PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: RFRP3 influences basal lamina degradation, cellular death, and progesterone secretion in cultured preantral ovarian follicles from the domestic cat
items: Gradual, temperature-induced change of secondary sexual characteristics in Trichogramma pretiosum infected with parthenogenesis-inducing Wolbachia
items: Visual search characteristics of precise map reading by orienteers
items: Revision of the Tanzanian dicynodont Dicynodon huenei (Therapsida: Anomodontia) from the Permian Usili Formation
items: Estimating the phylogeny of geoemydid turtles (Cryptodira) from landmark data: an assessment of different methods
items: Characterisation of bacteria isolated from the stingless bee, Heterotrigona itama, honey, bee bread and propolis
items: Phylogenomic analyses confirm a novel invasive North American Corbicula (Bivalvia: Cyrenidae) lineage
items: Seasonal dynamics of microbial diversity in the rhizosphere of Ulmus pumila L. var. sabulosa in a steppe desert area of Northern China
items: Root tolerance and biochemical response of Chinese lettuce (Lactuca sativa L.) genotypes to cadmium stress
items: Development of a multiplex RT-PCR assay for simultaneous detection of Cucumber green mottle mosaic virus and Acidovorax citrulli in watermelon

RFRP3 influences basal lamina degradation, cellular death, and progesterone secretion in cultured preantral ovarian follicles from the domestic cat
type: item
type: AcademicArticle
description: The hypothalamic neuropeptide RFRP3 can suppress hypothalamic GnRH neuron activation and inhibit gonadotropin release from the anterior pituitary. RFRP3 is also produced locally in the ovary and can inhibit steroidogenesis and follicle development in many vertebrates. However, almost nothing is known about the presence and regulatory action of RFRP3 in gonads of any carnivore species. Such knowledge is important for developing captive breeding programs for endangered carnivores and for inhibiting reproduction in feral species. Using the domestic cat as a model, our objectives were to (1) demonstrate the expression of feline RFRP3 (fRFRP3) and its receptor in the cat ovary and (2) assess the influence of fRFRP3 on ovarian follicle integrity, survival, and steroidogenesis in vitro. We first confirmed that fRFRP3 and its receptors (NPFFR1 and NPFFR2) were expressed in cat ovaries by sequencing PCR products from ovarian RNA. We then isolated and cultured preantral ovarian follicles in the presence of 10 or 1 µM fRFRP3 + FSH (1 µg/mL). We recorded the percentage of morphologically viable follicles (basal lamina integrity) over 8 days and calculated percentage survival of follicles on Day 8 (using fluorescent markers for cell survival and death). Last, we quantified progesterone accumulation in media. 10 µM fRFRP3 had no observable effect on viability, survival, or steroid production compared to follicles exposed to only FSH. However, 1 µM fRFRP3 decreased the percentage of morphologically viable follicles and the percentage of surviving follicles on Day 8. At the same time, 1 µM fRFRP3 increased the accumulation of progesterone in media. Our study shows, for the first time, direct action of RFRP3 on the follicle as a functional unit, and it is the first in a carnivore species. More broadly, our results support a conserved, inhibitory action of RFRP3 on ovarian follicle development and underscore the importance of comparative functional studies.
format: application/pdf
format: text/html
creator: Kathryn Wilsterman
creator: George E. Bentley
creator: Pierre Comizzoli
subject: Molecular Biology
subject: Veterinary Medicine
subject: Gynecology and Obstetrics
description: doi:10.7717/peerj.7540
publisher: PeerJ Inc.
rights: © 2019 Wilsterman et al.
abstract: The hypothalamic neuropeptide RFRP3 can suppress hypothalamic GnRH neuron activation and inhibit gonadotropin release from the anterior pituitary. RFRP3 is also produced locally in the ovary and can inhibit steroidogenesis and follicle development in many vertebrates. However, almost nothing is known about the presence and regulatory action of RFRP3 in gonads of any carnivore species. Such knowledge is important for developing captive breeding programs for endangered carnivores and for inhibiting reproduction in feral species. Using the domestic cat as a model, our objectives were to (1) demonstrate the expression of feline RFRP3 (fRFRP3) and its receptor in the cat ovary and (2) assess the influence of fRFRP3 on ovarian follicle integrity, survival, and steroidogenesis in vitro. We first confirmed that fRFRP3 and its receptors (NPFFR1 and NPFFR2) were expressed in cat ovaries by sequencing PCR products from ovarian RNA. We then isolated and cultured preantral ovarian follicles in the presence of 10 or 1 µM fRFRP3 + FSH (1 µg/mL). We recorded the percentage of morphologically viable follicles (basal lamina integrity) over 8 days and calculated percentage survival of follicles on Day 8 (using fluorescent markers for cell survival and death). Last, we quantified progesterone accumulation in media. 10 µM fRFRP3 had no observable effect on viability, survival, or steroid production compared to follicles exposed to only FSH. However, 1 µM fRFRP3 decreased the percentage of morphologically viable follicles and the percentage of surviving follicles on Day 8. At the same time, 1 µM fRFRP3 increased the accumulation of progesterone in media. Our study shows, for the first time, direct action of RFRP3 on the follicle as a functional unit, and it is the first in a carnivore species. More broadly, our results support a conserved, inhibitory action of RFRP3 on ovarian follicle development and underscore the importance of comparative functional studies.
bibliographic citation: Wilsterman et al. (2019) RFRP3 influences basal lamina degradation, cellular death, and progesterone secretion in cultured preantral ovarian follicles from the domestic cat. PeerJ 7:e7540 https://doi.org/10.7717/peerj.7540
date submitted: 2019-05-18
date accepted: 2019-07-23
issued: 2019-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wilsterman
  given name: Kathryn
author list: Agent
  family name: Bentley
  given name: George E.
author list: Agent
  family name: Comizzoli
  given name: Pierre
doi: 10.7717/peerj.7540
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-23
copyright: ©2019 Wilsterman et al.
attribution name: Wilsterman et al.

Gradual, temperature-induced change of secondary sexual characteristics in Trichogramma pretiosum infected with parthenogenesis-inducing Wolbachia
type: item
type: AcademicArticle
description: Intersex is an intermediate stage of sexual differentiation in insects. Determining intersex morphology and the cause of its production will aid in the understanding of the mechanism of sexual differentiation in insects. In this paper, Wolbachia-infected Trichogramma pretiosum (T. preW+) that shows thelytokous parthenogenesis were used as subjects. In order to determine the causes of the T. preW+ intersex and the influence of parental generation temperature on gradual changes in secondary masculinization in intersex offspring, we examined the occurrence of intersex offspring (F1 and F2 generation) after the parental generations were treated with high temperature (27, 29, 31, and 33 °C) and described the external morphology of the intersexes. The results showed that the T. preW+ parental generation temperature is positively correlated with the probability of intersex offspring. The probability of F1 intersex is significantly higher than that of F2 intersex in different high temperature. The degree of secondary masculinization in T. preW+ intersexes increases as parental generation temperature increases. In addition, our study first identified 11 intersex types in T. preW+ and found that the primary and secondary sexual characteristics showed a regular distribution. We also found that the D type and H type of intersex have the highest frequency of appearance. The external genitalia of most intersexes were female, and only three intersex types have male external genitalia. Conclusions were ultimately obtained: Wolbachia is a direct factor that causes the occurrence of intersexes, while high temperature is an indirect factor that determines the external morphology of intersexes. The effects of high temperature on T. preW+ intersexes is passed through the parental generation to offspring, and this maternal effect weakens as the number of generations increases. In T. preW+ intersex individuals, most exhibit female primary sexual characteristics, and secondary sexual chara…
format: application/pdf
format: text/html
creator: Su-fang Ning
creator: Jin-cheng Zhou
creator: Quan-quan Liu
creator: Qian Zhao
creator: Hui Dong
subject: Agricultural Science
subject: Biodiversity
subject: Entomology
subject: Evolutionary Studies
subject: Parasitology
description: doi:10.7717/peerj.7567
publisher: PeerJ Inc.
rights: © 2019 Ning et al.
abstract: Intersex is an intermediate stage of sexual differentiation in insects. Determining intersex morphology and the cause of its production will aid in the understanding of the mechanism of sexual differentiation in insects. In this paper, Wolbachia-infected Trichogramma pretiosum (T. preW+) that shows thelytokous parthenogenesis were used as subjects. In order to determine the causes of the T. preW+ intersex and the influence of parental generation temperature on gradual changes in secondary masculinization in intersex offspring, we examined the occurrence of intersex offspring (F1 and F2 generation) after the parental generations were treated with high temperature (27, 29, 31, and 33 °C) and described the external morphology of the intersexes. The results showed that the T. preW+ parental generation temperature is positively correlated with the probability of intersex offspring. The probability of F1 intersex is significantly higher than that of F2 intersex in different high temperature. The degree of secondary masculinization in T. preW+ intersexes increases as parental generation temperature increases. In addition, our study first identified 11 intersex types in T. preW+ and found that the primary and secondary sexual characteristics showed a regular distribution. We also found that the D type and H type of intersex have the highest frequency of appearance. The external genitalia of most intersexes were female, and only three intersex types have male external genitalia. Conclusions were ultimately obtained: Wolbachia is a direct factor that causes the occurrence of intersexes, while high temperature is an indirect factor that determines the external morphology of intersexes. The effects of high temperature on T. preW+ intersexes is passed through the parental generation to offspring, and this maternal effect weakens as the number of generations increases. In T. preW+ intersex individuals, most exhibit female primary sexual characteristics, and secondary sexual chara…
bibliographic citation: Ning et al. (2019) Gradual, temperature-induced change of secondary sexual characteristics in Trichogramma pretiosum infected with parthenogenesis-inducing Wolbachia. PeerJ 7:e7567 https://doi.org/10.7717/peerj.7567
date submitted: 2019-03-28
date accepted: 2019-07-29
issued: 2019-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ning
  given name: Su-fang
author list: Agent
  family name: Zhou
  given name: Jin-cheng
author list: Agent
  family name: Liu
  given name: Quan-quan
author list: Agent
  family name: Zhao
  given name: Qian
author list: Agent
  family name: Dong
  given name: Hui
doi: 10.7717/peerj.7567
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-23
copyright: © 2019 Ning et al.
attribution name: Ning et al.

Visual search characteristics of precise map reading by orienteers
type: item
type: AcademicArticle
description: This article compares the differences in eye movements between orienteers of different skill levels on map information searches and explores the visual search patterns of orienteers during precise map reading so as to explore the cognitive characteristics of orienteers’ visual search. We recruited 44 orienteers at different skill levels (experts, advanced beginners, and novices), and recorded their behavioral responses and eye movement data when reading maps of different complexities. We found that the complexity of map (complex vs. simple) affects the quality of orienteers’ route planning during precise map reading. Specifically, when observing complex maps, orienteers of higher competency tend to have a better quality of route planning (i.e., a shorter route planning time, a longer gaze time, and a more concentrate distribution of gazes). Expert orienteers demonstrated obvious cognitive advantages in the ability to find key information. We also found that in the stage of route planning, expert orienteers and advanced beginners first pay attention to the checkpoint description table. The expert group extracted information faster, and their attention was more concentrated, whereas the novice group paid less attention to the checkpoint description table, and their gaze was scattered. We found that experts regarded the information in the checkpoint description table as the key to the problem and they give priority to this area in route decision making. These results advance our understanding of professional knowledge and problem solving in orienteering.
format: application/pdf
format: text/html
creator: Yang Liu
subject: Neuroscience
subject: Psychiatry and Psychology
subject: Statistics
description: doi:10.7717/peerj.7592
publisher: PeerJ Inc.
rights: © 2019 Liu
abstract: This article compares the differences in eye movements between orienteers of different skill levels on map information searches and explores the visual search patterns of orienteers during precise map reading so as to explore the cognitive characteristics of orienteers’ visual search. We recruited 44 orienteers at different skill levels (experts, advanced beginners, and novices), and recorded their behavioral responses and eye movement data when reading maps of different complexities. We found that the complexity of map (complex vs. simple) affects the quality of orienteers’ route planning during precise map reading. Specifically, when observing complex maps, orienteers of higher competency tend to have a better quality of route planning (i.e., a shorter route planning time, a longer gaze time, and a more concentrate distribution of gazes). Expert orienteers demonstrated obvious cognitive advantages in the ability to find key information. We also found that in the stage of route planning, expert orienteers and advanced beginners first pay attention to the checkpoint description table. The expert group extracted information faster, and their attention was more concentrated, whereas the novice group paid less attention to the checkpoint description table, and their gaze was scattered. We found that experts regarded the information in the checkpoint description table as the key to the problem and they give priority to this area in route decision making. These results advance our understanding of professional knowledge and problem solving in orienteering.
bibliographic citation: Liu (2019) Visual search characteristics of precise map reading by orienteers. PeerJ 7:e7592 https://doi.org/10.7717/peerj.7592
date submitted: 2019-02-27
date accepted: 2019-07-30
issued: 2019-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Yang
doi: 10.7717/peerj.7592
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-23
copyright: © 2019 Liu
attribution name: Liu

Revision of the Tanzanian dicynodont Dicynodon huenei (Therapsida: Anomodontia) from the Permian Usili Formation
type: item
type: AcademicArticle
description: A single species of the dicynodontoid dicynodont Dicynodon is currently recognized from the late Permian Usili Formation of Tanzania: Dicynodon huenei Haughton, 1932. Restudy of the known Tanzanian materials of D. huenei demonstrates that they represent two distinct morphotypes, here considered separate taxa. The holotype of D. huenei is not referable to Dicynodon and instead is transferred to the genus Daptocephalus (but retained as a valid species, Daptocephalus huenei comb. nov.). A number of published dicynodontoid specimens from the Usili Formation, however, are referable to Dicynodon, and are here recognized as a new species (Dicynodon angielczyki sp. nov.) Dicynodon angielczyki can be distinguished from its South African congener Dicynodon lacerticeps by the presence of an expansion of the squamosal and jugal beneath the postorbital bar and a curved, posterolateral expansion of the squamosal behind the temporal fenestra. Inclusion of Dicynodon angielczyki and D. huenei in a phylogenetic analysis supports their referral to Dicynodon and Daptocephalus (respectively). These results indicate higher basinal endemism in large late Permian dicynodonts than previously thought, a sharp contrast to the cosmopolitanism in the group in the earliest Triassic.
format: application/pdf
format: text/html
creator: Christian F. Kammerer
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.7420
publisher: PeerJ Inc.
rights: © 2019 Kammerer
abstract: A single species of the dicynodontoid dicynodont Dicynodon is currently recognized from the late Permian Usili Formation of Tanzania: Dicynodon huenei Haughton, 1932. Restudy of the known Tanzanian materials of D. huenei demonstrates that they represent two distinct morphotypes, here considered separate taxa. The holotype of D. huenei is not referable to Dicynodon and instead is transferred to the genus Daptocephalus (but retained as a valid species, Daptocephalus huenei comb. nov.). A number of published dicynodontoid specimens from the Usili Formation, however, are referable to Dicynodon, and are here recognized as a new species (Dicynodon angielczyki sp. nov.) Dicynodon angielczyki can be distinguished from its South African congener Dicynodon lacerticeps by the presence of an expansion of the squamosal and jugal beneath the postorbital bar and a curved, posterolateral expansion of the squamosal behind the temporal fenestra. Inclusion of Dicynodon angielczyki and D. huenei in a phylogenetic analysis supports their referral to Dicynodon and Daptocephalus (respectively). These results indicate higher basinal endemism in large late Permian dicynodonts than previously thought, a sharp contrast to the cosmopolitanism in the group in the earliest Triassic.
bibliographic citation: Kammerer (2019) Revision of the Tanzanian dicynodont Dicynodon huenei (Therapsida: Anomodontia) from the Permian Usili Formation. PeerJ 7:e7420 https://doi.org/10.7717/peerj.7420
date submitted: 2019-05-07
date accepted: 2019-07-05
issued: 2019-08-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kammerer
  given name: Christian F.
doi: 10.7717/peerj.7420
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-22
copyright: © 2019 Kammerer
attribution name: Kammerer

Estimating the phylogeny of geoemydid turtles (Cryptodira) from landmark data: an assessment of different methods
type: item
type: AcademicArticle
description: Background In the last 20 years, a general picture of the evolutionary relationships between geoemydid turtles (ca. 70 species distributed over the Northern hemisphere) has emerged from the analysis of molecular data. However, there is a paucity of good traditional morphological characters that correlate with the phylogeny, which are essential for the robust integration of fossil and molecular data. Part of this problem might be due to intrinsic limitations of traditional discrete characters. Here, we explore the use of continuous data in the form of 3D coordinates of homologous landmarks on the turtle shell for phylogenetic inference and the phylogenetic placement of single species on a scaffold molecular tree. We focus on the performance yielded by sampling the carapace and/or plastral lobes and using various phylogenetic methods. Methods We digitised the landmark coordinates of the carapace and plastron of 42 and 46 extant geoemydid species, respectively. The configurations were superimposed and we estimated the phylogenetic tree of geoemydids with landmark analysis under parsimony, traditional Farris parsimony, unweighted squared-change parsimony, maximum likelihood with a Brownian motion model, and neighbour-joining on a matrix of pairwise Procrustes distances. We assessed the performance of those analyses by comparing the trees against a reference phylogeny obtained from seven molecular markers. For comparisons between trees we used difference measures based on quartets and splits. We used the same reference tree to evaluate phylogenetic placement performance by a leave-one-out validation procedure. Results Whatever method we used, similarity to the reference phylogeny was low. The carapace alone gave slightly better results than the plastron or the complete shell. Assessment of the potential for placement of single species on the reference tree with landmark data gave much better results, with similar accuracy and higher precision compared to the performance …
format: application/pdf
format: text/html
creator: Eduardo Ascarrunz
creator: Julien Claude
creator: Walter G. Joyce
subject: Evolutionary Studies
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.7476
publisher: PeerJ Inc.
rights: © 2019 Ascarrunz et al.
abstract: Background In the last 20 years, a general picture of the evolutionary relationships between geoemydid turtles (ca. 70 species distributed over the Northern hemisphere) has emerged from the analysis of molecular data. However, there is a paucity of good traditional morphological characters that correlate with the phylogeny, which are essential for the robust integration of fossil and molecular data. Part of this problem might be due to intrinsic limitations of traditional discrete characters. Here, we explore the use of continuous data in the form of 3D coordinates of homologous landmarks on the turtle shell for phylogenetic inference and the phylogenetic placement of single species on a scaffold molecular tree. We focus on the performance yielded by sampling the carapace and/or plastral lobes and using various phylogenetic methods. Methods We digitised the landmark coordinates of the carapace and plastron of 42 and 46 extant geoemydid species, respectively. The configurations were superimposed and we estimated the phylogenetic tree of geoemydids with landmark analysis under parsimony, traditional Farris parsimony, unweighted squared-change parsimony, maximum likelihood with a Brownian motion model, and neighbour-joining on a matrix of pairwise Procrustes distances. We assessed the performance of those analyses by comparing the trees against a reference phylogeny obtained from seven molecular markers. For comparisons between trees we used difference measures based on quartets and splits. We used the same reference tree to evaluate phylogenetic placement performance by a leave-one-out validation procedure. Results Whatever method we used, similarity to the reference phylogeny was low. The carapace alone gave slightly better results than the plastron or the complete shell. Assessment of the potential for placement of single species on the reference tree with landmark data gave much better results, with similar accuracy and higher precision compared to the performance …
bibliographic citation: Ascarrunz et al. (2019) Estimating the phylogeny of geoemydid turtles (Cryptodira) from landmark data: an assessment of different methods. PeerJ 7:e7476 https://doi.org/10.7717/peerj.7476
date submitted: 2019-04-18
date accepted: 2019-07-15
issued: 2019-08-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ascarrunz
  given name: Eduardo
author list: Agent
  family name: Claude
  given name: Julien
author list: Agent
  family name: Joyce
  given name: Walter G.
doi: 10.7717/peerj.7476
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-22
copyright: © 2019 Ascarrunz et al.
attribution name: Ascarrunz et al.

Characterisation of bacteria isolated from the stingless bee, Heterotrigona itama, honey, bee bread and propolis
type: item
type: AcademicArticle
description: Bacteria are present in stingless bee nest products. However, detailed information on their characteristics is scarce. Thus, this study aims to investigate the characteristics of bacterial species isolated from Malaysian stingless bee, Heterotrigona itama, nest products. Honey, bee bread and propolis were collected aseptically from four geographical localities of Malaysia. Total plate count (TPC), bacterial identification, phenotypic profile and enzymatic and antibacterial activities were studied. The results indicated that the number of TPC varies from one location to another. A total of 41 different bacterial isolates from the phyla Firmicutes, Proteobacteria and Actinobacteria were identified. Bacillus species were the major bacteria found. Therein, Bacillus cereus was the most frequently isolated species followed by Bacillus aryabhattai, Bacillus oleronius, Bacillus stratosphericus, Bacillus altitudinis, Bacillus amyloliquefaciens, Bacillus nealsonii, Bacillus toyonensis, Bacillus subtilis, Bacillus safensis, Bacillus pseudomycoides, Enterobacter asburiae, Enterobacter cloacae, Pantoea dispersa and Streptomyces kunmingensis. Phenotypic profile of 15 bacterial isolates using GEN III MicroPlate™ system revealed most of the isolates as capable to utilise carbohydrates as well as amino acids and carboxylic acids and derivatives. Proteolytic, lipolytic and cellulolytic activities as determined by enzymatic assays were detected in Bacillus stratosphericus PD6, Bacillus amyloliquefaciens PD9, Bacillus subtilis BD3 and Bacillus safensis BD9. Bacillus amyloliquefaciens PD9 showed broad-spectrum of antimicrobial activity against Gram-positive and Gram-negative bacteria in vitro. The multienzymes and antimicrobial activities exhibited by the bacterial isolates from H. itama nest products could provide potential sources of enzymes and antimicrobial compounds for biotechnological applications.
format: application/pdf
format: text/html
creator: Mohamad Syazwan Ngalimat
creator: Raja Noor Zaliha Raja Abd. Rahman
creator: Mohd Termizi Yusof
creator: Amir Syahir
creator: Suriana Sabri
subject: Biotechnology
subject: Entomology
subject: Microbiology
description: doi:10.7717/peerj.7478
publisher: PeerJ Inc.
rights: © 2019 Ngalimat et al.
abstract: Bacteria are present in stingless bee nest products. However, detailed information on their characteristics is scarce. Thus, this study aims to investigate the characteristics of bacterial species isolated from Malaysian stingless bee, Heterotrigona itama, nest products. Honey, bee bread and propolis were collected aseptically from four geographical localities of Malaysia. Total plate count (TPC), bacterial identification, phenotypic profile and enzymatic and antibacterial activities were studied. The results indicated that the number of TPC varies from one location to another. A total of 41 different bacterial isolates from the phyla Firmicutes, Proteobacteria and Actinobacteria were identified. Bacillus species were the major bacteria found. Therein, Bacillus cereus was the most frequently isolated species followed by Bacillus aryabhattai, Bacillus oleronius, Bacillus stratosphericus, Bacillus altitudinis, Bacillus amyloliquefaciens, Bacillus nealsonii, Bacillus toyonensis, Bacillus subtilis, Bacillus safensis, Bacillus pseudomycoides, Enterobacter asburiae, Enterobacter cloacae, Pantoea dispersa and Streptomyces kunmingensis. Phenotypic profile of 15 bacterial isolates using GEN III MicroPlate™ system revealed most of the isolates as capable to utilise carbohydrates as well as amino acids and carboxylic acids and derivatives. Proteolytic, lipolytic and cellulolytic activities as determined by enzymatic assays were detected in Bacillus stratosphericus PD6, Bacillus amyloliquefaciens PD9, Bacillus subtilis BD3 and Bacillus safensis BD9. Bacillus amyloliquefaciens PD9 showed broad-spectrum of antimicrobial activity against Gram-positive and Gram-negative bacteria in vitro. The multienzymes and antimicrobial activities exhibited by the bacterial isolates from H. itama nest products could provide potential sources of enzymes and antimicrobial compounds for biotechnological applications.
bibliographic citation: Ngalimat et al. (2019) Characterisation of bacteria isolated from the stingless bee, Heterotrigona itama, honey, bee bread and propolis. PeerJ 7:e7478 https://doi.org/10.7717/peerj.7478
date submitted: 2018-11-23
date accepted: 2019-07-15
issued: 2019-08-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ngalimat
  given name: Mohamad Syazwan
author list: Agent
  family name: Raja Abd. Rahman
  given name: Raja Noor Zaliha
author list: Agent
  family name: Yusof
  given name: Mohd Termizi
author list: Agent
  family name: Syahir
  given name: Amir
author list: Agent
  family name: Sabri
  given name: Suriana
doi: 10.7717/peerj.7478
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-22
copyright: © 2019 Ngalimat et al.
attribution name: Ngalimat et al.

Phylogenomic analyses confirm a novel invasive North American Corbicula (Bivalvia: Cyrenidae) lineage
type: item
type: AcademicArticle
description: The genus Corbicula consists of estuarine or freshwater clams native to temperate/tropical regions of Asia, Africa, and Australia that collectively encompass both sexual species and clonal (androgenetic) lineages. The latter have become globally invasive in freshwater systems and they represent some of the most successful aquatic invasive lineages. Previous studies have documented four invasive clonal lineages, Forms A, B, C, and Rlc, with varying known distributions. Form A (R in Europe) occurs globally, Form B is found solely in North America, mainly the western United States, Form C (S in Europe) occurs both in European watersheds and in South America, and Rlc is known from Europe. A putative fifth invasive morph, Form D, was recently described in the New World from the Illinois River (Great Lakes watershed), where it occurs in sympatry with Forms A and B. An initial study showed Form D to be conchologically distinct: possessing rust-colored rays and white nacre with purple teeth. However, its genetic distinctiveness using standard molecular markers (mitochondrial cytochrome c oxidase subunit I and nuclear ribosomal 28S RNA) was ambiguous. To resolve this issue, we performed a phylogenomic analysis using 1,699–30,027 nuclear genomic loci collected via the next generation double digested restriction-site associated DNA sequencing method. Our results confirmed Form D to be a distinct invasive New World lineage with a population genomic profile consistent with clonality. A majority (7/9) of the phylogenomic analyses recovered the four New World invasive Corbicula lineages (Forms A, B, C, and D) as members of a clonal clade, sister to the non-clonal Lake Biwa (Japan) endemic, Corbicula sandai. The age of the clonal clade was estimated at 1.49 million years (my; ± 0.401–2.955 my) whereas the estimated ages of the four invasive lineage crown clades ranged from 0.27 to 0.44 my. We recovered very little evidence of nuclear genomic admixture among the four invasive lineag…
format: application/pdf
format: text/html
creator: Amanda E. Haponski
creator: Diarmaid Ó Foighil
subject: Biodiversity
subject: Conservation Biology
subject: Evolutionary Studies
description: doi:10.7717/peerj.7484
publisher: PeerJ Inc.
rights: © 2019 Haponski and Ó Foighil
abstract: The genus Corbicula consists of estuarine or freshwater clams native to temperate/tropical regions of Asia, Africa, and Australia that collectively encompass both sexual species and clonal (androgenetic) lineages. The latter have become globally invasive in freshwater systems and they represent some of the most successful aquatic invasive lineages. Previous studies have documented four invasive clonal lineages, Forms A, B, C, and Rlc, with varying known distributions. Form A (R in Europe) occurs globally, Form B is found solely in North America, mainly the western United States, Form C (S in Europe) occurs both in European watersheds and in South America, and Rlc is known from Europe. A putative fifth invasive morph, Form D, was recently described in the New World from the Illinois River (Great Lakes watershed), where it occurs in sympatry with Forms A and B. An initial study showed Form D to be conchologically distinct: possessing rust-colored rays and white nacre with purple teeth. However, its genetic distinctiveness using standard molecular markers (mitochondrial cytochrome c oxidase subunit I and nuclear ribosomal 28S RNA) was ambiguous. To resolve this issue, we performed a phylogenomic analysis using 1,699–30,027 nuclear genomic loci collected via the next generation double digested restriction-site associated DNA sequencing method. Our results confirmed Form D to be a distinct invasive New World lineage with a population genomic profile consistent with clonality. A majority (7/9) of the phylogenomic analyses recovered the four New World invasive Corbicula lineages (Forms A, B, C, and D) as members of a clonal clade, sister to the non-clonal Lake Biwa (Japan) endemic, Corbicula sandai. The age of the clonal clade was estimated at 1.49 million years (my; ± 0.401–2.955 my) whereas the estimated ages of the four invasive lineage crown clades ranged from 0.27 to 0.44 my. We recovered very little evidence of nuclear genomic admixture among the four invasive lineag…
bibliographic citation: Haponski et al. (2019) Phylogenomic analyses confirm a novel invasive North American Corbicula (Bivalvia: Cyrenidae) lineage. PeerJ 7:e7484 https://doi.org/10.7717/peerj.7484
date submitted: 2019-03-25
date accepted: 2019-07-15
issued: 2019-08-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Haponski
  given name: Amanda E.
author list: Agent
  family name: Ó Foighil
  given name: Diarmaid
doi: 10.7717/peerj.7484
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-22
copyright: © 2019 Haponski and Ó Foighil
attribution name: Haponski and Ó Foighil

Seasonal dynamics of microbial diversity in the rhizosphere of Ulmus pumila L. var. sabulosa in a steppe desert area of Northern China
type: item
type: AcademicArticle
description: The seasonal dynamics of microbial diversity within the rhizosphere of Ulmus pumila L. var. sabulosa in the hinterland of the Otindag Sandy Land of China were investigated using high-throughput sequencing of bacterial 16S rRNA genes and fungal ITS region sequences. A significant level of bacterial and fungal diversity was observed overall, with detection of 7,676 bacterial Operational Taxonomic Units (OTUs) belonging to 40 bacteria phyla and 3,582 fungal OTUs belonging to six phyla. Proteobacteria, Actinobacteria, and Firmicutes were the dominant bacterial phyla among communities, while Ascomycota, Basidiomycota, and Zygomycota were the dominant phyla of fungal communities. Seasonal changes influenced the α-diversity and β-diversity of bacterial communities within elm rhizospheres more than for fungal communities. Inferred functional analysis of the bacterial communities identified evidence for 41 level two KEGG (Kyoto Encyclopedia of Genes and Genomes) orthology groups, while guild-based analysis of the fungal communities identified eight ecological guilds. Metabolism was the most prevalent bacterial functional group, while saprotrophs prevailed among the identified fungal ecological guilds. Soil moisture and soil nutrient content were important factors that affected the microbial community structures of elm rhizospheres across seasons. The present pilot study provides an important baseline investigation of elm rhizosphere microbial communities.
format: application/pdf
format: text/html
creator: Tianyu Liang
creator: Guang Yang
creator: Yunxia Ma
creator: Qingzhi Yao
creator: Yuan Ma
creator: Hui Ma
creator: Yang Hu
creator: Ying Yang
creator: Shaoxiong Wang
creator: Yiyong Pan
creator: Gangtie Li
subject: Biodiversity
subject: Ecology
description: doi:10.7717/peerj.7526
publisher: PeerJ Inc.
rights: © 2019 Liang et al.
abstract: The seasonal dynamics of microbial diversity within the rhizosphere of Ulmus pumila L. var. sabulosa in the hinterland of the Otindag Sandy Land of China were investigated using high-throughput sequencing of bacterial 16S rRNA genes and fungal ITS region sequences. A significant level of bacterial and fungal diversity was observed overall, with detection of 7,676 bacterial Operational Taxonomic Units (OTUs) belonging to 40 bacteria phyla and 3,582 fungal OTUs belonging to six phyla. Proteobacteria, Actinobacteria, and Firmicutes were the dominant bacterial phyla among communities, while Ascomycota, Basidiomycota, and Zygomycota were the dominant phyla of fungal communities. Seasonal changes influenced the α-diversity and β-diversity of bacterial communities within elm rhizospheres more than for fungal communities. Inferred functional analysis of the bacterial communities identified evidence for 41 level two KEGG (Kyoto Encyclopedia of Genes and Genomes) orthology groups, while guild-based analysis of the fungal communities identified eight ecological guilds. Metabolism was the most prevalent bacterial functional group, while saprotrophs prevailed among the identified fungal ecological guilds. Soil moisture and soil nutrient content were important factors that affected the microbial community structures of elm rhizospheres across seasons. The present pilot study provides an important baseline investigation of elm rhizosphere microbial communities.
bibliographic citation: Liang et al. (2019) Seasonal dynamics of microbial diversity in the rhizosphere of Ulmus pumila L. var. sabulosa in a steppe desert area of Northern China. PeerJ 7:e7526 https://doi.org/10.7717/peerj.7526
date submitted: 2019-01-09
date accepted: 2019-07-21
issued: 2019-08-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liang
  given name: Tianyu
author list: Agent
  family name: Yang
  given name: Guang
author list: Agent
  family name: Ma
  given name: Yunxia
author list: Agent
  family name: Yao
  given name: Qingzhi
author list: Agent
  family name: Ma
  given name: Yuan
author list: Agent
  family name: Ma
  given name: Hui
author list: Agent
  family name: Hu
  given name: Yang
author list: Agent
  family name: Yang
  given name: Ying
author list: Agent
  family name: Wang
  given name: Shaoxiong
author list: Agent
  family name: Pan
  given name: Yiyong
author list: Agent
  family name: Li
  given name: Gangtie
doi: 10.7717/peerj.7526
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-22
copyright: ©2019 Liang et al.
attribution name: Liang et al.

Root tolerance and biochemical response of Chinese lettuce (Lactuca sativa L.) genotypes to cadmium stress
type: item
type: AcademicArticle
description: This study was conducted to determine the root tolerance and biochemical responses of four Chinese Lactuca sativa L. genotypes (Lüsu, Lümeng, Yidali and Anyan) to cadmium (Cd2+) stress. Twenty-eight days old seedlings were exposed to Hoagland’s nutrient solution supplied with or without 100 µM CdCl2 and monitored for seven days in a climate controlled room. The 100 µM CdCl2 significantly (P < 0.001) decreased all the root morphological indexes of the four genotypes. However, Yidali, which possessed the smallest root system, exhibited greater root tolerance to Cd2+ by having the highest tolerance indexes for root volume (46%), surface area (61%), projected area (74%) and numbers of root forks (63%) and root tips (58%). Moreover, Cd2+ stress also caused increases in H2O2 contents in the roots but the increase was least in Yidali which showed greater root tolerance to Cd2+stress. The effect of Cd2+ stress on the contents of hormones in the roots depended on the genotypes. Under Cd2+ stress, abscisic acid correlated positively with indole-3-acetic acid (r = 0.669*), gibberellic acid (r = 0.630*) and cytokinin (r = 0.785**). The antioxidant enzyme activities and proline responses of the four genotypes to Cd2+ stress were similar. The SOD activity was decreased whiles the CAT and POD activities, as well as the contents of proline increased in all the genotypes under the stress condition. These results suggest that lettuce genotypes with smaller root systems could be more tolerant to Cd2+ stress compared to those with larger root systems.
format: application/pdf
format: text/html
creator: Mohammed Mujitaba Dawuda
creator: Weibiao Liao
creator: Linli Hu
creator: Jihua Yu
creator: Jianming Xie
creator: Alejandro Calderón-Urrea
creator: Xin Jin
creator: Yue Wu
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
description: doi:10.7717/peerj.7530
publisher: PeerJ Inc.
rights: © 2019 Dawuda et al.
abstract: This study was conducted to determine the root tolerance and biochemical responses of four Chinese Lactuca sativa L. genotypes (Lüsu, Lümeng, Yidali and Anyan) to cadmium (Cd2+) stress. Twenty-eight days old seedlings were exposed to Hoagland’s nutrient solution supplied with or without 100 µM CdCl2 and monitored for seven days in a climate controlled room. The 100 µM CdCl2 significantly (P < 0.001) decreased all the root morphological indexes of the four genotypes. However, Yidali, which possessed the smallest root system, exhibited greater root tolerance to Cd2+ by having the highest tolerance indexes for root volume (46%), surface area (61%), projected area (74%) and numbers of root forks (63%) and root tips (58%). Moreover, Cd2+ stress also caused increases in H2O2 contents in the roots but the increase was least in Yidali which showed greater root tolerance to Cd2+stress. The effect of Cd2+ stress on the contents of hormones in the roots depended on the genotypes. Under Cd2+ stress, abscisic acid correlated positively with indole-3-acetic acid (r = 0.669*), gibberellic acid (r = 0.630*) and cytokinin (r = 0.785**). The antioxidant enzyme activities and proline responses of the four genotypes to Cd2+ stress were similar. The SOD activity was decreased whiles the CAT and POD activities, as well as the contents of proline increased in all the genotypes under the stress condition. These results suggest that lettuce genotypes with smaller root systems could be more tolerant to Cd2+ stress compared to those with larger root systems.
bibliographic citation: Dawuda et al. (2019) Root tolerance and biochemical response of Chinese lettuce (Lactuca sativa L.) genotypes to cadmium stress. PeerJ 7:e7530 https://doi.org/10.7717/peerj.7530
date submitted: 2019-04-15
date accepted: 2019-07-22
issued: 2019-08-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dawuda
  given name: Mohammed Mujitaba
author list: Agent
  family name: Liao
  given name: Weibiao
author list: Agent
  family name: Hu
  given name: Linli
author list: Agent
  family name: Yu
  given name: Jihua
author list: Agent
  family name: Xie
  given name: Jianming
author list: Agent
  family name: Calderón-Urrea
  given name: Alejandro
author list: Agent
  family name: Jin
  given name: Xin
author list: Agent
  family name: Wu
  given name: Yue
doi: 10.7717/peerj.7530
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-22
copyright: ©2019 Dawuda et al.
attribution name: Dawuda et al.

Development of a multiplex RT-PCR assay for simultaneous detection of Cucumber green mottle mosaic virus and Acidovorax citrulli in watermelon
type: item
type: AcademicArticle
description: Watermelon (Citrullus lanatus Thunb.) is considered as a popular and nutritious fruit crop worldwide. Watermelon blood flesh disease caused by Cucumber green mottle mosaic virus (CGMMV) and bacterial fruit blotch caused by Acidovorax citrulli, are two major quarantine diseases of watermelon and result in considerable losses to global watermelon production. In this study, a multiplex reverse-transcription polymerase chain reaction (RT-PCR) method was developed for simultaneous detection of CGMMV and A. citrulli in both watermelon leaves and seeds. Two pairs of specific primers were designed based on the conserved sequences of the genomic RNA of CGMMV and the internal transcribed spacer of A. citrulli, respectively. Transcriptional elongation factor-1α from watermelon was added as an internal reference gene to prevent false negatives. No cross-reactivity was detected with other viral or bacterial pathogens infecting watermelon. Moreover, the multiplex RT-PCR showed high sensitivity and could simultaneously detect CGMMV and A. citrulli as little as 102 copies of plasmid DNA. This method was successfully applied to test field-collected watermelon leaves and stored seeds of cucurbitaceous crops. These results suggested that the developed multiplex RT-PCR technique is a rapid, efficient, and sensitive method for simultaneous detection of CGMMV and A. citrulli, providing technical support for monitoring, predicting, and preventing these two quarantine diseases. To our knowledge, this is the first report on simultaneous detection of a virus and a bacterium by multiplex RT-PCR in watermelon.
format: application/pdf
format: text/html
creator: Xinyue Bi
creator: Xiaodong Li
creator: Haibo Yu
creator: Mengnan An
creator: Rui Li
creator: Zihao Xia
creator: Yuanhua Wu
subject: Agricultural Science
subject: Biotechnology
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.7539
publisher: PeerJ Inc.
rights: © 2019 Bi et al.
abstract: Watermelon (Citrullus lanatus Thunb.) is considered as a popular and nutritious fruit crop worldwide. Watermelon blood flesh disease caused by Cucumber green mottle mosaic virus (CGMMV) and bacterial fruit blotch caused by Acidovorax citrulli, are two major quarantine diseases of watermelon and result in considerable losses to global watermelon production. In this study, a multiplex reverse-transcription polymerase chain reaction (RT-PCR) method was developed for simultaneous detection of CGMMV and A. citrulli in both watermelon leaves and seeds. Two pairs of specific primers were designed based on the conserved sequences of the genomic RNA of CGMMV and the internal transcribed spacer of A. citrulli, respectively. Transcriptional elongation factor-1α from watermelon was added as an internal reference gene to prevent false negatives. No cross-reactivity was detected with other viral or bacterial pathogens infecting watermelon. Moreover, the multiplex RT-PCR showed high sensitivity and could simultaneously detect CGMMV and A. citrulli as little as 102 copies of plasmid DNA. This method was successfully applied to test field-collected watermelon leaves and stored seeds of cucurbitaceous crops. These results suggested that the developed multiplex RT-PCR technique is a rapid, efficient, and sensitive method for simultaneous detection of CGMMV and A. citrulli, providing technical support for monitoring, predicting, and preventing these two quarantine diseases. To our knowledge, this is the first report on simultaneous detection of a virus and a bacterium by multiplex RT-PCR in watermelon.
bibliographic citation: Bi et al. (2019) Development of a multiplex RT-PCR assay for simultaneous detection of Cucumber green mottle mosaic virus and Acidovorax citrulli in watermelon. PeerJ 7:e7539 https://doi.org/10.7717/peerj.7539
date submitted: 2019-03-15
date accepted: 2019-07-23
issued: 2019-08-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bi
  given name: Xinyue
author list: Agent
  family name: Li
  given name: Xiaodong
author list: Agent
  family name: Yu
  given name: Haibo
author list: Agent
  family name: An
  given name: Mengnan
author list: Agent
  family name: Li
  given name: Rui
author list: Agent
  family name: Xia
  given name: Zihao
author list: Agent
  family name: Wu
  given name: Yuanhua
doi: 10.7717/peerj.7539
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-22
copyright: © 2019 Bi et al.
attribution name: Bi et al.

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