title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=45 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Licinophilus depressus n. gen., sp. n. (Eugregarinida: Stenophoridae) from Licinus depressus (Coleoptera: Carabidae) link: https://peerj.com/articles/20099 last-modified: 2025-10-01 description: The paper focuses on a new species of gregarines—Licinophilus depressus n. gen. sp. n., which was found in Licinus depressus (Paykull, 1790) (Coleoptera, Carabidae). The individuals of L. depressus ground beetle were collected on the bank of the Dnipro River, Ukraine and examined for the presence of gregarines in the guts. In the parasites discovered in the midguts, we measured the morphological parameters and their ratios, analyzing how they change in relation to the age of the specimens. According to our measurements, the species turned out to be incomparable to any of the ones described in the scientific literature. Because the gregarine specimens formed syzygies at late stages, were observed to have monogenous life cycle and a septum between the protomerite and deutomerite at all stages of development, and also rudimentary epimerite, they were classified to the Septatorina suborder, Stenophoricae superfamily, Stenophoridae family, and distinguished into a new genus due to the fluctuating septum between the protomerite and deutomerite.With age, the width of the segments does not change, while the gregarine increases in size due to significant elongation of the deutomerite. The most varying parameters of this species of gregarines were the deutomerite length (DL), the deutomerite length axis (DLA), and the total length of gregarine (TL) for which the coefficient of variation exceeded 30%. All the studied morphometric indices, except for the ratio of the deutomerite length to the deutomerite width (DL/DW), exhibited weak association with the age and sizes of gregarines. The indices such as the ratios of the epimerite length to the length of the protomerite-epimerite complex (EL/PECL), the protomerite length to the protomerite-epimerite complex (PL/PECL), the epimerite length to the epimerite width (EL/EW), the protomerite length to the protomerite width (PL/PW), the protomerite width to the septum width (PW/SW), the deutomerite width to the protomerite width (DW/PW), the nucleus length to nucleus width (NL/NW), and also DLA remained constant in this gregarine during growth, and therefore they can be used as constant diagnostic features. creator: Viktoriia Lazurska creator: Viktor V. Brygadyrenko uri: https://doi.org/10.7717/peerj.20099 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lazurska and Brygadyrenko title: Response of soil nematode community structure, diversity, and ecological network to elevation gradients in wild fruit forest of Tianshan Mountain, China link: https://peerj.com/articles/20090 last-modified: 2025-10-01 description: BackgroundThe Tianshan wild fruit forest is a special deciduous broad-leaved forest located in the mountains of central Asia.MethodsTo reveal how the Tianshan wild fruit forest ecosystem responds to environmental changes along an elevation gradient, we used the soil nematode index, which is widely recognized as a key indicator of soil health. This study focused on the nematode communities beneath Juglans cathayensis and Malus sieversii, two typical constructive species in the Tianshan wild fruit forest. Six elevation levels (1,480, 1,401, 1,351, 1,305, 1,252, and 1,207 m) were selected, and a nematode co-occurrence network was constructed for each elevation. We analyzed the abundance, diversity, ecological indices, and network complexity of soil nematode communities across different elevation gradients. In addition, we explored the relationships among environmental factors, soil multifunctionality, and nematode community characteristics.ResultsOur results showed that: (1) a total of 60,795 nematodes, representing 80 genera were collected. Total abundance, trophic group abundance, and diversity of nematodes peaked at middle elevations. However, in M. sieversii, nematode diversity increased with elevation. (2) The soil food web in the wild fruit forest exhibited a relatively high metabolic rate (nematode channel ratio > 0.5). (3) In J. cathayensis, the nematode ecological network was more complex and tightly interconnected at low elevations. whereas in M. sieversii, greater network complexity was observed at high elevations. (4) Environmental factors (organic matter, pH, total phosphorus, available potassium, total potassium) significantly affected the composition of nematode trophic groups (p < 0.05). Moreover, network complexity was a key factor influencing soil multifunctionality. This study provides a theoretical foundation for long-term monitoring of soil health in Tianshan wild fruit forest. creator: Yulu Zhang creator: Mengyu Yang creator: Wenxin Liu creator: Zhicheng Jiang creator: Yang Zhao creator: Gaofeng Li creator: Jing Cao creator: Minru Zhang creator: Haijun Yang creator: Dong Cui uri: https://doi.org/10.7717/peerj.20090 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhang et al. title: Rhodelphis edaphicus sp. nov.—a new lineage of predatory archaeplastids from agricultural soil link: https://peerj.com/articles/20071 last-modified: 2025-10-01 description: Predatory flagellated protists remain extremely poorly studied but often represent the most important deep-branching lineages of eukaryotic evolution. One of the most enigmatic and poorly studied predatory protist groups is Rhodelphidia. These are heterotrophic flagellates, yet belong to the primarily photosynthetic supergroup Archaeplastida and are related to red algae in particular. Here, we describe a new rhodelphid species and the first known soil representative of this group, Rhodelphis edaphicus sp. nov., which was isolated into a clonal culture from agricultural soil. The novel species actively phagocytoses the cells of other protists and bacteria. Using light and electron microscopy, we examined its morphology and identified several novel features, including complex tripartite mastigonemes—not previously reported for this taxon—which link rhodelphids with Cryptista. We expanded a previous 18S rRNA dataset for rhodelphids with environmental sequences and revealed the presence of a soil clade to which the new species belongs. A search of soil metabarcoding data yielded several unknown rhodelphid lineages. Analysis of the distribution of known species and environmental DNA data revealed that rhodelphids inhabit diverse geographic locations worldwide and are found in a variety of habitats, including marine and fresh waters, soils, and, most likely, anaerobic bottom sediments near fumaroles. The diversity of modern rhodelphid habitats, including soil ecosystems, highlights the different environments in which early stages of Archaeplastida evolution may have occurred. The identification and comprehensive study of new lineages of basal archaeplastids provides new insights into the complex evolutionary processes associated with early eukaryotic radiation, the emergence of photosynthesis and plastid evolution that gave rise to the diversification of numerous forms of algae and land plants. creator: Artem O. Belyaev creator: Dmitry G. Zagumyonnyi creator: Elena A. Gerasimova creator: German A. Sozonov creator: Denis V. Tikhonenkov uri: https://doi.org/10.7717/peerj.20071 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Belyaev et al. title: The first leech body fossil predates estimated hirudinidan origins by 200 million years link: https://peerj.com/articles/19962 last-modified: 2025-10-01 description: Clitellata is a major annelid clade comprising oligochaetes (e.g., earthworms) and hirudineans (e.g., leeches). Due to their scant fossil record, the origins of clitellates, particularly Hirudinea, are poorly known. Here, we describe the first leech body fossil, Macromyzon siluricus, gen. et sp. nov., from the Brandon Bridge Formation (Waukesha Lagerstätte). This fossil, which is preserved in exceptional detail, possesses several hirudinean soft-tissue synapomorphies–including a large sucker at the posterior end and sub-divided segments–and phylogenetic analyses resolve Macromyzon siluricus as a stem leech. Its age, 437.5–436.5 Ma, is consistent with early age estimates for the origin of clitellates, and predates molecular-clock-based estimates of hirudinidan origins by at least 200 million years. These findings suggest that the earliest true leeches were marine and that, contrary to prevailing hypotheses, were unlikely to have fed on vertebrate blood. creator: Danielle de Carle creator: Rafael Eiji Iwama creator: Andrew J. Wendruff creator: Loren E. Babcock creator: Karma Nanglu uri: https://doi.org/10.7717/peerj.19962 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 de Carle et al. title: Biochemical composition, β-glucan and phenolic content of a marine diatom Chaetoceros muelleri cultivated in Guillard’s modified medium link: https://peerj.com/articles/20098 last-modified: 2025-09-30 description: The biochemical compositions of diatoms are important for agricultural and pharmaceutical applications, and they vary according to nutrients and physical factors. To study the influence of carbonate and nitrogen source supplementation in the medium on the chemical composition of the marine diatom Chaetoceros muelleri, Guillard’s medium was modified for this study. Three types of Guillard medium were prepared including standard Guillard medium (T1), modified Guillard medium (0.005 g/L bicarbonate supplement, T2), and 50% nitrogen reducing medium (T3). Results showed that the maximum biomass was observed at T3 (5.75 × 106 cell/mL), which was significantly different (p < 0.05) from that at T1 (3.85 ± 0.13 × 106 cells/mL) but did not differ from that at T2 (4.03 ± 0.08 × 106 cells/mL). T3 contained the highest level of carbohydrates (13.71 ± 1.56 ), with a statistically significant difference (p < 0.05) from T1 (5.81 ± 0.50) and T2 (6.90 ± 1.14). The total lipid content in T3 (4.34 ± 0.03) was significantly greater (p < 0.05) than that in T1 (1.1 ± 0.08) and T2 (2.21 ± 0.62). The protein content in T1 (94.84 ± 0.08 mg/g) was significantly higher (p < 0.05) compared to that in T2 (31.39 ± 0.72 mg/g) and T3 (30.91 ± 0.38 mg/g). The highest β-glucan level was measured in T3 (0.4 1 ± 0.01 g/L), and statistical analysis revealed a significant difference (p < 0.05) from that in T1 (0.41 ± 0.01 gL−1) and T2 (0.41 ± 0.01 gL−1). The phenolic content in T1 was 14.91 ± 0.97, while those in T2 and T3 were 4.44 ± 0.11 and 4.16 ± 0.17 μg/mg gallic acid equivalents (GAE), respectively. Antioxidation examination revealed the highest value at 94.59 ± 0.04 mg mL−1 extract in T3, followed by T1 (89.21 ± 1.71 mg mL−1 extract) and T2 (10.66 ± 0.38). Phenolic content showed the values for T1, T2 and T3 were 49.44 ± 4.49, 47.61 ± 5.45, and 53.23 ± 6.61 mg ascorbic acid, respectively. Statistical analysis revealed that the phenolic content in T1 significantly higher differed (p < 0.05) from that in T2 and T3. In contrast, the 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid (ABTS) scavenging ability significantly differed (p < 0.05) among T3, T1, and T2 according to the 1,1-diphenyl-2-picrylhydrazyl (DPPH) scavenging ability and reducing power. The presence of β-glucan in the diatom extracts was confirmed by the FTIR spectrum data at wavenumbers 1,065 and 1,038 cm−1, whereas the LCMS spectrum confirmed the presence of gluconic acid at m/z 198, 196, and 194. Our results demonstrate that the modified Guillard T3 medium is optimal for cultivating C. muelleri to enhance the production of carbohydrates, lipids, proteins, and β-glucan. These findings are critical for advancing the large-scale production of diatom-derived biochemical components, particularly for pharmaceutical applications. creator: Sulaiman Madyod creator: Suwit Wuthisuthimethavee creator: Patchara Pedpradab creator: Rachow Khaochamnan creator: Suwanna Pholmai creator: Thitikorn Prombanchong uri: https://doi.org/10.7717/peerj.20098 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Madyod et al. title: Identification and analysis of the expansin gene family in yam link: https://peerj.com/articles/20093 last-modified: 2025-09-30 description: Expansins are a group of proteins that loosen plant cell walls and cellulose materials and are involved in regulating plant cell growth and diverse developmental processes. However, a systematic study of the Dioscorea opposita expansin (DoEXP) gene family has not yet been conducted. In this study, we used publicly available genomic data from yam to identify members of the DoEXP gene family and analyse its physicochemical properties, phylogeny and expression pattern using bioinformatics software. Thirty EXP genes were identified from the yam genome and can be classified into four subfamilies, DoEXPA, DoEXPB, DoEXLA, and DoEXLB, which are distributed across 14 chromosomes. All EXP proteins contain two conserved structural domains (DPBB_1 and expansin_C) and have highly similar motif compositions and exon–intron structures. Examination of the promoter regions of these genes revealed the presence of cis-acting elements associated with growth and development, phytohormone signaling, and abiotic stress. The collinearity analysis revealed that segmental duplication is the primary cause of the expansion of the DoEXP gene family. Gene Ontology (GO) enrichment analysis revealed that DoEXP genes (DoEXPs) are significantly associated with root elongation and cell differentiation processes. Utilizing quantitative real-time polymerase chain reaction (qPCR), the expression patterns of nine selected DoEXPs were validated. The results of this study are helpful for understanding the molecular functions of expansin proteins in yam tuber expansion and provide a theoretical basis for revealing the molecular regulatory mechanism of yam tuber growth and development. creator: Xing Qiao creator: Shuai Yuan creator: Jing Wei creator: Changzhou Li creator: Lan Lan creator: Xuerui He creator: Aiqin Wang creator: Jie Zhan creator: Longfei He creator: Dong Xiao uri: https://doi.org/10.7717/peerj.20093 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Qiao et al. title: DNA damage-dependent mechanisms of ionizing radiation-induced cellular senescence link: https://peerj.com/articles/20087 last-modified: 2025-09-30 description: Cellular senescence can be broadly categorized into replicative senescence and stress-induced premature senescence. Replicative senescence mainly results from the progressive shortening of telomeres during successive cell divisions, eventually leading to the arrest of cell division and the onset of senescence. In contrast, stress-induced premature senescence is typically triggered by environmental factors, such as ionizing radiation (IR). While the DNA damage induced by IR has been extensively studied, the specific mechanisms by which IR induces cellular senescence via DNA damage remain incompletely understood. This review focuses on IR-induced cellular senescence, particularly in the context of DNA damage. Understanding these mechanisms provides insight into the long-term effects of radiation on cellular senescence and lays the groundwork for future research into the effects of radiation on aging processes. creator: Jiebing Guan creator: Tuo Li creator: Feifei Ma creator: Ning Wang creator: Huanteng Zhang creator: Jiale Li creator: Jianguo Li creator: Chang Xu creator: Qiang Liu uri: https://doi.org/10.7717/peerj.20087 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Guan et al. title: Metagenomes and metagenome-assembled genomes from tidal lagoons at a New York City waterfront park link: https://peerj.com/articles/20081 last-modified: 2025-09-30 description: New York City parks serve as potential sites of both social and physical climate resilience, but relatively little is known about how microbial organisms and processes contribute to the functioning of these deeply human-impacted ecosystems. We report the sequencing and analysis of 15 shotgun metagenomes, including the reconstruction of 129 high-quality metagenome-assembled genomes, from tidal lagoons and bay water at Bush Terminal Piers Park in Brooklyn, NY sampled from July to September 2024. Our metagenomic database for this site provides an important baseline for ongoing studies of the microbial communities of public parks and waterfront areas in NYC. In particular, we provide rich functional and taxonomic annotations that enable the use of these metagenomes and metagenome-assembled genomes for a wide variety of downstream applications. creator: Sally Kong creator: Eliana Abrams creator: Yehuda Binik creator: Christina Cappelli creator: Mathew Chu creator: Taiyo Cornett creator: Isayah Culbertson creator: Epifania Garcia creator: Jada Henry creator: Kristy Lam creator: D.B. Lampman creator: Grace Morenko creator: Illusion Rivera creator: Tanasia Swift creator: Isabella Torres creator: Rayven Velez creator: Elliot Waxman creator: Serena Wessely creator: Anthony Yuen creator: Casey K. Lardner creator: J.L. Weissman uri: https://doi.org/10.7717/peerj.20081 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kong et al. title: Spatially explicit models of density improve estimates of Eastern Bering Sea beluga (Delphinapterus leucas) abundance and distribution from line-transect surveys link: https://peerj.com/articles/20077 last-modified: 2025-09-30 description: We investigate spatially explicit models and ensemble modeling techniques for estimating animal abundance from line-transect survey data. Spatially explicit models are expected to be statistically more efficient, resulting in more precise abundance estimates, than design-based abundance estimators that rely heavily on assumptions about survey design and realization. Ensemble modeling reduces error by averaging among models, and allows for model selection uncertainty to propagate to the abundance estimator. We develop density surface models using Matérn covariance functions and spline-based smooths for a case study, belugas (Delphinapterus leucas) from the Eastern Bering Sea (EBS) stock. EBS belugas are upper trophic level predators in a rapidly changing ecosystem and are a vital nutritional and cultural resource for Alaska Natives. Effective management of this stock requires regular monitoring to derive accurate and unbiased estimates of abundance. Since 1992, aerial line-transect surveys have been the primary means of surveying and estimating abundance of EBS belugas in the region. We compare EBS beluga abundance estimates for 2017 and 2022 that were derived using post-stratified, design-based abundance estimators with analogous estimates the we derive using spatially explicit and ensemble modeling methods. The estimated precision in the abundance estimates from the individual density surface models (DSMs) and the ensemble average of DSMs is higher than for the design-based estimator in both survey years. The design-based models estimated that there were 12,269 belugas in 2017 (coefficient of variation (CV) = 0.118) and 19,811 belugas within a larger study area in 2022 (CV = 0.343). The ensemble spatial models estimate that there were 11,654 belugas in 2017 (CV = 0.118) and 13,313 belugas in 2022 (CV = 0.216). Among the individual spatially explicit models, abundance estimates range from 11,242 to 11,963 (CV = 0.111 to 0.114) in 2017 and 12,023 to 15,593 (CV = 0.172 to 0.198) in 2022. Because spatial models identify spatial patterns in beluga density at finer resolutions than design-based models, we argue that ensembles of spatially explicit density models provide a reasonable path forward for estimating EBS beluga abundance and distribution in a way that is useful to management and conservation efforts. creator: Megan C. Ferguson creator: Paul B. Conn creator: James T. Thorson uri: https://doi.org/10.7717/peerj.20077 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ferguson et al. title: Morphological, phytochemical, and pharmacological properties of the genus Tamarix in Kazakhstan species: a review link: https://peerj.com/articles/20059 last-modified: 2025-09-30 description: The tree-like plants of the genus Tamarix belong to the Tamaricaceae family and predominantly grow in subtropical areas, steppes, and saline soils. These plants exhibit various pharmacological properties, including antioxidant, antidiabetic, anti-inflammatory, and antimicrobial characteristics. The current flora of Kazakhstan also includes 13 Tamarix species. Despite the diversity of the Tamarix taxon, the species discovered in the region have received limited investigation. Therefore, this review analyzed Kazakhstan and international-related scientific studies concerning the morphological, phytochemical, and pharmacological properties of 13 species within the Tamarix genus. The plants’ biological features and potential applications were also comprehensively analyzed. Consequently, this review significantly contributed to botanical science and practical pharmacology. Conservation and sustainable employment of the Tamarix species for medical purposes could also be developed. creator: Arailym Daulbayeva creator: Gulnara Kadyrbayeva creator: Kaldanay Kozhanova creator: Shazlin Shaharudin creator: Nurgali Rakhymbayev creator: Zoya Allambergenova creator: Rabiga Anarbayeva creator: Urziya Alimova creator: Aigerim Kantureyeva creator: Ainash Baidullaeva creator: Vladimir An creator: Bakkonat Kydyrbai uri: https://doi.org/10.7717/peerj.20059 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Daulbayeva et al.