ratio and seedling growth was evaluated. To verify the effect of seed coating on plant metabolism, we determined superoxide dismutase (SOD) activity and expression of the stress-related RSH (RelA/SpoT homologs). Results Our results showed that the T. viride strains used for seed coating significantly restricted the growth of all three pathogens, especially F. culmorum, for which the growth was inhibited by over 40%. Additionally, the new seed coating did not negatively affect the ability of the seeds to complete germination, increased seedling growth, and did not induce the plant stress response. To summarize, we have successfully developed a cost-effective and environmentally responsible seed coating, which will also be easy to exploit on an industrial scale.
format: application/pdf
format: text/html
creator: Sena Turkan
creator: Agnieszka Mierek-Adamska
creator: Milena Kulasek
creator: Wiktoria B. Konieczna
creator: Grażyna B. Dąbrowska
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.15392
publisher: PeerJ Inc.
rights: © 2023 Turkan et al.
abstract: Background To ensure food security in the face of climate change and the growing world population, multi-pronged measures should be taken. One promising approach uses plant growth-promoting fungi (PGPF), such as Trichoderma, to reduce the usage of agrochemicals and increase plant yield, stress tolerance, and nutritional value. However, large-scale applications of PGPF have been hampered by several constraints, and, consequently, usage on a large scale is still limited. Seed coating, a process that consists of covering seeds with low quantities of exogenous materials, is gaining attention as an efficient and feasible delivery system for PGPF. Methods We have designed a new seed coating composed of chitin, methylcellulose, and Trichoderma viride spores and assessed its effect on canola (Brassica napus L.) growth and development. For this purpose, we analyzed the antifungal activity of T. viride against common canola pathogenic fungi (Botrytis cinerea, Fusarium culmorum, and Colletotrichum sp.). Moreover, the effect of seed coating on germination ratio and seedling growth was evaluated. To verify the effect of seed coating on plant metabolism, we determined superoxide dismutase (SOD) activity and expression of the stress-related RSH (RelA/SpoT homologs). Results Our results showed that the T. viride strains used for seed coating significantly restricted the growth of all three pathogens, especially F. culmorum, for which the growth was inhibited by over 40%. Additionally, the new seed coating did not negatively affect the ability of the seeds to complete germination, increased seedling growth, and did not induce the plant stress response. To summarize, we have successfully developed a cost-effective and environmentally responsible seed coating, which will also be easy to exploit on an industrial scale.
bibliographic citation: Turkan et al. (2023) New seed coating containing Trichoderma viride with anti-pathogenic properties. PeerJ 11:e15392 https://doi.org/10.7717/peerj.15392
date submitted: 2022-10-14
date accepted: 2023-04-20
issued: 2023-06-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Turkan
  given name: Sena
author list: Agent
  family name: Mierek-Adamska
  given name: Agnieszka
author list: Agent
  family name: Kulasek
  given name: Milena
author list: Agent
  family name: Konieczna
  given name: Wiktoria B.
author list: Agent
  family name: Dąbrowska
  given name: Grażyna B.
doi: 10.7717/peerj.15392
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-01
copyright: © 2023 Turkan et al.
attribution name: Turkan et al.

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