PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Foliar microbiome transplants confer disease resistance in a critically-endangered plant
items: How can we reliably identify a taxon based on humeral morphology? Comparative morphology of desmostylian humeri
items: A unified approach to model peripheral nerves across different animal species
items: Anthropogenic water sources and the effects on Sonoran Desert small mammal communities
items: Preoperative cervical sagittal alignment parameters and their impacts on myelopathy in patients with cervical spondylotic myelopathy: a retrospective study
items: The role of MEF2 transcription factors in dehydration and anoxia survival in Rana sylvatica skeletal muscle
items: The response of soil microbial communities to variation in annual precipitation depends on soil nutritional status in an oligotrophic desert
items: Mobile acoustic transects miss rare bat species: implications of survey method and spatio-temporal sampling for monitoring bats
items: HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities
items: Indicators for the use of robotic labs in basic biomedical research: a literature analysis

Foliar microbiome transplants confer disease resistance in a critically-endangered plant
type: item
type: AcademicArticle
description: There has been very little effort to incorporate foliar microbiomes into plant conservation efforts even though foliar endophytes are critically important to the fitness and function of hosts. Many critically endangered plants that have been extirpated from the wild are dependent on regular fungicidal applications in greenhouses that cannot be maintained for remote out-planted populations, which quickly perish. These fungicides negatively impact potentially beneficial fungal symbionts, which may reduce plant defenses to pathogens once fungicide treatments are stopped. Using the host/parasite system of Phyllostegia kaalaensis and Neoerysiphe galeopsidis, we conducted experiments to test total foliar microbiome transplants from healthy wild relatives onto fungicide-dependent endangered plants in an attempt to mitigate disease and reduce dependency on fungicides. Plants were treated with total microbiome transplants or cultured subsets of this community and monitored for disease severity. High-throughput DNA screening of fungal ITS1 rDNA was used to track the leaf-associated fungal communities and evaluate the effectiveness of transplantation methods. Individuals receiving traditionally isolated fungal treatments showed no improvement, but those receiving applications of a simple leaf slurry containing an uncultured fungal community showed significant disease reduction, to which we partially attribute an increase in the mycoparasitic Pseudozyma aphidis. These results were replicated in two independent experimental rounds. Treated plants have since been moved to a native habitat and, as of this writing, remain disease-free. Our results demonstrate the effectiveness of a simple low-tech method for transferring beneficial microbes from healthy wild plants to greenhouse-raised plants with reduced symbiotic microbiota. This technique was effective at reducing disease, and in conferring increased survival to an out-planted population of critically endangered plants. It was n…
format: application/pdf
format: text/html
creator: Geoffrey Zahn
creator: Anthony S. Amend
subject: Conservation Biology
subject: Microbiology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.4020
publisher: PeerJ Inc.
rights: © 2017 Zahn and Amend
abstract: There has been very little effort to incorporate foliar microbiomes into plant conservation efforts even though foliar endophytes are critically important to the fitness and function of hosts. Many critically endangered plants that have been extirpated from the wild are dependent on regular fungicidal applications in greenhouses that cannot be maintained for remote out-planted populations, which quickly perish. These fungicides negatively impact potentially beneficial fungal symbionts, which may reduce plant defenses to pathogens once fungicide treatments are stopped. Using the host/parasite system of Phyllostegia kaalaensis and Neoerysiphe galeopsidis, we conducted experiments to test total foliar microbiome transplants from healthy wild relatives onto fungicide-dependent endangered plants in an attempt to mitigate disease and reduce dependency on fungicides. Plants were treated with total microbiome transplants or cultured subsets of this community and monitored for disease severity. High-throughput DNA screening of fungal ITS1 rDNA was used to track the leaf-associated fungal communities and evaluate the effectiveness of transplantation methods. Individuals receiving traditionally isolated fungal treatments showed no improvement, but those receiving applications of a simple leaf slurry containing an uncultured fungal community showed significant disease reduction, to which we partially attribute an increase in the mycoparasitic Pseudozyma aphidis. These results were replicated in two independent experimental rounds. Treated plants have since been moved to a native habitat and, as of this writing, remain disease-free. Our results demonstrate the effectiveness of a simple low-tech method for transferring beneficial microbes from healthy wild plants to greenhouse-raised plants with reduced symbiotic microbiota. This technique was effective at reducing disease, and in conferring increased survival to an out-planted population of critically endangered plants. It was n…
bibliographic citation: Zahn et al. (2017) Foliar microbiome transplants confer disease resistance in a critically-endangered plant. PeerJ 5:e4020 https://doi.org/10.7717/peerj.4020
date submitted: 2017-09-05
date accepted: 2017-10-20
issued: 2017-11-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zahn
  given name: Geoffrey
author list: Agent
  family name: Amend
  given name: Anthony S.
doi: 10.7717/peerj.4020
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-10
copyright: ©2017 Zahn and Amend
attribution name: Zahn and Amend

How can we reliably identify a taxon based on humeral morphology? Comparative morphology of desmostylian humeri
type: item
type: AcademicArticle
description: Desmostylia is a clade of marine mammals belonging to either Tethytheria or Perissodactyla. Rich fossil records of Desmostylia were found in the Oligocene to Miocene strata of the Northern Pacific Rim, especially in the northwestern region, which includes the Japanese archipelago. Fossils in many shapes and forms, including whole or partial skeletons, skulls, teeth, and fragmentary bones have been discovered from this region. Despite the prevalent availability of fossil records, detailed taxonomic identification based on fragmentary postcranial materials has been difficult owing to to our limited knowledge of the postcranial diagnostic features of many desmostylian taxa. In this study, I propose the utilization of diagnostic characters found in the humerus to identify desmostylian genus. These characters can be used to identify isolated desmostylian humeri at the genus level, contributing to a better understanding of the stratigraphic and geographic distributions of each genus.
format: application/pdf
format: text/html
creator: Kumiko Matsui
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.4011
publisher: PeerJ Inc.
rights: © 2017 Matsui
abstract: Desmostylia is a clade of marine mammals belonging to either Tethytheria or Perissodactyla. Rich fossil records of Desmostylia were found in the Oligocene to Miocene strata of the Northern Pacific Rim, especially in the northwestern region, which includes the Japanese archipelago. Fossils in many shapes and forms, including whole or partial skeletons, skulls, teeth, and fragmentary bones have been discovered from this region. Despite the prevalent availability of fossil records, detailed taxonomic identification based on fragmentary postcranial materials has been difficult owing to to our limited knowledge of the postcranial diagnostic features of many desmostylian taxa. In this study, I propose the utilization of diagnostic characters found in the humerus to identify desmostylian genus. These characters can be used to identify isolated desmostylian humeri at the genus level, contributing to a better understanding of the stratigraphic and geographic distributions of each genus.
bibliographic citation: Matsui (2017) How can we reliably identify a taxon based on humeral morphology? Comparative morphology of desmostylian humeri. PeerJ 5:e4011 https://doi.org/10.7717/peerj.4011
date submitted: 2017-07-19
date accepted: 2017-10-19
issued: 2017-11-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Matsui
  given name: Kumiko
doi: 10.7717/peerj.4011
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-10
copyright: ©2017 Matsui
attribution name: Matsui

A unified approach to model peripheral nerves across different animal species
type: item
type: AcademicArticle
description: Peripheral nerves are extremely complex biological structures. The knowledge of their response to stretch is crucial to better understand physiological and pathological states (e.g., due to overstretch). Since their mechanical response is deterministically related to the nature of the external stimuli, theoretical and computational tools were used to investigate their behaviour. In this work, a Yeoh-like polynomial strain energy function was used to reproduce the response of in vitro porcine nerve. Moreover, this approach was applied to different nervous structures coming from different animal species (rabbit, lobster, Aplysia) and tested for different amount of stretch (up to extreme ones). Starting from this theoretical background, in silico models of both porcine nerves and cerebro-abdominal connective of Aplysia were built to reproduce experimental data (R2 > 0.9). Finally, bi-dimensional in silico models were provided to reduce computational time of more than 90% with respect to the performances of fully three-dimensional models.
format: application/pdf
format: text/html
creator: Elisabetta Giannessi
creator: Maria Rita Stornelli
creator: Pier Nicola Sergi
subject: Bioengineering
subject: Computational Biology
subject: Neurology
description: doi:10.7717/peerj.4005
publisher: PeerJ Inc.
rights: © 2017 Giannessi et al.
abstract: Peripheral nerves are extremely complex biological structures. The knowledge of their response to stretch is crucial to better understand physiological and pathological states (e.g., due to overstretch). Since their mechanical response is deterministically related to the nature of the external stimuli, theoretical and computational tools were used to investigate their behaviour. In this work, a Yeoh-like polynomial strain energy function was used to reproduce the response of in vitro porcine nerve. Moreover, this approach was applied to different nervous structures coming from different animal species (rabbit, lobster, Aplysia) and tested for different amount of stretch (up to extreme ones). Starting from this theoretical background, in silico models of both porcine nerves and cerebro-abdominal connective of Aplysia were built to reproduce experimental data (R2 > 0.9). Finally, bi-dimensional in silico models were provided to reduce computational time of more than 90% with respect to the performances of fully three-dimensional models.
bibliographic citation: Giannessi et al. (2017) A unified approach to model peripheral nerves across different animal species. PeerJ 5:e4005 https://doi.org/10.7717/peerj.4005
date submitted: 2016-04-15
date accepted: 2017-10-18
issued: 2017-11-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Giannessi
  given name: Elisabetta
author list: Agent
  family name: Stornelli
  given name: Maria Rita
author list: Agent
  family name: Sergi
  given name: Pier Nicola
doi: 10.7717/peerj.4005
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-10
copyright: ©2017 Giannessi et al.
attribution name: Giannessi et al.

Anthropogenic water sources and the effects on Sonoran Desert small mammal communities
type: item
type: AcademicArticle
description: Anthropogenic water sources (AWS) are developed water sources used as a management tool for desert wildlife species. Studies documenting the effects of AWS are often focused on game species; whereas, the effects on non-target wildlife are less understood. We used live trapping techniques to investigate rodent abundance, biomass, and diversity metrics near AWS and paired control sites; we sampled vegetation to determine rodent-habitat associations in the Sauceda Mountains of the Sonoran Desert in Arizona. A total of 370 individual mammals representing three genera and eight species were captured in 4,800 trap nights from winter 2011 to spring 2012. A multi-response permutation procedure was used to identify differences in small mammal community abundance and biomass by season and treatment. Rodent abundance, biomass, and richness were greater at AWS compared to control sites. Patterns of abundance and biomass were driven by the desert pocket mouse (Chaetodipus penicillatus) which was the most common capture and two times more numerous at AWS compared to controls. Vegetation characteristics, explored using principal components analysis, were similar between AWS and controls. Two species that prefer vegetation structure, Bailey’s pocket mouse (C. baileyi) and white-throated woodrat (Neotoma albigula), had greater abundances and biomass near AWS and were associated with habitat having high cactus density. Although small mammals do not drink free-water, perhaps higher abundances of some species of desert rodents at AWS could be related to artificial structure associated with construction or other resources. Compared to the 30-year average of precipitation for the area, the period of our study occurred during a dry winter. During dry periods, perhaps AWS provide resources to rodents related to moisture.
format: application/pdf
format: text/html
creator: Aaron B. Switalski
creator: Heather L. Bateman
subject: Conservation Biology
subject: Ecohydrology
subject: Ecology
subject: Natural Resource Management
subject: Zoology
description: doi:10.7717/peerj.4003
publisher: PeerJ Inc.
rights: © 2017 Switalski and Bateman
abstract: Anthropogenic water sources (AWS) are developed water sources used as a management tool for desert wildlife species. Studies documenting the effects of AWS are often focused on game species; whereas, the effects on non-target wildlife are less understood. We used live trapping techniques to investigate rodent abundance, biomass, and diversity metrics near AWS and paired control sites; we sampled vegetation to determine rodent-habitat associations in the Sauceda Mountains of the Sonoran Desert in Arizona. A total of 370 individual mammals representing three genera and eight species were captured in 4,800 trap nights from winter 2011 to spring 2012. A multi-response permutation procedure was used to identify differences in small mammal community abundance and biomass by season and treatment. Rodent abundance, biomass, and richness were greater at AWS compared to control sites. Patterns of abundance and biomass were driven by the desert pocket mouse (Chaetodipus penicillatus) which was the most common capture and two times more numerous at AWS compared to controls. Vegetation characteristics, explored using principal components analysis, were similar between AWS and controls. Two species that prefer vegetation structure, Bailey’s pocket mouse (C. baileyi) and white-throated woodrat (Neotoma albigula), had greater abundances and biomass near AWS and were associated with habitat having high cactus density. Although small mammals do not drink free-water, perhaps higher abundances of some species of desert rodents at AWS could be related to artificial structure associated with construction or other resources. Compared to the 30-year average of precipitation for the area, the period of our study occurred during a dry winter. During dry periods, perhaps AWS provide resources to rodents related to moisture.
bibliographic citation: Switalski et al. (2017) Anthropogenic water sources and the effects on Sonoran Desert small mammal communities. PeerJ 5:e4003 https://doi.org/10.7717/peerj.4003
date submitted: 2017-06-15
date accepted: 2017-10-17
issued: 2017-11-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Switalski
  given name: Aaron B.
author list: Agent
  family name: Bateman
  given name: Heather L.
doi: 10.7717/peerj.4003
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-10
copyright: ©2017 Switalski and Bateman
attribution name: Switalski and Bateman

Preoperative cervical sagittal alignment parameters and their impacts on myelopathy in patients with cervical spondylotic myelopathy: a retrospective study
type: item
type: AcademicArticle
description: Background Cervical sagittal alignment plays an important role in the pathogenesis of cervical spondylotic myelopathy (CSM), but there are limited studies on the cervical sagittal parameters in CSM patients and their correlations with myelopathy. The aim of this study is to investigate the correlations among the preoperative cervical sagittal alignment parameters and their correlations with the development of myelopathy in patients with CSM. Methods We retrospectively collected 212 patients with CSM who underwent surgical interventions. Gender, age, modified Japanese Orthopedic Association score (mJOA), cervical lordosis (CL), C2–C7 sagittal vertical axis (C2–C7 SVA), T1 slope (T1S), neck tilt (NT) and thoracic inlet angle (TIA) were collected before operation. Interobserver and intraobserver reliability were calculated for all measurements (intraclass correlation coefficient, ICC). Data were analyzed with Pearson and Spearman correlation tests and multiple linear regression analysis. Results A total of 212 patients with CSM were included in this study (male: 136, female: 76) with an average age of 54.5 ± 10.1 years old. Intraobserver and interobserver reliability for all included radiographic parameters presented good to excellent agreement (ICC > 0.7). No significant differences in demographic and radiological parameters have been observed between males and females (P > 0.05). We found statistically significant correlations among the following parameters: age with CL (r = 0.135, P = 0.049), age with T1S (r = 0.222, P = 0.001), CL with T1S (r = 0.291, P < 0.001), CL with C2-C7 SVA (r = − 0.395, P < 0.001), mJOA with age (r = − 0.274, P < 0.001), mJOA with C2–C7 SVA (r = − 0.219, P < 0.001) and mJOA with T1S(r = − 0.171, p = 0.013). Linear regression analysis showed that C2–C7 SVA was the predictor of CL (adjusted R2 = 0.152, P < 0.001) and multiple linear regression showed that age combined with C2–C7 SVA was a sensitive predictor of mJOA (adjusted R2 = 0.106, P < …
format: application/pdf
format: text/html
creator: Wei Yuan
creator: Yue Zhu
creator: Haitao Zhu
creator: Cui Cui
creator: Lei Pei
creator: Zhuxi Huang
subject: Orthopedics
subject: Radiology and Medical Imaging
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.4027
publisher: PeerJ Inc.
rights: © 2017 Yuan et al.
abstract: Background Cervical sagittal alignment plays an important role in the pathogenesis of cervical spondylotic myelopathy (CSM), but there are limited studies on the cervical sagittal parameters in CSM patients and their correlations with myelopathy. The aim of this study is to investigate the correlations among the preoperative cervical sagittal alignment parameters and their correlations with the development of myelopathy in patients with CSM. Methods We retrospectively collected 212 patients with CSM who underwent surgical interventions. Gender, age, modified Japanese Orthopedic Association score (mJOA), cervical lordosis (CL), C2–C7 sagittal vertical axis (C2–C7 SVA), T1 slope (T1S), neck tilt (NT) and thoracic inlet angle (TIA) were collected before operation. Interobserver and intraobserver reliability were calculated for all measurements (intraclass correlation coefficient, ICC). Data were analyzed with Pearson and Spearman correlation tests and multiple linear regression analysis. Results A total of 212 patients with CSM were included in this study (male: 136, female: 76) with an average age of 54.5 ± 10.1 years old. Intraobserver and interobserver reliability for all included radiographic parameters presented good to excellent agreement (ICC > 0.7). No significant differences in demographic and radiological parameters have been observed between males and females (P > 0.05). We found statistically significant correlations among the following parameters: age with CL (r = 0.135, P = 0.049), age with T1S (r = 0.222, P = 0.001), CL with T1S (r = 0.291, P < 0.001), CL with C2-C7 SVA (r = − 0.395, P < 0.001), mJOA with age (r = − 0.274, P < 0.001), mJOA with C2–C7 SVA (r = − 0.219, P < 0.001) and mJOA with T1S(r = − 0.171, p = 0.013). Linear regression analysis showed that C2–C7 SVA was the predictor of CL (adjusted R2 = 0.152, P < 0.001) and multiple linear regression showed that age combined with C2–C7 SVA was a sensitive predictor of mJOA (adjusted R2 = 0.106, P < …
bibliographic citation: Yuan et al. (2017) Preoperative cervical sagittal alignment parameters and their impacts on myelopathy in patients with cervical spondylotic myelopathy: a retrospective study. PeerJ 5:e4027 https://doi.org/10.7717/peerj.4027
date submitted: 2017-07-17
date accepted: 2017-10-22
issued: 2017-11-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yuan
  given name: Wei
author list: Agent
  family name: Zhu
  given name: Yue
author list: Agent
  family name: Zhu
  given name: Haitao
author list: Agent
  family name: Cui
  given name: Cui
author list: Agent
  family name: Pei
  given name: Lei
author list: Agent
  family name: Huang
  given name: Zhuxi
doi: 10.7717/peerj.4027
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-09
copyright: ©2017 Yuan et al.
attribution name: Yuan et al.

The role of MEF2 transcription factors in dehydration and anoxia survival in Rana sylvatica skeletal muscle
type: item
type: AcademicArticle
description: The wood frog (Rana sylvatica) can endure freezing of up to 65% of total body water during winter. When frozen, wood frogs enter a dormant state characterized by a cessation of vital functions (i.e., no heartbeat, blood circulation, breathing, brain activity, or movement). Wood frogs utilize various behavioural and biochemical adaptations to survive extreme freezing and component anoxia and dehydration stresses, including a global suppression of metabolic functions and gene expression. The stress-responsive myocyte enhancer factor-2 (MEF2) transcription factor family regulates the selective expression of genes involved in glucose transport, protein quality control, and phosphagen homeostasis. This study examined the role of MEF2A and MEF2C proteins as well as select downstream targets (glucose transporter-4, calreticulin, and muscle and brain creatine kinase isozymes) in 40% dehydration and 24 h anoxia exposure at the transcriptional, translational, and post-translational levels using qRT-PCR, immunoblotting, and subcellular localization. Mef2a/c transcript levels remained constant during dehydration and anoxia. Total, cytoplasmic, and nuclear MEF2A/C and phospho-MEF2A/C protein levels remained constant during dehydration, whereas a decrease in total MEF2C levels was observed during rehydration. Total and phospho-MEF2A levels remained constant during anoxia, whereas total MEF2C levels decreased during 24 h anoxia and P-MEF2C levels increased during 4 h anoxia. In contrast, cytoplasmic MEF2A levels and nuclear phospho-MEF2A/C levels were upregulated during anoxia. MEF2 downstream targets remained constant during dehydration and anoxia, with the exception of glut4 which was upregulated during anoxia. These results suggest that the upregulated MEF2 response reported in wood frogs during freezing may in part stem from their cellular responses to surviving prolonged anoxia, rather than dehydration, leading to an increase in GLUT4 expression which may have an important ro…
format: application/pdf
format: text/html
creator: Myriam P. Hoyeck
creator: Hanane Hadj-Moussa
creator: Kenneth B. Storey
subject: Biochemistry
subject: Molecular Biology
description: doi:10.7717/peerj.4014
publisher: PeerJ Inc.
rights: © 2017 Hoyeck et al.
abstract: The wood frog (Rana sylvatica) can endure freezing of up to 65% of total body water during winter. When frozen, wood frogs enter a dormant state characterized by a cessation of vital functions (i.e., no heartbeat, blood circulation, breathing, brain activity, or movement). Wood frogs utilize various behavioural and biochemical adaptations to survive extreme freezing and component anoxia and dehydration stresses, including a global suppression of metabolic functions and gene expression. The stress-responsive myocyte enhancer factor-2 (MEF2) transcription factor family regulates the selective expression of genes involved in glucose transport, protein quality control, and phosphagen homeostasis. This study examined the role of MEF2A and MEF2C proteins as well as select downstream targets (glucose transporter-4, calreticulin, and muscle and brain creatine kinase isozymes) in 40% dehydration and 24 h anoxia exposure at the transcriptional, translational, and post-translational levels using qRT-PCR, immunoblotting, and subcellular localization. Mef2a/c transcript levels remained constant during dehydration and anoxia. Total, cytoplasmic, and nuclear MEF2A/C and phospho-MEF2A/C protein levels remained constant during dehydration, whereas a decrease in total MEF2C levels was observed during rehydration. Total and phospho-MEF2A levels remained constant during anoxia, whereas total MEF2C levels decreased during 24 h anoxia and P-MEF2C levels increased during 4 h anoxia. In contrast, cytoplasmic MEF2A levels and nuclear phospho-MEF2A/C levels were upregulated during anoxia. MEF2 downstream targets remained constant during dehydration and anoxia, with the exception of glut4 which was upregulated during anoxia. These results suggest that the upregulated MEF2 response reported in wood frogs during freezing may in part stem from their cellular responses to surviving prolonged anoxia, rather than dehydration, leading to an increase in GLUT4 expression which may have an important ro…
bibliographic citation: Hoyeck et al. (2017) The role of MEF2 transcription factors in dehydration and anoxia survival in Rana sylvatica skeletal muscle. PeerJ 5:e4014 https://doi.org/10.7717/peerj.4014
date submitted: 2017-09-07
date accepted: 2017-10-19
issued: 2017-11-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hoyeck
  given name: Myriam P.
author list: Agent
  family name: Hadj-Moussa
  given name: Hanane
author list: Agent
  family name: Storey
  given name: Kenneth B.
doi: 10.7717/peerj.4014
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-09
copyright: ©2017 Hoyeck et al.
attribution name: Hoyeck et al.

The response of soil microbial communities to variation in annual precipitation depends on soil nutritional status in an oligotrophic desert
type: item
type: AcademicArticle
description: Background Soil microbial communities (SMC) play a central role in the structure and function of desert ecosystems. However, the high variability of annual precipitation could results in the alteration of SMC and related biological processes depending on soil water potential. The nature of the physiological adjustments made by SMC in order to obtain energy and nutrients remains unclear under different soil resource availabilities in desert ecosystems. In order to examine this dynamic, the present study examined the effects of variation in annual precipitation on physiological adjustments by the SMC across two vegetation-soil systems of different soil organic matter input in an oligotrophic desert ecosystem. Methods We collected soil samples in the Cuatro Ciénegas Basin (Mexico) under two vegetation covers: rosetophylous scrub (RS) and grassland (G), that differ in terms of quantity and quality of organic matter. Collections were conducted during the years 2011, 2012, 2013 and 2014, over which a noticeable variation in the annual precipitation occurred. The ecoenzymatic activity involved in the decomposition of organic matter, and the concentration of dissolved, available and microbial biomass nutrients, were determined and compared between sites and years. Results In 2011, we observed differences in bacterial taxonomic composition between the two vegetation covers. The lowest values of dissolved, available and microbial nutrients in both cover types were found in 2012. The G soil showed higher values of dissolved and available nutrients in the wet years. Significant positive correlations were detected between precipitation and the ratios Cmic:Nmic and Cmic:Pmic in the RS soil and Cmic:Pmic and Nmic:Pmic in the G soil. The slopes of the regression with Cmic and Nmic were higher in the G soil and lower in the RS soil. Moreover, the SMC under each vegetation cover were co-limited by different nutrients and responded to the sum of water stress and nutrient limitation. D…
format: application/pdf
format: text/html
creator: Cristina Montiel-González
creator: Yunuen Tapia-Torres
creator: Valeria Souza
creator: Felipe García-Oliva
subject: Biodiversity
subject: Ecology
subject: Ecosystem Science
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.4007
publisher: PeerJ Inc.
rights: © 2017 Montiel-González et al.
abstract: Background Soil microbial communities (SMC) play a central role in the structure and function of desert ecosystems. However, the high variability of annual precipitation could results in the alteration of SMC and related biological processes depending on soil water potential. The nature of the physiological adjustments made by SMC in order to obtain energy and nutrients remains unclear under different soil resource availabilities in desert ecosystems. In order to examine this dynamic, the present study examined the effects of variation in annual precipitation on physiological adjustments by the SMC across two vegetation-soil systems of different soil organic matter input in an oligotrophic desert ecosystem. Methods We collected soil samples in the Cuatro Ciénegas Basin (Mexico) under two vegetation covers: rosetophylous scrub (RS) and grassland (G), that differ in terms of quantity and quality of organic matter. Collections were conducted during the years 2011, 2012, 2013 and 2014, over which a noticeable variation in the annual precipitation occurred. The ecoenzymatic activity involved in the decomposition of organic matter, and the concentration of dissolved, available and microbial biomass nutrients, were determined and compared between sites and years. Results In 2011, we observed differences in bacterial taxonomic composition between the two vegetation covers. The lowest values of dissolved, available and microbial nutrients in both cover types were found in 2012. The G soil showed higher values of dissolved and available nutrients in the wet years. Significant positive correlations were detected between precipitation and the ratios Cmic:Nmic and Cmic:Pmic in the RS soil and Cmic:Pmic and Nmic:Pmic in the G soil. The slopes of the regression with Cmic and Nmic were higher in the G soil and lower in the RS soil. Moreover, the SMC under each vegetation cover were co-limited by different nutrients and responded to the sum of water stress and nutrient limitation. D…
bibliographic citation: Montiel-González et al. (2017) The response of soil microbial communities to variation in annual precipitation depends on soil nutritional status in an oligotrophic desert. PeerJ 5:e4007 https://doi.org/10.7717/peerj.4007
date submitted: 2017-05-08
date accepted: 2017-10-18
issued: 2017-11-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Montiel-González
  given name: Cristina
author list: Agent
  family name: Tapia-Torres
  given name: Yunuen
author list: Agent
  family name: Souza
  given name: Valeria
author list: Agent
  family name: García-Oliva
  given name: Felipe
doi: 10.7717/peerj.4007
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-09
copyright: ©2017 Montiel-González et al.
attribution name: Montiel-González et al.

Mobile acoustic transects miss rare bat species: implications of survey method and spatio-temporal sampling for monitoring bats
type: item
type: AcademicArticle
description: Due to increasing threats facing bats, long-term monitoring protocols are needed to inform conservation strategies. Effective monitoring should be easily repeatable while capturing spatio-temporal variation. Mobile acoustic driving transect surveys (‘mobile transects’) have been touted as a robust, cost-effective method to monitor bats; however, it is not clear how well mobile transects represent dynamic bat communities, especially when used as the sole survey approach. To assist biologists who must select a single survey method due to resource limitations, we assessed the effectiveness of three acoustic survey methods at detecting species richness in a vast protected area (Everglades National Park): (1) mobile transects, (2) stationary surveys that were strategically located by sources of open water and (3) stationary surveys that were replicated spatially across the landscape. We found that mobile transects underrepresented bat species richness compared to stationary surveys across all major vegetation communities and in two distinct seasons (dry/cool and wet/warm). Most critically, mobile transects failed to detect three rare bat species, one of which is federally endangered. Spatially replicated stationary surveys did not estimate higher species richness than strategically located stationary surveys, but increased the rate at which species were detected in one vegetation community. The survey strategy that detected maximum species richness and the highest mean nightly species richness with minimal effort was a strategically located stationary detector in each of two major vegetation communities during the wet/warm season.
format: application/pdf
format: text/html
creator: Elizabeth C. Braun de Torrez
creator: Megan A. Wallrichs
creator: Holly K. Ober
creator: Robert A. McCleery
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.3940
publisher: PeerJ Inc.
rights: © 2017 Braun de Torrez et al.
abstract: Due to increasing threats facing bats, long-term monitoring protocols are needed to inform conservation strategies. Effective monitoring should be easily repeatable while capturing spatio-temporal variation. Mobile acoustic driving transect surveys (‘mobile transects’) have been touted as a robust, cost-effective method to monitor bats; however, it is not clear how well mobile transects represent dynamic bat communities, especially when used as the sole survey approach. To assist biologists who must select a single survey method due to resource limitations, we assessed the effectiveness of three acoustic survey methods at detecting species richness in a vast protected area (Everglades National Park): (1) mobile transects, (2) stationary surveys that were strategically located by sources of open water and (3) stationary surveys that were replicated spatially across the landscape. We found that mobile transects underrepresented bat species richness compared to stationary surveys across all major vegetation communities and in two distinct seasons (dry/cool and wet/warm). Most critically, mobile transects failed to detect three rare bat species, one of which is federally endangered. Spatially replicated stationary surveys did not estimate higher species richness than strategically located stationary surveys, but increased the rate at which species were detected in one vegetation community. The survey strategy that detected maximum species richness and the highest mean nightly species richness with minimal effort was a strategically located stationary detector in each of two major vegetation communities during the wet/warm season.
bibliographic citation: Braun de Torrez et al. (2017) Mobile acoustic transects miss rare bat species: implications of survey method and spatio-temporal sampling for monitoring bats. PeerJ 5:e3940 https://doi.org/10.7717/peerj.3940
date submitted: 2017-05-02
date accepted: 2017-09-26
issued: 2017-11-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Braun de Torrez
  given name: Elizabeth C.
author list: Agent
  family name: Wallrichs
  given name: Megan A.
author list: Agent
  family name: Ober
  given name: Holly K.
author list: Agent
  family name: McCleery
  given name: Robert A.
doi: 10.7717/peerj.3940
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-09
copyright: ©2017 Braun de Torrez et al.
attribution name: Braun de Torrez et al.

HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities
type: item
type: AcademicArticle
description: The development and application of metagenomic approaches have provided an opportunity to study and define horizontal gene transfer (HGT) on the level of microbial communities. However, no current metagenomic data simulation tools offers the option to introduce defined HGT within a microbial community. Here, we present HgtSIM, a pipeline to simulate HGT event among microbial community members with user-defined mutation levels. It was developed for testing and benchmarking pipelines for recovering HGTs from complex microbial datasets. HgtSIM is implemented in Python3 and is freely available at: https://github.com/songweizhi/HgtSIM.
format: application/pdf
format: text/html
creator: Weizhi Song
creator: Kerrin Steensen
creator: Torsten Thomas
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.4015
publisher: PeerJ Inc.
rights: © 2017 Song et al.
abstract: The development and application of metagenomic approaches have provided an opportunity to study and define horizontal gene transfer (HGT) on the level of microbial communities. However, no current metagenomic data simulation tools offers the option to introduce defined HGT within a microbial community. Here, we present HgtSIM, a pipeline to simulate HGT event among microbial community members with user-defined mutation levels. It was developed for testing and benchmarking pipelines for recovering HGTs from complex microbial datasets. HgtSIM is implemented in Python3 and is freely available at: https://github.com/songweizhi/HgtSIM.
bibliographic citation: Song et al. (2017) HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities. PeerJ 5:e4015 https://doi.org/10.7717/peerj.4015
date submitted: 2017-06-10
date accepted: 2017-10-19
issued: 2017-11-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: Weizhi
author list: Agent
  family name: Steensen
  given name: Kerrin
author list: Agent
  family name: Thomas
  given name: Torsten
doi: 10.7717/peerj.4015
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-08
copyright: ©2017 Song et al.
attribution name: Song et al.

Indicators for the use of robotic labs in basic biomedical research: a literature analysis
type: item
type: AcademicArticle
description: Robotic labs, in which experiments are carried out entirely by robots, have the potential to provide a reproducible and transparent foundation for performing basic biomedical laboratory experiments. In this article, we investigate whether these labs could be applicable in current experimental practice. We do this by text mining 1,628 papers for occurrences of methods that are supported by commercial robotic labs. Using two different concept recognition tools, we find that 86%–89% of the papers have at least one of these methods. This and our other results provide indications that robotic labs can serve as the foundation for performing many lab-based experiments.
format: application/pdf
format: text/html
creator: Paul Groth
creator: Jessica Cox
subject: Biochemistry
subject: Science Policy
subject: Computational Science
description: doi:10.7717/peerj.3997
publisher: PeerJ Inc.
rights: © 2017 Groth and Cox
abstract: Robotic labs, in which experiments are carried out entirely by robots, have the potential to provide a reproducible and transparent foundation for performing basic biomedical laboratory experiments. In this article, we investigate whether these labs could be applicable in current experimental practice. We do this by text mining 1,628 papers for occurrences of methods that are supported by commercial robotic labs. Using two different concept recognition tools, we find that 86%–89% of the papers have at least one of these methods. This and our other results provide indications that robotic labs can serve as the foundation for performing many lab-based experiments.
bibliographic citation: Groth et al. (2017) Indicators for the use of robotic labs in basic biomedical research: a literature analysis. PeerJ 5:e3997 https://doi.org/10.7717/peerj.3997
date submitted: 2017-06-26
date accepted: 2017-10-16
issued: 2017-11-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Groth
  given name: Paul
author list: Agent
  family name: Cox
  given name: Jessica
doi: 10.7717/peerj.3997
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-08
copyright: ©2017 Groth and Cox
attribution name: Groth and Cox

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