title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=501 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Optimizing lettuce yields and quality by incorporating movable downward lighting with a supplemental adjustable sideward lighting system in a plant factory link: https://peerj.com/articles/15401 last-modified: 2023-06-14 description: BackgroundLettuce is a vegetable that is increasingly consumed globally, given its nutritional quality. Plant factories with artificial lighting can produce high-yield and high-quality plants. High plant density in these systems speeds up leaf senescence. Wasted energy and lower yield raised labor expenses are some of the bottlenecks associated with this farming system. In order to increase lettuce yields and quality in the plant factory, it is essential to develop cultivating techniques using artificial lighting.MethodsRomaine lettuce was grown under a developed “movable downward lighting combined with supplemental adjustable sideward lighting system” (C-S) and under a system without supplemental sideward lighting (N-S) in a plant factory. The effects of C-S on lettuce’s photosynthetic characteristics, plant yield, and energy consumption relative to plants grown under a system without N-S were studied.ResultsRomaine lettuce growth and light energy consumption in the plant factory were both influenced favorably by supplementary adjustable sideward lighting. The number of leaves, stem diameter, fresh and dry weights, chlorophyll a and b concentration, and biochemical content (soluble sugar and protein) all increased sharply. The energy consumption was substantially higher in the N-S treatment than the C-S. creator: Mulowayi Mutombo Arcel creator: Ahmed Fathy Yousef creator: Zhen Hui Shen creator: Witness Joseph Nyimbo creator: Shu He Zheng uri: https://doi.org/10.7717/peerj.15401 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Mutombo Arcel et al. title: Spatial and temporal dynamics of the bacterial community under experimental warming in field-grown wheat link: https://peerj.com/articles/15428 last-modified: 2023-06-14 description: Climate change may lead to adverse effects on agricultural crops, plant microbiomes have the potential to help hosts counteract these effects. While plant–microbe interactions are known to be sensitive to temperature, how warming affects the community composition and functioning of plant microbiomes in most agricultural crops is still unclear. Here, we utilized a 10-year field experiment to investigate the effects of warming on root zone carbon availability, microbial activity and community composition at spatial (root, rhizosphere and bulk soil) and temporal (tillering, jointing and ripening stages of plants) scales in field-grown wheat (Triticum aestivum L.). The dissolved organic carbon and microbial activity in the rhizosphere were increased by soil warming and varied considerably across wheat growth stages. Warming exerted stronger effects on the microbial community composition in the root and rhizosphere samples than in the bulk soil. Microbial community composition, particularly the phyla Actinobacteria and Firmicutes, shifted considerably in response to warming. Interestingly, the abundance of a number of known copiotrophic taxa, such as Pseudomonas and Bacillus, and genera in Actinomycetales increased in the roots and rhizosphere under warming and the increase in these taxa implies that they may play a role in increasing the resilience of plants to warming. Taken together, we demonstrated that soil warming along with root proximity and plant growth status drives changes in the microbial community composition and function in the wheat root zone. creator: Jing Wang creator: Shuaimin Chen creator: Ruibo Sun creator: Binbin Liu creator: Tatoba Waghmode creator: Chunsheng Hu uri: https://doi.org/10.7717/peerj.15428 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wang et al. title: Detection of Echinococcus multilocularis in repurposed environmental DNA samples from river water link: https://peerj.com/articles/15431 last-modified: 2023-06-14 description: Environmental DNA (eDNA) is an increasingly popular tool in biological and ecological studies. As a biproduct of its increasing use, large number of eDNA samples are being collected and stored, that potentially contain information of many non-target species. One potential use for these eDNA samples is a surveillance and early detection of pathogens and parasites that are otherwise difficult to detect. Echinococcus multilocularis is such a parasite with serious zoonotic concern, and whose range has been expanding. If eDNA samples from various studies can be repurposed in detecting the parasite, it can significantly reduce the costs and efforts in surveillance and early detection of the parasite. We designed and tested a new set of primer-probe for detecting E. multilocularis mitochondrial DNA in environmental medium. Using this primer-probe set, we conducted real-time PCR on repurposed eDNA samples collected from three streams flowing through an area of Japan endemic to the parasite. We detected the DNA of E. multilocularis in one of the 128 samples (0.78%). The discovery suggests that while detecting E. multilocularis using eDNA samples is possible, the rate of detection appear to be very low. However, given the naturally low prevalence of the parasite among wild hosts in endemic areas, the repurposed eDNAs may still be a valid option for surveillance in newly introduced areas with the reduced cost and efforts. Further work is needed to assess and improve the effectiveness of using eDNA for detection of E. multilocularis. creator: Kensuke Mori creator: Akio Imamura creator: Itsuki Hirayama creator: Toshifumi Minamoto uri: https://doi.org/10.7717/peerj.15431 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Mori et al. title: Physiological response and transcriptome analyses of leguminous Indigofera bungeana Walp. to drought stress link: https://peerj.com/articles/15440 last-modified: 2023-06-14 description: ObjectiveIndigofera bungeana is a shrub with high quality protein that has been widely utilized for forage grass in the semi-arid regions of China. This study aimed to enrich the currently available knowledge and clarify the detailed drought stress regulatory mechanisms in I. bungeana, and provide a theoretical foundation for the cultivation and resistance breeding of forage crops.MethodsThis study evaluates the response mechanism to drought stress by exploiting multiple parameters and transcriptomic analyses of a 1-year-old seedlings of I. bungeana in a pot experiment.ResultsDrought stress significantly caused physiological changes in I. bungeana. The antioxidant enzyme activities and osmoregulation substance content of I. bungeana showed an increase under drought. Moreover, 3,978 and 6,923 differentially expressed genes were approved by transcriptome in leaves and roots. The transcription factors, hormone signal transduction, carbohydrate metabolism of regulatory network were observed to have increased. In both tissues, genes related to plant hormone signaling transduction pathway might play a more pivotal role in drought tolerance. Transcription factors families like basic helix-loop-helix (bHLH), vian myeloblastosis viral oncogene homolog (MYB), basic leucine zipper (bZIP) and the metabolic pathway related-genes like serine/threonine-phosphatase 2C (PP2C), SNF1-related protein kinase 2 (SnRK2), indole-3-acetic acid (IAA), auxin (AUX28), small auxin up-regulated rna (SAUR), sucrose synthase (SUS), sucrosecarriers (SUC) were highlighted for future research about drought stress resistance in Indigofera bungeana.ConclusionOur study posited I. bungeana mainly participate in various physiological and metabolic activities to response severe drought stress, by regulating the expression of the related genes in hormone signal transduction. These findings, which may be valuable for drought resistance breeding, and to clarify the drought stress regulatory mechanisms of I. bungeana and other plants. creator: Shuang Ma creator: Haiying Hu creator: Hao Zhang creator: Fenghua Ma creator: Zhihao Gao creator: Xueying Li uri: https://doi.org/10.7717/peerj.15440 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ma et al. title: Is coconut coir dust an efficient biofertilizer carrier for promoting coffee seedling growth and nutrient uptake? link: https://peerj.com/articles/15530 last-modified: 2023-06-14 description: BackgroundAs a method for sustainable agriculture, biofertilizers containing plant growth-promoting bacteria (PGPB) have been recommended as an alternative to chemical fertilizers. However, the short shelf-life of inoculants remains a limiting factor in the development of biofertilizer technology. The present study aimed to (i) evaluate the effectiveness of four different carriers (perlite, vermiculite, diatomite and coconut coir dust) on the shelf-life of S2-4a1 and R2-3b1 isolates over 60 days after inoculation and (ii) evaluate isolated bacteria as growth-promoting agents for coffee seedlings.MethodsThe rhizosphere soil-isolated S2-4a1 and plant-tissue-isolated R2-3b1 were chosen based on their P and K-solubilizing capacities and their ability to produce IAA. To evaluate the alternative carriers, two selected isolates were inoculated with the four different carriers and incubated at 25 °C for 60 days. The bacterial survival, pH, and EC in each carrier were investigated. In addition, coconut coir dust inoculated with the selected isolates was applied to the soil in pots planted with coffee (Coffea arabica). At 90 days following application, variables such as biomass and total N, P, K, Ca, and Mg uptakes of coffee seedlings were examined.ResultsThe results showed that after 60 days of inoculation at 25 °C, the population of S2-4a1 and R2-3b1 in coconut coir dust carriers was 1.3 and 2.15 × 108 CFU g−1, respectively. However, there were no significant differences among carriers (P > 0.05). The results of the present study suggested that coconut coir dust can be used as an alternative carrier for S2-4a1 and R2-3b1 isolates. The significant differences in pH and EC were observed by different carriers (P < 0.01) after inoculation with both bacterial isolates. However, pH and EC declined significantly only with coconut coir dust during the incubation period. In addition, coconut coir dust-based bioformulations of both S2-4a1 and R2-3b1 enhanced plant growth and nutrient uptake (P, K, Ca, Mg), providing evidence that isolated bacteria possess additional growth-promoting properties. creator: Yupa Chromkaew creator: Thewin Kaeomuangmoon creator: Nipon Mawan creator: Nilita Mukjang creator: Nuttapon Khongdee uri: https://doi.org/10.7717/peerj.15530 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chromkaew et al. title: Three new species of Axinulus (Bivalvia: Thyasiridae) from the Japan and Kuril-Kamchatka trenches and abyssal zone of the northern Pacific Ocean link: https://peerj.com/articles/15543 last-modified: 2023-06-14 description: The Thyasiridae is one of the most species-rich families of bivalves in the deep-sea areas of the northern Pacific Ocean. Many thyasirid species form abundant populations in these regions and play an important role in the functioning of deep-sea benthic communities. However, most of these deep-sea thyasirid species have not been identified and many of them are new to science. Based on the material of bivalves collected by eight deep-sea expeditions in the northern Pacific Ocean during the period from 1954 to 2016, three new species of the genus Axinulus (Axinulus krylovae sp. nov., A. alatus sp. nov., and A. cristatus sp. nov.) are described from the Kuril-Kamchatka and Japan trenches, the Bering Sea, and other deep-water regions of the northern Pacific Ocean (3,200–9,583 m depth). The new species are distinguished due to a unique and complex sculpture of the prodissoconch, including tubercles and numerous thin folds of varying length and shape, as well as due to a thickening of the shell in the adductor scar areas, thus rendering the scars raised above the inner surface of the shell. Comparisons with all species of the genus Axinulus are provided. creator: Gennady M. Kamenev uri: https://doi.org/10.7717/peerj.15543 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Kamenev title: Expression, localization, and function of P4HB in the spermatogenesis of Chinese mitten crab (Eriocheir sinensis) link: https://peerj.com/articles/15547 last-modified: 2023-06-14 description: BackgroundThe sperm of Chinese mitten crab (Eriocheir sinensis) have special noncondensed nuclei. The formation and stability of the special nuclei are closely related to the correct folding of proteins during spermatogenesis. P4HB plays a key role in protein folding, but its expression and role in the spermatogenesis of E. sinensis are unclear.ObjectiveTo investigate the expression and distribution characteristics of P4HB in the spermatogenesis of E. sinensis as well as its possible role.MethodsThe testis tissues of adult and juvenile E. sinensis were used as materials. We utilized a variety of techniques, including homology modeling, phylogenetic analysis, RT-qPCR, western blotting, and immunofluorescence staining to predict the protein structure and sequence homology of P4HB, analyze its expression in the testis tissues, and localize and semi-quantitatively assess its expression in different male germ cells.ResultsThe sequence of P4HB protein in E. sinensis shared a high similarity of 58.09% with the human protein disulfide isomerase, and the phylogenetic tree analysis indicated that the protein sequence was highly conserved among crustaceans, arthropods, and other animals species. P4HB was found to be expressed in both juvenile and adult E. sinensis testis tissues, with different localization patterns observed all over the developmental stages of male germ cells. It was higher expressed in the spermatogonia, spermatocytes, and stage I spermatids, followed by the mature sperm than in the stage II and III spermatids. The subcellular localization analysis revealed that P4HB was predominantly expressed in the cytoplasm, cell membrane, and extracellular matrix in the spermatogonia, spermatocytes, stage I and stage II spermatids, with some present in specific regions of the nuclei in the spermatogonia. In contrast, P4HB was mainly localized in the nuclei of stage III spermatids and sperm, with little expression observed in the cytoplasm.ConclusionP4HB was expressed in the testis tissues of both adult and juvenile E. sinensis, but the expression and localization were different in male germ cells at various developmental stages. The observed differences in the expression and localization of P4HB may be an essential factor in maintaining the cell morphology and structure of diverse male germ cells in E. sinensis. Additionally, P4HB expressed in the nuclei of spermatogonia, late spermatids, and sperm may play an indispensable role in maintaining the stability of the noncondensed spermatozoal nuclei in E. sinensis. creator: Yulian Tang creator: Anni Ni creator: Shu Li creator: Lishuang Sun creator: Genliang Li uri: https://doi.org/10.7717/peerj.15547 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Tang et al. title: Accounting for spatial habitat and management boundaries when estimating forest bird population distribution and density: inferences from a soap film smoother link: https://peerj.com/articles/15558 last-modified: 2023-06-14 description: Birds are often obligate to specific habitats which can result in study areas with complex boundaries due to sudden changes in vegetation or other features. This can result in study areas with concave arcs or that include holes of unsuitable habitat such as lakes or agricultural fields. Spatial models used to produce species’ distribution and density estimates need to respect such boundaries to make informed decisions for species conservation and management. The soap film smoother is one model for complex study regions which controls the boundary behaviour, ensuring realistic values at the edges of the region. We apply the soap film smoother to account for boundary effects and compare it with thin plate regression spline (TPRS) smooth and design-based conventional distance sampling methods to produce abundance estimates from point-transect distance sampling collected data on Hawai‘i ‘Ākepa Loxops coccineus in the Hakalau Forest Unit of the Big Island National Wildlife Refuge Complex, Hawai‘i Island, USA. The soap film smoother predicted zero or near zero densities in the northern part of the domain and two hotspots (in the southern and central parts of the domain). Along the boundary the soap film model predicted relatively high densities where ‘Ākepa occur in the adjacent forest and near zero elsewhere. The design-based and soap film abundance estimates were nearly identical. The width of the soap film confidence interval was 16.5% and 0.8% wider than the width of the TPRS smooth and design-based confidence intervals, respectively. The peaks in predicted densities along the boundary indicates leakage by the TPRS smooth. We provide a discussion of the statistical methods, biological findings and management implications of applying soap film smoothers to estimate forest bird population status. creator: Richard J. Camp creator: David L. Miller creator: Stephen T. Buckland creator: Steve J. Kendall uri: https://doi.org/10.7717/peerj.15558 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: What are the Andean Colombian anurans? Empirical regionalization proposals vs. observed patterns of compositional dissimilarity link: https://peerj.com/articles/15217 last-modified: 2023-06-13 description: BackgroundDefining Andean anurans through their altitudinal limits has been a common practice in species lists, studies of responses to climate change among others, especially in the northern Andes. At least three proposals to differentiate Andean anurans from lowland anurans through elevation and at least one to differentiate Andean anurans from high mountain anurans have been formulated. However, the most frequently used altitudinal limits are not based on theoretical or numerical support, but on observations or practical definitions. Additionally, these proposals have been applied equally to different portions of the Andes, ignoring the fact that even between slopes of the same mountain, environmental conditions (and therefore the distribution of species) may differ. The objective of this work was to evaluate the concordance between the altitudinal distribution of anurans in the Colombian Andes and four different altitudinal delimitation proposals.MethodsWe constructed our study area in a manner that allowed us to include species from the Andean region (as traditionally defined) and adjacent lowlands, because if the boundaries criteria were applied they would separate the species of the latter by themselves. We divided the study area into eight entities according to the watershed and the course of the most important rivers. We conducted a bibliographic search for all anurans in the cordilleras and inter-Andean valleys of Colombia and complemented the search with information on anurans for the region available in the GBIF. After curing the species distribution points, we generated elevation bands of 200 m amplitude for both the study area and for each Andean entity. Subsequently, we performed a cluster analysis to evaluate the grouping of the elevation bands according to their species composition.ResultsIn none of the cases (neither for the entire study area nor for any of the entities) we found a correspondence of any of the traditionally used boundaries and the altitudinal distribution of Anurans in the Andean region of Colombia. Instead, on average, the altitudinal delimitation proposals arbitrarily spanned the altitudinal distribution of about one third of the species distributed in the study area.ConclusionsWe suggest that, although, based on our results, some Andean entities can be divided according to the altitudinal composition of the species that occur in them, we did not find any results that support the idea of a generalizable altitudinal limit for the Colombian Andes. Thus, to avoid biases in studies that may later be used by decision makers, the selection of anuran species in studies in the Colombian Andes should be based on biogeographic, phylogenetic or natural history criteria and not on altitudinal limits as they have been used. creator: Jorge Mario Herrera-Lopera creator: Viviana Andrea Ramírez Castaño creator: Carlos A. Cultid-Medina uri: https://doi.org/10.7717/peerj.15217 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Herrera-Lopera et al. title: A review of visual sustained attention: neural mechanisms and computational models link: https://peerj.com/articles/15351 last-modified: 2023-06-13 description: Sustained attention is one of the basic abilities of humans to maintain concentration on relevant information while ignoring irrelevant information over extended periods. The purpose of the review is to provide insight into how to integrate neural mechanisms of sustained attention with computational models to facilitate research and application. Although many studies have assessed attention, the evaluation of humans’ sustained attention is not sufficiently comprehensive. Hence, this study provides a current review on both neural mechanisms and computational models of visual sustained attention. We first review models, measurements, and neural mechanisms of sustained attention and propose plausible neural pathways for visual sustained attention. Next, we analyze and compare the different computational models of sustained attention that the previous reviews have not systematically summarized. We then provide computational models for automatically detecting vigilance states and evaluation of sustained attention. Finally, we outline possible future trends in the research field of sustained attention. creator: Huimin Huang creator: Rui Li creator: Junsong Zhang uri: https://doi.org/10.7717/peerj.15351 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Huang et al.