PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Spiculous skeleton formation in the freshwater sponge Ephydatia fluviatilis under hypergravity conditions
items: Temperature-mediated feeding between spring-associated and riverine-associated congeners, with implications for community segregation
items: Using the wax moth larva Galleria mellonella infection model to detect emerging bacterial pathogens
items: Role of the larval feeding morphology and digestive enzyme activity in the early development of the polychaete Boccardia wellingtonensis
items: Secreted Frizzled-related protein 4 inhibits the regeneration of hair follicles
items: Primulina anisocymosa (Gesneriaceae), a new species with a unique inflorescence structure from Guangdong, China
items: Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies
items: Long-term effects of straw and straw-derived biochar on soil aggregation and fungal community in a rice–wheat rotation system
items: Functional polymorphisms of the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster are associated with dyslipidemia in a sex-specific pattern
items: A Tournaisian (earliest Carboniferous) conglomerate-preserved non-marine faunal assemblage and its environmental and sedimentological context

Spiculous skeleton formation in the freshwater sponge Ephydatia fluviatilis under hypergravity conditions
type: item
type: AcademicArticle
description: Successful dispersal of freshwater sponges depends on the formation of dormant sponge bodies (gemmules) under adverse conditions. Gemmule formation allows the sponge to overcome critical environmental conditions, for example, desiccation or freezing, and to re-establish as a fully developed sponge when conditions are more favorable. A key process in sponge development from hatched gemmules is the construction of the silica skeleton. Silica spicules form the structural support for the three-dimensional filtration system the sponge uses to filter food particles from ambient water. We studied the effect of different hypergravity forces (1, 2.5, 5, 10, and 20 × g for 48 h)—as measure for environmental stress—on the ability of developing sponges to set-up their spiculous skeleton. Additionally, we assessed whether the addition of nutrients (i.e., dissolved 13C- and 15N-labeled amino acids) compensates for this stress. Our results show that freshwater sponges can withstand prolonged periods of hypergravity exposure and successfully set-up their skeleton, even after 48 h under 20 × g. Developing sponges were found to take up and assimilate dissolved food before forming a functional filtering system. However, fed and non-fed sponges showed no differences in skeleton formation and relative surface area growth, suggesting that the gemmules’ intrinsic energy fulfills the processes of skeleton construction. Additionally, non-fed sponges formed oscula significantly more often than fed sponges, especially under higher g-forces. This suggests that the eventual formation of a filtration system might be stimulated by food deprivation and environmentally stressful conditions. These findings indicate that the process of spiculous skeleton formation is energy-efficient and highly resilient. The uptake of dissolved food substances by freshwater sponges may contribute to the cycling of dissolved organic matter in freshwater ecosystems where sponges are abundant.
format: application/pdf
format: text/html
creator: Martijn C. Bart
creator: Sebastiaan J. de Vet
creator: Didier M. de Bakker
creator: Brittany E. Alexander
creator: Dick van Oevelen
creator: E. Emiel van Loon
creator: Jack J.W.A. van Loon
creator: Jasper M. de Goeij
subject: Ecology
subject: Freshwater Biology
description: doi:10.7717/peerj.6055
publisher: PeerJ Inc.
rights: © 2019 Bart et al.
abstract: Successful dispersal of freshwater sponges depends on the formation of dormant sponge bodies (gemmules) under adverse conditions. Gemmule formation allows the sponge to overcome critical environmental conditions, for example, desiccation or freezing, and to re-establish as a fully developed sponge when conditions are more favorable. A key process in sponge development from hatched gemmules is the construction of the silica skeleton. Silica spicules form the structural support for the three-dimensional filtration system the sponge uses to filter food particles from ambient water. We studied the effect of different hypergravity forces (1, 2.5, 5, 10, and 20 × g for 48 h)—as measure for environmental stress—on the ability of developing sponges to set-up their spiculous skeleton. Additionally, we assessed whether the addition of nutrients (i.e., dissolved 13C- and 15N-labeled amino acids) compensates for this stress. Our results show that freshwater sponges can withstand prolonged periods of hypergravity exposure and successfully set-up their skeleton, even after 48 h under 20 × g. Developing sponges were found to take up and assimilate dissolved food before forming a functional filtering system. However, fed and non-fed sponges showed no differences in skeleton formation and relative surface area growth, suggesting that the gemmules’ intrinsic energy fulfills the processes of skeleton construction. Additionally, non-fed sponges formed oscula significantly more often than fed sponges, especially under higher g-forces. This suggests that the eventual formation of a filtration system might be stimulated by food deprivation and environmentally stressful conditions. These findings indicate that the process of spiculous skeleton formation is energy-efficient and highly resilient. The uptake of dissolved food substances by freshwater sponges may contribute to the cycling of dissolved organic matter in freshwater ecosystems where sponges are abundant.
bibliographic citation: Bart et al. (2019) Spiculous skeleton formation in the freshwater sponge Ephydatia fluviatilis under hypergravity conditions. PeerJ 6:e6055 https://doi.org/10.7717/peerj.6055
date submitted: 2018-08-30
date accepted: 2018-10-30
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bart
  given name: Martijn C.
author list: Agent
  family name: de Vet
  given name: Sebastiaan J.
author list: Agent
  family name: de Bakker
  given name: Didier M.
author list: Agent
  family name: Alexander
  given name: Brittany E.
author list: Agent
  family name: van Oevelen
  given name: Dick
author list: Agent
  family name: van Loon
  given name: E. Emiel
author list: Agent
  family name: van Loon
  given name: Jack J.W.A.
author list: Agent
  family name: de Goeij
  given name: Jasper M.
doi: 10.7717/peerj.6055
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: © 2019 Bart et al.
attribution name: Bart et al.

Temperature-mediated feeding between spring-associated and riverine-associated congeners, with implications for community segregation
type: item
type: AcademicArticle
description: Freshwater fish communities segregate along water temperature gradients attributed in part to temperature-mediated physiological processes that affect species fitness. In spring complexes of southwest USA, spring complexes with narrow range of water temperatures are dominated by a community of fishes (i.e., spring-associated fishes), whereas riverine habitats with wide-range of water temperatures are dominated by a different community of fishes (i.e., riverine-associated fishes). The purpose of this study was to test a prediction of the concept that temperature-mediated species performance is a mechanism in maintaining community segregation. We predicted that a spring-associated fish (Largespring Gambusia Gambusia geiseri) would feed first and more often in a pairing with a riverine-associated fish (Western Mosquitofish G. affinis) at an average spring temperature (23 °C) and that the riverine-associated fish would feed first and more often in a pairing with the spring-associated fish at a warm riverine temperature (30 °C). Among four trails consisting of 30 pairings, at the spring complex temperature (23 °C), Largespring Gambusia had a greater number of first feeds (mean ± 1 SD, 5.0 ± 0.82) than Western Mosquitofish (2.5 ± 1.73) and had greater mean number of total feeds (1.9 ± 0.31) than Western Mosquitofish (0.81 ± 0.70). At the riverine environment temperature (30 °C), Western Mosquitofish had a greater number of first feeds (5.25 ± 1.71) than Largespring Gambusia (2.5 ± 1.73) and had greater mean number of total feeds (2.78 ± 1.05) than Largespring Gambusia (0.94 ± 0.68). Our findings suggest that temperature-mediated species performance could be maintaining segregation between the two fish communities. This study benefits our understanding of distributional patterns and improves threat assessments of stenothermal aquatic organisms.
format: application/pdf
format: text/html
creator: Cody A. Craig
creator: Jeremy D. Maikoetter
creator: Timothy H. Bonner
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Freshwater Biology
description: doi:10.7717/peerj.6144
publisher: PeerJ Inc.
rights: © 2019 Craig et al.
abstract: Freshwater fish communities segregate along water temperature gradients attributed in part to temperature-mediated physiological processes that affect species fitness. In spring complexes of southwest USA, spring complexes with narrow range of water temperatures are dominated by a community of fishes (i.e., spring-associated fishes), whereas riverine habitats with wide-range of water temperatures are dominated by a different community of fishes (i.e., riverine-associated fishes). The purpose of this study was to test a prediction of the concept that temperature-mediated species performance is a mechanism in maintaining community segregation. We predicted that a spring-associated fish (Largespring Gambusia Gambusia geiseri) would feed first and more often in a pairing with a riverine-associated fish (Western Mosquitofish G. affinis) at an average spring temperature (23 °C) and that the riverine-associated fish would feed first and more often in a pairing with the spring-associated fish at a warm riverine temperature (30 °C). Among four trails consisting of 30 pairings, at the spring complex temperature (23 °C), Largespring Gambusia had a greater number of first feeds (mean ± 1 SD, 5.0 ± 0.82) than Western Mosquitofish (2.5 ± 1.73) and had greater mean number of total feeds (1.9 ± 0.31) than Western Mosquitofish (0.81 ± 0.70). At the riverine environment temperature (30 °C), Western Mosquitofish had a greater number of first feeds (5.25 ± 1.71) than Largespring Gambusia (2.5 ± 1.73) and had greater mean number of total feeds (2.78 ± 1.05) than Largespring Gambusia (0.94 ± 0.68). Our findings suggest that temperature-mediated species performance could be maintaining segregation between the two fish communities. This study benefits our understanding of distributional patterns and improves threat assessments of stenothermal aquatic organisms.
bibliographic citation: Craig et al. (2019) Temperature-mediated feeding between spring-associated and riverine-associated congeners, with implications for community segregation. PeerJ 6:e6144 https://doi.org/10.7717/peerj.6144
date submitted: 2018-08-13
date accepted: 2018-11-20
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Craig
  given name: Cody A.
author list: Agent
  family name: Maikoetter
  given name: Jeremy D.
author list: Agent
  family name: Bonner
  given name: Timothy H.
doi: 10.7717/peerj.6144
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: © 2019 Craig et al.
attribution name: Craig et al.

Using the wax moth larva Galleria mellonella infection model to detect emerging bacterial pathogens
type: item
type: AcademicArticle
description: Climate change, changing farming practices, social and demographic changes and rising levels of antibiotic resistance are likely to lead to future increases in opportunistic bacterial infections that are more difficult to treat. Uncovering the prevalence and identity of pathogenic bacteria in the environment is key to assessing transmission risks. We describe the first use of the Wax moth larva Galleria mellonella, a well-established model for the mammalian innate immune system, to selectively enrich and characterize pathogens from coastal environments in the South West of the UK. Whole-genome sequencing of highly virulent isolates revealed amongst others a Proteus mirabilis strain carrying the Salmonella SGI1 genomic island not reported from the UK before and the recently described species Vibrio injenensis hitherto only reported from human patients in Korea. Our novel method has the power to detect bacterial pathogens in the environment that potentially pose a serious risk to public health.
format: application/pdf
format: text/html
creator: Rafael J. Hernandez
creator: Elze Hesse
creator: Andrea J. Dowling
creator: Nicola M. Coyle
creator: Edward J. Feil
creator: Will H. Gaze
creator: Michiel Vos
subject: Microbiology
subject: Infectious Diseases
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.6150
publisher: PeerJ Inc.
rights: © 2019 Hernandez et al.
abstract: Climate change, changing farming practices, social and demographic changes and rising levels of antibiotic resistance are likely to lead to future increases in opportunistic bacterial infections that are more difficult to treat. Uncovering the prevalence and identity of pathogenic bacteria in the environment is key to assessing transmission risks. We describe the first use of the Wax moth larva Galleria mellonella, a well-established model for the mammalian innate immune system, to selectively enrich and characterize pathogens from coastal environments in the South West of the UK. Whole-genome sequencing of highly virulent isolates revealed amongst others a Proteus mirabilis strain carrying the Salmonella SGI1 genomic island not reported from the UK before and the recently described species Vibrio injenensis hitherto only reported from human patients in Korea. Our novel method has the power to detect bacterial pathogens in the environment that potentially pose a serious risk to public health.
bibliographic citation: Hernandez et al. (2019) Using the wax moth larva Galleria mellonella infection model to detect emerging bacterial pathogens. PeerJ 6:e6150 https://doi.org/10.7717/peerj.6150
date submitted: 2018-10-19
date accepted: 2018-11-23
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hernandez
  given name: Rafael J.
author list: Agent
  family name: Hesse
  given name: Elze
author list: Agent
  family name: Dowling
  given name: Andrea J.
author list: Agent
  family name: Coyle
  given name: Nicola M.
author list: Agent
  family name: Feil
  given name: Edward J.
author list: Agent
  family name: Gaze
  given name: Will H.
author list: Agent
  family name: Vos
  given name: Michiel
doi: 10.7717/peerj.6150
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: © 2019 Hernandez et al.
attribution name: Hernandez et al.

Role of the larval feeding morphology and digestive enzyme activity in the early development of the polychaete Boccardia wellingtonensis
type: item
type: AcademicArticle
description: In marine invertebrates, the modes of development at early stages are related to the type and capacity of larval feeding to achieve growth. Therefore, studying the factors that determine larval feeding strategies can help to understand the diversity of life histories and evolution of marine invertebrates. The polychaete Boccardia wellingtonensis is a poecilogonous species that encapsulates and incubates its offspring. This species produces two types of larvae: (1) larvae that do not feed within the capsule and hatch as planktotrophic larvae (indirect development), and (2) adelphophagic larvae that feed on nurse eggs and other larvae inside the capsule to hatch as advanced larvae or juveniles (direct development). Otherwise, the larval types are indistinguishable at the same stage of development. The non-apparent morphological differences between both types of larvae suggest that other factors are influencing their feeding behavior. This work studied the potential role of the activity of 19 digestive enzymes on the different feeding capacities of planktotrophic and adelphophagic larvae of B. wellingtonensis. Also, differences in larval feeding structures and the larval capacity to feed from intracapsular fluid were evaluated by electron and fluorescence microscopy. Results showed that both types of larvae present similar feeding structures and had the capacity to ingest intracapsular fluid protein. Adelphophagic larvae showed overall the highest activities of digestive enzymes. Significant differences between larval types were observed in nine enzymes related to the use of internal and external nutritional sources. Given that larval feeding is closely related to larval development in species with encapsulation, this work supports that the study of the digestive enzymatic machinery of larvae may contribute to understanding the evolution of developmental modes.
format: application/pdf
format: text/html
creator: Daniel Doherty-Weason
creator: Fernanda X. Oyarzun
creator: Luciano Vera
creator: Miguel Bascur
creator: Fabián Guzmán
creator: Francisco Silva
creator: Ángel Urzúa
creator: Antonio Brante
subject: Evolutionary Studies
subject: Marine Biology
description: doi:10.7717/peerj.6151
publisher: PeerJ Inc.
rights: © 2019 Doherty-Weason et al.
abstract: In marine invertebrates, the modes of development at early stages are related to the type and capacity of larval feeding to achieve growth. Therefore, studying the factors that determine larval feeding strategies can help to understand the diversity of life histories and evolution of marine invertebrates. The polychaete Boccardia wellingtonensis is a poecilogonous species that encapsulates and incubates its offspring. This species produces two types of larvae: (1) larvae that do not feed within the capsule and hatch as planktotrophic larvae (indirect development), and (2) adelphophagic larvae that feed on nurse eggs and other larvae inside the capsule to hatch as advanced larvae or juveniles (direct development). Otherwise, the larval types are indistinguishable at the same stage of development. The non-apparent morphological differences between both types of larvae suggest that other factors are influencing their feeding behavior. This work studied the potential role of the activity of 19 digestive enzymes on the different feeding capacities of planktotrophic and adelphophagic larvae of B. wellingtonensis. Also, differences in larval feeding structures and the larval capacity to feed from intracapsular fluid were evaluated by electron and fluorescence microscopy. Results showed that both types of larvae present similar feeding structures and had the capacity to ingest intracapsular fluid protein. Adelphophagic larvae showed overall the highest activities of digestive enzymes. Significant differences between larval types were observed in nine enzymes related to the use of internal and external nutritional sources. Given that larval feeding is closely related to larval development in species with encapsulation, this work supports that the study of the digestive enzymatic machinery of larvae may contribute to understanding the evolution of developmental modes.
bibliographic citation: Doherty-Weason et al. (2019) Role of the larval feeding morphology and digestive enzyme activity in the early development of the polychaete Boccardia wellingtonensis. PeerJ 7:e6151 https://doi.org/10.7717/peerj.6151
date submitted: 2018-08-13
date accepted: 2018-11-22
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Doherty-Weason
  given name: Daniel
author list: Agent
  family name: Oyarzun
  given name: Fernanda X.
author list: Agent
  family name: Vera
  given name: Luciano
author list: Agent
  family name: Bascur
  given name: Miguel
author list: Agent
  family name: Guzmán
  given name: Fabián
author list: Agent
  family name: Silva
  given name: Francisco
author list: Agent
  family name: Urzúa
  given name: Ángel
author list: Agent
  family name: Brante
  given name: Antonio
doi: 10.7717/peerj.6151
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: ©2019 Doherty-Weason et al.
attribution name: Doherty-Weason et al.

Secreted Frizzled-related protein 4 inhibits the regeneration of hair follicles
type: item
type: AcademicArticle
description: Secreted Frizzled-related Protein 4 (sFRP4) belongs to Wnt inhibitors. Previously, we reported that sFRP4 inhibited the differentiation of melanocyte. Here, by using of immunostaining, we showed that sFRP4 is expressed in both human and mouse hair follicles, especially in the outer root sheath and inner root sheath. To reveal the role of sFRP4 in hair follicle growth and hair cycle, we induced synchronized hair cycle in the dorsal skin of mice by depilation, and injected sFRP4 intradermally into the skin. By hematoxylin and eosin staining, we found that the regeneration of hair follicles was inhibited by sFRP4. However, the structure of hair follicles remained complete. Compared with phosphate buffer saline-treated hair follicles, the sFRP4-treated hair follicles still had the same expression pattern of keratins. Our findings reveal that sFRP4 inhibits but not blocks the regeneration of hair follicles, and supply a potential therapeutic application to treat hair follicle regeneration disorders.
format: application/pdf
format: text/html
creator: Haiying Guo
creator: Yizhan Xing
creator: Fang Deng
creator: Ke Yang
creator: Yuhong Li
subject: Cell Biology
subject: Dermatology
description: doi:10.7717/peerj.6153
publisher: PeerJ Inc.
rights: © 2019 Guo et al.
abstract: Secreted Frizzled-related Protein 4 (sFRP4) belongs to Wnt inhibitors. Previously, we reported that sFRP4 inhibited the differentiation of melanocyte. Here, by using of immunostaining, we showed that sFRP4 is expressed in both human and mouse hair follicles, especially in the outer root sheath and inner root sheath. To reveal the role of sFRP4 in hair follicle growth and hair cycle, we induced synchronized hair cycle in the dorsal skin of mice by depilation, and injected sFRP4 intradermally into the skin. By hematoxylin and eosin staining, we found that the regeneration of hair follicles was inhibited by sFRP4. However, the structure of hair follicles remained complete. Compared with phosphate buffer saline-treated hair follicles, the sFRP4-treated hair follicles still had the same expression pattern of keratins. Our findings reveal that sFRP4 inhibits but not blocks the regeneration of hair follicles, and supply a potential therapeutic application to treat hair follicle regeneration disorders.
bibliographic citation: Guo et al. (2019) Secreted Frizzled-related protein 4 inhibits the regeneration of hair follicles. PeerJ 6:e6153 https://doi.org/10.7717/peerj.6153
date submitted: 2018-08-28
date accepted: 2018-11-24
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Haiying
author list: Agent
  family name: Xing
  given name: Yizhan
author list: Agent
  family name: Deng
  given name: Fang
author list: Agent
  family name: Yang
  given name: Ke
author list: Agent
  family name: Li
  given name: Yuhong
doi: 10.7717/peerj.6153
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: © 2019 Guo et al.
attribution name: Guo et al.

Primulina anisocymosa (Gesneriaceae), a new species with a unique inflorescence structure from Guangdong, China
type: item
type: AcademicArticle
description: A new Primulina species from Guangdong, China with an unusual inflorescence is described here. Primulina anisocymosa is vegetatively most similar to P. bobaiensis. It can be distinguished from all species within Primulina morphologically by its unique zigzag monochasial cyme and infructescence. To confirm the phylogenetic relationships and generic placement of this species, not only morphological anatomical features but also chromosome and DNA sequence data were examined and analysed here. Two samples from different populations identified as Primulina anisocymosa are monophyletic and were nested in a monophyletic clade within Primulina with high branch support. The somatic chromosome number of the new species is also reported (2n = 36), supporting its placement in the genus.
format: application/pdf
format: text/html
creator: Xin Hong
creator: Jeremy Keene
creator: Zhi-Jing Qiu
creator: Fang Wen
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.6157
publisher: PeerJ Inc.
rights: © 2019 Hong et al.
abstract: A new Primulina species from Guangdong, China with an unusual inflorescence is described here. Primulina anisocymosa is vegetatively most similar to P. bobaiensis. It can be distinguished from all species within Primulina morphologically by its unique zigzag monochasial cyme and infructescence. To confirm the phylogenetic relationships and generic placement of this species, not only morphological anatomical features but also chromosome and DNA sequence data were examined and analysed here. Two samples from different populations identified as Primulina anisocymosa are monophyletic and were nested in a monophyletic clade within Primulina with high branch support. The somatic chromosome number of the new species is also reported (2n = 36), supporting its placement in the genus.
bibliographic citation: Hong et al. (2019) Primulina anisocymosa (Gesneriaceae), a new species with a unique inflorescence structure from Guangdong, China. PeerJ 7:e6157 https://doi.org/10.7717/peerj.6157
date submitted: 2018-08-01
date accepted: 2018-11-25
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hong
  given name: Xin
author list: Agent
  family name: Keene
  given name: Jeremy
author list: Agent
  family name: Qiu
  given name: Zhi-Jing
author list: Agent
  family name: Wen
  given name: Fang
doi: 10.7717/peerj.6157
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: ©2019 Hong et al.
attribution name: Hong et al.

Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies
type: item
type: AcademicArticle
description: Metagenomic and meta-barcode DNA sequencing has rapidly become a widely-used technique for investigating a range of questions, particularly related to health and environmental monitoring. There has also been a proliferation of bioinformatic tools for analysing metagenomic and amplicon datasets, which makes selecting adequate tools a significant challenge. A number of benchmark studies have been undertaken; however, these can present conflicting results. In order to address this issue we have applied a robust Z-score ranking procedure and a network meta-analysis method to identify software tools that are consistently accurate for mapping DNA sequences to taxonomic hierarchies. Based upon these results we have identified some tools and computational strategies that produce robust predictions.
format: application/pdf
format: text/html
creator: Paul P. Gardner
creator: Renee J. Watson
creator: Xochitl C. Morgan
creator: Jenny L. Draper
creator: Robert D. Finn
creator: Sergio E. Morales
creator: Matthew B. Stott
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.6160
publisher: PeerJ Inc.
rights: © 2019 Gardner et al.
abstract: Metagenomic and meta-barcode DNA sequencing has rapidly become a widely-used technique for investigating a range of questions, particularly related to health and environmental monitoring. There has also been a proliferation of bioinformatic tools for analysing metagenomic and amplicon datasets, which makes selecting adequate tools a significant challenge. A number of benchmark studies have been undertaken; however, these can present conflicting results. In order to address this issue we have applied a robust Z-score ranking procedure and a network meta-analysis method to identify software tools that are consistently accurate for mapping DNA sequences to taxonomic hierarchies. Based upon these results we have identified some tools and computational strategies that produce robust predictions.
bibliographic citation: Gardner et al. (2019) Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies. PeerJ 7:e6160 https://doi.org/10.7717/peerj.6160
date submitted: 2017-11-08
date accepted: 2018-11-14
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gardner
  given name: Paul P.
author list: Agent
  family name: Watson
  given name: Renee J.
author list: Agent
  family name: Morgan
  given name: Xochitl C.
author list: Agent
  family name: Draper
  given name: Jenny L.
author list: Agent
  family name: Finn
  given name: Robert D.
author list: Agent
  family name: Morales
  given name: Sergio E.
author list: Agent
  family name: Stott
  given name: Matthew B.
doi: 10.7717/peerj.6160
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: ©2019 Gardner et al.
attribution name: Gardner et al.

Long-term effects of straw and straw-derived biochar on soil aggregation and fungal community in a rice–wheat rotation system
type: item
type: AcademicArticle
description: Background Soil aggregation is fundamental for soil functioning and agricultural productivity. Aggregate formation depends on microbial activity influencing the production of exudates and hyphae, which in turn act as binding materials. Fungi are also important for improving soil quality and promoting plant growth in a symbiotic manner. There is a scarcity of findings comparing the long-term impacts of different yearly double-crop straw return modes (e.g., straw return to the field and straw-derived biochar return to the field) on soil aggregation and fungal community structure in rice–wheat rotation systems. Methods The effects of 6-year continuous straw and straw-derived biochar amendment on soil physicochemical properties and the fungal community were evaluated in an intensively managed crop rotation system (rice–wheat). Soil samples of different aggregates (macroaggregates, microaggregates, and silt clay) from four different fertilization regimes (control, CK; traditional inorganic fertilization, CF; straw returned to field, CS; straw-derived biochar addition, CB) were obtained, and Illumina MiSeq sequencing analysis of the fungal internal transcribed spacer gene was performed. Results Compared to CF, CS and CB enhanced soil organic carbon, total nitrogen, and aggregation in 0–20 and 20–40 cm soil, with CB exhibiting a stronger effect. Additionally, agrowaste addition increased the mean weight diameter and the geometric diameter and decreased the fractal dimension (p < 0.05). Principal coordinates analysis indicated that fertilization management affected fungal community structure and aggregation distribution. In addition, CS increased fungal community richness and diversity, compared to CK, CB decreased these aspects. Ascomycota, unclassified_k_Fungi, and Basidiomycota were the dominant phyla in all soil samples. At the genus level, CB clearly increased fungi decomposing biosolids (Articulospora in macroaggregates in 0–20 cm soil and Neurospora in macroaggregate…
format: application/pdf
format: text/html
creator: Naling Bai
creator: Hanlin Zhang
creator: Shuangxi Li
creator: Xianqing Zheng
creator: Juanqin Zhang
creator: Haiyun Zhang
creator: Sheng Zhou
creator: Huifeng Sun
creator: Weiguang Lv
subject: Ecology
subject: Microbiology
description: doi:10.7717/peerj.6171
publisher: PeerJ Inc.
rights: © 2019 Bai et al.
abstract: Background Soil aggregation is fundamental for soil functioning and agricultural productivity. Aggregate formation depends on microbial activity influencing the production of exudates and hyphae, which in turn act as binding materials. Fungi are also important for improving soil quality and promoting plant growth in a symbiotic manner. There is a scarcity of findings comparing the long-term impacts of different yearly double-crop straw return modes (e.g., straw return to the field and straw-derived biochar return to the field) on soil aggregation and fungal community structure in rice–wheat rotation systems. Methods The effects of 6-year continuous straw and straw-derived biochar amendment on soil physicochemical properties and the fungal community were evaluated in an intensively managed crop rotation system (rice–wheat). Soil samples of different aggregates (macroaggregates, microaggregates, and silt clay) from four different fertilization regimes (control, CK; traditional inorganic fertilization, CF; straw returned to field, CS; straw-derived biochar addition, CB) were obtained, and Illumina MiSeq sequencing analysis of the fungal internal transcribed spacer gene was performed. Results Compared to CF, CS and CB enhanced soil organic carbon, total nitrogen, and aggregation in 0–20 and 20–40 cm soil, with CB exhibiting a stronger effect. Additionally, agrowaste addition increased the mean weight diameter and the geometric diameter and decreased the fractal dimension (p < 0.05). Principal coordinates analysis indicated that fertilization management affected fungal community structure and aggregation distribution. In addition, CS increased fungal community richness and diversity, compared to CK, CB decreased these aspects. Ascomycota, unclassified_k_Fungi, and Basidiomycota were the dominant phyla in all soil samples. At the genus level, CB clearly increased fungi decomposing biosolids (Articulospora in macroaggregates in 0–20 cm soil and Neurospora in macroaggregate…
bibliographic citation: Bai et al. (2019) Long-term effects of straw and straw-derived biochar on soil aggregation and fungal community in a rice–wheat rotation system. PeerJ 6:e6171 https://doi.org/10.7717/peerj.6171
date submitted: 2018-10-14
date accepted: 2018-11-27
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bai
  given name: Naling
author list: Agent
  family name: Zhang
  given name: Hanlin
author list: Agent
  family name: Li
  given name: Shuangxi
author list: Agent
  family name: Zheng
  given name: Xianqing
author list: Agent
  family name: Zhang
  given name: Juanqin
author list: Agent
  family name: Zhang
  given name: Haiyun
author list: Agent
  family name: Zhou
  given name: Sheng
author list: Agent
  family name: Sun
  given name: Huifeng
author list: Agent
  family name: Lv
  given name: Weiguang
doi: 10.7717/peerj.6171
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: © 2019 Bai et al.
attribution name: Bai et al.

Functional polymorphisms of the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster are associated with dyslipidemia in a sex-specific pattern
type: item
type: AcademicArticle
description: Background Dyslipidemia contributes to the risk of many diseases, including stroke, cardiovascular disease and metabolic-related diseases. Previous studies have indicated that single nucleotide polymorphisms (SNPs) are associated with different levels of serum lipid. Therefore, this study explored the relationship between the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster gene polymorphisms and dyslipidemia in the total sample population and stratified by genders in a northeast Chinese population. Methods A total of 3,850 participants from Jilin Province, China, were enrolled in our study, and their serum lipid levels were measured. Six functional SNPs (APOA1 rs5072, APOC3 rs5128, APOA4 rs5104, APOA5 rs651821, ZPR1 rs2075294 and BUD13 rs10488698) were genotyped using polymerase chain reaction and MALDI-TOF-MS. Logistic regression analysis was performed to explore the relationship of APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster gene polymorphisms with dyslipidemia. Linkage disequilibrium and haplotype analyses were performed with the SNPStats program and Haploview software. Results All SNPs conformed to Hardy–Weinberg equilibrium. Logistic regression analysis revealed that rs5072, rs5128 and rs651821 were associated with hypertriglyceridemia, rs5104 and rs651821 were associated with low-HDL cholesterolemia in overall group. rs651821 was associated with hypertriglyceridemia and low-HDL cholesterolemia in both the male and female group. However, among females, rs5072 was observed to be associated with hypertriglyceridemia. Haplotype analysis showed that haplotypes TGCCGC and CAGCGC were associated with dyslipidemia in the overall, male and female groups. Conclusion SNPs in the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster were associated with dyslipidemia. Furthermore, the association of APOA1 rs5072 in this gene cluster with dyslipidemia differed between genders; thus, additional studies are needed to confirm this conclusion, and the mechanisms underlying these results warrant further exp…
format: application/pdf
format: text/html
creator: Wei Bai
creator: Changgui Kou
creator: Lili Zhang
creator: Yueyue You
creator: Weiying Yu
creator: Wanqing Hua
creator: Yuanyuan Li
creator: Yaqin Yu
creator: Tiancheng Zhao
creator: Yanhua Wu
subject: Biochemistry
subject: Genetics
subject: Epidemiology
subject: Public Health
description: doi:10.7717/peerj.6175
publisher: PeerJ Inc.
rights: © 2019 Bai et al.
abstract: Background Dyslipidemia contributes to the risk of many diseases, including stroke, cardiovascular disease and metabolic-related diseases. Previous studies have indicated that single nucleotide polymorphisms (SNPs) are associated with different levels of serum lipid. Therefore, this study explored the relationship between the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster gene polymorphisms and dyslipidemia in the total sample population and stratified by genders in a northeast Chinese population. Methods A total of 3,850 participants from Jilin Province, China, were enrolled in our study, and their serum lipid levels were measured. Six functional SNPs (APOA1 rs5072, APOC3 rs5128, APOA4 rs5104, APOA5 rs651821, ZPR1 rs2075294 and BUD13 rs10488698) were genotyped using polymerase chain reaction and MALDI-TOF-MS. Logistic regression analysis was performed to explore the relationship of APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster gene polymorphisms with dyslipidemia. Linkage disequilibrium and haplotype analyses were performed with the SNPStats program and Haploview software. Results All SNPs conformed to Hardy–Weinberg equilibrium. Logistic regression analysis revealed that rs5072, rs5128 and rs651821 were associated with hypertriglyceridemia, rs5104 and rs651821 were associated with low-HDL cholesterolemia in overall group. rs651821 was associated with hypertriglyceridemia and low-HDL cholesterolemia in both the male and female group. However, among females, rs5072 was observed to be associated with hypertriglyceridemia. Haplotype analysis showed that haplotypes TGCCGC and CAGCGC were associated with dyslipidemia in the overall, male and female groups. Conclusion SNPs in the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster were associated with dyslipidemia. Furthermore, the association of APOA1 rs5072 in this gene cluster with dyslipidemia differed between genders; thus, additional studies are needed to confirm this conclusion, and the mechanisms underlying these results warrant further exp…
bibliographic citation: Bai et al. (2019) Functional polymorphisms of the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster are associated with dyslipidemia in a sex-specific pattern. PeerJ 6:e6175 https://doi.org/10.7717/peerj.6175
date submitted: 2018-05-29
date accepted: 2018-11-26
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bai
  given name: Wei
author list: Agent
  family name: Kou
  given name: Changgui
author list: Agent
  family name: Zhang
  given name: Lili
author list: Agent
  family name: You
  given name: Yueyue
author list: Agent
  family name: Yu
  given name: Weiying
author list: Agent
  family name: Hua
  given name: Wanqing
author list: Agent
  family name: Li
  given name: Yuanyuan
author list: Agent
  family name: Yu
  given name: Yaqin
author list: Agent
  family name: Zhao
  given name: Tiancheng
author list: Agent
  family name: Wu
  given name: Yanhua
doi: 10.7717/peerj.6175
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: © 2019 Bai et al.
attribution name: Bai et al.

A Tournaisian (earliest Carboniferous) conglomerate-preserved non-marine faunal assemblage and its environmental and sedimentological context
type: item
type: AcademicArticle
description: A conglomerate bed from the Tournaisian Ballagan Formation of Scotland preserves a rich array of vertebrate and other nonmarine fossils providing an insight into the wider ecosystem and paleoenvironment that existed during this pivotal stage of Earth history. It challenges hypotheses of a long-lasting post-extinction trough following the end-Devonian extinction event. The fauna recovered includes a wide size range of tetrapods, rhizodonts, and dipnoans, from tiny juveniles or small-bodied taxa up to large adults, and more than one taxon of each group is likely. Some fauna, such as actinopterygians and chondrichthyans, are rare as macrofauna but are better represented in the microfossil assemblage. The fauna provides evidence of the largest Carboniferous lungfish ever found. The specimens are preserved in a localized, poorly-sorted conglomerate which was deposited in the deepest part of a river channel, the youngest of a group of channels. In addition to the fossils (micro- and macro-), the conglomerate includes locally-derived clasts of paleosols and other distinctive elements of the surrounding floodplains. Charcoal fragments represent small woody axes and possible larger trunk tissue from arborescent pteridosperms. Preservation of the fossils indicates some aerial exposure prior to transport, with abrasion from rolling. The findings presented here contrast with other published trends in vertebrate size that are used to interpret a reduction in maximum sizes during the Tournaisian. The richness of the fauna runs counter to the assumption of a depauperate nonmarine fauna following the end-Devonian Hangenberg event, and charcoal content highlights the occurrence of fire, with the requisite levels of atmospheric oxygen during that stage.
format: application/pdf
format: text/html
creator: Jennifer A. Clack
creator: Carys E. Bennett
creator: Sarah J. Davies
creator: Andrew C. Scott
creator: Janet E. Sherwin
creator: Timothy R. Smithson
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.5972
publisher: PeerJ Inc.
rights: © 2019 Clack et al.
abstract: A conglomerate bed from the Tournaisian Ballagan Formation of Scotland preserves a rich array of vertebrate and other nonmarine fossils providing an insight into the wider ecosystem and paleoenvironment that existed during this pivotal stage of Earth history. It challenges hypotheses of a long-lasting post-extinction trough following the end-Devonian extinction event. The fauna recovered includes a wide size range of tetrapods, rhizodonts, and dipnoans, from tiny juveniles or small-bodied taxa up to large adults, and more than one taxon of each group is likely. Some fauna, such as actinopterygians and chondrichthyans, are rare as macrofauna but are better represented in the microfossil assemblage. The fauna provides evidence of the largest Carboniferous lungfish ever found. The specimens are preserved in a localized, poorly-sorted conglomerate which was deposited in the deepest part of a river channel, the youngest of a group of channels. In addition to the fossils (micro- and macro-), the conglomerate includes locally-derived clasts of paleosols and other distinctive elements of the surrounding floodplains. Charcoal fragments represent small woody axes and possible larger trunk tissue from arborescent pteridosperms. Preservation of the fossils indicates some aerial exposure prior to transport, with abrasion from rolling. The findings presented here contrast with other published trends in vertebrate size that are used to interpret a reduction in maximum sizes during the Tournaisian. The richness of the fauna runs counter to the assumption of a depauperate nonmarine fauna following the end-Devonian Hangenberg event, and charcoal content highlights the occurrence of fire, with the requisite levels of atmospheric oxygen during that stage.
bibliographic citation: Clack et al. (2019) A Tournaisian (earliest Carboniferous) conglomerate-preserved non-marine faunal assemblage and its environmental and sedimentological context. PeerJ 6:e5972 https://doi.org/10.7717/peerj.5972
date submitted: 2018-08-06
date accepted: 2018-10-19
issued: 2019-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Clack
  given name: Jennifer A.
author list: Agent
  family name: Bennett
  given name: Carys E.
author list: Agent
  family name: Davies
  given name: Sarah J.
author list: Agent
  family name: Scott
  given name: Andrew C.
author list: Agent
  family name: Sherwin
  given name: Janet E.
author list: Agent
  family name: Smithson
  given name: Timothy R.
doi: 10.7717/peerj.5972
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-03
copyright: © 2019 Clack et al.
attribution name: Clack et al.

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