PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A new species of Proceratophrys Miranda-Ribeiro, 1920 (Anura, Odontophrynidae) from Southern Amazonia, Brazil
items: Independent validation of downscaled climate estimates from a coastal Alaska watershed using local historical weather journals
items: Estrogen receptor alpha regulates the expression of adipogenic genes genetically and epigenetically in rat bone marrow-derived mesenchymal stem cells
items: Seagrass contribution to blue carbon in a shallow karstic coastal area of the Gulf of Mexico
items: Carbon and nitrogen metabolism under nitrogen variation affects flavonoid accumulation in the leaves of Coreopsis tinctoria
items: Acoustic individuality in the hissing calls of the male black grouse (Lyrurus tetrix)
items: The importance of molecular characters when morphological variability hinders diagnosability: systematics of the moon jellyfish genus Aurelia (Cnidaria: Scyphozoa)
items: Cbl upregulates cysH for hydrogen sulfide production in Aeromonas veronii
items: Apis andreniformis associated Actinomycetes show antimicrobial activity against black rot pathogen (Xanthomonas campestris pv. campestris)
items: Tackling the phylogenetic conundrum of Hydroidolina (Cnidaria: Medusozoa: Hydrozoa) by assessing competing tree topologies with targeted high-throughput sequencing

A new species of Proceratophrys Miranda-Ribeiro, 1920 (Anura, Odontophrynidae) from Southern Amazonia, Brazil
type: item
type: AcademicArticle
description: Based on concordant differences in morphology, male advertisement call, and 16S mtDNA barcode distance, we describe a new species of Proceratophrys from southern Amazonia, in the states of Mato Grosso and Pará, Brazil. The new species is most similar to P. concavitympanum and P. ararype but differs from these species by its proportionally larger eyes and features of the advertisement call. Additionally, genetic distance between the new species and its congeners is 3.0–10.4% based on a fragment of the 16S rRNA gene, which is greater than the threshold typically characterizing distinct species of anurans. Using an integrative approach (molecular, bioacoustics, and adult morphology), we were able to distinguish the new species from other congeneric species. The new species is known only from the type locality where it is threatened by illegal logging and gold mining as well as hydroelectric dams.
format: application/pdf
format: text/html
creator: Diego J. Santana
creator: Leandro Alves da Silva
creator: Anathielle Caroline Sant’Anna
creator: Donald B. Shepard
creator: Sarah Mângia
subject: Biodiversity
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12012
publisher: PeerJ Inc.
rights: © 2021 Santana et al.
abstract: Based on concordant differences in morphology, male advertisement call, and 16S mtDNA barcode distance, we describe a new species of Proceratophrys from southern Amazonia, in the states of Mato Grosso and Pará, Brazil. The new species is most similar to P. concavitympanum and P. ararype but differs from these species by its proportionally larger eyes and features of the advertisement call. Additionally, genetic distance between the new species and its congeners is 3.0–10.4% based on a fragment of the 16S rRNA gene, which is greater than the threshold typically characterizing distinct species of anurans. Using an integrative approach (molecular, bioacoustics, and adult morphology), we were able to distinguish the new species from other congeneric species. The new species is known only from the type locality where it is threatened by illegal logging and gold mining as well as hydroelectric dams.
bibliographic citation: Santana et al. (2021) A new species of Proceratophrys Miranda-Ribeiro, 1920 (Anura, Odontophrynidae) from Southern Amazonia, Brazil. PeerJ 9:e12012 https://doi.org/10.7717/peerj.12012
date submitted: 2021-04-09
date accepted: 2021-07-28
issued: 2021-09-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Santana
  given name: Diego J.
author list: Agent
  family name: Silva
  given name: Leandro Alves da
author list: Agent
  family name: Sant’Anna
  given name: Anathielle Caroline
author list: Agent
  family name: Shepard
  given name: Donald B.
author list: Agent
  family name: Mângia
  given name: Sarah
doi: 10.7717/peerj.12012
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-10
copyright: © 2021 Santana et al.
attribution name: Santana et al.

Independent validation of downscaled climate estimates from a coastal Alaska watershed using local historical weather journals
type: item
type: AcademicArticle
description: Downscaling coarse global and regional climate models allows researchers to access weather and climate data at finer temporal and spatial resolution, but there remains a need to compare these models with empirical data sources to assess model accuracy. Here, we validate a widely used software for generating North American downscaled climate data, ClimateNA, with a novel empirical data source, 20th century weather journals kept by Admiralty Island, Alaska homesteader, Allen Hasselborg. Using Hasselborg’s journals, we calculated monthly precipitation and monthly mean of the maximum daily air temperature across the years 1926 to 1954 and compared these to ClimateNA data generated from the Hasselborg homestead location and adjacent areas. To demonstrate the utility and potential implications of this validation for other disciplines such as hydrology, we used an established regression equation to generate time series of 95% low duration flow estimates for the month of August using mean annual precipitation from ClimateNA predictions and Hasselborg data. Across 279 months, we found strong correlation between modeled and observed measurements of monthly precipitation (ρ = 0.74) and monthly mean of the maximum daily air temperature (ρ = 0.98). Monthly precipitation residuals (calculated as ClimateNA data - Hasselborg data) generally demonstrated heteroscedasticity around zero, but a negative trend in residual values starting during the last decade of observations may have been due to a shift to the cold-phase Pacific Decadal Oscillation. Air temperature residuals demonstrated a consistent but small positive bias, with ClimateNA tending to overestimate air temperature relative to Hasselborg’s journals. The degree of correlation between weather patterns observed at the Hasselborg homestead site and ClimateNA data extracted from spatial grid cells across the region varied by wet and dry climate years. Monthly precipitation from both data sources tended to be more similar acros…
format: application/pdf
format: text/html
creator: Emily R. Williamson
creator: Christopher J. Sergeant
subject: Ecosystem Science
subject: Climate Change Biology
subject: Atmospheric Chemistry
subject: Ecohydrology
description: doi:10.7717/peerj.12055
publisher: PeerJ Inc.
rights: © 2021 Williamson and Sergeant
abstract: Downscaling coarse global and regional climate models allows researchers to access weather and climate data at finer temporal and spatial resolution, but there remains a need to compare these models with empirical data sources to assess model accuracy. Here, we validate a widely used software for generating North American downscaled climate data, ClimateNA, with a novel empirical data source, 20th century weather journals kept by Admiralty Island, Alaska homesteader, Allen Hasselborg. Using Hasselborg’s journals, we calculated monthly precipitation and monthly mean of the maximum daily air temperature across the years 1926 to 1954 and compared these to ClimateNA data generated from the Hasselborg homestead location and adjacent areas. To demonstrate the utility and potential implications of this validation for other disciplines such as hydrology, we used an established regression equation to generate time series of 95% low duration flow estimates for the month of August using mean annual precipitation from ClimateNA predictions and Hasselborg data. Across 279 months, we found strong correlation between modeled and observed measurements of monthly precipitation (ρ = 0.74) and monthly mean of the maximum daily air temperature (ρ = 0.98). Monthly precipitation residuals (calculated as ClimateNA data - Hasselborg data) generally demonstrated heteroscedasticity around zero, but a negative trend in residual values starting during the last decade of observations may have been due to a shift to the cold-phase Pacific Decadal Oscillation. Air temperature residuals demonstrated a consistent but small positive bias, with ClimateNA tending to overestimate air temperature relative to Hasselborg’s journals. The degree of correlation between weather patterns observed at the Hasselborg homestead site and ClimateNA data extracted from spatial grid cells across the region varied by wet and dry climate years. Monthly precipitation from both data sources tended to be more similar acros…
bibliographic citation: Williamson et al. (2021) Independent validation of downscaled climate estimates from a coastal Alaska watershed using local historical weather journals. PeerJ 9:e12055 https://doi.org/10.7717/peerj.12055
date submitted: 2021-04-01
date accepted: 2021-08-04
issued: 2021-09-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Williamson
  given name: Emily R.
author list: Agent
  family name: Sergeant
  given name: Christopher J.
doi: 10.7717/peerj.12055
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-10
copyright: ©2021 Williamson and Sergeant
attribution name: Williamson and Sergeant

Estrogen receptor alpha regulates the expression of adipogenic genes genetically and epigenetically in rat bone marrow-derived mesenchymal stem cells
type: item
type: AcademicArticle
description: Regulation of the efficacy of epigenetic modifiers is regarded as an important control mechanism in the determination and differentiation of stem cell fate. Studies are showing that the effect of estrogen is important in the differentiation of mesenchymal stem cells (MSCs) into adipocytes, osteocytes, and chondrocytes. Activation of certain transcription factors and epigenetic modifications in related genes play an active role in the initiation and completion of adipogenic differentiation. Understanding the role of estrogen in diseases such as obesity, which increases with the onset of menopause, will pave the way for more effective use of estrogen as a therapeutic option. Demonstration of the differentiation tendencies of MSCs change in the presence/absence of estrogen, especially the evaluation of reversible epigenetic changes, will provide valuable information for clinical applications. In this study, the effect of estrogen on the expression of genes involved in adipogenic differentiation of MSCs and accompanying epigenetic modifications was investigated. Our results showed that estrogen affects the expression of adipogenesis-related transcription factors such as PPARy, C/EBPα and Adipsin. In addition, after estrogen treatment, increased accumulation of estrogen receptor alpha (ERα) and repressive epigenetic markers such as H3K27me2 and H3K27me3 were observed on the promoter of given transcription factors. By using co-immunoprecipitation experiments we were also able to show that ERα physically interacts with the zeste homolog 2 (EZH2) H3K27 methyltransferase in MSCs. We propose that the increase of H3K27me2 and H3K27me3 markers on adipogenic genes upon estrogen treatment may be mediated by the direct interaction of ERα and EZH2. Taken together, these findings suggest that estrogen has a role as an epigenetic switcher in the regulation of H3K27 methylation leading to suppression of adipogenic differentiation of MSC.
format: application/pdf
format: text/html
creator: Ceylan V. Bitirim
creator: Zeynep B. Ozer
creator: Kamil C. Akcali
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Gynecology and Obstetrics
subject: Women’s Health
description: doi:10.7717/peerj.12071
publisher: PeerJ Inc.
rights: © 2021 Bitirim et al.
abstract: Regulation of the efficacy of epigenetic modifiers is regarded as an important control mechanism in the determination and differentiation of stem cell fate. Studies are showing that the effect of estrogen is important in the differentiation of mesenchymal stem cells (MSCs) into adipocytes, osteocytes, and chondrocytes. Activation of certain transcription factors and epigenetic modifications in related genes play an active role in the initiation and completion of adipogenic differentiation. Understanding the role of estrogen in diseases such as obesity, which increases with the onset of menopause, will pave the way for more effective use of estrogen as a therapeutic option. Demonstration of the differentiation tendencies of MSCs change in the presence/absence of estrogen, especially the evaluation of reversible epigenetic changes, will provide valuable information for clinical applications. In this study, the effect of estrogen on the expression of genes involved in adipogenic differentiation of MSCs and accompanying epigenetic modifications was investigated. Our results showed that estrogen affects the expression of adipogenesis-related transcription factors such as PPARy, C/EBPα and Adipsin. In addition, after estrogen treatment, increased accumulation of estrogen receptor alpha (ERα) and repressive epigenetic markers such as H3K27me2 and H3K27me3 were observed on the promoter of given transcription factors. By using co-immunoprecipitation experiments we were also able to show that ERα physically interacts with the zeste homolog 2 (EZH2) H3K27 methyltransferase in MSCs. We propose that the increase of H3K27me2 and H3K27me3 markers on adipogenic genes upon estrogen treatment may be mediated by the direct interaction of ERα and EZH2. Taken together, these findings suggest that estrogen has a role as an epigenetic switcher in the regulation of H3K27 methylation leading to suppression of adipogenic differentiation of MSC.
bibliographic citation: Bitirim et al. (2021) Estrogen receptor alpha regulates the expression of adipogenic genes genetically and epigenetically in rat bone marrow-derived mesenchymal stem cells. PeerJ 9:e12071 https://doi.org/10.7717/peerj.12071
date submitted: 2021-03-03
date accepted: 2021-08-05
issued: 2021-09-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bitirim
  given name: Ceylan V.
author list: Agent
  family name: Ozer
  given name: Zeynep B.
author list: Agent
  family name: Akcali
  given name: Kamil C.
doi: 10.7717/peerj.12071
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-10
copyright: © 2021 Bitirim et al.
attribution name: Bitirim et al.

Seagrass contribution to blue carbon in a shallow karstic coastal area of the Gulf of Mexico
type: item
type: AcademicArticle
description: Seagrass meadows provide multiple ecosystem services, including carbon sequestration. However, seagrass meadows are among the most threatened ecosystems worldwide. Determining the magnitude of the carbon stocks in seagrass meadows at the regional scale allows for the estimation of their global magnitude and identification of their importance in regional environmental mitigation strategies. The objective of the present study was to determine the structure of seagrass meadows in the Los Petenes Biosfera Reserve (LPBR) and evaluate their contributions to sinks of carbon in this system, located in Yucatan, which is considered the region with the largest seagrass extension in Mexico. Analyses of the seagrass meadows were executed following standardized protocols (spectral analysis, and isotope and carbon stock analyses). The LPBR stores an average of 2.2 ± 1.7 Mg C ha−1 in living biomass and 318 ± 215 Mg C ha−1 in sediment (top 1 m), and this carbon stock decreases with water depth. The seagrass community extends 149,613 ha, which represents the largest organic carbon stock (47 Tg C) documented in seagrass meadows in Mexico. Macroalgae and seagrass represent 76% of the organic carbon stored in sediment. If LPBR seagrass meadows are lost due to natural or anthropogenic impacts, 173 Tg CO2eqemissions could be released, which corresponds to the emissions generated by fossil fuel combustion of 27% of the current Mexican population. This information emphasizes the importance of seagrass meadows as a carbon sink in the region and their contribution to climate change mitigation, thus allowing for the implementation of necessary conservation strategies.
format: application/pdf
format: text/html
creator: Tania C. Cota Lucero
creator: Jorge A. Herrera-Silveira
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
subject: Climate Change Biology
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.12109
publisher: PeerJ Inc.
rights: © 2021 Cota Lucero and Herrera-Silveira
abstract: Seagrass meadows provide multiple ecosystem services, including carbon sequestration. However, seagrass meadows are among the most threatened ecosystems worldwide. Determining the magnitude of the carbon stocks in seagrass meadows at the regional scale allows for the estimation of their global magnitude and identification of their importance in regional environmental mitigation strategies. The objective of the present study was to determine the structure of seagrass meadows in the Los Petenes Biosfera Reserve (LPBR) and evaluate their contributions to sinks of carbon in this system, located in Yucatan, which is considered the region with the largest seagrass extension in Mexico. Analyses of the seagrass meadows were executed following standardized protocols (spectral analysis, and isotope and carbon stock analyses). The LPBR stores an average of 2.2 ± 1.7 Mg C ha−1 in living biomass and 318 ± 215 Mg C ha−1 in sediment (top 1 m), and this carbon stock decreases with water depth. The seagrass community extends 149,613 ha, which represents the largest organic carbon stock (47 Tg C) documented in seagrass meadows in Mexico. Macroalgae and seagrass represent 76% of the organic carbon stored in sediment. If LPBR seagrass meadows are lost due to natural or anthropogenic impacts, 173 Tg CO2eqemissions could be released, which corresponds to the emissions generated by fossil fuel combustion of 27% of the current Mexican population. This information emphasizes the importance of seagrass meadows as a carbon sink in the region and their contribution to climate change mitigation, thus allowing for the implementation of necessary conservation strategies.
bibliographic citation: Cota Lucero et al. (2021) Seagrass contribution to blue carbon in a shallow karstic coastal area of the Gulf of Mexico. PeerJ 9:e12109 https://doi.org/10.7717/peerj.12109
date submitted: 2021-01-05
date accepted: 2021-08-14
issued: 2021-09-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cota Lucero
  given name: Tania C.
author list: Agent
  family name: Herrera-Silveira
  given name: Jorge A.
doi: 10.7717/peerj.12109
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-10
copyright: ©2021 Cota Lucero and Herrera-Silveira
attribution name: Cota Lucero and Herrera-Silveira

Carbon and nitrogen metabolism under nitrogen variation affects flavonoid accumulation in the leaves of Coreopsis tinctoria
type: item
type: AcademicArticle
description: Flavonoids are phytochemicals present in medicinal plants and contribute to human health. Coreopsis tinctoria, a species rich in flavonoids, has long been used in traditional medicine and as a food resource. N (nitrogen) fertilization can reduce flavonoid accumulation in C. tinctoria. However, there is limited knowledge regarding N regulatory mechanisms. The aim of this study was to determine the effect of N availability on flavonoid biosynthesis in C. tinctoria and to investigate the relationship between C (carbon) and N metabolism coupled with flavonoid synthesis under controlled conditions. C. tinctoria seedlings were grown hydroponically under five different N levels (0, 0.625, 1.250, 2.500 and 5.000 mM). The related indexes of C, N and flavonoid metabolism of C. tinctoria under N variation were measured and analysed. N availability (low and moderate N levels) regulates enzyme activities related to C and N metabolism, promotes the accumulation of carbohydrates, reduces N metabolite levels, and enhances the internal C/N balance. The flavonoid content in roots and stalks remained relatively stable, while that in leaves peaked at low or intermediate N levels. Flavonoids are closely related to phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), 4-coumarate: coenzyme A ligase (4CL), and chalcone-thioase (CHS) activity, significantly positively correlated with carbohydrates and negatively correlated with N metabolites. Thus, C and N metabolism can not only control the distribution of C in amino acid and carbohydrate biosynthesis pathways but also change the distribution in flavonoid biosynthesis pathways, which also provides meaningful information for maintaining high yields while ensuring the nutritional value of crop plants.
format: application/pdf
format: text/html
creator: Zhiyuan Li
creator: Hong Jiang
creator: Huizhuan Yan
creator: Xiumei Jiang
creator: Yan Ma
creator: Yong Qin
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
description: doi:10.7717/peerj.12152
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Flavonoids are phytochemicals present in medicinal plants and contribute to human health. Coreopsis tinctoria, a species rich in flavonoids, has long been used in traditional medicine and as a food resource. N (nitrogen) fertilization can reduce flavonoid accumulation in C. tinctoria. However, there is limited knowledge regarding N regulatory mechanisms. The aim of this study was to determine the effect of N availability on flavonoid biosynthesis in C. tinctoria and to investigate the relationship between C (carbon) and N metabolism coupled with flavonoid synthesis under controlled conditions. C. tinctoria seedlings were grown hydroponically under five different N levels (0, 0.625, 1.250, 2.500 and 5.000 mM). The related indexes of C, N and flavonoid metabolism of C. tinctoria under N variation were measured and analysed. N availability (low and moderate N levels) regulates enzyme activities related to C and N metabolism, promotes the accumulation of carbohydrates, reduces N metabolite levels, and enhances the internal C/N balance. The flavonoid content in roots and stalks remained relatively stable, while that in leaves peaked at low or intermediate N levels. Flavonoids are closely related to phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), 4-coumarate: coenzyme A ligase (4CL), and chalcone-thioase (CHS) activity, significantly positively correlated with carbohydrates and negatively correlated with N metabolites. Thus, C and N metabolism can not only control the distribution of C in amino acid and carbohydrate biosynthesis pathways but also change the distribution in flavonoid biosynthesis pathways, which also provides meaningful information for maintaining high yields while ensuring the nutritional value of crop plants.
bibliographic citation: Li et al. (2021) Carbon and nitrogen metabolism under nitrogen variation affects flavonoid accumulation in the leaves of Coreopsis tinctoria. PeerJ 9:e12152 https://doi.org/10.7717/peerj.12152
date submitted: 2021-05-11
date accepted: 2021-08-22
issued: 2021-09-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Zhiyuan
author list: Agent
  family name: Jiang
  given name: Hong
author list: Agent
  family name: Yan
  given name: Huizhuan
author list: Agent
  family name: Jiang
  given name: Xiumei
author list: Agent
  family name: Ma
  given name: Yan
author list: Agent
  family name: Qin
  given name: Yong
doi: 10.7717/peerj.12152
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-10
copyright: © 2021 Li et al.
attribution name: Li et al.

Acoustic individuality in the hissing calls of the male black grouse (Lyrurus tetrix)
type: item
type: AcademicArticle
description: Acoustic individuality may well play a big role during the mating season of many birds. Black grouse (Lyrurus tetrix) produces two different long-distance calls during mating on leks: rookooing and hissing calls. The first one represents low frequency series of bubbling sounds and the second one represents hissing sound. This hissing represents a signal not produced by the syrinx. We analyzed 426 hissing calls from 24 individuals in Finland and Scotland. We conducted cross-validated discrimination analyses (DFA). The discrimination model classified each call with almost 78% accuracy (conventional result) and the validated DFA revealed 71% output, that is much higher than classification by chance (4%). The most important variables were Frequency 95%, 1st Quartile Frequency, Aggregate Entropy and Duration 90%. We also tested whether between individual variation is higher than within individual variation using PIC (Potential for individual coding) and we found that all acoustic parameters had PIC > 1. We confirmed that hissing call of black grouse is individually distinct. In comparison to the signals produced by the syrinx, non-vocal sounds have been studied rarely and according to our knowledge, this is the second evidence of vocal individuality in avian hissing sounds which are not produced by syrinx. Individuality in the vocalization of the male black grouse may aid females in mating partner selection, and for males it may enable competitor recognition and assessment. Individually distinct hissing calls could be of possible use to monitor individuals on leks. Such a method could overcome problems during traditional monitoring methods of this species, when one individual can be counted multiple times, because catching and traditional marking is problematic in this species.
format: application/pdf
format: text/html
creator: Lucie Hambálková
creator: Richard Policht
creator: Jiří Horák
creator: Vlastimil Hart
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.11837
publisher: PeerJ Inc.
rights: © 2021 Hambálková et al.
abstract: Acoustic individuality may well play a big role during the mating season of many birds. Black grouse (Lyrurus tetrix) produces two different long-distance calls during mating on leks: rookooing and hissing calls. The first one represents low frequency series of bubbling sounds and the second one represents hissing sound. This hissing represents a signal not produced by the syrinx. We analyzed 426 hissing calls from 24 individuals in Finland and Scotland. We conducted cross-validated discrimination analyses (DFA). The discrimination model classified each call with almost 78% accuracy (conventional result) and the validated DFA revealed 71% output, that is much higher than classification by chance (4%). The most important variables were Frequency 95%, 1st Quartile Frequency, Aggregate Entropy and Duration 90%. We also tested whether between individual variation is higher than within individual variation using PIC (Potential for individual coding) and we found that all acoustic parameters had PIC > 1. We confirmed that hissing call of black grouse is individually distinct. In comparison to the signals produced by the syrinx, non-vocal sounds have been studied rarely and according to our knowledge, this is the second evidence of vocal individuality in avian hissing sounds which are not produced by syrinx. Individuality in the vocalization of the male black grouse may aid females in mating partner selection, and for males it may enable competitor recognition and assessment. Individually distinct hissing calls could be of possible use to monitor individuals on leks. Such a method could overcome problems during traditional monitoring methods of this species, when one individual can be counted multiple times, because catching and traditional marking is problematic in this species.
bibliographic citation: Hambálková et al. (2021) Acoustic individuality in the hissing calls of the male black grouse (Lyrurus tetrix). PeerJ 9:e11837 https://doi.org/10.7717/peerj.11837
date submitted: 2020-10-08
date accepted: 2021-07-01
issued: 2021-09-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hambálková
  given name: Lucie
author list: Agent
  family name: Policht
  given name: Richard
author list: Agent
  family name: Horák
  given name: Jiří
author list: Agent
  family name: Hart
  given name: Vlastimil
doi: 10.7717/peerj.11837
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-09
copyright: © 2021 Hambálková et al.
attribution name: Hambálková et al.

The importance of molecular characters when morphological variability hinders diagnosability: systematics of the moon jellyfish genus Aurelia (Cnidaria: Scyphozoa)
type: item
type: AcademicArticle
description: Cryptic species have been detected across Metazoa, and while no apparent morphological features distinguish them, it should not impede taxonomists from formal descriptions. We accepted this challenge for the jellyfish genus Aurelia, which has a long and confusing taxonomic history. We demonstrate that morphological variability in Aurelia medusae overlaps across very distant geographic localities. Even though some morphological features seem responsible for most of the variation, regional geographic patterns of dissimilarities are lacking. This is further emphasized by morphological differences found when comparing lab-cultured Aurelia coerulea medusae with the diagnostic features in its recent redescription. Previous studies have also highlighted the difficulties in distinguishing Aurelia polyps and ephyrae, and their morphological plasticity. Therefore, mostly based on genetic data, we recognize 28 species of Aurelia, of which seven were already described, 10 are formally described herein, four are resurrected and seven remain undescribed. We present diagnostic genetic characters for all species and designate type materials for newly described and some resurrected species. Recognizing moon jellyfish diversity with formal names is vital for conservation efforts and other studies. This work clarifies the practical implications of molecular genetic data as diagnostic characters, and sheds light on the patterns and processes that generate crypsis.
format: application/pdf
format: text/html
creator: Jonathan W. Lawley
creator: Edgar Gamero-Mora
creator: Maximiliano M. Maronna
creator: Luciano M. Chiaverano
creator: Sérgio N. Stampar
creator: Russell R. Hopcroft
creator: Allen G. Collins
creator: André C. Morandini
subject: Biodiversity
subject: Marine Biology
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.11954
publisher: PeerJ Inc.
rights: © 2021 Lawley et al.
abstract: Cryptic species have been detected across Metazoa, and while no apparent morphological features distinguish them, it should not impede taxonomists from formal descriptions. We accepted this challenge for the jellyfish genus Aurelia, which has a long and confusing taxonomic history. We demonstrate that morphological variability in Aurelia medusae overlaps across very distant geographic localities. Even though some morphological features seem responsible for most of the variation, regional geographic patterns of dissimilarities are lacking. This is further emphasized by morphological differences found when comparing lab-cultured Aurelia coerulea medusae with the diagnostic features in its recent redescription. Previous studies have also highlighted the difficulties in distinguishing Aurelia polyps and ephyrae, and their morphological plasticity. Therefore, mostly based on genetic data, we recognize 28 species of Aurelia, of which seven were already described, 10 are formally described herein, four are resurrected and seven remain undescribed. We present diagnostic genetic characters for all species and designate type materials for newly described and some resurrected species. Recognizing moon jellyfish diversity with formal names is vital for conservation efforts and other studies. This work clarifies the practical implications of molecular genetic data as diagnostic characters, and sheds light on the patterns and processes that generate crypsis.
bibliographic citation: Lawley et al. (2021) The importance of molecular characters when morphological variability hinders diagnosability: systematics of the moon jellyfish genus Aurelia (Cnidaria: Scyphozoa). PeerJ 9:e11954 https://doi.org/10.7717/peerj.11954
date submitted: 2021-05-03
date accepted: 2021-07-21
issued: 2021-09-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lawley
  given name: Jonathan W.
author list: Agent
  family name: Gamero-Mora
  given name: Edgar
author list: Agent
  family name: Maronna
  given name: Maximiliano M.
author list: Agent
  family name: Chiaverano
  given name: Luciano M.
author list: Agent
  family name: Stampar
  given name: Sérgio N.
author list: Agent
  family name: Hopcroft
  given name: Russell R.
author list: Agent
  family name: Collins
  given name: Allen G.
author list: Agent
  family name: Morandini
  given name: André C.
doi: 10.7717/peerj.11954
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-09
copyright: © 2021 Lawley et al.
attribution name: Lawley et al.

Cbl upregulates cysH for hydrogen sulfide production in Aeromonas veronii
type: item
type: AcademicArticle
description: Endogenous hydrogen sulfide (H2S) is generated in many metabolism pathways, and has been recognized as a second messenger against antibiotics and reactive oxygen species (ROS). In Aeromonas veronii, Small Protein B (SmpB) plays an important role in resisting stress. The absence of smpB could trigger sulfate assimilation pathway to adapt the nutrient deficiency, of which was mediated by up-regulation of cbl and cys genes and followed with enhancing H2S production. To figure out the mutual regulations of cbl and cys genes, a series of experiments were performed. Compared with the wild type, cysH was down-regulated significantly in cbl deletion by qRT-PCR. The fluorescence analysis further manifested that Cbl had a positive regulatory effect on the promoter of cysJIH. Bacterial one-hybrid analysis and electrophoretic mobility shift assay (EMSA) verified that Cbl bound with the promoter of cysJIH. Collectively, the tolerance to adversity could be maintained by the production of H2S when SmpB was malfunctioned, of which the activity of cysJIH promoter was positively regulated by upstream Cbl protein. The outcomes also suggested the enormous potentials of Aeromonas veronii in environmental adaptability.
format: application/pdf
format: text/html
creator: Yidong Zhang
creator: Zebin Liu
creator: Yanqiong Tang
creator: Xiang Ma
creator: Hongqian Tang
creator: Hong Li
creator: Zhu Liu
subject: Biochemistry
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.12058
publisher: PeerJ Inc.
rights: © 2021 Zhang et al.
abstract: Endogenous hydrogen sulfide (H2S) is generated in many metabolism pathways, and has been recognized as a second messenger against antibiotics and reactive oxygen species (ROS). In Aeromonas veronii, Small Protein B (SmpB) plays an important role in resisting stress. The absence of smpB could trigger sulfate assimilation pathway to adapt the nutrient deficiency, of which was mediated by up-regulation of cbl and cys genes and followed with enhancing H2S production. To figure out the mutual regulations of cbl and cys genes, a series of experiments were performed. Compared with the wild type, cysH was down-regulated significantly in cbl deletion by qRT-PCR. The fluorescence analysis further manifested that Cbl had a positive regulatory effect on the promoter of cysJIH. Bacterial one-hybrid analysis and electrophoretic mobility shift assay (EMSA) verified that Cbl bound with the promoter of cysJIH. Collectively, the tolerance to adversity could be maintained by the production of H2S when SmpB was malfunctioned, of which the activity of cysJIH promoter was positively regulated by upstream Cbl protein. The outcomes also suggested the enormous potentials of Aeromonas veronii in environmental adaptability.
bibliographic citation: Zhang et al. (2021) Cbl upregulates cysH for hydrogen sulfide production in Aeromonas veronii. PeerJ 9:e12058 https://doi.org/10.7717/peerj.12058
date submitted: 2021-03-30
date accepted: 2021-08-04
issued: 2021-09-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yidong
author list: Agent
  family name: Liu
  given name: Zebin
author list: Agent
  family name: Tang
  given name: Yanqiong
author list: Agent
  family name: Ma
  given name: Xiang
author list: Agent
  family name: Tang
  given name: Hongqian
author list: Agent
  family name: Li
  given name: Hong
author list: Agent
  family name: Liu
  given name: Zhu
doi: 10.7717/peerj.12058
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-09
copyright: © 2021 Zhang et al.
attribution name: Zhang et al.

Apis andreniformis associated Actinomycetes show antimicrobial activity against black rot pathogen (Xanthomonas campestris pv. campestris)
type: item
type: AcademicArticle
description: This study aimed to investigate cultivable actinomycetes associated with rare honey bee species in Thailand and their antagonistic activity against plant pathogenic bacteria. Actinomycetes were selectively isolated from the black dwarf honey bee (Apis andreniformis). A total of 64 actinomycete isolates were obtained with Streptomyces as the predominant genus (84.4%) followed by Micromonospora (7.8%), Nonomuraea (4.7%) and Actinomadura (3.1%). All isolates were screened for antimicrobial activity against Xanthomonas campestris pv. campestris, Pectobacterium carotovorum and Pseudomonas syringae pv. sesame. Three isolates inhibited the growth of X. campestris pv. campestris during in vitro screening. The crude extracts of two isolates (ASC3-2 and ASC5-7P) had a minimum inhibitory concentration (MIC) of 128 mg L−1against X. campestris pv. campestris. For isolate ACZ2-27, its crude extract showed stronger inhibitory effect with a lower MIC value of 64 mg L−1 against X. campestris pv. campestris. These three active isolates were identified as members of the genus Streptomyces based on their 16S rRNA gene sequences. Phylogenetic analysis based on the maximum likelihood algorithm showed that isolate ACZ2-27, ASC3-2 and ASC5-7P were closely related to Streptomyces misionensis NBRC 13063T (99.71%), Streptomyces cacaoi subsp. cacaoi NBRC 12748T (100%) and Streptomyces puniceus NBRC 12811T (100%), respectively. In addition, representative isolates from non-Streptomyces groups were identified by 16S rRNA gene sequence analysis. High similarities were found with members of the genera Actinomadura, Micromonospora and Nonomuraea. Our study provides evidence of actinomycetes associated with the black dwarf honey bee including members of rare genera. Antimicrobial potential of these insect associated Streptomyces was also demonstrated especially the antibacterial activity against phytopathogenic bacteria.
format: application/pdf
format: text/html
creator: Yaowanoot Promnuan
creator: Saran Promsai
creator: Wasu Pathom-aree
creator: Sujinan Meelai
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.12097
publisher: PeerJ Inc.
rights: © 2021 Promnuan et al.
abstract: This study aimed to investigate cultivable actinomycetes associated with rare honey bee species in Thailand and their antagonistic activity against plant pathogenic bacteria. Actinomycetes were selectively isolated from the black dwarf honey bee (Apis andreniformis). A total of 64 actinomycete isolates were obtained with Streptomyces as the predominant genus (84.4%) followed by Micromonospora (7.8%), Nonomuraea (4.7%) and Actinomadura (3.1%). All isolates were screened for antimicrobial activity against Xanthomonas campestris pv. campestris, Pectobacterium carotovorum and Pseudomonas syringae pv. sesame. Three isolates inhibited the growth of X. campestris pv. campestris during in vitro screening. The crude extracts of two isolates (ASC3-2 and ASC5-7P) had a minimum inhibitory concentration (MIC) of 128 mg L−1against X. campestris pv. campestris. For isolate ACZ2-27, its crude extract showed stronger inhibitory effect with a lower MIC value of 64 mg L−1 against X. campestris pv. campestris. These three active isolates were identified as members of the genus Streptomyces based on their 16S rRNA gene sequences. Phylogenetic analysis based on the maximum likelihood algorithm showed that isolate ACZ2-27, ASC3-2 and ASC5-7P were closely related to Streptomyces misionensis NBRC 13063T (99.71%), Streptomyces cacaoi subsp. cacaoi NBRC 12748T (100%) and Streptomyces puniceus NBRC 12811T (100%), respectively. In addition, representative isolates from non-Streptomyces groups were identified by 16S rRNA gene sequence analysis. High similarities were found with members of the genera Actinomadura, Micromonospora and Nonomuraea. Our study provides evidence of actinomycetes associated with the black dwarf honey bee including members of rare genera. Antimicrobial potential of these insect associated Streptomyces was also demonstrated especially the antibacterial activity against phytopathogenic bacteria.
bibliographic citation: Promnuan et al. (2021) Apis andreniformis associated Actinomycetes show antimicrobial activity against black rot pathogen (Xanthomonas campestris pv. campestris). PeerJ 9:e12097 https://doi.org/10.7717/peerj.12097
date submitted: 2021-03-02
date accepted: 2021-08-10
issued: 2021-09-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Promnuan
  given name: Yaowanoot
author list: Agent
  family name: Promsai
  given name: Saran
author list: Agent
  family name: Pathom-aree
  given name: Wasu
author list: Agent
  family name: Meelai
  given name: Sujinan
doi: 10.7717/peerj.12097
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-09
copyright: ©2021 Promnuan et al.
attribution name: Promnuan et al.

Tackling the phylogenetic conundrum of Hydroidolina (Cnidaria: Medusozoa: Hydrozoa) by assessing competing tree topologies with targeted high-throughput sequencing
type: item
type: AcademicArticle
description: Higher-level relationships of the Hydrozoan subclass Hydroidolina, which encompasses the vast majority of medusozoan cnidarian species diversity, have been elusive to confidently infer. The most widely adopted phylogenetic framework for Hydroidolina based on ribosomal RNA data received low support for several higher level relationships. To address this issue, we developed a set of RNA baits to target more than a hundred loci from the genomes of a broad taxonomic sample of Hydroidolina for high-throughput sequencing. Using these data, we inferred the relationships of Hydroidolina using maximum likelihood and Bayesian approaches. Both inference methods yielded well-supported phylogenetic hypotheses that largely agree with each other. Using maximum likelihood and Baysian hypothesis testing frameworks, we found that several alternate topological hypotheses proposed previously may be rejected in light of the genomic data generated for this study. Both the maximum likelihood and Bayesian topologies inferred herein consistently score well across testing frameworks, suggesting that their consensus represents the most likely phylogenetic hypothesis of Hydroidolina. This phylogenetic framework places Aplanulata as sister lineage to the remainder of Hydroidolina. This is a strong deviation from previous phylogenetic analyses that placed Capitata or Siphonophorae as sister group to the remainder of Hydroidolina. Considering that Aplanulata represents a lineage comprised of species that for the most part possess a life cycle involving a solitary polyp and free-swimming medusa stage, the phylogenetic hypotheses presented herein have potentially large implications for clarifying the evolution of life cycles, coloniality, and the division of labor in Hydrozoa as taxon sampling for phylogenetic analyses becomes more complete.
format: application/pdf
format: text/html
creator: Bastian Bentlage
creator: Allen G. Collins
subject: Evolutionary Studies
subject: Marine Biology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.12104
publisher: PeerJ Inc.
rights: © 2021 ©2021 Bentlage and Collins
abstract: Higher-level relationships of the Hydrozoan subclass Hydroidolina, which encompasses the vast majority of medusozoan cnidarian species diversity, have been elusive to confidently infer. The most widely adopted phylogenetic framework for Hydroidolina based on ribosomal RNA data received low support for several higher level relationships. To address this issue, we developed a set of RNA baits to target more than a hundred loci from the genomes of a broad taxonomic sample of Hydroidolina for high-throughput sequencing. Using these data, we inferred the relationships of Hydroidolina using maximum likelihood and Bayesian approaches. Both inference methods yielded well-supported phylogenetic hypotheses that largely agree with each other. Using maximum likelihood and Baysian hypothesis testing frameworks, we found that several alternate topological hypotheses proposed previously may be rejected in light of the genomic data generated for this study. Both the maximum likelihood and Bayesian topologies inferred herein consistently score well across testing frameworks, suggesting that their consensus represents the most likely phylogenetic hypothesis of Hydroidolina. This phylogenetic framework places Aplanulata as sister lineage to the remainder of Hydroidolina. This is a strong deviation from previous phylogenetic analyses that placed Capitata or Siphonophorae as sister group to the remainder of Hydroidolina. Considering that Aplanulata represents a lineage comprised of species that for the most part possess a life cycle involving a solitary polyp and free-swimming medusa stage, the phylogenetic hypotheses presented herein have potentially large implications for clarifying the evolution of life cycles, coloniality, and the division of labor in Hydrozoa as taxon sampling for phylogenetic analyses becomes more complete.
bibliographic citation: Bentlage et al. (2021) Tackling the phylogenetic conundrum of Hydroidolina (Cnidaria: Medusozoa: Hydrozoa) by assessing competing tree topologies with targeted high-throughput sequencing. PeerJ 9:e12104 https://doi.org/10.7717/peerj.12104
date submitted: 2020-12-03
date accepted: 2021-08-11
issued: 2021-09-09
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Bentlage
  given name: Bastian
author list: Agent
  family name: Collins
  given name: Allen G.
doi: 10.7717/peerj.12104
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-09
copyright: ©2021 Bentlage and Collins
attribution name: ©2021 Bentlage and Collins

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