title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=313 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Phylogeny and divergence time estimation of Io moths and relatives (Lepidoptera: Saturniidae: Automeris) link: https://peerj.com/articles/17365 last-modified: 2024-05-30 description: The saturniid moth genus Automeris includes 145 described species. Their geographic distribution ranges from the eastern half of North America to as far south as Peru. Automeris moths are cryptically colored, with forewings that resemble dead leaves, and conspicuously colored, elaborate eyespots hidden on their hindwings. Despite their charismatic nature, the evolutionary history and relationships within Automeris and between closely related genera, remain poorly understood. In this study, we present the most comprehensive phylogeny of Automeris to date, including 80 of the 145 described species. We also incorporate two morphologically similar hemileucine genera, Pseudautomeris and Leucanella, as well as a morphologically distinct genus, Molippa. We obtained DNA data from both dry-pinned and ethanol-stored museum specimens and conducted Anchored Hybrid Enrichment (AHE) sequencing to assemble a high-quality dataset for phylogenetic analysis. The resulting phylogeny supports Automeris as a paraphyletic genus, with Leucanella and Pseudautomeris nested within, with the most recent common ancestor dating back to 21 mya. This study lays the foundation for future research on various aspects of Automeris biology, including geographical distribution patterns, potential drivers of speciation, and ecological adaptations such as antipredator defense mechanisms. creator: Chelsea Skojec creator: Chandra Earl creator: Christian D. Couch creator: Paul Masonick creator: Akito Y. Kawahara uri: https://doi.org/10.7717/peerj.17365 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Skojec et al. title: Zoonotic spillover and viral mutations from low and middle-income countries: improving prevention strategies and bridging policy gaps link: https://peerj.com/articles/17394 last-modified: 2024-05-30 description: The increasing frequency of zoonotic spillover events and viral mutations in low and middle-income countries presents a critical global health challenge. Contributing factors encompass cultural practices like bushmeat consumption, wildlife trade for traditional medicine, habitat disruption, and the encroachment of impoverished settlements onto natural habitats. The existing “vaccine gap” in many developing countries exacerbates the situation by allowing unchecked viral replication and the emergence of novel mutant viruses. Despite global health policies addressing the root causes of zoonotic disease emergence, there is a significant absence of concrete prevention-oriented initiatives, posing a potential risk to vulnerable populations. This article is targeted at policymakers, public health professionals, researchers, and global health stakeholders, particularly those engaged in zoonotic disease prevention and control in low and middle-income countries. The article underscores the importance of assessing potential zoonotic diseases at the animal-human interface and comprehending historical factors contributing to spillover events. To bridge policy gaps, comprehensive strategies are proposed that include education, collaborations, specialized task forces, environmental sampling, and the establishment of integrated diagnostic laboratories. These strategies advocate simplicity and unity, breaking down barriers, and placing humanity at the forefront of addressing global health challenges. Such a strategic and mental shift is crucial for constructing a more resilient and equitable world in the face of emerging zoonotic threats. creator: Zulfqarul Haq creator: Junaid Nazir creator: Tasaduq Manzoor creator: Afnan Saleem creator: H. Hamadani creator: Azmat Alam Khan creator: Sahar Saleem Bhat creator: Priyanka Jha creator: Syed Mudasir Ahmad uri: https://doi.org/10.7717/peerj.17394 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Haq et al. title: The COVID-19 pandemic “anthropause” decreased plastic ingestion in neotropic cormorants Nannopterum brasilianus in Lima, Peru link: https://peerj.com/articles/17407 last-modified: 2024-05-30 description: BackgroundThe anthropause during the recent COVID-19 pandemic provided a unique opportunity to examine the impact of human activity on seabirds. Lockdowns in Peru prevented people from visiting coastal areas, thereby reducing garbage disposal on beaches and the movement of microplastics into the ocean. This cessation of activities likely led to a temporary decrease in plastic pollution in coastal regions. We aimed to investigate this phenomenon in inshore-feeding neotropic cormorants (Nannopterum brasilianus) along the Circuito de Playas Costa Verde (CPCV), situated on the coastal strip of Lima, Peru (∼ 11 million people).MethodsWe collected and analyzed fresh pellets along the CPCV before (over 11 months) and during the pandemic lockdowns (over 8 months).ResultsOur findings revealed a significant reduction in the occurrence of plastic in pellets during the pandemic period (% Oc = 2.47, n = 647 pellets) compared to pre-pandemic conditions (% Oc = 7.13, n = 800 pellets). The most common plastic debris item found in the pellets was threadlike microplastic. Additionally, our study highlights the direct correlation between human presence on beaches and the quantity of microplastics (mainly threadlike) found in cormorant pellets. We suggest that the reintroduction of these materials into the sea, previously accumulated on the coast, is likely facilitated by the movement and activity of beachgoers toward the ocean. creator: Laura Catalina Porras-Parra creator: Carlos B. Zavalaga creator: Alvaro Rios uri: https://doi.org/10.7717/peerj.17407 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Porras-Parra et al. title: Metagenomic insight into taxonomic composition, environmental filtering and functional redundancy for shaping worldwide modern non-lithifying microbial mats link: https://peerj.com/articles/17412 last-modified: 2024-05-30 description: Modern microbial mats are relictual communities mostly found in extreme environments worldwide. Despite their significance as representatives of the ancestral Earth and their important roles in biogeochemical cycling, research on microbial mats has largely been localized, focusing on site-specific descriptions and environmental change experiments. Here, we present a global comparative analysis of non-lithifying microbial mats, integrating environmental measurements with metagenomic data from 62 samples across eight sites, including two new samples from the recently discovered Archaean Domes from Cuatro Ciénegas, Mexico. Our results revealed a notable influence of environmental filtering on both taxonomic and functional compositions of microbial mats. Functional redundancy appears to confer resilience to mats, with essential metabolic pathways conserved across diverse and highly contrasting habitats. We identified six highly correlated clusters of taxa performing similar ecological functions, suggesting niche partitioning and functional specialization as key mechanisms shaping community structure. Our findings provide insights into the ecological principles governing microbial mats, and lay the foundation for future research elucidating the intricate interplay between environmental factors and microbial community dynamics. creator: Mariette Viladomat Jasso creator: Manuel García-Ulloa creator: Icoquih Zapata-Peñasco creator: Luis E. Eguiarte creator: Valeria Souza uri: https://doi.org/10.7717/peerj.17412 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Viladomat Jasso et al. title: Seasonal dynamics and environmental drivers of tissue and mucus microbiomes in the staghorn coral Acropora pulchra link: https://peerj.com/articles/17421 last-modified: 2024-05-30 description: BackgroundRainfall-induced coastal runoff represents an important environmental impact in near-shore coral reefs that may affect coral-associated bacterial microbiomes. Shifts in microbiome community composition and function can stress corals and ultimately cause mortality and reef declines. Impacts of environmental stress may be site specific and differ between coral microbiome compartments (e.g., tissue versus mucus). Coastal runoff and associated water pollution represent a major stressor for near-shore reef-ecosystems in Guam, Micronesia.MethodsAcropora pulchra colonies growing on the West Hagåtña reef flat in Guam were sampled over a period of 8 months spanning the 2021 wet and dry seasons. To examine bacterial microbiome diversity and composition, samples of A. pulchra tissue and mucus were collected during late April, early July, late September, and at the end of December. Samples were collected from populations in two different habitat zones, near the reef crest (farshore) and close to shore (nearshore). Seawater samples were collected during the same time period to evaluate microbiome dynamics of the waters surrounding coral colonies. Tissue, mucus, and seawater microbiomes were characterized using 16S DNA metabarcoding in conjunction with Illumina sequencing. In addition, water samples were collected to determine fecal indicator bacteria (FIB) concentrations as an indicator of water pollution. Water temperatures were recorded using data loggers and precipitation data obtained from a nearby rain gauge. The correlation structure of environmental parameters (temperature and rainfall), FIB concentrations, and A. pulchra microbiome diversity was evaluated using a structural equation model. Beta diversity analyses were used to investigate spatio-temporal trends of microbiome composition.ResultsAcropora pulchra microbiome diversity differed between tissues and mucus, with mucus microbiome diversity being similar to the surrounding seawater. Rainfall and associated fluctuations of FIB concentrations were correlated with changes in tissue and mucus microbiomes, indicating their role as drivers of A. pulchra microbiome diversity. A. pulchra tissue microbiome composition remained relatively stable throughout dry and wet seasons; tissues were dominated by Endozoicomonadaceae, coral endosymbionts and putative indicators of coral health. In nearshore A. pulchra tissue microbiomes, Simkaniaceae, putative obligate coral endosymbionts, were more abundant than in A. pulchra colonies growing near the reef crest (farshore). A. pulchra mucus microbiomes were more diverse during the wet season than the dry season, a distinction that was also associated with drastic shifts in microbiome composition. This study highlights the seasonal dynamics of coral microbiomes and demonstrates that microbiome diversity and composition may differ between coral tissues and the surface mucus layer. creator: Therese C. Miller creator: Bastian Bentlage uri: https://doi.org/10.7717/peerj.17421 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Miller and Bentlage title: The unexpected effect of the compound microbial agent NP-M2 on microbial community dynamics in a nonylphenol-contaminated soil: the self-stability of soil ecosystem link: https://peerj.com/articles/17424 last-modified: 2024-05-30 description: BackgroundNonylphenol (NP) is widely recognized as a crucial environmental endocrine-disrupting chemical and persistent toxic substance. The remediation of NP-contaminated sites primarily relies on biological degradation. Compound microbial products, as opposed to pure strains, possess a greater variety of metabolic pathways and can thrive in a wider range of environmental conditions. This characteristic is believed to facilitate the synergistic degradation of pollutants. Limited research has been conducted to thoroughly examine the potential compatibility of compound microbial agents with indigenous microflora, their ability to function effectively in practical environments, their capacity to enhance the dissipation of NP, and their potential to improve soil physicochemical and biological characteristics.MethodsIn order to efficiently eliminate NP in contaminated soil in an eco-friendly manner, a simulation study was conducted to investigate the impact of bioaugmentation using the functional compound microbial agent NP-M2 at varying concentrations (50 and 200 mg/L) on the dynamics of the soil microbial community. The treatments were set as follows: sterilized soil with 50 mg/kg NP (CK50) or 200 mg/kg NP (CK200); non-sterilized soil with 50 mg/kg NP (TU50) or 200 mg/kg NP (TU200); non-sterilized soil with the compound microbial agent NP-M2 at 50 mg/kg NP (J50) or 200 mg/kg NP (J200). Full-length 16S rRNA analysis was performed using the PacBio Sequel II platform.ResultsBoth the indigenous microbes (TU50 and TU200 treatments) and the application of NP-M2 (J50 and J200 treatments) exhibited rapid NP removal, with removal rates ranging from 93% to 99%. The application of NP-M2 further accelerated the degradation rate of NP for a subtle lag period. Although the different treatments had minimal impacts on the soil bacterial α-diversity, they significantly altered the β-diversity and composition of the bacterial community. The dominant phyla were Proteobacteria (35.54%–44.14%), Acidobacteria (13.55%–17.07%), Planctomycetes (10.78%–11.42%), Bacteroidetes (5.60%–10.74%), and Actinobacteria (6.44%–8.68%). The core species were Luteitalea_pratensis, Pyrinomonas_methylaliphatogenes, Fimbriiglobus_ruber, Longimicrobium_terrae, and Massilia_sp003590855. The bacterial community structure and taxon distribution in polluted soils were significantly influenced by the activities of soil catalase, sucrase, and polyphenol oxidase, which were identified as the major environmental factors. Notably, the concentration of NP and, to a lesser extent, the compound microbial agent NP-M2 were found to cause major shifts in the bacterial community. This study highlights the importance of conducting bioremediation experiments in conjunction with microbiome assessment to better understand the impact of bioaugmentation/biostimulation on the potential functions of complex microbial communities present in contaminated soils, which is essential for bioremediation success. creator: Zhaoliang Chen creator: Juanqin Zhang creator: Weiguang Lv creator: Hanlin Zhang creator: Shuangxi Li creator: Haiyun Zhang creator: Yue Shen creator: Chunnu Geng creator: Naling Bai uri: https://doi.org/10.7717/peerj.17424 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Chen et al. title: Sucrose rinse modulates the salivary behavior of carbonic anhydrase VI and its buffering capacity: a longitudinal study in 4 to 6.5-year-old children link: https://peerj.com/articles/17429 last-modified: 2024-05-30 description: BackgroundCarbonic anhydrase VI (CA VI) is crucial in regulating oral pH and predicting susceptibility to dental caries. The hypothesis posits that caries activity may alter the CA VI function, diminishing its capacity to regulate pH effectively and potentially exacerbating cariogenic challenges. This 1-year cohort study sought to investigate the enzymatic activity of salivary CA VI and buffering capacity following a 20% sucrose rinse in 4 to 6.5-year-old children.MethodThis research involved 46 volunteers categorized into three groups based on their caries status after follow-up: caries-free (CFee), arrested caries (CArrested), and caries active (CActive). Children underwent visible biofilm examination and saliva collection for salivary flow rate, buffering capacity, and CA VI analyses before and after a 20% sucrose rinse.ResultsA reduction in the buffering capacity was observed after sucrose rinse in all groups. The CA VI activity decreased significantly in CFee and CArrested groups after sucrose rinse, although it did not change in the CActive group. An improvement in the buffering capacity and salivary flow rate was found at follow-up when compared with the baseline. After 1-year follow-up, buffering capacity and salivary flow rate increased in all groups, whilst the CA VI activity reduced only in CFree and CArrested children.ConclusionSucrose rinse universally reduces the salivary buffering capacity, while caries activity may disrupt CA VI activity response during a cariogenic challenge. After a year, increased salivary flow enhances buffering capacity but not CA VI activity in caries-active children. creator: Thayse Rodrigues de Souza creator: Bruna Raquel Zancope creator: Emerson Tavares de Sousa creator: Thais Manzano Parisotto creator: Marcelo Rocha Marques creator: Marinês Nobre dos Santos uri: https://doi.org/10.7717/peerj.17429 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Souza et al. title: Crizotinib inhibits the metabolism of tramadol by non-competitive suppressing the activities of CYP2D1 and CYP3A2 link: https://peerj.com/articles/17446 last-modified: 2024-05-30 description: ObjectivesTo investigate the interaction between tramadol and representative tyrosine kinase inhibitors, and to study the inhibition mode of drug-interaction.MethodsLiver microsomal catalyzing assay was developed. Sprague-Dawley rats were administrated tramadol with or without selected tyrosine kinase inhibitors. Samples were prepared and ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS) was used for analysis. Besides, liver, kidney, and small intestine were collected and morphology was examined by hematoxyline-eosin (H&E) staining. Meanwhile, liver microsomes were prepared and carbon monoxide differential ultraviolet radiation (UV) spectrophotometric quantification was performed.ResultsAmong the screened inhibitors, crizotinib takes the highest potency in suppressing the metabolism of tramadol in rat/human liver microsome, following non-competitive inhibitory mechanism. In vivo, when crizotinib was co-administered, the AUC value of tramadol increased compared with the control group. Besides, no obvious pathological changes were observed, including cell morphology, size, arrangement, nuclear morphology with the levels of alanine transaminase (ALT) and aspartate transaminase (AST) increased after multiple administration of crizotinib. Meanwhile, the activities of CYP2D1 and CYP3A2 as well as the total cytochrome P450 abundance were found to be decreased in rat liver of combinational group.ConclusionsCrizotinib can inhibit the metabolism of tramadol. Therefore, this recipe should be vigilant to prevent adverse reactions. creator: Nanyong Gao creator: Xiaoyu Xu creator: Feng Ye creator: Xin-yue Li creator: Chengqi Lin creator: Xiu-wei Shen creator: Jianchang Qian uri: https://doi.org/10.7717/peerj.17446 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Gao et al. title: Analysis of rotational grazing management for sheep in mixed grassland link: https://peerj.com/articles/17453 last-modified: 2024-05-30 description: Sown mixed grassland is rarely used for livestock raising and grazing; however, different forages can provide various nutrients for livestock, which may be beneficial to animal health and welfare. We established a sown mixed grassland and adopted a rotational grazing system, monitored the changes in aboveground biomass and sheep weights during the summer grazing period, measured the nutrients of forage by near-infrared spectroscopy, tested the contents of medium- and long-chain fatty acids by gas chromatography, and explored an efficient sheep fattening system that is suitable for agro-pastoral interlacing areas. The results showed that the maximum forage supply in a single grazing paddock was 4.6 kg DM/d, the highest dry matter intake (DMI) was 1.80 kg DM/ewe/d, the average daily weight gain (ADG) was 193.3 g, the DMI and ADG were significantly correlated (P < 0.05), and the average feed weight gain ratio (F/G) reached 8.02. The average crude protein and metabolizable energy intake by sheep were 286 g/ewe/d and 18.5 MJ/ewe/d respectively, and the n-6/n-3 ratio of polyunsaturated fatty acids in mutton was 2.84. The results indicated that the sheep fattening system had high feed conversion efficiency, could improve the yield and quality of sheep, and could be promoted in suitable regions. creator: Zongyong Tong creator: Xianlin Dai creator: Yu Wang creator: Xianglin Li creator: Feng He creator: Guomei Yin uri: https://doi.org/10.7717/peerj.17453 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Tong et al. title: Genomic insights into CKX genes: key players in cotton fibre development and abiotic stress responses link: https://peerj.com/articles/17462 last-modified: 2024-05-30 description: Cytokinin oxidase/dehydrogenase (CKX), responsible for irreversible cytokinin degradation, also controls plant growth and development and response to abiotic stress. While the CKX gene has been studied in other plants extensively, its function in cotton is still unknown. Therefore, a genome-wide study to identify the CKX gene family in the four cotton species was conducted using transcriptomics, quantitative real-time PCR (qRT-PCR) and bioinformatics. As a result, in G. hirsutum and G. barbadense (the tetraploid cotton species), 87 and 96 CKX genes respectively and 62 genes each in G. arboreum and G. raimondii, were identified. Based on the evolutionary studies, the cotton CKX gene family has been divided into five distinct subfamilies. It was observed that CKX genes in cotton have conserved sequence logos and gene family expansion was due to segmental duplication or whole genome duplication (WGD). Collinearity and multiple synteny studies showed an expansion of gene families during evolution and purifying selection pressure has been exerted. G. hirsutum CKX genes displayed multiple exons/introns, uneven chromosomal distribution, conserved protein motifs, and cis-elements related to growth and stress in their promoter regions. Cis-elements related to resistance, physiological metabolism and hormonal regulation were identified within the promoter regions of the CKX genes. Expression analysis under different stress conditions (cold, heat, drought and salt) revealed different expression patterns in the different tissues. Through virus-induced gene silencing (VIGS), the GhCKX34A gene was found to improve cold resistance by modulating antioxidant-related activity. Since GhCKX29A is highly expressed during fibre development, we hypothesize that the increased expression of GhCKX29A in fibres has significant effects on fibre elongation. Consequently, these results contribute to our understanding of the involvement of GhCKXs in both fibre development and response to abiotic stress. creator: Rasmieh Hamid creator: Feba Jacob creator: Zahra Ghorbanzadeh creator: Mojtaba Khayam Nekouei creator: Mehrshad Zeinalabedini creator: Mohsen Mardi creator: Akram Sadeghi creator: Sushil Kumar creator: Mohammad Reza Ghaffari uri: https://doi.org/10.7717/peerj.17462 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hamid et al.