title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=725 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Phosphorus flow analysis of different crops in Dongying District, Shandong Province, China, 1995–2016 link: https://peerj.com/articles/13274 last-modified: 2022-04-19 description: Investigating the phosphorus (P) sources, pathways, and final sinks are important to reduce P pollution and improve P management. In this study, substance flow analysis (SFA) was performed for P flow analysis from 1995 to 2016 in different crops of Dongying District, a core region of the alluvial delta at the estuary of the Yellow River. The results showed that P input steadily increased from 1.48 × 104 t in 1995 to 2.16 × 104 t in 2007, and then decreased from 1.90 × 104 t in 2010 to 1.78 × 104 t in 2016. Chemical fertilizers made the highest contribution to P input. The cotton with the highest P load was on the top of P load risk ranks. More importantly, this study applied the Partial Least Squares Path Modeling (PLS-PM) model for P flow analysis and established the numerical relationship between the variables (including fertilizers, straws return-to-field, harvested grains, discarded straw, and P erosion and runoff), P use efficiency (PUE) and P load. The analysis revealed that fertilizer and crop production are the key factors affecting the PUE. Therefore, optimizing the use of P-fertilizer whilst maintaining yields can be an effective strategy to improve the local region PUE. creator: Huan He creator: Lvqing Zhang creator: Hongwei Zang creator: Mingxing Sun creator: Cheng Lv creator: Shuangshuang Li creator: Liyong Bai creator: Wenyuan Han creator: Jiulan Dai uri: https://doi.org/10.7717/peerj.13274 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 He et al. title: Analysis of fungal dynamic changes in the natural fermentation broth of ‘Hongyang’ kiwifruit link: https://peerj.com/articles/13286 last-modified: 2022-04-19 description: ‘Hongyang’ kiwifruit (Actinidia chinensis Planch.) is an ideal kiwifruit wine variety. At present, there is no research on the dynamic changes of yeast during the natural fermentation of kiwifruit wine. In this study, a high-throughput was employed to analyze the fungal population composition and diversity in the samples cultured in yeast extract peptone dextrose (YPD) medium and enriched in the natural fermentation process of ‘Hongyang’ kiwifruit at four time points, day one (D1T), day three (D3T), day five (D5T), and day fifteen (D15T). Five hundred and eighty-two operational taxonomic units (OTUs) were obtained from 131 genera and 178 species samples. The diversity analysis results showed that in the early natural fermentation stage, the dominant species was Aureobasidium pullulans, and as natural fermentation proceeded, the genus Pichia became the dominant species. Pichia kluyveri was an important species at the later stages of natural fermentation. An analysis of the metabolic pathways shows that P. kluyveri plays an aromatic-producing role in the natural fermentation of ‘Hongyang’ kiwifruit. These results could provide a theoretical basis for the studies of kiwifruit fungal diversity and fungal changes during fermentation. The findings could fix a major deficiency in the production of kiwifruit fruit wine, which lacks a specific flavor-producing yeast species or strain. creator: Zhiming Zhang creator: Yuhong Gao creator: Wenjuan Zhao creator: Zhuo Wei creator: Xiaozhen Liu creator: Hanyao Zhang uri: https://doi.org/10.7717/peerj.13286 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: Exposure of adult sea urchin Strongylocentrotus intermedius to stranded heavy fuel oil causes developmental toxicity on larval offspring link: https://peerj.com/articles/13298 last-modified: 2022-04-19 description: Heavy fuel oil (HFO) spills pose serious threat to coastlines and sensitive resources. Stranded HFO that occurs along the coastline could cause long-term and massive damage to the marine environment and indirectly affect the survival of parental marine invertebrates. However, our understanding of the complex associations within invertebrates is primarily limited, particularly in terms of the toxicity effects on the offspring when parents are exposed to stranded HFO. Here, we investigated the persistent effects on the early development stage of the offspring following stranded HFO exposure on the sea urchin Strongylocentrotus intermedius. After 21 d exposure, sea urchins exhibited a significant decrease in the reproductive capacity; while the reactive oxygen species level, 3-nitrotyrosine protein level, protein carbonyl level, and heat shock proteins 70 expression in the gonadal tissues and gametes significantly increased as compared to the controls, indicating that HFO exposure could cause development toxicity on offspring in most traits of larval size. These results suggested that the stranded HFO exposure could increase oxidative stress of gonadal tissues, impair reproductive functions in parental sea urchins, and subsequently impact on development of their offspring. This study provides valuable information regarding the persistent toxicity effects on the offspring following stranded HFO exposure on sea urchins. creator: Xuanbo Wang creator: Xishan Li creator: Deqi Xiong creator: Hang Ren creator: Huishu Chen creator: Zhonglei Ju uri: https://doi.org/10.7717/peerj.13298 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: Unconscious priming shares a common resource pool with the manipulation subsystem link: https://peerj.com/articles/13312 last-modified: 2022-04-19 description: BackgroundWorking memory can be subdivided into two relatively independent subordinate systems, the maintenance subsystem and the manipulation subsystem. Although the two subsystems are quite heterogeneous, research thus far has not adequately distinguished the resource pools of the two subsystems. Additionally, previous research on the relationship between working memory and unconscious priming is paradoxical. Different subsystems leading to different effects on unconscious priming might be the reason for the paradoxical research. Therefore, the current article aimed to distinguish the resource pools among two working-memory subsystems and to investigate the relationship between the two subsystems and unconscious priming.MethodsTo address these issues, a maintenance dual-task and a manipulation dual-task program were developed. Each participant had to separately perform the two dual tasks in a balanced order. In each dual task, participants first completed a masked priming task accompanied by working-memory load. As a control, participants completed a prime identification test to confirm that the processing of the masked prime was at the unconscious level. The maintenance dual task comprised sandwich masking trials accompanied by Sternberg trials, while the manipulation dual task comprised sandwich masking trials accompanied by N-back trials.ResultsThe results of the prime identification test indicated that the participants could not consciously perceive the masked prime of both dual tasks. The results of the working-memory task of both dual tasks indicated that the load manipulation was successful for both dual tasks. Most importantly, the results of the masking task of both dual tasks showed that an increase in working-memory load decreased the magnitude of unconscious priming in the manipulation dual task, whereas an increase in working-memory load did not decrease unconscious priming in the maintenance dual task. These observations demonstrate that the manipulation subsystem, rather than the maintenance subsystem, interferes with unconscious priming. Together with previous research, we propose a two-pool attention resource model to explain the modulation of working memory on unconscious priming by dissociating the executive resource pool of the manipulation system from the retention resource pool of the maintenance system. Thus, the current work confirms and extends the extant literature about the dependence of unconscious processing on attention resources by suggesting that unconscious priming shares a common resource pool with the manipulation subsystem. creator: Xuechen Mao creator: Anmin Li uri: https://doi.org/10.7717/peerj.13312 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Mao and Li title: Association of toll-like receptors single nucleotide polymorphisms with HBV and HCV infection: research status link: https://peerj.com/articles/13335 last-modified: 2022-04-19 description: BackgroundHepatitis B virus (HBV) and hepatitis C virus (HCV) infections have become increasingly severe worldwide and are a threat to public health. There have been a number of studies conducted recently on the relationship of single nucleotide polymorphisms (SNPs) to innate immune receptor genes such as toll-like receptors (TLRs). Some literature suggests that SNPs of TLRs are associated with HBV and HCV infection. We summarized the role of TLRs gene polymorphisms associated with HBV and HCV infections and explored their possible mechanisms of action.MethodologyPubMed and Web of Science were used to perform the literature review. Related articles and references were identified and used to analyze the role of TLRs gene polymorphism in HBV and HCV infection.ResultsTLRs gene polymorphisms may have beneficial or detrimental effects in HBV and HCV infection, and some SNPs can affect disease progression or prognosis. They affect the disease state by altering gene expression or protein synthesis; however, the mechanism of action is not clearly understood.ConclusionsSingle nucleotide polymorphisms of TLRs play a role in HBV and HCV infection, but the mechanism of action still needs to be explored in future studies. creator: Yaxin Xu creator: Wentao Xue creator: Hongwei Gao creator: Jiabo Cui creator: Lingzhi Zhao creator: Chongge You uri: https://doi.org/10.7717/peerj.13335 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Xu et al. title: Water stress and nitrogen supply affect floral traits and pollination of the white mustard, Sinapis alba (Brassicaceae) link: https://peerj.com/articles/13009 last-modified: 2022-04-18 description: Changes in environmental conditions are likely to have a complex effect on the growth of plants, their phenology, plant-pollinator interactions, and reproductive success. The current world is facing an ongoing climate change along with other human-induced environmental changes. Most research has focused on the impact of increasing temperature as a major driving force for climate change, but other factors may have important impacts on plant traits and pollination too and these effects may vary from season to season. In addition, it is likely that the effects of multiple environmental factors, such as increasing temperature, water availability, and nitrogen enrichment are not independent. Therefore, we tested the impact of two key factors—water, and nitrogen supply—on plant traits, pollination, and seed production in Sinapis alba (Brassicaceae) in three seasons defined as three temperature conditions with two levels of water and nitrogen supply in a factorial design. We collected data on multiple vegetative and floral traits and assessed the response of pollinators in the field. Additionally, we evaluated the effect of growing conditions on seed set in plants exposed to pollinators and in hand-pollinated plants. Our results show that water stress impaired vegetative growth, decreased flower production, and reduced visitation by pollinators and seed set, while high amount of nitrogen increased nectar production under low water availability in plants grown in the spring. Temperature modulated the effect of water and nitrogen availability on vegetative and floral traits and strongly affected flowering phenology and flower production. We demonstrated that changes in water and nitrogen availability alter plant vegetative and floral traits, which impacts flower visitation and consequently plant reproduction. We conclude that ongoing environmental changes such as increasing temperature, altered precipitation regimes and nitrogen enrichment may thus affect plant-pollinator interactions with negative consequences for the reproduction of wild plants and insect-pollinated crops. creator: Asma Akter creator: Jan Klečka uri: https://doi.org/10.7717/peerj.13009 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Akter and Klečka title: Concentration and quantification of Tilapia tilapinevirus from water using a simple iron flocculation coupled with probe-based RT-qPCR link: https://peerj.com/articles/13157 last-modified: 2022-04-18 description: BackgroundTilapia tilapinevirus, also known as tilapia lake virus (TiLV), is a significant virus that is responsible for the die-off of farmed tilapia across the globe. The detection and quantification of the virus using environmental RNA (eRNA) from pond water samples represents a potentially non-invasive and routine strategy for monitoring pathogens and early disease forecasting in aquaculture systems.MethodsHere, we report a simple iron flocculation method for concentrating viruses in water, together with a newly-developed hydrolysis probe quantitative RT-qPCR method for the detection and quantification of TiLV.ResultsThe RT-qPCR method designed to target a conserved region of the TiLV genome segment 9 has a detection limit of 10 viral copies per µL of template. The method had a 100% analytical specificity and sensitivity for TiLV. The optimized iron flocculation method was able to recover 16.11 ± 3.3% of the virus from water samples spiked with viral cultures. Tilapia and water samples were collected for use in the detection and quantification of TiLV disease during outbreaks in an open-caged river farming system and two earthen fish farms. TiLV was detected from both clinically sick and asymptomatic fish. Most importantly, the virus was successfully detected from water samples collected from different locations in the affected farms (i.e., river water samples from affected cages (8.50 × 103 to 2.79 × 105 copies/L) and fish-rearing water samples, sewage, and reservoir (4.29 × 103 to 3.53 × 104 copies/L)). By contrast, TiLV was not detected in fish or water samples collected from two farms that had previously experienced TiLV outbreaks and from one farm that had never experienced a TiLV outbreak. In summary, this study suggests that the eRNA detection system using iron flocculation, coupled with probe based-RT-qPCR, is feasible for use in the concentration and quantification of TiLV from water. This approach may be useful for the non-invasive monitoring of TiLV in tilapia aquaculture systems and may support evidence-based decisions on biosecurity interventions needed. creator: Suwimon Taengphu creator: Pattanapon Kayansamruaj creator: Yasuhiko Kawato creator: Jerome Delamare-Deboutteville creator: Chadag Vishnumurthy Mohan creator: Ha Thanh Dong creator: Saengchan Senapin uri: https://doi.org/10.7717/peerj.13157 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Taengphu et al. title: Differentiation patterns of emperor moths (Lepidoptera: Saturniidae: Saturniinae) of a continental island: divergent evolutionary history driven by Pleistocene glaciations link: https://peerj.com/articles/13240 last-modified: 2022-04-18 description: BackgroundOn the basis of molecular dating, Pleistocene glaciations have been proposed as the major driving force of biota speciation in the Palearctic and the pre-Quaternary origin of Amazonian taxa. However, the major driving factors in East Asia remain unclear. All 16 saturniine species inhabiting Taiwan with congeners of populations, subspecies, or species in East Asia constitute research objects for addressing the mode of speciation because of the repeated formation and disappearance of a landbridge from the Asian mainland to Taiwan during glacial cycles.MethodsThe genetic divergences of mitochondrial cytochrome c oxidase subunit I (COI) and 16S rDNA and the nuclear 28S rDNA of the saturniine species from Taiwan and the Asian mainland were assessed to determine the monophyly of each genus and species of Saturniinae. Moreover, 519 saturniine COI sequences of 114 taxa from adjacent East and Southeast Asian populations and closely related species were retrieved from GenBank and analyzed. The differentiation timing and possible origination of the insular saturniines were elucidated based on phylogenetic relationships, haplotype networks, and lineage calibrations.ResultsApproximately 90% of intraspecific COI divergence was <2%; all divergences exceeding 2% originated from comparisons between allopatric populations or subspecies. Relationship analyses revealed that multiple introductions likely occurred in insular saturniines and that some East Asian saturniines were paraphyletic as deduced by analyzing endemic insular species. Calibration dating revealed that Taiwanese endemic saturniines split from sibling Asian species 0.2–2.7 million years ago (Mya), whereas subspecific-level and population-level splitting events occurred 0.1–1.7 Mya and 0.2–1.2 Mya, respectively. Moreover, phylogenetic patterns combined with geographical distributions revealed that hill-distributed Taiwanese saturniines are closely related to those from southern China and Southeast Asia, whereas saturniines inhabiting altitudes higher than 1,500 m in Taiwan have siblings distributed in temperate Northeast Asia.DiscussionThe Global DNA Barcoding Initiative was successfully applied to study the population genetic structure in species. Most Formosan saturniines are distinct and monophyletic, reflecting the vicariant barrier of the Taiwan Strait; Pleistocene glacial cycles provided opportunities for insular saturniines to experience repeated isolation from and secondary contact with the continental mainland. Each insular saturniine may have evolved with a unique differentiation timing pattern that possibly emerged in the Early, Middle, or Late Pleistocene with these patterns differing from the consistent pattern that occurred in the temperate Palearctic and tropical Amazonian regions. Moreover, multiple migrations or artificial genetic admixtures may have also occurred, as suggested by the coexistence of two divergent lineages in a few Taiwanese saturniines. creator: Wen-Bin Yeh creator: Cheng-Lung Tsai creator: Thai-Hong Pham creator: Shipher Wu creator: Chia-Wei Chang creator: Hong-Minh Bui uri: https://doi.org/10.7717/peerj.13240 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yeh et al. title: Five new mitogenomes sequences of Calidridine sandpipers (Aves: Charadriiformes) and comparative mitogenomics of genus Calidris link: https://peerj.com/articles/13268 last-modified: 2022-04-18 description: BackgroundThe genus Calidris (Charadriiformes, Scolopacidae) includes shorebirds known as dunlin, knots, and sanderlings. The relationships between species nested within Calidris, including Eurynorynchus, Limicola and Aphriza, are not well-resolved.MethodsSamples were collected from Xiaoyangkou, Rudong County, Jiangsu Province, China. Mitogenomes were sequenced using the Illumina Novaseq 6000 platform for PE 2 × 150 bp sequencing, and then checked for PCR products. Protein-coding genes were determined using an Open Reading Frame Finder. tRNAscan-SE, MITOS, and ARWEN were used to confirm tRNA and rRNA annotations. Bioinformatic analyses were conducted using DnaSP 5.1 and MEGA X. Phylogenic trees were constructed using maximum likelihood and Bayesian analyses.ResultsWe sequenced and annotated the mitogenome of five species and obtained four complete mitogenomes and one nearly complete mitogenome. Circular mitogenomes displayed moderate size variation, with a mean length of 16,747 bp, ranging from 16,642 to 16,791 bp. The mitogenome encoded a control region and a typical set of 37 genes containing two rRNA genes, 13 protein-coding genes, and 22 tRNA genes. There were four start codons, four stop codons, and one incomplete stop codon (T–). The nucleotide composition was consistently AT-biased. The average uncorrected pairwise distances revealed heterogeneity in the evolutionary rate for each gene; the COIII had a slow evolutionary rate, whereas the ATP8 gene had a fast rate. dN/dS analysis indicated that the protein-coding genes were under purifying selection. The genetic distances between species showed that the greatest genetic distance was between Eurynorhynchus pygmeus and Limicola falcinellus (22.5%), and the shortest was between E. pygmeus and Calidris ruficollis (12.8%). Phylogenetic trees revealed that Calidris is not a monophyletic genus, as species from the genera Eurynorynchus and Limicola were nested within Calidris. The molecular data obtained in this study are valuable for research on the taxonomy, population genetics, and evolution of birds in the genus Calidris. creator: Wan Chen creator: Keer Miao creator: Junqi Wang creator: Hao Wang creator: Wan Sun creator: Sijia Yuan creator: Site Luo creator: Chaochao Hu creator: Qing Chang uri: https://doi.org/10.7717/peerj.13268 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Chen et al. title: Mitogenomics and phylogenetics of twelve species of African Saturniidae (Lepidoptera) link: https://peerj.com/articles/13275 last-modified: 2022-04-18 description: African Saturniidae (Lepidoptera) include numerous species consumed at the caterpillar stage throughout the continent, and their importance to local communities as a source of nutrition and seasonal income cannot be overestimated. However, baseline genetic data with utility for the characterization of their diversity, phylogeography and phylogenetic relationships have remained scarce compared to their Asian counterparts. To bridge this gap, we sequenced the mitochondrial genomes of 12 species found in southern Africa for comparative mitogenomics and phylogenetic reconstruction of the family, including the first representatives of the tribes Eochroini and Micragonini. Mitochondrial gene content and organization were conserved across all Saturniidae included in the analyses. The phylogenetic positions of the 12 species were assessed in the context of publicly available mitogenomes using Bayesian inference and maximum likelihood (ML) methods. The monophyly of the tribes Saturniini, Attacini, Bunaeini and Micragonini, the sister relationship between Saturniini and Attacini, and the placement of Eochroa trimenii and Rhodinia fugax in the tribes Eochroini and Attacini, respectively, were strongly supported. These results contribute to significantly expanding genetic data available for African Saturniidae and allow for the development of new mitochondrial markers in future studies. creator: Zwannda Nethavhani creator: Rieze Straeuli creator: Kayleigh Hiscock creator: Ruan Veldtman creator: Andrew Morton creator: Rolf G. Oberprieler creator: Barbara van Asch uri: https://doi.org/10.7717/peerj.13275 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Nethavhani et al.