title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=919
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Planktonic associations between medusae (classes Scyphozoa and Hydrozoa) and epifaunal crustaceans
link: https://peerj.com/articles/11281
last-modified: 2021-04-23
description: Jellyfish are known to carry various epibionts, including many of the subphylum Crustacea. However, the associations between gelatinous zooplankton and other invertebrates have been chronically overlooked. Crustacea, a massive clade of economically, ecologically, and culturally important species, includes many taxa that utilize gelatinous zooplankton for food, transport, and protection as both adults and juveniles. Here we compile 211 instances of epifaunal crustaceans recorded on Hydromedusae and Scyphomedusae from a century of literature. These include 78 identified crustacean species in 65 genera across nine orders found upon 37 Hydromedusa species and 48 Scyphomedusae. The crustacean life stage, location, nature of the association with the medusa, years, months, and depths are compiled to form a comprehensive view of the current state of the literature. Additionally, this review highlights areas where the current literature is lacking, particularly noting our poor understanding of the relationships between juvenile crabs of commercially valuable species and medusae.
creator: Kaden Muffett
creator: Maria Pia Miglietta
uri: https://doi.org/10.7717/peerj.11281
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Muffett and Miglietta

title: Bosminopsis deitersi (Crustacea: Cladocera) as an ancient species group: a revision
link: https://peerj.com/articles/11310
last-modified: 2021-04-23
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).
creator: Petr G. Garibian
creator: Dmitry P. Karabanov
creator: Anna N. Neretina
creator: Derek J. Taylor
creator: Alexey A. Kotov
uri: https://doi.org/10.7717/peerj.11310
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Garibian et al.

title: Bloom evenness modulates the influence of bloom abundance on insect community structure in suburban gardens
link: https://peerj.com/articles/11132
last-modified: 2021-04-22
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.
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
uri: https://doi.org/10.7717/peerj.11132
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Braatz et al.

title: Evolutionary genomics of endangered Hawaiian tree snails (Achatinellidae: Achatinellinae) for conservation of adaptive capacity
link: https://peerj.com/articles/10993
last-modified: 2021-04-22
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 capacity to adapt to rapidly changing environmental conditions.
creator: Melissa R. Price
creator: Michael G. Hadfield
creator: Ingrid S.S. Knapp
creator: Robert J. Toonen
creator: Zac H. Forsman
uri: https://doi.org/10.7717/peerj.10993
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Price et al.

title: The biosonar of the boto: evidence of differences among species of river dolphins (Inia spp.) from the Amazon
link: https://peerj.com/articles/11105
last-modified: 2021-04-22
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.
creator: Jéssica F. Melo
creator: Thiago O. S. Amorim
creator: Mariana Paschoalini
creator: Artur Andriolo
uri: https://doi.org/10.7717/peerj.11105
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Melo et al.

title: Commercial arbuscular mycorrhizal fungal inoculant failed to establish in a vineyard despite priority advantage
link: https://peerj.com/articles/11119
last-modified: 2021-04-22
description: BackgroundArbuscular 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.MethodsHere, 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).ResultsWe 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.
creator: Corrina Thomsen
creator: Laura Loverock
creator: Vasilis Kokkoris
creator: Taylor Holland
creator: Patricia A. Bowen
creator: Miranda Hart
uri: https://doi.org/10.7717/peerj.11119
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Thomsen et al.

title: Transcriptome analysis of the liver of Eospalax fontanierii under hypoxia
link: https://peerj.com/articles/11166
last-modified: 2021-04-22
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.
creator: Zhiqiang Hao
creator: Lulu Xu
creator: Li Zhao
creator: Jianping He
creator: Guanglin Li
creator: Jingang Li
uri: https://doi.org/10.7717/peerj.11166
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Hao et al.

title: Soil microbial diversity in organic and non-organic pasture systems
link: https://peerj.com/articles/11184
last-modified: 2021-04-22
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-organic management (use of inorganic-fertilizers and herbicides). Results indicate that when pastures are converted to organic production systems, soil microbial richness and diversity may increase, thereby resulting in enhanced soil microbiome diversity and overall ecosystem services.
creator: Mohan Acharya
creator: Amanda J. Ashworth
creator: Yichao Yang
creator: Joan M. Burke
creator: Jung Ae Lee
creator: Roshani Sharma Acharya
uri: https://doi.org/10.7717/peerj.11184
license: https://creativecommons.org/publicdomain/zero/1.0/
rights: ©2021 Acharya et al.

title: The rise in climate change-induced federal fishery disasters in the United States
link: https://peerj.com/articles/11186
last-modified: 2021-04-22
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.
creator: Lyall Bellquist
creator: Vienna Saccomanno
creator: Brice X. Semmens
creator: Mary Gleason
creator: Jono Wilson
uri: https://doi.org/10.7717/peerj.11186
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Bellquist et al.

title: The antimicrobial activity of silver acetate against Acinetobacter baumannii in a Galleria mellonella infection model
link: https://peerj.com/articles/11196
last-modified: 2021-04-22
description: BackgroundThe 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.MethodsHerein 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.ResultsWe 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.
creator: Eden Mannix-Fisher
creator: Samantha McLean
uri: https://doi.org/10.7717/peerj.11196
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Mannix-Fisher and McLean