PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: From morphology to molecules: a combined source approach to untangle the taxonomy of Clessinia (Gastropoda, Odontostomidae), endemic land snails from the Dry Chaco ecoregion
items: Density-dependent changes in the distribution of Southern Right Whales (Eubalaena australis) in the breeding ground Peninsula Valdés
items: Micro-remediation of chromium contaminated soils
items: Importance of biotic predictors in estimation of potential invasive areas: the example of the tortoise beetle Eurypedus nigrosignatus, in Hispaniola
items: Simultaneous preservation of the DNA quality, the community composition and the density of freshwater oligochaetes for the development of genetically based biological indices
items: Bacterial diversity and community in Qula from the Qinghai–Tibetan Plateau in China
items: Drivers and assemblies of soil eukaryotic microbes among different soil habitat types in a semi-arid mountain in China
items: Aberrant repair initiated by the adenine-DNA glycosylase does not play a role in UV-induced mutagenesis in Escherichia coli
items: Association between dry eye disease and asthma: a nationwide population-based study
items: An experimental comparison of composite and grab sampling of stream water for metagenetic analysis of environmental DNA

From morphology to molecules: a combined source approach to untangle the taxonomy of Clessinia (Gastropoda, Odontostomidae), endemic land snails from the Dry Chaco ecoregion
type: item
type: AcademicArticle
description: Background Land gastropods of the Dry Chaco merit special attention because they comprise a highly diverse but barely studied group. Clessinia Doering, 1875 are typical inhabitants of this ecoregion. The inclusion of their distribution areas into Spixia range, their shell shape similarities, and a former molecular study raised doubts on the monophyly of this genus. The present study review the species of Clessinia, under a morphological, geometric morphometrics, and molecular combined approach. Methods Adults were collected, photographed, measured, and dissected for anatomical studies. Shell ultrastructure was studied with scanning electron microscope. Geometric morphometric analyses on shells were performed testing if they gave complementary information to anatomy. Two mitochondrial genes, and a nuclear region were studied. Phylogenetic reconstructions to explore the relationships of DNA sequences here obtained to those of Clessinia and Spixia species from GenBank were performed. Results Species description on shell, periostracal ornamentation and anatomy is provided. We raised former Clessinia cordovana striata to species rank, naming it as Clessinia tulumbensis sp. nov. The periostracum, consisting of hairs and lamellae, has taxonomic importance for species identification. Shell morphometric analyses, inner sculpture of penis and proportion of the epiphallus and penis, were useful tools to species identification. Nuclear markers do not exhibit enough genetic variation to determine species relationships. Based on the mitochondrial markers, genetic distances among Clessinia species were greater than 10%, and while C. cordovana, C. nattkemperi, and C. pagoda were recognized as distinct evolutionary genetic species, the distinction between C. stelzneri and C. tulumbensis sp. nov. was not evident. Clessinia and Spixia were paraphyletic in the molecular phylogenetic analyses. Species of Clessinia here treated have narrow distributional areas and are endemic to the Chac…
format: application/pdf
format: text/html
creator: Maria Gabriela Cuezzo
creator: Maria Jose Miranda
creator: Roberto Eugenio Vogler
creator: Ariel Anibal Beltramino
subject: Biodiversity
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.5986
publisher: PeerJ Inc.
rights: © 2018 Cuezzo et al.
abstract: Background Land gastropods of the Dry Chaco merit special attention because they comprise a highly diverse but barely studied group. Clessinia Doering, 1875 are typical inhabitants of this ecoregion. The inclusion of their distribution areas into Spixia range, their shell shape similarities, and a former molecular study raised doubts on the monophyly of this genus. The present study review the species of Clessinia, under a morphological, geometric morphometrics, and molecular combined approach. Methods Adults were collected, photographed, measured, and dissected for anatomical studies. Shell ultrastructure was studied with scanning electron microscope. Geometric morphometric analyses on shells were performed testing if they gave complementary information to anatomy. Two mitochondrial genes, and a nuclear region were studied. Phylogenetic reconstructions to explore the relationships of DNA sequences here obtained to those of Clessinia and Spixia species from GenBank were performed. Results Species description on shell, periostracal ornamentation and anatomy is provided. We raised former Clessinia cordovana striata to species rank, naming it as Clessinia tulumbensis sp. nov. The periostracum, consisting of hairs and lamellae, has taxonomic importance for species identification. Shell morphometric analyses, inner sculpture of penis and proportion of the epiphallus and penis, were useful tools to species identification. Nuclear markers do not exhibit enough genetic variation to determine species relationships. Based on the mitochondrial markers, genetic distances among Clessinia species were greater than 10%, and while C. cordovana, C. nattkemperi, and C. pagoda were recognized as distinct evolutionary genetic species, the distinction between C. stelzneri and C. tulumbensis sp. nov. was not evident. Clessinia and Spixia were paraphyletic in the molecular phylogenetic analyses. Species of Clessinia here treated have narrow distributional areas and are endemic to the Chac…
bibliographic citation: Cuezzo et al. (2018) From morphology to molecules: a combined source approach to untangle the taxonomy of Clessinia (Gastropoda, Odontostomidae), endemic land snails from the Dry Chaco ecoregion. PeerJ 6:e5986 https://doi.org/10.7717/peerj.5986
date submitted: 2018-06-05
date accepted: 2018-10-23
issued: 2018-12-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cuezzo
  given name: Maria Gabriela
author list: Agent
  family name: Miranda
  given name: Maria Jose
author list: Agent
  family name: Vogler
  given name: Roberto Eugenio
author list: Agent
  family name: Beltramino
  given name: Ariel Anibal
doi: 10.7717/peerj.5986
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-06
copyright: © 2018 Cuezzo et al.
attribution name: Cuezzo et al.

Density-dependent changes in the distribution of Southern Right Whales (Eubalaena australis) in the breeding ground Peninsula Valdés
type: item
type: AcademicArticle
description: Background The Southern Right Whale (Eubalaena australis) population of the South–western Atlantic Ocean is recovering. In the breeding ground of Peninsula Valdés, as a consequence of the population growth, expansion to new areas by some types of groups and a change in the habitat use patterns at the coastal area were recorded. Methods We analysed information gathered from aerial surveys conducted along the coast of Peninsula Valdés in 15 years of effective sampling in a 19-year span. These surveys were divided into four periods (1999–2000; 2004–2007; 2008–2012 and 2013–2016) and estimated the density of whales in a 620 km of coast divided into segments of five km. Results The density of the whales increased to near three whales per km2 (averaged over each period) in the high-density areas. When this mean number was reached, the significant changes in density in the adjacent areas were detected in the following period. These changes were a decrease in density in the high-density areas and an increase of density in the low-density areas. Discussion We propose that a threshold in density elicits a response in habitat use, with the Mother-calf pairs remaining in the area, while the other groups are displaced to new areas.
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creator: Nicolas Sueyro
creator: Enrique Alberto Crespo
creator: Magdalena Arias
creator: Mariano Alberto Coscarella
subject: Ecology
subject: Marine Biology
subject: Population Biology
description: doi:10.7717/peerj.5957
publisher: PeerJ Inc.
rights: © 2018 Sueyro et al.
abstract: Background The Southern Right Whale (Eubalaena australis) population of the South–western Atlantic Ocean is recovering. In the breeding ground of Peninsula Valdés, as a consequence of the population growth, expansion to new areas by some types of groups and a change in the habitat use patterns at the coastal area were recorded. Methods We analysed information gathered from aerial surveys conducted along the coast of Peninsula Valdés in 15 years of effective sampling in a 19-year span. These surveys were divided into four periods (1999–2000; 2004–2007; 2008–2012 and 2013–2016) and estimated the density of whales in a 620 km of coast divided into segments of five km. Results The density of the whales increased to near three whales per km2 (averaged over each period) in the high-density areas. When this mean number was reached, the significant changes in density in the adjacent areas were detected in the following period. These changes were a decrease in density in the high-density areas and an increase of density in the low-density areas. Discussion We propose that a threshold in density elicits a response in habitat use, with the Mother-calf pairs remaining in the area, while the other groups are displaced to new areas.
bibliographic citation: Sueyro et al. (2018) Density-dependent changes in the distribution of Southern Right Whales (Eubalaena australis) in the breeding ground Peninsula Valdés. PeerJ 6:e5957 https://doi.org/10.7717/peerj.5957
date submitted: 2018-07-03
date accepted: 2018-10-17
issued: 2018-12-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sueyro
  given name: Nicolas
author list: Agent
  family name: Crespo
  given name: Enrique Alberto
author list: Agent
  family name: Arias
  given name: Magdalena
author list: Agent
  family name: Coscarella
  given name: Mariano Alberto
doi: 10.7717/peerj.5957
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-06
copyright: © 2018 Sueyro et al.
attribution name: Sueyro et al.

Micro-remediation of chromium contaminated soils
type: item
type: AcademicArticle
description: Bacteria are tiny organisms which are ubiquitously found in the environment. These microscopic living bodies are responsible for the flow of nutrients in biogeochemical cycles and fertility imparted to the soil. Release of excessive chromium in agricultural soils due to rapid growth of industries may result in minimizing the fertility of soil in future, which will lead to reduction in crop production. Plant growth promoting bacteria (PGPB) are beneficial to the environment, some of which can tolerate chromium and protect plants against heavy metal stress. The current study aims to identify such chromium-tolerant auxin-producing rhizobacteria and to investigate their inoculation effects on the growth characteristics of Lens culinaris in chromium polluted soils by using two different chromium salts i.e., K2Cr2O7 and K2CrO4 in varying concentrations (0, 50, 100, 200, 400 and 500 µgml−1). The results revealed that Bacillus species are efficient in significantly reducing the deleterious effects of Cr. These effective bacterial strains were able to stimulate the growth of metal effected plants of Lens culinaris which were grown in chromium contaminated environment. Therefore, these plant growth promoting rhizobacteria PGPRs, having both auxin production potential and chromium-resistance ability, are considered as efficient micro-factories against chromium pollution.
format: application/pdf
format: text/html
creator: Hadia -e- Fatima
creator: Ambreen Ahmed
subject: Microbiology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.6076
publisher: PeerJ Inc.
rights: © 2018 Fatima and Ahmed
abstract: Bacteria are tiny organisms which are ubiquitously found in the environment. These microscopic living bodies are responsible for the flow of nutrients in biogeochemical cycles and fertility imparted to the soil. Release of excessive chromium in agricultural soils due to rapid growth of industries may result in minimizing the fertility of soil in future, which will lead to reduction in crop production. Plant growth promoting bacteria (PGPB) are beneficial to the environment, some of which can tolerate chromium and protect plants against heavy metal stress. The current study aims to identify such chromium-tolerant auxin-producing rhizobacteria and to investigate their inoculation effects on the growth characteristics of Lens culinaris in chromium polluted soils by using two different chromium salts i.e., K2Cr2O7 and K2CrO4 in varying concentrations (0, 50, 100, 200, 400 and 500 µgml−1). The results revealed that Bacillus species are efficient in significantly reducing the deleterious effects of Cr. These effective bacterial strains were able to stimulate the growth of metal effected plants of Lens culinaris which were grown in chromium contaminated environment. Therefore, these plant growth promoting rhizobacteria PGPRs, having both auxin production potential and chromium-resistance ability, are considered as efficient micro-factories against chromium pollution.
bibliographic citation: Fatima et al. (2018) Micro-remediation of chromium contaminated soils. PeerJ 6:e6076 https://doi.org/10.7717/peerj.6076
date submitted: 2018-07-12
date accepted: 2018-11-05
issued: 2018-12-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fatima
  given name: Hadia -e-
author list: Agent
  family name: Ahmed
  given name: Ambreen
doi: 10.7717/peerj.6076
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-05
copyright: ©2018 Fatima and Ahmed
attribution name: Fatima and Ahmed

Importance of biotic predictors in estimation of potential invasive areas: the example of the tortoise beetle Eurypedus nigrosignatus, in Hispaniola
type: item
type: AcademicArticle
description: Climatic variables have been the main predictors employed in ecological niche modeling and species distribution modeling, although biotic interactions are known to affect species’ spatial distributions via mechanisms such as predation, competition, and mutualism. Biotic interactions can affect species’ responses to abiotic environmental changes differently along environmental gradients, and abiotic environmental changes can likewise influence the nature of biotic interactions. Understanding whether and how to integrate variables at different scales in ecological niche models is essential to better estimate spatial distributions of species on macroecological scales and their responses to change. We report the leaf beetle Eurypedus nigrosignatus as an alien species in the Dominican Republic and investigate whether biotic factors played a meaningful role in the distributional expansion of the species into the Caribbean. We evaluate ecological niche models built with an additive gradient of unlinked biotic predictors—host plants, using likelihood-based model evaluation criteria (Akaike information criterion and Bayesian information criterion) within a range of regularization multiplier parameter values. Our results support the argument that ecological niche models should be more inclusive, as selected biotic predictors can improve the performance of models, despite the increased model complexity, and show that biotic interactions matter at macroecological scales. Moreover, we provide an alternative approach to select optimal combination of relevant variables, to improve estimation of potential invasive areas using global minimum model likelihood scores.
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creator: Marianna V.P. Simões
creator: A. Townsend Peterson
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Entomology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.6052
publisher: PeerJ Inc.
rights: © 2018 Simões and Peterson
abstract: Climatic variables have been the main predictors employed in ecological niche modeling and species distribution modeling, although biotic interactions are known to affect species’ spatial distributions via mechanisms such as predation, competition, and mutualism. Biotic interactions can affect species’ responses to abiotic environmental changes differently along environmental gradients, and abiotic environmental changes can likewise influence the nature of biotic interactions. Understanding whether and how to integrate variables at different scales in ecological niche models is essential to better estimate spatial distributions of species on macroecological scales and their responses to change. We report the leaf beetle Eurypedus nigrosignatus as an alien species in the Dominican Republic and investigate whether biotic factors played a meaningful role in the distributional expansion of the species into the Caribbean. We evaluate ecological niche models built with an additive gradient of unlinked biotic predictors—host plants, using likelihood-based model evaluation criteria (Akaike information criterion and Bayesian information criterion) within a range of regularization multiplier parameter values. Our results support the argument that ecological niche models should be more inclusive, as selected biotic predictors can improve the performance of models, despite the increased model complexity, and show that biotic interactions matter at macroecological scales. Moreover, we provide an alternative approach to select optimal combination of relevant variables, to improve estimation of potential invasive areas using global minimum model likelihood scores.
bibliographic citation: Simões et al. (2018) Importance of biotic predictors in estimation of potential invasive areas: the example of the tortoise beetle Eurypedus nigrosignatus, in Hispaniola. PeerJ 6:e6052 https://doi.org/10.7717/peerj.6052
date submitted: 2018-08-01
date accepted: 2018-11-01
issued: 2018-12-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Simões
  given name: Marianna V.P.
author list: Agent
  family name: Peterson
  given name: A. Townsend
doi: 10.7717/peerj.6052
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-05
copyright: © 2018 Simões and Peterson
attribution name: Simões and Peterson

Simultaneous preservation of the DNA quality, the community composition and the density of freshwater oligochaetes for the development of genetically based biological indices
type: item
type: AcademicArticle
description: Introduction Oligochaetes are recognized as valuable bioindicators of sediment quality in streams and lakes. The development of an oligochaete index based on the identification of specimens using DNA barcodes requires a method for simultaneously preserving the DNA quality and information on the specimen density and oligochaete community composition. Absolute ethanol optimally preserves DNA but fixation of freshwater oligochaetes with this medium can cause disintegration and fragmentation of specimens. Here, we investigated the possibility to preserve oligochaete specimens in low-pH formalin and in neutral buffered formalin for up to four weeks before genetic analyses and tested if the addition of absolute ethanol to formalin-fixed oligochaetes resulted in a loss of specimens and/or species. Methods We performed guanidine extraction and polymerase chain reaction (PCR) amplification/sequencing of a fragment of the cytochrome c oxidase I (COI) gene on tissue fragments preserved in low-pH formalin for up to 3 weeks and in neutral buffered formalin for up to 4 weeks. In addition, we compared the density and taxonomic composition of formalin-fixed oligochaetes of several sieved sediment samples before and after the addition of absolute ethanol. Results The COI fragment of all oligochaete specimens preserved in neutral buffered formalin for up to 28 days was successfully amplified by PCR and obtained sequences were complete and of high quality. The amplification success rate for low-pH formalin fixed specimens declined after 7 days of storage. The addition of absolute ethanol to formalin-fixed oligochaete communities did not alter density or diversity estimates. Discussion Our results indicate that sediment samples can be stored in neutral buffered formalin for up to 4 weeks and the sieved material can then be transferred to absolute ethanol, without affecting DNA quality, density and community composition of oligochaetes. Based on these results, a protocol for preserving …
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format: text/html
creator: Régis Vivien
creator: Inge Werner
creator: Benoit J.D. Ferrari
subject: Biodiversity
subject: Ecology
subject: Genetics
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.6050
publisher: PeerJ Inc.
rights: © 2018 Vivien et al.
abstract: Introduction Oligochaetes are recognized as valuable bioindicators of sediment quality in streams and lakes. The development of an oligochaete index based on the identification of specimens using DNA barcodes requires a method for simultaneously preserving the DNA quality and information on the specimen density and oligochaete community composition. Absolute ethanol optimally preserves DNA but fixation of freshwater oligochaetes with this medium can cause disintegration and fragmentation of specimens. Here, we investigated the possibility to preserve oligochaete specimens in low-pH formalin and in neutral buffered formalin for up to four weeks before genetic analyses and tested if the addition of absolute ethanol to formalin-fixed oligochaetes resulted in a loss of specimens and/or species. Methods We performed guanidine extraction and polymerase chain reaction (PCR) amplification/sequencing of a fragment of the cytochrome c oxidase I (COI) gene on tissue fragments preserved in low-pH formalin for up to 3 weeks and in neutral buffered formalin for up to 4 weeks. In addition, we compared the density and taxonomic composition of formalin-fixed oligochaetes of several sieved sediment samples before and after the addition of absolute ethanol. Results The COI fragment of all oligochaete specimens preserved in neutral buffered formalin for up to 28 days was successfully amplified by PCR and obtained sequences were complete and of high quality. The amplification success rate for low-pH formalin fixed specimens declined after 7 days of storage. The addition of absolute ethanol to formalin-fixed oligochaete communities did not alter density or diversity estimates. Discussion Our results indicate that sediment samples can be stored in neutral buffered formalin for up to 4 weeks and the sieved material can then be transferred to absolute ethanol, without affecting DNA quality, density and community composition of oligochaetes. Based on these results, a protocol for preserving …
bibliographic citation: Vivien et al. (2018) Simultaneous preservation of the DNA quality, the community composition and the density of freshwater oligochaetes for the development of genetically based biological indices. PeerJ 6:e6050 https://doi.org/10.7717/peerj.6050
date submitted: 2018-09-05
date accepted: 2018-11-01
issued: 2018-12-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vivien
  given name: Régis
author list: Agent
  family name: Werner
  given name: Inge
author list: Agent
  family name: Ferrari
  given name: Benoit J.D.
doi: 10.7717/peerj.6050
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-05
copyright: ©2018 Vivien et al.
attribution name: Vivien et al.

Bacterial diversity and community in Qula from the Qinghai–Tibetan Plateau in China
type: item
type: AcademicArticle
description: Qula is a cheese-like product usually prepared with unpasteurized yak milk under open conditions, with both endogenous and exogenous microorganisms involved in the fermentation process. In the present study, 15 Qula samples were collected from five different regions in China to investigate the diversity of microbial communities using high-throughput sequencing targeting the V3–V4 region of 16S rRNA gene. The bacterial diversity significantly differed among samples of different origins, indicating a possible effect of geography. The result also showed that microbial communities significantly differed in samples of different origin and these differences were greater at the genus than the phylum level. A total of six phyla were identified in the samples, and Firmicutes and Proteobacteria had a relative abundance >20%. A total of 73 bacterial genera were identified in the samples. Two dominant genera (Lactobacillus and Acetobacter) were common to all samples, and a total of 47 operational taxonomic units at different levels significantly differed between samples of different origin. The predicted functional genes of the bacteria present in samples also indicated differences in bacterial communities between the samples of different origin. The network analysis showed that microbial interactions between bacterial communities in Qula were very complex. This study lays a foundation for further investigations into its food ecology.
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format: text/html
creator: Yan Zhu
creator: Yingying Cao
creator: Min Yang
creator: Pengchen Wen
creator: Lei Cao
creator: Jiang Ma
creator: Zhongmin Zhang
creator: Weibing Zhang
subject: Food Science and Technology
subject: Microbiology
description: doi:10.7717/peerj.6044
publisher: PeerJ Inc.
rights: © 2018 Zhu et al.
abstract: Qula is a cheese-like product usually prepared with unpasteurized yak milk under open conditions, with both endogenous and exogenous microorganisms involved in the fermentation process. In the present study, 15 Qula samples were collected from five different regions in China to investigate the diversity of microbial communities using high-throughput sequencing targeting the V3–V4 region of 16S rRNA gene. The bacterial diversity significantly differed among samples of different origins, indicating a possible effect of geography. The result also showed that microbial communities significantly differed in samples of different origin and these differences were greater at the genus than the phylum level. A total of six phyla were identified in the samples, and Firmicutes and Proteobacteria had a relative abundance >20%. A total of 73 bacterial genera were identified in the samples. Two dominant genera (Lactobacillus and Acetobacter) were common to all samples, and a total of 47 operational taxonomic units at different levels significantly differed between samples of different origin. The predicted functional genes of the bacteria present in samples also indicated differences in bacterial communities between the samples of different origin. The network analysis showed that microbial interactions between bacterial communities in Qula were very complex. This study lays a foundation for further investigations into its food ecology.
bibliographic citation: Zhu et al. (2018) Bacterial diversity and community in Qula from the Qinghai–Tibetan Plateau in China. PeerJ 6:e6044 https://doi.org/10.7717/peerj.6044
date submitted: 2018-02-28
date accepted: 2018-10-31
issued: 2018-12-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Yan
author list: Agent
  family name: Cao
  given name: Yingying
author list: Agent
  family name: Yang
  given name: Min
author list: Agent
  family name: Wen
  given name: Pengchen
author list: Agent
  family name: Cao
  given name: Lei
author list: Agent
  family name: Ma
  given name: Jiang
author list: Agent
  family name: Zhang
  given name: Zhongmin
author list: Agent
  family name: Zhang
  given name: Weibing
doi: 10.7717/peerj.6044
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-05
copyright: © 2018 Zhu et al.
attribution name: Zhu et al.

Drivers and assemblies of soil eukaryotic microbes among different soil habitat types in a semi-arid mountain in China
type: item
type: AcademicArticle
description: The effects of environmental and species structure on soil eukaryotic microbes inhabiting semi-arid mountains remain unclear. Furthermore, whether community assembly differs in a variety of soil habitat types, for example, artificial forest, artificial bush, farmland, and natural grassland, is not well understood. Here, we explored species diversity and composition of soil eukaryotic microbes south of the Taihang Mountains (mid-western region of China) using Illumina sequencing of the 18S rRNA gene (V4) region on the MiSeq platform. The results suggest that the forest soil habitat type improved the diversity and abundance of soil eukaryotic microbes that will benefit the restoration of degraded soil. The SAR (Stramenopiles, Alveolates, Rhizaria) supergroup and Metazoa were the dominant soil eukaryotic microbial groups at the phylum level. About 26% of all operational taxonomic units were common among the different soil habitat types. The O-elements, water content, soil organic matter, and elevation significantly influenced the abundance of soil eukaryote communities (P < 0.05). Our findings provide some reference for the effectiveness of local ecological restoration and the establishment of a soil eukaryotic microbe resource databases in a semi-arid area.
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format: text/html
creator: He Zhao
creator: Xuanzhen Li
creator: Zhiming Zhang
creator: Yong Zhao
creator: Peng Chen
creator: Yiwei Zhu
subject: Natural Resource Management
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
subject: Forestry
description: doi:10.7717/peerj.6042
publisher: PeerJ Inc.
rights: © 2018 Zhao et al.
abstract: The effects of environmental and species structure on soil eukaryotic microbes inhabiting semi-arid mountains remain unclear. Furthermore, whether community assembly differs in a variety of soil habitat types, for example, artificial forest, artificial bush, farmland, and natural grassland, is not well understood. Here, we explored species diversity and composition of soil eukaryotic microbes south of the Taihang Mountains (mid-western region of China) using Illumina sequencing of the 18S rRNA gene (V4) region on the MiSeq platform. The results suggest that the forest soil habitat type improved the diversity and abundance of soil eukaryotic microbes that will benefit the restoration of degraded soil. The SAR (Stramenopiles, Alveolates, Rhizaria) supergroup and Metazoa were the dominant soil eukaryotic microbial groups at the phylum level. About 26% of all operational taxonomic units were common among the different soil habitat types. The O-elements, water content, soil organic matter, and elevation significantly influenced the abundance of soil eukaryote communities (P < 0.05). Our findings provide some reference for the effectiveness of local ecological restoration and the establishment of a soil eukaryotic microbe resource databases in a semi-arid area.
bibliographic citation: Zhao et al. (2018) Drivers and assemblies of soil eukaryotic microbes among different soil habitat types in a semi-arid mountain in China. PeerJ 6:e6042 https://doi.org/10.7717/peerj.6042
date submitted: 2018-07-04
date accepted: 2018-10-30
issued: 2018-12-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: He
author list: Agent
  family name: Li
  given name: Xuanzhen
author list: Agent
  family name: Zhang
  given name: Zhiming
author list: Agent
  family name: Zhao
  given name: Yong
author list: Agent
  family name: Chen
  given name: Peng
author list: Agent
  family name: Zhu
  given name: Yiwei
doi: 10.7717/peerj.6042
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-05
copyright: © 2018 Zhao et al.
attribution name: Zhao et al.

Aberrant repair initiated by the adenine-DNA glycosylase does not play a role in UV-induced mutagenesis in Escherichia coli
type: item
type: AcademicArticle
description: Background DNA repair is essential to counteract damage to DNA induced by endo- and exogenous factors, to maintain genome stability. However, challenges to the faithful discrimination between damaged and non-damaged DNA strands do exist, such as mismatched pairs between two regular bases resulting from spontaneous deamination of 5-methylcytosine or DNA polymerase errors during replication. To counteract these mutagenic threats to genome stability, cells evolved the mismatch-specific DNA glycosylases that can recognize and remove regular DNA bases in the mismatched DNA duplexes. The Escherichia coli adenine-DNA glycosylase (MutY/MicA) protects cells against oxidative stress-induced mutagenesis by removing adenine which is mispaired with 7,8-dihydro-8-oxoguanine (8oxoG) in the base excision repair pathway. However, MutY does not discriminate between template and newly synthesized DNA strands. Therefore the ability to remove A from 8oxoG•A mispair, which is generated via misincorporation of an 8-oxo-2′-deoxyguanosine-5′-triphosphate precursor during DNA replication and in which A is the template base, can induce A•T→C•G transversions. Furthermore, it has been demonstrated that human MUTYH, homologous to the bacterial MutY, might be involved in the aberrant processing of ultraviolet (UV) induced DNA damage. Methods Here, we investigated the role of MutY in UV-induced mutagenesis in E. coli. MutY was probed on DNA duplexes containing cyclobutane pyrimidine dimers (CPD) and pyrimidine (6–4) pyrimidone photoproduct (6–4PP). UV irradiation of E. coli induces Save Our Souls (SOS) response characterized by increased production of DNA repair enzymes and mutagenesis. To study the role of MutY in vivo, the mutation frequencies to rifampicin-resistant (RifR) after UV irradiation of wild type and mutant E. coli strains were measured. Results We demonstrated that MutY does not excise Adenine when it is paired with CPD and 6–4PP adducts in duplex DNA. At the same time, MutY excises …
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creator: Caroline Zutterling
creator: Aibek Mursalimov
creator: Ibtissam Talhaoui
creator: Zhanat Koshenov
creator: Zhiger Akishev
creator: Amangeldy K. Bissenbaev
creator: Gerard Mazon
creator: Nicolas E. Geacintov
creator: Didier Gasparutto
creator: Regina Groisman
creator: Dmitry O. Zharkov
creator: Bakhyt T. Matkarimov
creator: Murat Saparbaev
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.6029
publisher: PeerJ Inc.
rights: © 2018 Zutterling et al.
abstract: Background DNA repair is essential to counteract damage to DNA induced by endo- and exogenous factors, to maintain genome stability. However, challenges to the faithful discrimination between damaged and non-damaged DNA strands do exist, such as mismatched pairs between two regular bases resulting from spontaneous deamination of 5-methylcytosine or DNA polymerase errors during replication. To counteract these mutagenic threats to genome stability, cells evolved the mismatch-specific DNA glycosylases that can recognize and remove regular DNA bases in the mismatched DNA duplexes. The Escherichia coli adenine-DNA glycosylase (MutY/MicA) protects cells against oxidative stress-induced mutagenesis by removing adenine which is mispaired with 7,8-dihydro-8-oxoguanine (8oxoG) in the base excision repair pathway. However, MutY does not discriminate between template and newly synthesized DNA strands. Therefore the ability to remove A from 8oxoG•A mispair, which is generated via misincorporation of an 8-oxo-2′-deoxyguanosine-5′-triphosphate precursor during DNA replication and in which A is the template base, can induce A•T→C•G transversions. Furthermore, it has been demonstrated that human MUTYH, homologous to the bacterial MutY, might be involved in the aberrant processing of ultraviolet (UV) induced DNA damage. Methods Here, we investigated the role of MutY in UV-induced mutagenesis in E. coli. MutY was probed on DNA duplexes containing cyclobutane pyrimidine dimers (CPD) and pyrimidine (6–4) pyrimidone photoproduct (6–4PP). UV irradiation of E. coli induces Save Our Souls (SOS) response characterized by increased production of DNA repair enzymes and mutagenesis. To study the role of MutY in vivo, the mutation frequencies to rifampicin-resistant (RifR) after UV irradiation of wild type and mutant E. coli strains were measured. Results We demonstrated that MutY does not excise Adenine when it is paired with CPD and 6–4PP adducts in duplex DNA. At the same time, MutY excises …
bibliographic citation: Zutterling et al. (2018) Aberrant repair initiated by the adenine-DNA glycosylase does not play a role in UV-induced mutagenesis in Escherichia coli. PeerJ 6:e6029 https://doi.org/10.7717/peerj.6029
date submitted: 2018-09-12
date accepted: 2018-10-30
issued: 2018-12-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zutterling
  given name: Caroline
author list: Agent
  family name: Mursalimov
  given name: Aibek
author list: Agent
  family name: Talhaoui
  given name: Ibtissam
author list: Agent
  family name: Koshenov
  given name: Zhanat
author list: Agent
  family name: Akishev
  given name: Zhiger
author list: Agent
  family name: Bissenbaev
  given name: Amangeldy K.
author list: Agent
  family name: Mazon
  given name: Gerard
author list: Agent
  family name: Geacintov
  given name: Nicolas E.
author list: Agent
  family name: Gasparutto
  given name: Didier
author list: Agent
  family name: Groisman
  given name: Regina
author list: Agent
  family name: Zharkov
  given name: Dmitry O.
author list: Agent
  family name: Matkarimov
  given name: Bakhyt T.
author list: Agent
  family name: Saparbaev
  given name: Murat
doi: 10.7717/peerj.6029
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-05
copyright: © 2018 Zutterling et al.
attribution name: Zutterling et al.

Association between dry eye disease and asthma: a nationwide population-based study
type: item
type: AcademicArticle
description: Background Dry eye disease (DED), a chronic ocular disease, is associated with numerous medical issues, including asthma. However, studies on these associations are limited. In this study, we investigated the incidence of DED among patients with asthma and its correlation with other allergic comorbidities. Methods We retrospectively analyzed data from the National Health Insurance Research Database of Taiwan. We compared the data of 41,229 patients with asthma with those of 164,916 sex- and age-matched non-asthma controls. We followed up the patient and control groups from 1998 to 2010, and compared the rate of DED in these two groups. We further analyzed the allergic comorbidities and asthma-related medication use among the patients with asthma to verify whether these factors were associated with DED. Results The patients in the asthma group were more likely to have DED than were the controls (6.35% vs. 4.92%, p < 0.0001). In the asthma group, female had a higher risk of DED (odds ratio (OR) = 1.70, 95% confidence interval (CI) [1.57–1.85]) than males did. After adjustment for sex, age, income, urbanization, and the other two allergic comorbidities, patients with allergic rhinitis (adjusted OR = 1.58, 95% CI [1.46–1.72]) and urticaria (adjusted OR = 1.25, 95% CI [1.12–1.38]) were more likely to have DED, but not patients with atopic dermatitis (adjusted OR = 1.17, 95% CI [0.98–1.40]). Patients with asthma who had prescriptions of leukotriene receptor antagonists (LTRAs) (adjusted OR = 1.29, 95% CI [1.01–1.64]), oral antihistamines (adjusted OR = 2.02, 95% CI [1.84–2.21]), and inhaled corticosteroids (adjusted OR = 1.19, 95% CI [1.04–1.36]) exhibited association with DED. Discussion Our findings reveal that patients with asthma—particularly females—were more likely to have DED, with comorbidities such as allergic rhinitis and urticaria, and prescriptions including LTRAs, antihistamines, and inhaled corticosteroids. The results suggest that in clinical practice, phys…
format: application/pdf
format: text/html
creator: Yung-Chieh Huang
creator: Wei-Cheng Chan
creator: Jiaan-Der Wang
creator: Lin-Shien Fu
creator: Yu-Tse Tsan
subject: Allergy and Clinical Immunology
subject: Immunology
description: doi:10.7717/peerj.5941
publisher: PeerJ Inc.
rights: © 2018 Huang et al.
abstract: Background Dry eye disease (DED), a chronic ocular disease, is associated with numerous medical issues, including asthma. However, studies on these associations are limited. In this study, we investigated the incidence of DED among patients with asthma and its correlation with other allergic comorbidities. Methods We retrospectively analyzed data from the National Health Insurance Research Database of Taiwan. We compared the data of 41,229 patients with asthma with those of 164,916 sex- and age-matched non-asthma controls. We followed up the patient and control groups from 1998 to 2010, and compared the rate of DED in these two groups. We further analyzed the allergic comorbidities and asthma-related medication use among the patients with asthma to verify whether these factors were associated with DED. Results The patients in the asthma group were more likely to have DED than were the controls (6.35% vs. 4.92%, p < 0.0001). In the asthma group, female had a higher risk of DED (odds ratio (OR) = 1.70, 95% confidence interval (CI) [1.57–1.85]) than males did. After adjustment for sex, age, income, urbanization, and the other two allergic comorbidities, patients with allergic rhinitis (adjusted OR = 1.58, 95% CI [1.46–1.72]) and urticaria (adjusted OR = 1.25, 95% CI [1.12–1.38]) were more likely to have DED, but not patients with atopic dermatitis (adjusted OR = 1.17, 95% CI [0.98–1.40]). Patients with asthma who had prescriptions of leukotriene receptor antagonists (LTRAs) (adjusted OR = 1.29, 95% CI [1.01–1.64]), oral antihistamines (adjusted OR = 2.02, 95% CI [1.84–2.21]), and inhaled corticosteroids (adjusted OR = 1.19, 95% CI [1.04–1.36]) exhibited association with DED. Discussion Our findings reveal that patients with asthma—particularly females—were more likely to have DED, with comorbidities such as allergic rhinitis and urticaria, and prescriptions including LTRAs, antihistamines, and inhaled corticosteroids. The results suggest that in clinical practice, phys…
bibliographic citation: Huang et al. (2018) Association between dry eye disease and asthma: a nationwide population-based study. PeerJ 6:e5941 https://doi.org/10.7717/peerj.5941
date submitted: 2018-06-08
date accepted: 2018-10-16
issued: 2018-12-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Yung-Chieh
author list: Agent
  family name: Chan
  given name: Wei-Cheng
author list: Agent
  family name: Wang
  given name: Jiaan-Der
author list: Agent
  family name: Fu
  given name: Lin-Shien
author list: Agent
  family name: Tsan
  given name: Yu-Tse
doi: 10.7717/peerj.5941
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-05
copyright: © 2018 Huang et al.
attribution name: Huang et al.

An experimental comparison of composite and grab sampling of stream water for metagenetic analysis of environmental DNA
type: item
type: AcademicArticle
description: Use of environmental DNA (eDNA) to assess distributions of aquatic and semi-aquatic macroorganisms is promising, but sampling schemes may need to be tailored to specific objectives. Given the potentially high variance in aquatic eDNA among replicate grab samples, compositing smaller water volumes collected over a period of time may be more effective for some applications. In this study, we compared eDNA profiles from composite water samples aggregated over three hours with grab water samples. Both sampling patterns were performed with identical autosamplers paired at two different sites in a headwater stream environment, augmented with exogenous fish eDNA from an upstream rearing facility. Samples were filtered through 0.8 μm cellulose nitrate filters and DNA was extracted with a cetyl trimethylammonium bromide procedure. Eukaryotic and bacterial community profiles were derived by amplicon sequencing of 12S ribosomal, 16S ribosomal, and cytochrome oxidase I loci. Operational taxa were assigned to genus with a lowest common ancestor approach for eukaryotes and to family with the RDP Classifier software for prokaryotes. Eukaryotic community profiles were more consistent with composite sampling than grab sampling. Downstream, rarefaction curves suggested faster taxon accumulation for composite samples, and estimated richness was higher for composite samples as a set than for grab samples. Upstream, composite sampling produced lower estimated richness than grab samples, but with overlapping standard errors. Furthermore, a bimodal pattern of richness as a function of sequence counts suggested the impact of clumped particles on upstream samples. Bacterial profiles were insensitive to sample method, consistent with the more even dispersion expected for bacteria compared with eukaryotic eDNA. Overall, samples composited over 3 h performed equal to or better than triplicate grab sampling for quantitative community metrics, despite the higher total sequencing effort provided …
format: application/pdf
format: text/html
creator: Robert S. Cornman
creator: James E. McKenna
creator: Jennifer Fike
creator: Sara J. Oyler-McCance
creator: Robin Johnson
subject: Aquaculture, Fisheries and Fish Science
subject: Bioinformatics
subject: Ecosystem Science
subject: Freshwater Biology
description: doi:10.7717/peerj.5871
publisher: PeerJ Inc.
rights: © 2018
abstract: Use of environmental DNA (eDNA) to assess distributions of aquatic and semi-aquatic macroorganisms is promising, but sampling schemes may need to be tailored to specific objectives. Given the potentially high variance in aquatic eDNA among replicate grab samples, compositing smaller water volumes collected over a period of time may be more effective for some applications. In this study, we compared eDNA profiles from composite water samples aggregated over three hours with grab water samples. Both sampling patterns were performed with identical autosamplers paired at two different sites in a headwater stream environment, augmented with exogenous fish eDNA from an upstream rearing facility. Samples were filtered through 0.8 μm cellulose nitrate filters and DNA was extracted with a cetyl trimethylammonium bromide procedure. Eukaryotic and bacterial community profiles were derived by amplicon sequencing of 12S ribosomal, 16S ribosomal, and cytochrome oxidase I loci. Operational taxa were assigned to genus with a lowest common ancestor approach for eukaryotes and to family with the RDP Classifier software for prokaryotes. Eukaryotic community profiles were more consistent with composite sampling than grab sampling. Downstream, rarefaction curves suggested faster taxon accumulation for composite samples, and estimated richness was higher for composite samples as a set than for grab samples. Upstream, composite sampling produced lower estimated richness than grab samples, but with overlapping standard errors. Furthermore, a bimodal pattern of richness as a function of sequence counts suggested the impact of clumped particles on upstream samples. Bacterial profiles were insensitive to sample method, consistent with the more even dispersion expected for bacteria compared with eukaryotic eDNA. Overall, samples composited over 3 h performed equal to or better than triplicate grab sampling for quantitative community metrics, despite the higher total sequencing effort provided …
bibliographic citation: Cornman et al. (2018) An experimental comparison of composite and grab sampling of stream water for metagenetic analysis of environmental DNA. PeerJ 6:e5871 https://doi.org/10.7717/peerj.5871
date submitted: 2018-06-28
date accepted: 2018-10-03
issued: 2018-12-05
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Cornman
  given name: Robert S.
author list: Agent
  family name: McKenna
  given name: James E.
author list: Agent
  family name: Fike
  given name: Jennifer
author list: Agent
  family name: Oyler-McCance
  given name: Sara J.
author list: Agent
  family name: Johnson
  given name: Robin
doi: 10.7717/peerj.5871
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-05

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