PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Bosminopsis deitersi (Crustacea: Cladocera) as an ancient species group: a revision
items: Bloom evenness modulates the influence of bloom abundance on insect community structure in suburban gardens
items: Evolutionary genomics of endangered Hawaiian tree snails (Achatinellidae: Achatinellinae) for conservation of adaptive capacity
items: The biosonar of the boto: evidence of differences among species of river dolphins (Inia spp.) from the Amazon
items: Commercial arbuscular mycorrhizal fungal inoculant failed to establish in a vineyard despite priority advantage
items: Transcriptome analysis of the liver of Eospalax fontanierii under hypoxia
items: Soil microbial diversity in organic and non-organic pasture systems
items: The rise in climate change-induced federal fishery disasters in the United States
items: The antimicrobial activity of silver acetate against Acinetobacter baumannii in a Galleria mellonella infection model
items: https://peerj.com/articles/11283

Bosminopsis deitersi (Crustacea: Cladocera) as an ancient species group: a revision
type: item
type: AcademicArticle
description: Water fleas (Crustacea: Cladocera) of the Family Bosminidae have been studied since the founding of paleolimnology and freshwater ecology. However, one species, Bosminopsis deitersi, stands out for its exceptional multicontinental range and broad ecological requirements. Here we use an integrated morphological and multilocus genetic approach to address the species problem in B. deitersi. We analyzed 32 populations of B. deitersi s. lat. Two nuclear and two mitochondrial loci were used to carry out the bGMYC, mPTP and STACEY algorithms for species delimitation. Detailed morphological study was also carried out across continents. The evidence indicated a widely distributed cryptic species in the Old World (Bosminopsis zernowi) that is genetically divergent from B. deitersi s.str. We revised the taxonomy and redescribed the species in this complex. Our sampling indicated that B. zernowi had weak genetic differentiation across its range. A molecular clock and biogeographic analysis with fossil calibrations suggested a Mesozoic origin for the Bosminopsis deitersi group. Our evidence rejects the single species hypothesis for B. deitersi and is consistent with an ancient species group (potentially Mesozoic) that shows marked morphological conservation. The family Bosminidae, then, has examples of both rapid morphological evolution (Holocene Bosmina), and morphological stasis (Bosminopsis).
format: application/pdf
format: text/html
creator: Petr G. Garibian
creator: Dmitry P. Karabanov
creator: Anna N. Neretina
creator: Derek J. Taylor
creator: Alexey A. Kotov
subject: Biodiversity
subject: Biogeography
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.11310
publisher: PeerJ Inc.
rights: © 2021 Garibian et al.
abstract: Water fleas (Crustacea: Cladocera) of the Family Bosminidae have been studied since the founding of paleolimnology and freshwater ecology. However, one species, Bosminopsis deitersi, stands out for its exceptional multicontinental range and broad ecological requirements. Here we use an integrated morphological and multilocus genetic approach to address the species problem in B. deitersi. We analyzed 32 populations of B. deitersi s. lat. Two nuclear and two mitochondrial loci were used to carry out the bGMYC, mPTP and STACEY algorithms for species delimitation. Detailed morphological study was also carried out across continents. The evidence indicated a widely distributed cryptic species in the Old World (Bosminopsis zernowi) that is genetically divergent from B. deitersi s.str. We revised the taxonomy and redescribed the species in this complex. Our sampling indicated that B. zernowi had weak genetic differentiation across its range. A molecular clock and biogeographic analysis with fossil calibrations suggested a Mesozoic origin for the Bosminopsis deitersi group. Our evidence rejects the single species hypothesis for B. deitersi and is consistent with an ancient species group (potentially Mesozoic) that shows marked morphological conservation. The family Bosminidae, then, has examples of both rapid morphological evolution (Holocene Bosmina), and morphological stasis (Bosminopsis).
bibliographic citation: Garibian et al. (2021) Bosminopsis deitersi (Crustacea: Cladocera) as an ancient species group: a revision. PeerJ 9:e11310 https://doi.org/10.7717/peerj.11310
date submitted: 2021-01-21
date accepted: 2021-03-29
issued: 2021-04-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Garibian
  given name: Petr G.
author list: Agent
  family name: Karabanov
  given name: Dmitry P.
author list: Agent
  family name: Neretina
  given name: Anna N.
author list: Agent
  family name: Taylor
  given name: Derek J.
author list: Agent
  family name: Kotov
  given name: Alexey A.
doi: 10.7717/peerj.11310
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-23
copyright: © 2021 Garibian et al.
attribution name: Garibian et al.

Bloom evenness modulates the influence of bloom abundance on insect community structure in suburban gardens
type: item
type: AcademicArticle
description: As land use change drives global insect declines, the value of enhancing habitat in urban and suburban landscapes has become increasingly important for flower-visiting insects. In order to help identify best landscaping practices, we conducted plant surveys and insect bowl-trap surveys in 34 suburban yards for 21 months in Gainesville, FL, USA, which resulted in 274 paired days of plant and insect survey data. We assessed the impact of nearest greenspace size, distance to greenspace, yard area, plant richness, plant type, bloom abundance, bloom richness and bloom evenness on insect abundance and richness. Our samples include 34,972 insects captured, 485,827 blooms counted and 774 species of plants recorded. We found that bloom evenness had a modulating effect on bloom abundance—a more even sample of the same number of blooms would have a disproportionately greater positive impact on flower visitor richness, insect richness and insect abundance. Bloom abundance was also highly significant and positively associated with flower visitor abundance, but nearest greenspace size, distance to greenspace, plant type (native vs. non-native vs. Florida Friendly), and yard area were not found to be important factors. Plant richness was a highly significant factor, but its effect size was very small.
format: application/pdf
format: text/html
creator: Elizabeth Y. Braatz
creator: Zachariah J. Gezon
creator: Kristin Rossetti
creator: Lily T. Maynard
creator: Jonathan S. Bremer
creator: Geena M. Hill
creator: Marissa A. Streifel
creator: Jaret C. Daniels
subject: Conservation Biology
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.11132
publisher: PeerJ Inc.
rights: © 2021 Braatz et al.
abstract: As land use change drives global insect declines, the value of enhancing habitat in urban and suburban landscapes has become increasingly important for flower-visiting insects. In order to help identify best landscaping practices, we conducted plant surveys and insect bowl-trap surveys in 34 suburban yards for 21 months in Gainesville, FL, USA, which resulted in 274 paired days of plant and insect survey data. We assessed the impact of nearest greenspace size, distance to greenspace, yard area, plant richness, plant type, bloom abundance, bloom richness and bloom evenness on insect abundance and richness. Our samples include 34,972 insects captured, 485,827 blooms counted and 774 species of plants recorded. We found that bloom evenness had a modulating effect on bloom abundance—a more even sample of the same number of blooms would have a disproportionately greater positive impact on flower visitor richness, insect richness and insect abundance. Bloom abundance was also highly significant and positively associated with flower visitor abundance, but nearest greenspace size, distance to greenspace, plant type (native vs. non-native vs. Florida Friendly), and yard area were not found to be important factors. Plant richness was a highly significant factor, but its effect size was very small.
bibliographic citation: Braatz et al. (2021) Bloom evenness modulates the influence of bloom abundance on insect community structure in suburban gardens. PeerJ 9:e11132 https://doi.org/10.7717/peerj.11132
date submitted: 2020-08-24
date accepted: 2021-03-01
issued: 2021-04-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Braatz
  given name: Elizabeth Y.
author list: Agent
  family name: Gezon
  given name: Zachariah J.
author list: Agent
  family name: Rossetti
  given name: Kristin
author list: Agent
  family name: Maynard
  given name: Lily T.
author list: Agent
  family name: Bremer
  given name: Jonathan S.
author list: Agent
  family name: Hill
  given name: Geena M.
author list: Agent
  family name: Streifel
  given name: Marissa A.
author list: Agent
  family name: Daniels
  given name: Jaret C.
doi: 10.7717/peerj.11132
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-22
copyright: © 2021 Braatz et al.
attribution name: Braatz et al.

Evolutionary genomics of endangered Hawaiian tree snails (Achatinellidae: Achatinellinae) for conservation of adaptive capacity
type: item
type: AcademicArticle
description: Phylogenomic studies can provide insights into speciation, adaptation, and extinction, while providing a roadmap for conservation. Hawaiian tree snails are a model system for an adaptive radiation facing an extinction crisis. In the last 5 years, nearly all populations of Hawaiian tree snails across the 30 remaining species in the subfamily Achatinellinae (Achatinellidae) have declined from hundreds or thousands in the wild down to undetectable levels. Nearly 100 species historically occurred across dramatic environmental gradients on five of the Hawaiian Islands, but habitat loss, overcollection, and predation by invasive species have decimated populations. As such, this system offers the opportunity to integrate efforts to conserve evolutionary potential into conservation planning for a rapidly declining subfamily. Here, we used genome-wide, restriction-site associated DNA sequencing (RADseq), along with mitochondrial genome reconstruction, to resolve evolutionary relationships to inform conservation efforts. Phylogenetic analysis of nearly 400k genome-wide SNPs from 59 populations and 25 species across six genera in the family Achatinellidae, was generally concordant with taxonomy, geography, and mtDNA with several notable exceptions; mtDNA was unable to resolve some deeper nodes (e.g., the monophyly of Achatinella), while SNP data did not resolve as many shallow nodes. Both phylogenetic and coalescent analysis revealed deep divergences between populations within Achatinella mustelina that were consistent with species-level differences. Given cryptic species-level divergence within populations that are geographically proximate, they are at higher risk of extirpation from invasive predators and climate change than previously assumed. This study clarifies evolutionary relationships within this model system for adaptive radiation, forming the basis for conservation strategies such as translocation, captive rearing, and hybridization trials to prevent the loss of cap…
format: application/pdf
format: text/html
creator: Melissa R. Price
creator: Michael G. Hadfield
creator: Ingrid S.S. Knapp
creator: Robert J. Toonen
creator: Zac H. Forsman
subject: Biodiversity
subject: Conservation Biology
subject: Evolutionary Studies
subject: Genomics
subject: Natural Resource Management
description: doi:10.7717/peerj.10993
publisher: PeerJ Inc.
rights: © 2021 Price et al.
abstract: Phylogenomic studies can provide insights into speciation, adaptation, and extinction, while providing a roadmap for conservation. Hawaiian tree snails are a model system for an adaptive radiation facing an extinction crisis. In the last 5 years, nearly all populations of Hawaiian tree snails across the 30 remaining species in the subfamily Achatinellinae (Achatinellidae) have declined from hundreds or thousands in the wild down to undetectable levels. Nearly 100 species historically occurred across dramatic environmental gradients on five of the Hawaiian Islands, but habitat loss, overcollection, and predation by invasive species have decimated populations. As such, this system offers the opportunity to integrate efforts to conserve evolutionary potential into conservation planning for a rapidly declining subfamily. Here, we used genome-wide, restriction-site associated DNA sequencing (RADseq), along with mitochondrial genome reconstruction, to resolve evolutionary relationships to inform conservation efforts. Phylogenetic analysis of nearly 400k genome-wide SNPs from 59 populations and 25 species across six genera in the family Achatinellidae, was generally concordant with taxonomy, geography, and mtDNA with several notable exceptions; mtDNA was unable to resolve some deeper nodes (e.g., the monophyly of Achatinella), while SNP data did not resolve as many shallow nodes. Both phylogenetic and coalescent analysis revealed deep divergences between populations within Achatinella mustelina that were consistent with species-level differences. Given cryptic species-level divergence within populations that are geographically proximate, they are at higher risk of extirpation from invasive predators and climate change than previously assumed. This study clarifies evolutionary relationships within this model system for adaptive radiation, forming the basis for conservation strategies such as translocation, captive rearing, and hybridization trials to prevent the loss of cap…
bibliographic citation: Price et al. (2021) Evolutionary genomics of endangered Hawaiian tree snails (Achatinellidae: Achatinellinae) for conservation of adaptive capacity. PeerJ 9:e10993 https://doi.org/10.7717/peerj.10993
date submitted: 2019-12-21
date accepted: 2021-02-01
issued: 2021-04-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Price
  given name: Melissa R.
author list: Agent
  family name: Hadfield
  given name: Michael G.
author list: Agent
  family name: Knapp
  given name: Ingrid S.S.
author list: Agent
  family name: Toonen
  given name: Robert J.
author list: Agent
  family name: Forsman
  given name: Zac H.
doi: 10.7717/peerj.10993
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-22
copyright: © 2021 Price et al.
attribution name: Price et al.

The biosonar of the boto: evidence of differences among species of river dolphins (Inia spp.) from the Amazon
type: item
type: AcademicArticle
description: Echolocation clicks can reflect the anatomy of the vocalizing animal, enabling the distinction of species. River dolphins from the family Iniidae are formally represented by one species and two subspecies (Inia geoffrensis geoffrensis and I. g. humboldtiana). Additionally, two other species have been proposed (I. boliviensis and I. araguaiaensis) regarding its level of restricted distribution and morph-genetics differences. For the Committee on Taxonomy of the Society for Marine Mammalogy, the specific status of the proposed species relies on further knowledge on morphology, ecology, and genetics. Given that species-specific status is required for conservation efforts, we described and compared the echolocation clicks of Inia spp., searching for specific differences on their vocalizations. The sounds were captured with a Cetacean Research ™ C54XRS (+3/−20 dB, −185 dB re: 1V/μPa) in Guaviare River (Orinoco basin), Madeira River (Madeira basin), Xingu River (Amazon Basin), and Araguaia River (Tocantins-Araguaia basin). We found significant differences in all analyzed parameters (peak frequency, 3 dB bandwidth, 10 dB bandwidth and inter-click interval) for all species and subspecies. Differences in acoustical parameters of clicks are mainly related to the animal’s internal morphology, thus this study may potentially support with information for the species-level classification mostly of I. araguaiaensis (the Araguaian boto). Classifying the Araguaian boto separately from I. geoffrensis has important implications for the species in terms of conservation status, since it is restricted to a highly impacted river system.
format: application/pdf
format: text/html
creator: Jéssica F. Melo
creator: Thiago O. S. Amorim
creator: Mariana Paschoalini
creator: Artur Andriolo
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.11105
publisher: PeerJ Inc.
rights: © 2021 Melo et al.
abstract: Echolocation clicks can reflect the anatomy of the vocalizing animal, enabling the distinction of species. River dolphins from the family Iniidae are formally represented by one species and two subspecies (Inia geoffrensis geoffrensis and I. g. humboldtiana). Additionally, two other species have been proposed (I. boliviensis and I. araguaiaensis) regarding its level of restricted distribution and morph-genetics differences. For the Committee on Taxonomy of the Society for Marine Mammalogy, the specific status of the proposed species relies on further knowledge on morphology, ecology, and genetics. Given that species-specific status is required for conservation efforts, we described and compared the echolocation clicks of Inia spp., searching for specific differences on their vocalizations. The sounds were captured with a Cetacean Research ™ C54XRS (+3/−20 dB, −185 dB re: 1V/μPa) in Guaviare River (Orinoco basin), Madeira River (Madeira basin), Xingu River (Amazon Basin), and Araguaia River (Tocantins-Araguaia basin). We found significant differences in all analyzed parameters (peak frequency, 3 dB bandwidth, 10 dB bandwidth and inter-click interval) for all species and subspecies. Differences in acoustical parameters of clicks are mainly related to the animal’s internal morphology, thus this study may potentially support with information for the species-level classification mostly of I. araguaiaensis (the Araguaian boto). Classifying the Araguaian boto separately from I. geoffrensis has important implications for the species in terms of conservation status, since it is restricted to a highly impacted river system.
bibliographic citation: Melo et al. (2021) The biosonar of the boto: evidence of differences among species of river dolphins (Inia spp.) from the Amazon. PeerJ 9:e11105 https://doi.org/10.7717/peerj.11105
date submitted: 2020-09-02
date accepted: 2021-02-22
issued: 2021-04-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Melo
  given name: Jéssica F.
author list: Agent
  family name: Amorim
  given name: Thiago O. S.
author list: Agent
  family name: Paschoalini
  given name: Mariana
author list: Agent
  family name: Andriolo
  given name: Artur
doi: 10.7717/peerj.11105
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-22
copyright: © 2021 Melo et al.
attribution name: Melo et al.

Commercial arbuscular mycorrhizal fungal inoculant failed to establish in a vineyard despite priority advantage
type: item
type: AcademicArticle
description: Background Arbuscular mycorrhizal (AM) fungi associate with most plants and can increase nutrient uptake. As a result, commercial inoculants called “biofertilizers” containing AM fungi have been developed and marketed to increase plant performance. However, successful establishment of these inoculants remains a challenge, and may be negatively impacted by competition with fungi already present (priority effects). Perennial agriculture may be more amenable if inoculants can be successfully established on crops prior to field planting. Methods Here, we inoculate grapevine (Vitis vinifera) with a commercial inoculant in three treatments designed to manipulate the strength and direction of priority effects and quantified the abundance of the fungal strain before and after introduction using droplet digital PCR (ddPCR). Results We found that the introduced strain did not establish in any treatment, even with priority advantage, and inoculated vines did not differ in performance from non-inoculated vines. Fungal abundance was not greater than in pre-inoculation soil samples during any of the five years sampled and may have been impaired by high available phosphorus levels in the soil. This study highlights the need to understand and evaluate how the management of the agricultural system will affect establishment before introduction of “biofertilizers”, which is often unpredictable.
format: application/pdf
format: text/html
creator: Corrina Thomsen
creator: Laura Loverock
creator: Vasilis Kokkoris
creator: Taylor Holland
creator: Patricia A. Bowen
creator: Miranda Hart
subject: Agricultural Science
subject: Ecology
subject: Mycology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.11119
publisher: PeerJ Inc.
rights: © 2021 Thomsen et al.
abstract: Background Arbuscular mycorrhizal (AM) fungi associate with most plants and can increase nutrient uptake. As a result, commercial inoculants called “biofertilizers” containing AM fungi have been developed and marketed to increase plant performance. However, successful establishment of these inoculants remains a challenge, and may be negatively impacted by competition with fungi already present (priority effects). Perennial agriculture may be more amenable if inoculants can be successfully established on crops prior to field planting. Methods Here, we inoculate grapevine (Vitis vinifera) with a commercial inoculant in three treatments designed to manipulate the strength and direction of priority effects and quantified the abundance of the fungal strain before and after introduction using droplet digital PCR (ddPCR). Results We found that the introduced strain did not establish in any treatment, even with priority advantage, and inoculated vines did not differ in performance from non-inoculated vines. Fungal abundance was not greater than in pre-inoculation soil samples during any of the five years sampled and may have been impaired by high available phosphorus levels in the soil. This study highlights the need to understand and evaluate how the management of the agricultural system will affect establishment before introduction of “biofertilizers”, which is often unpredictable.
bibliographic citation: Thomsen et al. (2021) Commercial arbuscular mycorrhizal fungal inoculant failed to establish in a vineyard despite priority advantage. PeerJ 9:e11119 https://doi.org/10.7717/peerj.11119
date submitted: 2020-11-26
date accepted: 2021-02-25
issued: 2021-04-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thomsen
  given name: Corrina
author list: Agent
  family name: Loverock
  given name: Laura
author list: Agent
  family name: Kokkoris
  given name: Vasilis
author list: Agent
  family name: Holland
  given name: Taylor
author list: Agent
  family name: Bowen
  given name: Patricia A.
author list: Agent
  family name: Hart
  given name: Miranda
doi: 10.7717/peerj.11119
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-22
copyright: ©2021 Thomsen et al.
attribution name: Thomsen et al.

Transcriptome analysis of the liver of Eospalax fontanierii under hypoxia
type: item
type: AcademicArticle
description: Hypoxia can induce cell damage, inflammation, carcinogenesis, and inhibit liver regeneration in non-adapted species. Because of their excellent hypoxia adaptation features, subterranean rodents have been widely studied to clarify the mechanism of hypoxia adaptation. Eospalax fontanierii, which is a subterranean rodent found in China, can survive for more than 10 h under 4% O2 without observable injury, while Sprague-Dawley rats can survive for less than 6 h under the same conditions. To explore the potential mechanism of hypoxia responses in E. fontanierii, we performed RNA-seq analysis of the liver in E. fontanierii exposed to different oxygen levels (6.5% 6h, 10.5% 44h, and 21%). Based on the bioinformatics analysis, 39,439 unigenes were assembled, and 56.78% unigenes were annotated using public databases (Nr, GO, Swiss-Prot, KEGG, and Pfam). In total, 725 differentially expressed genes (DEGs) were identified in the response to hypoxia; six with important functions were validated by qPCR. Those DEGs were mainly involved in processes related to lipid metabolism, steroid catabolism, glycolysis/gluconeogenesis, and the AMPK and PPAR signaling pathway. By analyzing the expression patterns of important genes related to energy associated metabolism under hypoxia, we found that fatty acid oxidation and gluconeogenesis were increased, while protein synthesis and fatty acid synthesis were decreased. Furthermore, the upregulated expression of specific genes with anti-apoptosis or anti-oxidation functions under hypoxia may contribute to the mechanism by which E. fontanierii tolerates hypoxia. Our results provide an understanding of the response to hypoxia in E. fontanierii, and have potential value for biomedical studies.
format: application/pdf
format: text/html
creator: Zhiqiang Hao
creator: Lulu Xu
creator: Li Zhao
creator: Jianping He
creator: Guanglin Li
creator: Jingang Li
subject: Animal Behavior
subject: Bioinformatics
subject: Molecular Biology
subject: Zoology
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.11166
publisher: PeerJ Inc.
rights: © 2021 Hao et al.
abstract: Hypoxia can induce cell damage, inflammation, carcinogenesis, and inhibit liver regeneration in non-adapted species. Because of their excellent hypoxia adaptation features, subterranean rodents have been widely studied to clarify the mechanism of hypoxia adaptation. Eospalax fontanierii, which is a subterranean rodent found in China, can survive for more than 10 h under 4% O2 without observable injury, while Sprague-Dawley rats can survive for less than 6 h under the same conditions. To explore the potential mechanism of hypoxia responses in E. fontanierii, we performed RNA-seq analysis of the liver in E. fontanierii exposed to different oxygen levels (6.5% 6h, 10.5% 44h, and 21%). Based on the bioinformatics analysis, 39,439 unigenes were assembled, and 56.78% unigenes were annotated using public databases (Nr, GO, Swiss-Prot, KEGG, and Pfam). In total, 725 differentially expressed genes (DEGs) were identified in the response to hypoxia; six with important functions were validated by qPCR. Those DEGs were mainly involved in processes related to lipid metabolism, steroid catabolism, glycolysis/gluconeogenesis, and the AMPK and PPAR signaling pathway. By analyzing the expression patterns of important genes related to energy associated metabolism under hypoxia, we found that fatty acid oxidation and gluconeogenesis were increased, while protein synthesis and fatty acid synthesis were decreased. Furthermore, the upregulated expression of specific genes with anti-apoptosis or anti-oxidation functions under hypoxia may contribute to the mechanism by which E. fontanierii tolerates hypoxia. Our results provide an understanding of the response to hypoxia in E. fontanierii, and have potential value for biomedical studies.
bibliographic citation: Hao et al. (2021) Transcriptome analysis of the liver of Eospalax fontanierii under hypoxia. PeerJ 9:e11166 https://doi.org/10.7717/peerj.11166
date submitted: 2020-09-14
date accepted: 2021-03-05
issued: 2021-04-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hao
  given name: Zhiqiang
author list: Agent
  family name: Xu
  given name: Lulu
author list: Agent
  family name: Zhao
  given name: Li
author list: Agent
  family name: He
  given name: Jianping
author list: Agent
  family name: Li
  given name: Guanglin
author list: Agent
  family name: Li
  given name: Jingang
doi: 10.7717/peerj.11166
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-22
copyright: ©2021 Hao et al.
attribution name: Hao et al.

Soil microbial diversity in organic and non-organic pasture systems
type: item
type: AcademicArticle
description: Understanding the effects of organic pasture management on the soil microbiome is important for sustainable forage production since soil microbiome diversity contributes to improved nutrient cycling, soil structure, plant growth, and environmental resiliency; however, the soil microbiome response to pasture management is largely unknown. This study assessed the soil microbial diversity, richness, and community structure following 10 years of pasture management (organic or non-organic) of the V4 region of the 16S rRNA using the Illumina MiSeq platform. Soil samples were collected from 0–15 cm in July and August from 2017–2018 and soil nutrient properties (nutrients, carbon, nitrogen, and pH) quantified and correlated with soil microbial diversity. Overall, greater soil bacterial species richness (P ≤ 0.05) occurred in organic relative to non-organic (conventional) systems. Management affected bacterial species richness (Chao1), with greater richness occurring in organic pasture soils and less richness occurring in non-organic systems (P ≤ 0.05). Similarly, management affected bacterial evenness (Simpson’s index), with a more diverse community occurring in organically managed soils relative to non-organic pastures (P ≤ 0.05). Linear discriminant analysis effect size analysis showed statistically significant and biologically consistent differences in bacterial taxa in organic compared with non-organic soils. Therefore, there was a shift in bacterial community structure in organic relative to non-organic soils (P ≤ 0.05). Additionally, soil nutrients (Fe, Mg, Ni, S, Al, K, Cd, and Cu), pH, C, and N were correlated with one or more dominant bacterial phyla (Gemmatimonadetes, Planctomycetes, Firmicutes, Chloroflexi, Actinobacteria, and Acidobacteria). Overall, pasture management affected soil microbial diversity, with greater diversity occurring in organic than non-organic systems, likely owing to applications of organic poultry litter in organic systems compared to non-o…
format: application/pdf
format: text/html
creator: Mohan Acharya
creator: Amanda J. Ashworth
creator: Yichao Yang
creator: Joan M. Burke
creator: Jung Ae Lee
creator: Roshani Sharma Acharya
subject: Agricultural Science
subject: Bioinformatics
subject: Microbiology
subject: Molecular Biology
subject: Soil Science
description: doi:10.7717/peerj.11184
publisher: PeerJ Inc.
rights: © 2021 Acharya et al.
abstract: Understanding the effects of organic pasture management on the soil microbiome is important for sustainable forage production since soil microbiome diversity contributes to improved nutrient cycling, soil structure, plant growth, and environmental resiliency; however, the soil microbiome response to pasture management is largely unknown. This study assessed the soil microbial diversity, richness, and community structure following 10 years of pasture management (organic or non-organic) of the V4 region of the 16S rRNA using the Illumina MiSeq platform. Soil samples were collected from 0–15 cm in July and August from 2017–2018 and soil nutrient properties (nutrients, carbon, nitrogen, and pH) quantified and correlated with soil microbial diversity. Overall, greater soil bacterial species richness (P ≤ 0.05) occurred in organic relative to non-organic (conventional) systems. Management affected bacterial species richness (Chao1), with greater richness occurring in organic pasture soils and less richness occurring in non-organic systems (P ≤ 0.05). Similarly, management affected bacterial evenness (Simpson’s index), with a more diverse community occurring in organically managed soils relative to non-organic pastures (P ≤ 0.05). Linear discriminant analysis effect size analysis showed statistically significant and biologically consistent differences in bacterial taxa in organic compared with non-organic soils. Therefore, there was a shift in bacterial community structure in organic relative to non-organic soils (P ≤ 0.05). Additionally, soil nutrients (Fe, Mg, Ni, S, Al, K, Cd, and Cu), pH, C, and N were correlated with one or more dominant bacterial phyla (Gemmatimonadetes, Planctomycetes, Firmicutes, Chloroflexi, Actinobacteria, and Acidobacteria). Overall, pasture management affected soil microbial diversity, with greater diversity occurring in organic than non-organic systems, likely owing to applications of organic poultry litter in organic systems compared to non-o…
bibliographic citation: Acharya et al. (2021) Soil microbial diversity in organic and non-organic pasture systems. PeerJ 9:e11184 https://doi.org/10.7717/peerj.11184
date submitted: 2020-10-21
date accepted: 2021-03-08
issued: 2021-04-22
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Acharya
  given name: Mohan
author list: Agent
  family name: Ashworth
  given name: Amanda J.
author list: Agent
  family name: Yang
  given name: Yichao
author list: Agent
  family name: Burke
  given name: Joan M.
author list: Agent
  family name: Lee
  given name: Jung Ae
author list: Agent
  family name: Sharma Acharya
  given name: Roshani
doi: 10.7717/peerj.11184
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-22
copyright: ©2021 Acharya et al.
attribution name: Acharya et al.

The rise in climate change-induced federal fishery disasters in the United States
type: item
type: AcademicArticle
description: Commercial, recreational, and indigenous fisheries are critical to coastal economies and communities in the United States. For over three decades, the federal government has formally recognized the impact of fishery disasters via federal declarations. Despite these impacts, national syntheses of the dynamics, impacts, and causes of fishery disasters are lacking. We developed a nationwide Federal Fishery Disaster database using National Oceanic and Atmospheric Administration (NOAA) fishery disaster declarations and fishery revenue data. From 1989-2020, there were 71 federally approved fishery disasters (eleven are pending), which spanned every federal fisheries management region and coastal state in the country. To date, we estimate fishery disasters resulted in $2B (2019 USD) in Congressional allocations, and an additional, conservative estimate of $3.2B (2019 USD) in direct revenue loss. Despite this scale of impact, the disaster assistance process is largely ad hoc and lacks sufficient detail to properly assess allocation fairness and benefit. Nonetheless, fishery disasters increased in frequency over time, and the causes of disasters included a broad range of anthropogenic and environmental factors, with a recent shift to disasters now almost exclusively caused by extreme environmental events (e.g., marine heatwaves, hurricanes, and harmful algal blooms). Nationwide, 84.5% of fishery disasters were either partially or entirely attributed to extreme environmental events. As climate change drives higher rates of such extreme events, and as natural disaster assistance requests reach an all-time high, the federal system for fisheries disaster declaration and mitigation must evolve in order to effectively protect both fisheries sustainability and societal benefit.
format: application/pdf
format: text/html
creator: Lyall Bellquist
creator: Vienna Saccomanno
creator: Brice X. Semmens
creator: Mary Gleason
creator: Jono Wilson
subject: Aquaculture, Fisheries and Fish Science
subject: Science Policy
subject: Coupled Natural and Human Systems
subject: Climate Change Biology
description: doi:10.7717/peerj.11186
publisher: PeerJ Inc.
rights: © 2021 Bellquist et al.
abstract: Commercial, recreational, and indigenous fisheries are critical to coastal economies and communities in the United States. For over three decades, the federal government has formally recognized the impact of fishery disasters via federal declarations. Despite these impacts, national syntheses of the dynamics, impacts, and causes of fishery disasters are lacking. We developed a nationwide Federal Fishery Disaster database using National Oceanic and Atmospheric Administration (NOAA) fishery disaster declarations and fishery revenue data. From 1989-2020, there were 71 federally approved fishery disasters (eleven are pending), which spanned every federal fisheries management region and coastal state in the country. To date, we estimate fishery disasters resulted in $2B (2019 USD) in Congressional allocations, and an additional, conservative estimate of $3.2B (2019 USD) in direct revenue loss. Despite this scale of impact, the disaster assistance process is largely ad hoc and lacks sufficient detail to properly assess allocation fairness and benefit. Nonetheless, fishery disasters increased in frequency over time, and the causes of disasters included a broad range of anthropogenic and environmental factors, with a recent shift to disasters now almost exclusively caused by extreme environmental events (e.g., marine heatwaves, hurricanes, and harmful algal blooms). Nationwide, 84.5% of fishery disasters were either partially or entirely attributed to extreme environmental events. As climate change drives higher rates of such extreme events, and as natural disaster assistance requests reach an all-time high, the federal system for fisheries disaster declaration and mitigation must evolve in order to effectively protect both fisheries sustainability and societal benefit.
bibliographic citation: Bellquist et al. (2021) The rise in climate change-induced federal fishery disasters in the United States. PeerJ 9:e11186 https://doi.org/10.7717/peerj.11186
date submitted: 2020-11-26
date accepted: 2021-03-09
issued: 2021-04-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bellquist
  given name: Lyall
author list: Agent
  family name: Saccomanno
  given name: Vienna
author list: Agent
  family name: Semmens
  given name: Brice X.
author list: Agent
  family name: Gleason
  given name: Mary
author list: Agent
  family name: Wilson
  given name: Jono
doi: 10.7717/peerj.11186
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-22
copyright: ©2021 Bellquist et al.
attribution name: Bellquist et al.

The antimicrobial activity of silver acetate against Acinetobacter baumannii in a Galleria mellonella infection model
type: item
type: AcademicArticle
description: Background The increasing prevalence of bacterial infections that are resistant to antibiotic treatment has caused the scientific and medical communities to look for alternate remedies aimed at prevention and treatment. In addition to researching novel antimicrobials, there has also been much interest in revisiting some of the earliest therapies used by man. One such antimicrobial is silver; its use stretches back to the ancient Greeks but interest in its medicinal properties has increased in recent years due to the rise in antibiotic resistance. Currently antimicrobial silver is found in everything from lunch boxes to medical device implants. Though much is claimed about the antimicrobial efficacy of silver salts the research in this area is mixed. Methods Herein we investigated the efficacy of silver acetate against a carbapenem resistant strain of Acinetobacter baumannii to determine the in vitro activity of this silver salt against a World Health Organisation designated category I critical pathogen. Furthermore, we use the Galleria mellonella larvae model to assess toxicity of the compound and its efficacy in treating infections in a live host. Results We found that silver acetate can be delivered safely to Galleria at medically relevant and antimicrobial levels without detriment to the larvae and that administration of silver acetate to an infection model significantly improved survival. This demonstrates the selective toxicity of silver acetate for bacterial pathogens but also highlights the need for administration of well-defined doses of the antimicrobial to provide an efficacious treatment.
format: application/pdf
format: text/html
creator: Eden Mannix-Fisher
creator: Samantha McLean
subject: Entomology
subject: Microbiology
subject: Toxicology
description: doi:10.7717/peerj.11196
publisher: PeerJ Inc.
rights: © 2021 Mannix-Fisher and McLean
abstract: Background The increasing prevalence of bacterial infections that are resistant to antibiotic treatment has caused the scientific and medical communities to look for alternate remedies aimed at prevention and treatment. In addition to researching novel antimicrobials, there has also been much interest in revisiting some of the earliest therapies used by man. One such antimicrobial is silver; its use stretches back to the ancient Greeks but interest in its medicinal properties has increased in recent years due to the rise in antibiotic resistance. Currently antimicrobial silver is found in everything from lunch boxes to medical device implants. Though much is claimed about the antimicrobial efficacy of silver salts the research in this area is mixed. Methods Herein we investigated the efficacy of silver acetate against a carbapenem resistant strain of Acinetobacter baumannii to determine the in vitro activity of this silver salt against a World Health Organisation designated category I critical pathogen. Furthermore, we use the Galleria mellonella larvae model to assess toxicity of the compound and its efficacy in treating infections in a live host. Results We found that silver acetate can be delivered safely to Galleria at medically relevant and antimicrobial levels without detriment to the larvae and that administration of silver acetate to an infection model significantly improved survival. This demonstrates the selective toxicity of silver acetate for bacterial pathogens but also highlights the need for administration of well-defined doses of the antimicrobial to provide an efficacious treatment.
bibliographic citation: Mannix-Fisher et al. (2021) The antimicrobial activity of silver acetate against Acinetobacter baumannii in a Galleria mellonella infection model. PeerJ 9:e11196 https://doi.org/10.7717/peerj.11196
date submitted: 2020-12-09
date accepted: 2021-03-09
issued: 2021-04-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mannix-Fisher
  given name: Eden
author list: Agent
  family name: McLean
  given name: Samantha
doi: 10.7717/peerj.11196
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-22
copyright: © 2021 Mannix-Fisher and McLean
attribution name: Mannix-Fisher and McLean

https://peerj.com/articles/11283
type: item
type: AcademicArticle
title: Stable isotope and fatty acid analyses reveal significant differences in trophic niches of smooth hammerhead Sphyrna zygaena (Carcharhiniformes) among three nursery areas in northern Humboldt Current System
description: Fishery pressure on nursery areas of smooth hammerhead in northern Peruvian coast have become a serious threat to sustainability of this resource. Even though, some management actions focused on conservation of the smooth hammerhead populations were proposed in recent years, their scientific foundations are often limited, and biomass of smooth hammerhead in Peruvian waters continues to decrease. To inform management and conservation, this study aims to evaluate the trophic niche of smooth hammerhead juveniles from three nursery areas in the northern Peruvian coast using stable isotope and fatty acid analyses. First, we compared the environmental characteristics of each nursery area (i.e., sea surface temperature and chlorophyll-a concentration) and concluded that nursery areas differed significantly and consistently in sea surface temperature. Subsequently, we evaluated isotopic composition of carbon and nitrogen and fatty acid profiles of muscle and liver tissues collected from juvenile smooth hammerhead from each nursery area. We found that juvenile smooth hammerhead captured in San José were enriched in heavier 13C and 15N isotopes compared to those captured in Máncora and Salaverry. Furthermore, the broadest isotopic niches were observed in juveniles from Máncora, whereas isotopic niches of juveniles from Salaverry and San José were narrower. This difference is primarily driven by the Humboldt Current System and associated upwelling of cold and nutrient rich water that drives increased primary production in San José and, to a less extent, in Salaverry. Compared to smooth hammerhead juveniles from Máncora, those from San José and Salaverry were characterised by higher essential fatty acid concentrations related to pelagic and migratory prey. We conclude that smooth hammerhead juveniles from three nursery areas in the northern Peruvian coast differ significantly in their trophic niches. Thus, management and conservation efforts should consider each nursery area as…
format: application/pdf
format: text/html
creator: Eduardo Segura-Cobeña
creator: Joanna Alfaro-Shigueto
creator: Jeffrey Mangel
creator: Angel Urzua
creator: Konrad Górski
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Population Biology
description: doi:10.7717/peerj.11283
publisher: PeerJ Inc.
rights: © 2021 Segura-Cobeña et al.
abstract: Fishery pressure on nursery areas of smooth hammerhead in northern Peruvian coast have become a serious threat to sustainability of this resource. Even though, some management actions focused on conservation of the smooth hammerhead populations were proposed in recent years, their scientific foundations are often limited, and biomass of smooth hammerhead in Peruvian waters continues to decrease. To inform management and conservation, this study aims to evaluate the trophic niche of smooth hammerhead juveniles from three nursery areas in the northern Peruvian coast using stable isotope and fatty acid analyses. First, we compared the environmental characteristics of each nursery area (i.e., sea surface temperature and chlorophyll-a concentration) and concluded that nursery areas differed significantly and consistently in sea surface temperature. Subsequently, we evaluated isotopic composition of carbon and nitrogen and fatty acid profiles of muscle and liver tissues collected from juvenile smooth hammerhead from each nursery area. We found that juvenile smooth hammerhead captured in San José were enriched in heavier 13C and 15N isotopes compared to those captured in Máncora and Salaverry. Furthermore, the broadest isotopic niches were observed in juveniles from Máncora, whereas isotopic niches of juveniles from Salaverry and San José were narrower. This difference is primarily driven by the Humboldt Current System and associated upwelling of cold and nutrient rich water that drives increased primary production in San José and, to a less extent, in Salaverry. Compared to smooth hammerhead juveniles from Máncora, those from San José and Salaverry were characterised by higher essential fatty acid concentrations related to pelagic and migratory prey. We conclude that smooth hammerhead juveniles from three nursery areas in the northern Peruvian coast differ significantly in their trophic niches. Thus, management and conservation efforts should consider each nursery area as…
bibliographic citation: Segura-Cobeña et al. (2021) Stable isotope and fatty acid analyses reveal significant differences in trophic niches of smooth hammerhead Sphyrna zygaena (Carcharhiniformes) among three nursery areas in northern Humboldt Current System. PeerJ 9:e11283 https://doi.org/10.7717/peerj.11283
date submitted: 2020-12-07
date accepted: 2021-03-24
issued: 2021-04-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Segura-Cobeña
  given name: Eduardo
author list: Agent
  family name: Alfaro-Shigueto
  given name: Joanna
author list: Agent
  family name: Mangel
  given name: Jeffrey
author list: Agent
  family name: Urzua
  given name: Angel
author list: Agent
  family name: Górski
  given name: Konrad
doi: 10.7717/peerj.11283
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-22
copyright: ©2021 Segura-Cobeña et al.
attribution name: Segura-Cobeña et al.

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