PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Inter-domain microbial diversity within the coral holobiont Siderastrea siderea from two depth habitats
items: A new species of Amazonian snouted treefrog (Hylidae: Scinax) with description of a novel species-habitat association for an aquatic breeding frog
items: CCR6+ Th cell distribution differentiates systemic lupus erythematosus patients based on anti-dsDNA antibody status
items: A simple molecular technique for distinguishing species reveals frequent misidentification of Hawaiian corals in the genus Pocillopora
items: Forecasting biodiversity in breeding birds using best practices
items: Calpain activation and disturbance of autophagy are induced in cortical neurons in vitro by exposure to HA/β-Ga2O3:Cr3+ nanoparticles
items: Bioreactor virome metagenomics sequencing using DNA spike-ins
items: Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs
items: An Indo-Pacific damselfish (Neopomacentrus cyanomos) in the Gulf of Mexico: origin and mode of introduction
items: Detection of stable community structures within gut microbiota co-occurrence networks from different human populations

Inter-domain microbial diversity within the coral holobiont Siderastrea siderea from two depth habitats
type: item
type: AcademicArticle
description: Corals host diverse microbial communities that are involved in acclimatization, pathogen defense, and nutrient cycling. Surveys of coral-associated microbes have been particularly directed toward Symbiodinium and bacteria. However, a holistic understanding of the total microbiome has been hindered by a lack of analyses bridging taxonomically disparate groups. Using high-throughput amplicon sequencing, we simultaneously characterized the Symbiodinium, bacterial, and fungal communities associated with the Caribbean coral Siderastrea siderea collected from two depths (17 and 27 m) on Conch reef in the Florida Keys. S. siderea hosted an exceptionally diverse Symbiodinium community, structured differently between sampled depth habitats. While dominated at 27 m by a Symbiodinium belonging to clade C, at 17 m S. siderea primarily hosted a mixture of clade B types. Most fungal operational taxonomic units were distantly related to available reference sequences, indicating the presence of a high degree of fungal novelty within the S. siderea holobiont and a lack of knowledge on the diversity of fungi on coral reefs. Network analysis showed that co-occurrence patterns in the S. siderea holobiont were prevalent among bacteria, however, also detected between fungi and bacteria. Overall, our data show a drastic shift in the associated Symbiodinium community between depths on Conch Reef, which might indicate that alteration in this community is an important mechanism facilitating local physiological adaptation of the S. siderea holobiont. In contrast, bacterial and fungal communities were not structured differently between depth habitats.
format: application/pdf
format: text/html
creator: Guido Bonthond
creator: Daniel G. Merselis
creator: Katherine E. Dougan
creator: Trevor Graff
creator: William Todd
creator: James W. Fourqurean
creator: Mauricio Rodriguez-Lanetty
subject: Marine Biology
subject: Microbiology
description: doi:10.7717/peerj.4323
publisher: PeerJ Inc.
rights: © 2018 Bonthond et al.
abstract: Corals host diverse microbial communities that are involved in acclimatization, pathogen defense, and nutrient cycling. Surveys of coral-associated microbes have been particularly directed toward Symbiodinium and bacteria. However, a holistic understanding of the total microbiome has been hindered by a lack of analyses bridging taxonomically disparate groups. Using high-throughput amplicon sequencing, we simultaneously characterized the Symbiodinium, bacterial, and fungal communities associated with the Caribbean coral Siderastrea siderea collected from two depths (17 and 27 m) on Conch reef in the Florida Keys. S. siderea hosted an exceptionally diverse Symbiodinium community, structured differently between sampled depth habitats. While dominated at 27 m by a Symbiodinium belonging to clade C, at 17 m S. siderea primarily hosted a mixture of clade B types. Most fungal operational taxonomic units were distantly related to available reference sequences, indicating the presence of a high degree of fungal novelty within the S. siderea holobiont and a lack of knowledge on the diversity of fungi on coral reefs. Network analysis showed that co-occurrence patterns in the S. siderea holobiont were prevalent among bacteria, however, also detected between fungi and bacteria. Overall, our data show a drastic shift in the associated Symbiodinium community between depths on Conch Reef, which might indicate that alteration in this community is an important mechanism facilitating local physiological adaptation of the S. siderea holobiont. In contrast, bacterial and fungal communities were not structured differently between depth habitats.
bibliographic citation: Bonthond et al. (2018) Inter-domain microbial diversity within the coral holobiont Siderastrea siderea from two depth habitats. PeerJ 6:e4323 https://doi.org/10.7717/peerj.4323
date submitted: 2017-08-16
date accepted: 2018-01-13
issued: 2018-02-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bonthond
  given name: Guido
author list: Agent
  family name: Merselis
  given name: Daniel G.
author list: Agent
  family name: Dougan
  given name: Katherine E.
author list: Agent
  family name: Graff
  given name: Trevor
author list: Agent
  family name: Todd
  given name: William
author list: Agent
  family name: Fourqurean
  given name: James W.
author list: Agent
  family name: Rodriguez-Lanetty
  given name: Mauricio
doi: 10.7717/peerj.4323
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-02-09
copyright: © 2018 Bonthond et al.
attribution name: Bonthond et al.

A new species of Amazonian snouted treefrog (Hylidae: Scinax) with description of a novel species-habitat association for an aquatic breeding frog
type: item
type: AcademicArticle
description: The genus Scinax is one of the most specious genera of treefrogs of the family Hylidae. Despite the high number of potential new species of Scinax revealed in recent studies, the rate of species descriptions for Amazonia has been low in the last decade. A potential cause of this low rate may be the existence of morphologically cryptic species. Describing new species may not only impact the taxonomy and systematics of a group of organisms but also benefit other fields of biology. Ecological studies conducted in megadiverse regions, such as Amazonia, often meet challenging questions concerning insufficient knowledge of organismal alpha taxonomy. Due to that, detecting species-habitat associations is dependent on our ability to properly identify species. In this study, we first provide a description of a new species (including its tadpoles) of the genus Scinax distributed along heterogeneous landscapes in southern Amazonia; and secondly assess the influence of environmental heterogeneity on the new species’ abundance and distribution. Scinax ruberoculatus sp. nov. differs from all nominal congeners by its small size (SVL 22.6–25.9 mm in males and 25.4–27.5 mm in females), by having a dark brown spot on the head and scapular region shaped mainly like the moth Copiopteryx semiramis (or a human molar in lateral view, or a triangle), bicolored reddish and grey iris, snout truncate in dorsal view, bilobate vocal sac in males, by its advertisement call consisting of a single pulsed note with duration of 0.134–0.331 s, 10–23 pulses per note, and dominant frequency 1,809–1,895 Hz. Both occurrence and abundance of the new species are significantly influenced by silt content in the soil. This finding brings the first evidence that edaphic factors influence species-habitat association in Amazonian aquatic breeding frogs.
format: application/pdf
format: text/html
creator: Miquéias Ferrão
creator: Rafael de Fraga
creator: Jiří Moravec
creator: Igor L. Kaefer
creator: Albertina P. Lima
subject: Ecology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.4321
publisher: PeerJ Inc.
rights: © 2018 Ferrão et al.
abstract: The genus Scinax is one of the most specious genera of treefrogs of the family Hylidae. Despite the high number of potential new species of Scinax revealed in recent studies, the rate of species descriptions for Amazonia has been low in the last decade. A potential cause of this low rate may be the existence of morphologically cryptic species. Describing new species may not only impact the taxonomy and systematics of a group of organisms but also benefit other fields of biology. Ecological studies conducted in megadiverse regions, such as Amazonia, often meet challenging questions concerning insufficient knowledge of organismal alpha taxonomy. Due to that, detecting species-habitat associations is dependent on our ability to properly identify species. In this study, we first provide a description of a new species (including its tadpoles) of the genus Scinax distributed along heterogeneous landscapes in southern Amazonia; and secondly assess the influence of environmental heterogeneity on the new species’ abundance and distribution. Scinax ruberoculatus sp. nov. differs from all nominal congeners by its small size (SVL 22.6–25.9 mm in males and 25.4–27.5 mm in females), by having a dark brown spot on the head and scapular region shaped mainly like the moth Copiopteryx semiramis (or a human molar in lateral view, or a triangle), bicolored reddish and grey iris, snout truncate in dorsal view, bilobate vocal sac in males, by its advertisement call consisting of a single pulsed note with duration of 0.134–0.331 s, 10–23 pulses per note, and dominant frequency 1,809–1,895 Hz. Both occurrence and abundance of the new species are significantly influenced by silt content in the soil. This finding brings the first evidence that edaphic factors influence species-habitat association in Amazonian aquatic breeding frogs.
bibliographic citation: Ferrão et al. (2018) A new species of Amazonian snouted treefrog (Hylidae: Scinax) with description of a novel species-habitat association for an aquatic breeding frog. PeerJ 6:e4321 https://doi.org/10.7717/peerj.4321
date submitted: 2017-07-13
date accepted: 2018-01-13
issued: 2018-02-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ferrão
  given name: Miquéias
author list: Agent
  family name: Fraga
  given name: Rafael de
author list: Agent
  family name: Moravec
  given name: Jiří
author list: Agent
  family name: Kaefer
  given name: Igor L.
author list: Agent
  family name: Lima
  given name: Albertina P.
doi: 10.7717/peerj.4321
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-02-09
copyright: ©2018 Ferrão et al.
attribution name: Ferrão et al.

CCR6+ Th cell distribution differentiates systemic lupus erythematosus patients based on anti-dsDNA antibody status
type: item
type: AcademicArticle
description: Background Systemic lupus erythematosus (SLE) disease has been shown to be associated with the generation of multiple auto-antibodies. Among these, anti-dsDNA antibodies (anti-DNAs) are specific and play a pathogenic role in SLE. Indeed, anti-DNA+ SLE patients display a worse disease course. The generation of these pathogenic anti-DNAs has been attributed to the interaction between aberrant T helper (Th) cells and autoimmune B cells. Thus, in this study we have investigated whether CCR6+Th cells have the ability to differentiate SLE patients based on anti-DNA status, and if their distribution has any correlation with disease activity. Methods We recruited 25 anti-DNA+ and 25 anti-DNA− treatment-naive onset SLE patients, matched for various clinical characteristics in our nested matched case-control study. CCR6+ Th cells and their additional subsets were analyzed in each patient by flow cytometry. Results Anti-DNA+ SLE patients specifically had a higher percentage of Th cells expressing CCR6 and CXCR3. Further analysis of CCR6+ Th cell subsets showed that anti-DNA+ SLE patients had elevated proportions of Th9, Th17, Th17.1 and CCR4/CXCR3 double-negative (DN) cells. However, the proportions of CCR6− Th subsets, including Th1 and Th2 cells, did not show any association with anti-DNA status. Finally, we identified a correlation between CCR6+ Th subsets and clinical indicators, specifically in anti-DNA+ SLE patients. Conclusions Our data indicated that CCR6+ Th cells and their subsets were elevated and correlated with disease activity in anti-DNA+ SLE patients. We speculated that CCR6+ Th cells may contribute to distinct disease severity in anti-DNA+ SLE patients.
format: application/pdf
format: text/html
creator: Wei Zhong
creator: Zhenyu Jiang
creator: Jiang Wu
creator: Yanfang Jiang
creator: Ling Zhao
subject: Cell Biology
subject: Immunology
subject: Rheumatology
description: doi:10.7717/peerj.4294
publisher: PeerJ Inc.
rights: © 2018 Zhong et al.
abstract: Background Systemic lupus erythematosus (SLE) disease has been shown to be associated with the generation of multiple auto-antibodies. Among these, anti-dsDNA antibodies (anti-DNAs) are specific and play a pathogenic role in SLE. Indeed, anti-DNA+ SLE patients display a worse disease course. The generation of these pathogenic anti-DNAs has been attributed to the interaction between aberrant T helper (Th) cells and autoimmune B cells. Thus, in this study we have investigated whether CCR6+Th cells have the ability to differentiate SLE patients based on anti-DNA status, and if their distribution has any correlation with disease activity. Methods We recruited 25 anti-DNA+ and 25 anti-DNA− treatment-naive onset SLE patients, matched for various clinical characteristics in our nested matched case-control study. CCR6+ Th cells and their additional subsets were analyzed in each patient by flow cytometry. Results Anti-DNA+ SLE patients specifically had a higher percentage of Th cells expressing CCR6 and CXCR3. Further analysis of CCR6+ Th cell subsets showed that anti-DNA+ SLE patients had elevated proportions of Th9, Th17, Th17.1 and CCR4/CXCR3 double-negative (DN) cells. However, the proportions of CCR6− Th subsets, including Th1 and Th2 cells, did not show any association with anti-DNA status. Finally, we identified a correlation between CCR6+ Th subsets and clinical indicators, specifically in anti-DNA+ SLE patients. Conclusions Our data indicated that CCR6+ Th cells and their subsets were elevated and correlated with disease activity in anti-DNA+ SLE patients. We speculated that CCR6+ Th cells may contribute to distinct disease severity in anti-DNA+ SLE patients.
bibliographic citation: Zhong et al. (2018) CCR6+ Th cell distribution differentiates systemic lupus erythematosus patients based on anti-dsDNA antibody status. PeerJ 6:e4294 https://doi.org/10.7717/peerj.4294
date submitted: 2017-09-11
date accepted: 2018-01-05
issued: 2018-02-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhong
  given name: Wei
author list: Agent
  family name: Jiang
  given name: Zhenyu
author list: Agent
  family name: Wu
  given name: Jiang
author list: Agent
  family name: Jiang
  given name: Yanfang
author list: Agent
  family name: Zhao
  given name: Ling
doi: 10.7717/peerj.4294
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-02-09
copyright: ©2018 Zhong et al.
attribution name: Zhong et al.

A simple molecular technique for distinguishing species reveals frequent misidentification of Hawaiian corals in the genus Pocillopora
type: item
type: AcademicArticle
description: Species within the scleractinian genus Pocillopora Lamarck 1816 exhibit extreme phenotypic plasticity, making identification based on morphology difficult. However, the mitochondrial open reading frame (mtORF) marker provides a useful genetic tool for identification of most species in this genus, with a notable exception of P. eydouxi and P. meandrina. Based on recent genomic work, we present a quick and simple, gel-based restriction fragment length polymorphism (RFLP) method for the identification of all six Pocillopora species occurring in Hawai‘i by amplifying either the mtORF region, a newly discovered histone region, or both, and then using the restriction enzymes targeting diagnostic sequences we unambiguously identify each species. Using this approach, we documented frequent misidentification of Pocillopora species based on colony morphology. We found that P. acuta colonies are frequently mistakenly identified as P. damicornis in Kāne‘ohe Bay, O‘ahu. We also found that P. meandrina likely has a northern range limit in the Northwest Hawaiian Islands, above which P. ligulata was regularly mistaken for P. meandrina.
format: application/pdf
format: text/html
creator: Erika C. Johnston
creator: Zac H. Forsman
creator: Robert J. Toonen
subject: Genetics
subject: Marine Biology
subject: Taxonomy
description: doi:10.7717/peerj.4355
publisher: PeerJ Inc.
rights: © 2018 Johnston et al.
abstract: Species within the scleractinian genus Pocillopora Lamarck 1816 exhibit extreme phenotypic plasticity, making identification based on morphology difficult. However, the mitochondrial open reading frame (mtORF) marker provides a useful genetic tool for identification of most species in this genus, with a notable exception of P. eydouxi and P. meandrina. Based on recent genomic work, we present a quick and simple, gel-based restriction fragment length polymorphism (RFLP) method for the identification of all six Pocillopora species occurring in Hawai‘i by amplifying either the mtORF region, a newly discovered histone region, or both, and then using the restriction enzymes targeting diagnostic sequences we unambiguously identify each species. Using this approach, we documented frequent misidentification of Pocillopora species based on colony morphology. We found that P. acuta colonies are frequently mistakenly identified as P. damicornis in Kāne‘ohe Bay, O‘ahu. We also found that P. meandrina likely has a northern range limit in the Northwest Hawaiian Islands, above which P. ligulata was regularly mistaken for P. meandrina.
bibliographic citation: Johnston et al. (2018) A simple molecular technique for distinguishing species reveals frequent misidentification of Hawaiian corals in the genus Pocillopora. PeerJ 6:e4355 https://doi.org/10.7717/peerj.4355
date submitted: 2017-10-04
date accepted: 2018-01-20
issued: 2018-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Johnston
  given name: Erika C.
author list: Agent
  family name: Forsman
  given name: Zac H.
author list: Agent
  family name: Toonen
  given name: Robert J.
doi: 10.7717/peerj.4355
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-02-08
copyright: ©2018 Johnston et al.
attribution name: Johnston et al.

Forecasting biodiversity in breeding birds using best practices
type: item
type: AcademicArticle
description: Biodiversity forecasts are important for conservation, management, and evaluating how well current models characterize natural systems. While the number of forecasts for biodiversity is increasing, there is little information available on how well these forecasts work. Most biodiversity forecasts are not evaluated to determine how well they predict future diversity, fail to account for uncertainty, and do not use time-series data that captures the actual dynamics being studied. We addressed these limitations by using best practices to explore our ability to forecast the species richness of breeding birds in North America. We used hindcasting to evaluate six different modeling approaches for predicting richness. Hindcasts for each method were evaluated annually for a decade at 1,237 sites distributed throughout the continental United States. All models explained more than 50% of the variance in richness, but none of them consistently outperformed a baseline model that predicted constant richness at each site. The best practices implemented in this study directly influenced the forecasts and evaluations. Stacked species distribution models and “naive” forecasts produced poor estimates of uncertainty and accounting for this resulted in these models dropping in the relative performance compared to other models. Accounting for observer effects improved model performance overall, but also changed the rank ordering of models because it did not improve the accuracy of the “naive” model. Considering the forecast horizon revealed that the prediction accuracy decreased across all models as the time horizon of the forecast increased. To facilitate the rapid improvement of biodiversity forecasts, we emphasize the value of specific best practices in making forecasts and evaluating forecasting methods.
format: application/pdf
format: text/html
creator: David J. Harris
creator: Shawn D. Taylor
creator: Ethan P. White
subject: Ecology
subject: Data Mining and Machine Learning
subject: Climate Change Biology
description: doi:10.7717/peerj.4278
publisher: PeerJ Inc.
rights: © 2018 Harris et al.
abstract: Biodiversity forecasts are important for conservation, management, and evaluating how well current models characterize natural systems. While the number of forecasts for biodiversity is increasing, there is little information available on how well these forecasts work. Most biodiversity forecasts are not evaluated to determine how well they predict future diversity, fail to account for uncertainty, and do not use time-series data that captures the actual dynamics being studied. We addressed these limitations by using best practices to explore our ability to forecast the species richness of breeding birds in North America. We used hindcasting to evaluate six different modeling approaches for predicting richness. Hindcasts for each method were evaluated annually for a decade at 1,237 sites distributed throughout the continental United States. All models explained more than 50% of the variance in richness, but none of them consistently outperformed a baseline model that predicted constant richness at each site. The best practices implemented in this study directly influenced the forecasts and evaluations. Stacked species distribution models and “naive” forecasts produced poor estimates of uncertainty and accounting for this resulted in these models dropping in the relative performance compared to other models. Accounting for observer effects improved model performance overall, but also changed the rank ordering of models because it did not improve the accuracy of the “naive” model. Considering the forecast horizon revealed that the prediction accuracy decreased across all models as the time horizon of the forecast increased. To facilitate the rapid improvement of biodiversity forecasts, we emphasize the value of specific best practices in making forecasts and evaluating forecasting methods.
bibliographic citation: Harris et al. (2018) Forecasting biodiversity in breeding birds using best practices. PeerJ 6:e4278 https://doi.org/10.7717/peerj.4278
date submitted: 2017-09-19
date accepted: 2017-12-29
issued: 2018-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Harris
  given name: David J.
author list: Agent
  family name: Taylor
  given name: Shawn D.
author list: Agent
  family name: White
  given name: Ethan P.
doi: 10.7717/peerj.4278
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-02-08
copyright: ©2018 Harris et al.
attribution name: Harris et al.

Calpain activation and disturbance of autophagy are induced in cortical neurons in vitro by exposure to HA/β-Ga2O3:Cr3+ nanoparticles
type: item
type: AcademicArticle
description: The toxicity of engineered nanoparticles remains a concern. The knowledge of biohazards associated with particular nanoparticles is crucial to make this cutting-edge technology more beneficial and safe. Here, we evaluated the toxicity of Ga2O3 nanoparticles (NPs), which are frequently used to enhance the performance of metal catalysts in a variety of catalytic reactions. The potential inflammatory signaling associated with the toxicity of HA/β-Ga2O3:Cr3+ NPs in primary cortical neurons was examined. We observed a dose-dependent decrease in cell viability and an increase in apoptosis in neurons following various concentrations (0, 1, 5, 25, 50, 100 µg/ml) of HA/β-Ga2O3:Cr3+ NPs treatment. Consistently, constitutively active forms of calcineurin (48 kDa) were significantly elevated in cultured primary cortical neurons, which was consistent with calpain activation indicated by the breakdown products of spectrin. Moreover, HA/β-Ga2O3:Cr3+ NPs result in the elevation of LC3-II formation, SQSTM/p62, and Cathepsin B, whereas phosphorylation of CaMKII (Thr286) and Synapsin I (Ser603) were downregulated in the same context. Taken together, these results demonstrate for the first time that calpain activation and a disturbance of autophagy signaling are evoked by exposure to HA/β-Ga2O3:Cr3+ NPs, which may contribute to neuronal injury in vitro.
format: application/pdf
format: text/html
creator: Yu Lei
creator: Chengkun Wang
creator: Quan Jiang
creator: Xiaoyi Sun
creator: Yongzhong Du
creator: Yaofeng Zhu
creator: Yingmei Lu
subject: Biochemistry
subject: Neuroscience
subject: Toxicology
subject: Neurology
description: doi:10.7717/peerj.4365
publisher: PeerJ Inc.
rights: © 2018 Lei et al.
abstract: The toxicity of engineered nanoparticles remains a concern. The knowledge of biohazards associated with particular nanoparticles is crucial to make this cutting-edge technology more beneficial and safe. Here, we evaluated the toxicity of Ga2O3 nanoparticles (NPs), which are frequently used to enhance the performance of metal catalysts in a variety of catalytic reactions. The potential inflammatory signaling associated with the toxicity of HA/β-Ga2O3:Cr3+ NPs in primary cortical neurons was examined. We observed a dose-dependent decrease in cell viability and an increase in apoptosis in neurons following various concentrations (0, 1, 5, 25, 50, 100 µg/ml) of HA/β-Ga2O3:Cr3+ NPs treatment. Consistently, constitutively active forms of calcineurin (48 kDa) were significantly elevated in cultured primary cortical neurons, which was consistent with calpain activation indicated by the breakdown products of spectrin. Moreover, HA/β-Ga2O3:Cr3+ NPs result in the elevation of LC3-II formation, SQSTM/p62, and Cathepsin B, whereas phosphorylation of CaMKII (Thr286) and Synapsin I (Ser603) were downregulated in the same context. Taken together, these results demonstrate for the first time that calpain activation and a disturbance of autophagy signaling are evoked by exposure to HA/β-Ga2O3:Cr3+ NPs, which may contribute to neuronal injury in vitro.
bibliographic citation: Lei et al. (2018) Calpain activation and disturbance of autophagy are induced in cortical neurons in vitro by exposure to HA/β-Ga2O3:Cr3+ nanoparticles. PeerJ 6:e4365 https://doi.org/10.7717/peerj.4365
date submitted: 2017-09-21
date accepted: 2018-01-23
issued: 2018-02-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lei
  given name: Yu
author list: Agent
  family name: Wang
  given name: Chengkun
author list: Agent
  family name: Jiang
  given name: Quan
author list: Agent
  family name: Sun
  given name: Xiaoyi
author list: Agent
  family name: Du
  given name: Yongzhong
author list: Agent
  family name: Zhu
  given name: Yaofeng
author list: Agent
  family name: Lu
  given name: Yingmei
doi: 10.7717/peerj.4365
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-02-07
copyright: ©2018 Lei et al.
attribution name: Lei et al.

Bioreactor virome metagenomics sequencing using DNA spike-ins
type: item
type: AcademicArticle
description: With the emergence of Next Generation Sequencing, major advances were made with regard to identifying viruses in natural environments. However, bioinformatical research on viruses is still limited because of the low amounts of viral DNA that can be obtained for analysis. To overcome this limitation, DNA is often amplified with multiple displacement amplification (MDA), which may cause an unavoidable bias. Here, we describe a case study in which the virome of a bioreactor is sequenced using Ion Torrent technology. DNA-spiking of samples is compared with MDA-amplified samples. DNA for spiking was obtained by amplifying a bacterial 16S rRNA gene. After sequencing, the 16S rRNA gene reads were removed by mapping to the Silva database. Three samples were tested, a whole genome from Enterobacteria P1 Phage and two viral metagenomes from an infected bioreactor. For one sample, the new DNA-spiking protocol was compared with the MDA technique. When MDA was applied, the overall GC content of the reads showed a bias towards lower GC%, indicating a change in composition of the DNA sample. Assemblies using all available reads from both MDA and the DNA-spiked samples resulted in six viral genomes. All six genomes could be almost completely retrieved (97.9%–100%) when mapping the reads from the DNA-spiked sample to those six genomes. In contrast, 6.3%–77.7% of three viral genomes was covered by reads obtained using the MDA amplification method and only three were nearly fully covered (97.4%–100%). This case study shows that DNA-spiking could be a simple and inexpensive alternative with very low bias for sequencing of metagenomes for which low amounts of DNA are available.
format: application/pdf
format: text/html
creator: Geert Cremers
creator: Lavinia Gambelli
creator: Theo van Alen
creator: Laura van Niftrik
creator: Huub J.M. Op den Camp
subject: Biodiversity
subject: Genomics
subject: Microbiology
subject: Virology
description: doi:10.7717/peerj.4351
publisher: PeerJ Inc.
rights: © 2018 Cremers et al.
abstract: With the emergence of Next Generation Sequencing, major advances were made with regard to identifying viruses in natural environments. However, bioinformatical research on viruses is still limited because of the low amounts of viral DNA that can be obtained for analysis. To overcome this limitation, DNA is often amplified with multiple displacement amplification (MDA), which may cause an unavoidable bias. Here, we describe a case study in which the virome of a bioreactor is sequenced using Ion Torrent technology. DNA-spiking of samples is compared with MDA-amplified samples. DNA for spiking was obtained by amplifying a bacterial 16S rRNA gene. After sequencing, the 16S rRNA gene reads were removed by mapping to the Silva database. Three samples were tested, a whole genome from Enterobacteria P1 Phage and two viral metagenomes from an infected bioreactor. For one sample, the new DNA-spiking protocol was compared with the MDA technique. When MDA was applied, the overall GC content of the reads showed a bias towards lower GC%, indicating a change in composition of the DNA sample. Assemblies using all available reads from both MDA and the DNA-spiked samples resulted in six viral genomes. All six genomes could be almost completely retrieved (97.9%–100%) when mapping the reads from the DNA-spiked sample to those six genomes. In contrast, 6.3%–77.7% of three viral genomes was covered by reads obtained using the MDA amplification method and only three were nearly fully covered (97.4%–100%). This case study shows that DNA-spiking could be a simple and inexpensive alternative with very low bias for sequencing of metagenomes for which low amounts of DNA are available.
bibliographic citation: Cremers et al. (2018) Bioreactor virome metagenomics sequencing using DNA spike-ins. PeerJ 6:e4351 https://doi.org/10.7717/peerj.4351
date submitted: 2017-04-03
date accepted: 2018-01-19
issued: 2018-02-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cremers
  given name: Geert
author list: Agent
  family name: Gambelli
  given name: Lavinia
author list: Agent
  family name: van Alen
  given name: Theo
author list: Agent
  family name: van Niftrik
  given name: Laura
author list: Agent
  family name: Op den Camp
  given name: Huub J.M.
doi: 10.7717/peerj.4351
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-02-07
copyright: ©2018 Cremers et al.
attribution name: Cremers et al.

Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs
type: item
type: AcademicArticle
description: Phenotypic differences between closely related taxa or populations can arise through genetic variation or be environmentally induced, leading to altered transcription of genes during development. Comparative developmental studies of closely related species or variable populations within species can help to elucidate the molecular mechanisms related to evolutionary divergence and speciation. Studies of Arctic charr (Salvelinus alpinus) and related salmonids have revealed considerable phenotypic variation among populations and in Arctic charr many cases of extensive variation within lakes (resource polymorphism) have been recorded. One example is the four Arctic charr morphs in the ∼10,000 year old Lake Thingvallavatn, which differ in numerous morphological and life history traits. We set out to investigate the molecular and developmental roots of this polymorphism by studying gene expression in embryos of three of the morphs reared in a common garden set-up. We performed RNA-sequencing, de-novo transcriptome assembly and compared gene expression among morphs during an important timeframe in early development, i.e., preceding the formation of key trophic structures. Expectedly, developmental time was the predominant explanatory variable. As the data were affected by some form of RNA-degradation even though all samples passed quality control testing, an estimate of 3′-bias was the second most common explanatory variable. Importantly, morph, both as an independent variable and as interaction with developmental time, affected the expression of numerous transcripts. Transcripts with morph effect, separated the three morphs at the expression level, with the two benthic morphs being more similar. However, Gene Ontology analyses did not reveal clear functional enrichment of transcripts between groups. Verification via qPCR confirmed differential expression of several genes between the morphs, including regulatory genes such as AT-Rich Interaction Domain 4A (arid4a) and trans…
format: application/pdf
format: text/html
creator: Jóhannes Guðbrandsson
creator: Sigríður Rut Franzdóttir
creator: Bjarni Kristófer Kristjánsson
creator: Ehsan Pashay Ahi
creator: Valerie Helene Maier
creator: Kalina Hristova Kapralova
creator: Sigurður Sveinn Snorrason
creator: Zophonías Oddur Jónsson
creator: Arnar Pálsson
subject: Developmental Biology
subject: Evolutionary Studies
subject: Genomics
subject: Molecular Biology
subject: Freshwater Biology
description: doi:10.7717/peerj.4345
publisher: PeerJ Inc.
rights: © 2018 Guðbrandsson et al.
abstract: Phenotypic differences between closely related taxa or populations can arise through genetic variation or be environmentally induced, leading to altered transcription of genes during development. Comparative developmental studies of closely related species or variable populations within species can help to elucidate the molecular mechanisms related to evolutionary divergence and speciation. Studies of Arctic charr (Salvelinus alpinus) and related salmonids have revealed considerable phenotypic variation among populations and in Arctic charr many cases of extensive variation within lakes (resource polymorphism) have been recorded. One example is the four Arctic charr morphs in the ∼10,000 year old Lake Thingvallavatn, which differ in numerous morphological and life history traits. We set out to investigate the molecular and developmental roots of this polymorphism by studying gene expression in embryos of three of the morphs reared in a common garden set-up. We performed RNA-sequencing, de-novo transcriptome assembly and compared gene expression among morphs during an important timeframe in early development, i.e., preceding the formation of key trophic structures. Expectedly, developmental time was the predominant explanatory variable. As the data were affected by some form of RNA-degradation even though all samples passed quality control testing, an estimate of 3′-bias was the second most common explanatory variable. Importantly, morph, both as an independent variable and as interaction with developmental time, affected the expression of numerous transcripts. Transcripts with morph effect, separated the three morphs at the expression level, with the two benthic morphs being more similar. However, Gene Ontology analyses did not reveal clear functional enrichment of transcripts between groups. Verification via qPCR confirmed differential expression of several genes between the morphs, including regulatory genes such as AT-Rich Interaction Domain 4A (arid4a) and trans…
bibliographic citation: Guðbrandsson et al. (2018) Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs. PeerJ 6:e4345 https://doi.org/10.7717/peerj.4345
date submitted: 2017-10-02
date accepted: 2018-01-19
issued: 2018-02-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guðbrandsson
  given name: Jóhannes
author list: Agent
  family name: Franzdóttir
  given name: Sigríður Rut
author list: Agent
  family name: Kristjánsson
  given name: Bjarni Kristófer
author list: Agent
  family name: Ahi
  given name: Ehsan Pashay
author list: Agent
  family name: Maier
  given name: Valerie Helene
author list: Agent
  family name: Kapralova
  given name: Kalina Hristova
author list: Agent
  family name: Snorrason
  given name: Sigurður Sveinn
author list: Agent
  family name: Jónsson
  given name: Zophonías Oddur
author list: Agent
  family name: Pálsson
  given name: Arnar
doi: 10.7717/peerj.4345
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-02-07
copyright: ©2018 Guðbrandsson et al.
attribution name: Guðbrandsson et al.

An Indo-Pacific damselfish (Neopomacentrus cyanomos) in the Gulf of Mexico: origin and mode of introduction
type: item
type: AcademicArticle
description: The Indo-West Pacific (IWP) coral-reef damselfish Neopomacentrus cyanomos is well established across the south-west Gulf of Mexico (SwGoMx). Comparisons of mtDNA sequences of the SwGoMx population with those from conspecifics from 16 sites scattered across its native geographic range show that the SwGoMx population is derived from two of four native lineages: one from the north-west Pacific Ocean, the other from the northern Indian Ocean. Three hypotheses address how this species was introduced to the SwGoMX: (1) aquarium release; (2) borne by cargo-ship; and (3) carried by offshore petroleum platform (petro-platform). The first is unlikely because this species rarely features in the aquarium trade, and “N. cyanomos” traded to the USA from the sole IWP source we are aware of are a misidentified congener, N. taeniurus. The second hypothesis is unlikely because shipping has not been associated with the introduction of alien damselfishes, there is little international shipping between the IWP and the SwGoMx, and voyages between those areas would be lengthy and along environmentally unfavorable routes. Various lines of evidence support the third hypothesis: (i) bio-fouled petro-platforms represent artificial reefs that can sustain large and diverse populations of tropical reef-fishes, including N. cyanomos in the SwGoMx; (ii) relocation of such platforms has been implicated in trans-oceanic introductions leading to establishment of non-native populations of such fishes; and (iii) genetic characteristics of the SwGoMx population indicate that it was established by a large and diverse group of founders drawn from the IWP regions where many petro-platforms currently in the SwGoMx and other Atlantic offshore oilfields originated.
format: application/pdf
format: text/html
creator: D. Ross Robertson
creator: Omar Dominguez-Dominguez
creator: Benjamin Victor
creator: Nuno Simoes
subject: Aquaculture, Fisheries and Fish Science
subject: Biogeography
subject: Genetics
subject: Marine Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.4328
publisher: PeerJ Inc.
rights: © 2018 Robertson et al.
abstract: The Indo-West Pacific (IWP) coral-reef damselfish Neopomacentrus cyanomos is well established across the south-west Gulf of Mexico (SwGoMx). Comparisons of mtDNA sequences of the SwGoMx population with those from conspecifics from 16 sites scattered across its native geographic range show that the SwGoMx population is derived from two of four native lineages: one from the north-west Pacific Ocean, the other from the northern Indian Ocean. Three hypotheses address how this species was introduced to the SwGoMX: (1) aquarium release; (2) borne by cargo-ship; and (3) carried by offshore petroleum platform (petro-platform). The first is unlikely because this species rarely features in the aquarium trade, and “N. cyanomos” traded to the USA from the sole IWP source we are aware of are a misidentified congener, N. taeniurus. The second hypothesis is unlikely because shipping has not been associated with the introduction of alien damselfishes, there is little international shipping between the IWP and the SwGoMx, and voyages between those areas would be lengthy and along environmentally unfavorable routes. Various lines of evidence support the third hypothesis: (i) bio-fouled petro-platforms represent artificial reefs that can sustain large and diverse populations of tropical reef-fishes, including N. cyanomos in the SwGoMx; (ii) relocation of such platforms has been implicated in trans-oceanic introductions leading to establishment of non-native populations of such fishes; and (iii) genetic characteristics of the SwGoMx population indicate that it was established by a large and diverse group of founders drawn from the IWP regions where many petro-platforms currently in the SwGoMx and other Atlantic offshore oilfields originated.
bibliographic citation: Robertson et al. (2018) An Indo-Pacific damselfish (Neopomacentrus cyanomos) in the Gulf of Mexico: origin and mode of introduction. PeerJ 6:e4328 https://doi.org/10.7717/peerj.4328
date submitted: 2017-11-08
date accepted: 2018-01-15
issued: 2018-02-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Robertson
  given name: D. Ross
author list: Agent
  family name: Dominguez-Dominguez
  given name: Omar
author list: Agent
  family name: Victor
  given name: Benjamin
author list: Agent
  family name: Simoes
  given name: Nuno
doi: 10.7717/peerj.4328
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-02-07
copyright: ©2018 Robertson et al.
attribution name: Robertson et al.

Detection of stable community structures within gut microbiota co-occurrence networks from different human populations
type: item
type: AcademicArticle
description: Microbes in the gut microbiome form sub-communities based on shared niche specialisations and specific interactions between individual taxa. The inter-microbial relationships that define these communities can be inferred from the co-occurrence of taxa across multiple samples. Here, we present an approach to identify comparable communities within different gut microbiota co-occurrence networks, and demonstrate its use by comparing the gut microbiota community structures of three geographically diverse populations. We combine gut microbiota profiles from 2,764 British, 1,023 Dutch, and 639 Israeli individuals, derive co-occurrence networks between their operational taxonomic units, and detect comparable communities within them. Comparing populations we find that community structure is significantly more similar between datasets than expected by chance. Mapping communities across the datasets, we also show that communities can have similar associations to host phenotypes in different populations. This study shows that the community structure within the gut microbiota is stable across populations, and describes a novel approach that facilitates comparative community-centric microbiome analyses.
format: application/pdf
format: text/html
creator: Matthew A. Jackson
creator: Marc Jan Bonder
creator: Zhana Kuncheva
creator: Jonas Zierer
creator: Jingyuan Fu
creator: Alexander Kurilshikov
creator: Cisca Wijmenga
creator: Alexandra Zhernakova
creator: Jordana T. Bell
creator: Tim D. Spector
creator: Claire J. Steves
subject: Bioinformatics
subject: Ecology
subject: Microbiology
description: doi:10.7717/peerj.4303
publisher: PeerJ Inc.
rights: © 2018 Jackson et al.
abstract: Microbes in the gut microbiome form sub-communities based on shared niche specialisations and specific interactions between individual taxa. The inter-microbial relationships that define these communities can be inferred from the co-occurrence of taxa across multiple samples. Here, we present an approach to identify comparable communities within different gut microbiota co-occurrence networks, and demonstrate its use by comparing the gut microbiota community structures of three geographically diverse populations. We combine gut microbiota profiles from 2,764 British, 1,023 Dutch, and 639 Israeli individuals, derive co-occurrence networks between their operational taxonomic units, and detect comparable communities within them. Comparing populations we find that community structure is significantly more similar between datasets than expected by chance. Mapping communities across the datasets, we also show that communities can have similar associations to host phenotypes in different populations. This study shows that the community structure within the gut microbiota is stable across populations, and describes a novel approach that facilitates comparative community-centric microbiome analyses.
bibliographic citation: Jackson et al. (2018) Detection of stable community structures within gut microbiota co-occurrence networks from different human populations. PeerJ 6:e4303 https://doi.org/10.7717/peerj.4303
date submitted: 2017-10-23
date accepted: 2018-01-10
issued: 2018-02-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jackson
  given name: Matthew A.
author list: Agent
  family name: Bonder
  given name: Marc Jan
author list: Agent
  family name: Kuncheva
  given name: Zhana
author list: Agent
  family name: Zierer
  given name: Jonas
author list: Agent
  family name: Fu
  given name: Jingyuan
author list: Agent
  family name: Kurilshikov
  given name: Alexander
author list: Agent
  family name: Wijmenga
  given name: Cisca
author list: Agent
  family name: Zhernakova
  given name: Alexandra
author list: Agent
  family name: Bell
  given name: Jordana T.
author list: Agent
  family name: Spector
  given name: Tim D.
author list: Agent
  family name: Steves
  given name: Claire J.
doi: 10.7717/peerj.4303
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-02-07
copyright: ©2018 Jackson et al.
attribution name: Jackson et al.

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