Effects of vegetation restoration on soil quality in fragile karst ecosystems of southwest China
Soil quality assessment is important for karst ecosystems where soil erosion is significant. A large amount of vegetation restoration has been implemented since the early 21st century in degraded karst areas across southwestern China. However, the impacts on soil quality of different restoration types rarely have been compared systematically. In the current study, we investigated the soil quality after a number of vegetation restoration projects as well as their adjacent cropland by analyzing soil samples. Six vegetation restoration types were evaluated, including one natural restoration (natural shrubland, protected for 13 years), three economic forests (4 years Eucalyptus robusta, 4 years Prunus salicina and 6 years Zenia insignis) and two mixed forests (1 year Juglans regia–crop and 13 years Toona sinensis-Pennisetum purpureum ). We evaluated the benefits of different restoration types more accurately by setting each adjacent cropland as the control and setting the variation between the corresponding restored and control site as the evaluation object so that the background differences of six sites could be eliminated. The results indicated that natural shrubland, Toona sinensis-Pennisetum purpureum and Zenia insignis were effective in improving soil quality index (SQI) in degraded karst cropland largely due to their higher SOC and TN content. The variation of SQI (VSQI) of natural shrubland was significantly higher than that in Eucalyptus robusta, Prunus salicina and Juglans regia-crop in total soil layer (0–30 cm) (P < 0.05), indicating natural shrubland had better capacity to improve soil quality. The boosting regression tree model revealed that vegetation restoration type explained 73.49% and restoration time explained 10.30% of the variation in VSQI, which confirmed that vegetation restoration type and restoration time are critical for achieving soil reserves. Therefore, it is vital to select appropriate vegetation type in restoration projects and recovery for a long time in order to achieve better soil quality. The current study provides a theoretical basis on which to assess the effects of different vegetation restoration types on the heterogeneous degraded karst areas.
Guan et al. (2020) Effects of vegetation restoration on soil quality in fragile karst ecosystems of southwest China. PeerJ 8:e9456 https://doi.org/10.7717/peerj.9456
Effects of microbial evolution dominate those of experimental host-mediated indirect selection
Microbes ubiquitously inhabit animals and plants, often affecting their host’s phenotype. As a result, even in a constant genetic background, the host’s phenotype may evolve through indirect selection on the microbiome. ‘Microbiome engineering’ offers a promising novel approach for attaining desired host traits but has been attempted only a few times. Building on the known role of the microbiome on development in fruit flies, we attempted to evolve earlier-eclosing flies by selecting on microbes in the growth media. We carried out parallel evolution experiments in no- and high-sugar diets by transferring media associated with fast-developing fly lines over the course of four selection cycles. In each cycle, we used sterile eggs from the same inbred population, and assayed mean fly eclosion times. Ultimately, flies eclosed seven to twelve hours earlier, depending on the diet, but microbiome engineering had no effect relative to a random-selection control treatment. 16S rRNA gene sequencing showed that the microbiome did evolve, particularly in the no sugar diet, with an increase in Shannon diversity over time. Thus, while microbiome evolution did affect host eclosion times, these effects were incidental. Instead, any experimentally enforced selection effects were swamped by uncontrolled microbial evolution, likely resulting in its adaptation to the media. These results imply that selection on host phenotypes must be strong enough to overcome other selection pressures simultaneously operating on the microbiome. The independent evolutionary trajectories of the host and the microbiome may limit the extent to which indirect selection on the microbiome can ultimately affect host phenotype. Random-selection lines accounting for independent microbial evolution are essential for experimental microbiome engineering studies.
Arora et al. (2020) Effects of microbial evolution dominate those of experimental host-mediated indirect selection. PeerJ 8:e9350 https://doi.org/10.7717/peerj.9350
Spawning of French grunts, Haemulon flavolineatum, in recirculating aquarium systems
Background Because the French grunt, Haemulon flavolineatum, is an ecologically important reef fish prized by both recreational anglers and public aquariums, the wild population requires limits on harvests. Yet, the environmental conditions conducive for French grunt spawning in aquarium settings is not well understood. Therefore, the goal of this study was to document the conditions leading to voluntary spawning and the number of eggs produced by French grunts without the use of hormones or artificial insemination. Methods We hypothesized and verified that it is possible for French grunts to spontaneously spawn in human care. Forty individuals were collected around the Florida Keys and haphazardly stocked in five recirculating seawater systems each containing two 250-L circular tanks. Over the course of 87 days, eggs were collected daily from each system and environmental parameters were monitored. Results Total daily number of eggs released ranged from 0 to 207,644 eggs. Of the observed environmental parameters, temperature and alkalinity had the greatest impact on number of eggs released. This study demonstrates that it is possible for French grunts to reproduce in captivity with little environmental manipulation, thus an ideal candidate to culture for the zoo/aquarium industry.
Maurer et al. (2020) Spawning of French grunts, Haemulon flavolineatum, in recirculating aquarium systems. PeerJ 8:e9417 https://doi.org/10.7717/peerj.9417
Habitat association in the critically endangered Mangshan pit viper (Protobothrops mangshanensis), a species endemic to China
Habitat directly affects the population size and geographical distribution of wildlife species, including the Mangshan pit viper (Protobothrops mangshanensis), a critically endangered snake species endemic to China. We searched for Mangshan pit viper using randomly arranged transects in their area of distribution and assessed their habitat association using plots, with the goals of gaining a better understanding of the habitat features associated with P. mangshanensis detection and determining if the association with these features varies across season. We conducted transect surveys, found 48 individual snakes, and measured 11 habitat variables seasonally in used and random plots in Hunan Mangshan National Nature Reserve over a period of 5 years (2012–2016). The important habitat variables for predicting Mangshan pit viper detection were fallen log density, shrub density, leaf litter cover, herb cover and distance to water. In spring, summer and autumn, Mangshan pit viper detection was always positively associated with fallen log density. In summer, Mangshan pit viper detection was related to such habitats with high canopy cover, high shrub density and high herb cover. In autumn, snakes generally occurred in habitats near water in areas with high fallen log density and tall shrubs height. Our study is the first to demonstrate the relationship between Mangshan pit viper detection and specific habitat components. Mangshan pit viper detection was associated with habitat features such as with a relatively high fallen log density and shrub density, moderately high leaf litter cover, sites near stream, and with lower herb cover. The pattern of the relationship between snakes and habitats was not consistent across the seasons. Identifying the habitat features associated with Mangshan pit viper detection can better inform the forestry department on managing natural reserves to meet the habitat requirements for this critically endangered snake species.
Zhang et al. (2020) Habitat association in the critically endangered Mangshan pit viper (Protobothrops mangshanensis), a species endemic to China. PeerJ 8:e9439 https://doi.org/10.7717/peerj.9439
Bioindicator potential of Ricinus communis to simulated rainfall containing potassium fluoride
Background Fluoride pollution is a global problem because of its high phytotoxicity. Fluoride is released in air, water and soil through industrial processes, where it damages various plant species. Ricinus communis is widely distributed in Brazil, India and China and has been extensively used as a phytoremediation species in heavy metal-contaminated soils. However, few studies regarding the effect of air pollutants on R. communis have been published, and no information about the exposure of this species to fluoride is available. Therefore, the aim of the present study was to investigate the effects of fluoride on R. communis morphoanatomical and physiological responses using simulated rainfall containing potassium fluoride (KF). Methods Young plants at approximately 10 days after emergence were treated daily with KF using simulated rainfall at 0, 1.5, 3.0 and 4.5 mg L−1, for 37 consecutive days. Chlorophyll a fluorescence, gas exchange, anatomical characteristics and fluoride accumulation in the roots and leaves were evaluated after this period. Results No visual or anatomical symptoms were observed for the first three treatments. Necrosis and chlorosis were visually evident after the 37th day of KF application at 4.5 mg L−1, followed by changes in parenchyma tissues, cell collapse and phenolic compound accumulation at the end of the experiment. No damage was observed in terms of photosynthetic photochemical and biochemical stages. Maintenance of physiological characteristics in the presence of fluoride accumulation in roots and leaves were shown to be important fluoride biomarkers. These characteristics suggest that R. communis is tolerant to 1.5 and 3.0 mg L−1 KF, and is anatomically sensitive at 4.5 mg L−1 KF.
Rodrigues et al. (2020) Bioindicator potential of Ricinus communis to simulated rainfall containing potassium fluoride. PeerJ 8:e9445 https://doi.org/10.7717/peerj.9445
A novel bamboo sheet chair and its influence on sitting comfort
Background In today’s economy, workers spend increasingly more time in seated positions, leading to a growing scientific interest in chair design. In this study we used body pressure distribution tests to compare a novel bamboo chair with unique structural features to other commonly-used chairs. We studied the bamboo sheet chair’s physical characteristics and comfort to provide a scientific theoretical basis for common use seat design. Methods A total of 25 (14 male and 11 female) subjects participated in the study. Subjects were divided into six groups according to their body characteristics parameters included stature, weight, shoulder breadth, hip breadth, waist width, popliteal height, buttocks-popliteal length, and buttock-abdomen depth, with three groups for males and three groups for females. Each subject was required to complete specified body pressure tests for three different experimental chairs for three minutes and subjective comfort evaluations were also administered. The pressure indexes were measured from the seat pan and backrest and calculated with MATLAB 2015b, which mainly included maximum pressure (Pm), average pressure (Pa), pressure exponent (Pe) and contact area index (PAI). Three pressure threshold limits of 0.67 kPa, 4.00 kPa and 9.33 kPa and four contact surface indexes were used in the experiment to reflect the contact area between human and chair. Results The contact areas in the backrest (52.96 ± 32.94 cm2) and seat pan (307.75 ± 90.31 cm2) in the middle-to-high threshold pressure range, and the contact areas of the backrest (4.34 ± 5.95 cm2) in the high threshold pressure range of bamboo sheet chair were smaller than the corresponding indexes of the common office chair (81.430 ± 45.04 cm2, p = 0.00; 394.39 ± 98.99 cm2, p = 0.02; 13.54 ± 12.00 cm2, p = 0.00, respectively). The pressure index (2.68 ± 0.88 kPa), maximum pressure (6.66 ± 2.05 kPa), and average pressure (2.42 ± 0.59 kPa) values of the bamboo sheet chair backrest were also found to be lower than those of the office chair (4.32 ± 1.62 kPa, p = 0.00; 10.50 ± 3.88 kPa, p = 0.00; 3.43 ± 0.97 kPa, p = 0.00, respectively). The average pressure on the seat pan was greater than 4 kPa for all subjects, while the average pressure on the seat pan was greater than 9.33 kPa for male subjects with a body mass index (BMI) of 27.48. Discussion The bamboo sheet chair’s contact areas within the middle-to-high and high-pressure threshold ranges of the backrest and seat pan were smaller than those of the office chair, indicating that the bamboo sheet chair is effective at relieving pressure. Human body characteristics must be considered in the design of seat functional size. Buttocks-popliteal length, weight, body mass index, body shape and weight distribution, all have important effects on the distribution of body pressure at the human-chair interface.
Yuan et al. (2020) A novel bamboo sheet chair and its influence on sitting comfort. PeerJ 8:e9476 https://doi.org/10.7717/peerj.9476
Analysis of deubiquitinase OTUD5 as a biomarker and therapeutic target for cervical cancer by bioinformatic analysis
OTU deubiquitinase 5 (OTUD5), as a member of the ovarian tumor protease (OTU) family, was previously reported to play important roles in DNA repair and immunity. However, little is known about its function in tumors. Cervical cancer is a malignant tumor that seriously endangers the lives of women. Here, we found that low expression of OTUD5 in cervical cancer is associated with poor prognosis. Its expression is associated with tumor stage, metastatic nodes and tumor subtypes such as those related to the phosphatidylinositol–3–kinase (PI3K)–AKT signaling, epithelial-mesenchymal transition (EMT) and hormones. In addtion, we analyzed the coexpressed genes, related miRNAs, transcription factors, kinases, E3s and interacting proteins of OTUD5. We demonstrated that OTUD5 affects the expression levels of WD repeat domain 45 (WDR45), ubiquitin-specific peptidase 11 (USP11), GRIP1 associated protein 1 (GRIPAP1) and RNA binding motif protein 10 (RBM10). Moreover, hsa-mir-137, hsa-mir-1913, hsa-mir-937, hsa-mir-607, hsa-mir-3149 and hsa-mir-144 may inhibit the expression of OTUD5. Furthermore, we performed enrichment analysis of 22 coexpressed genes, 33 related miRNAs and 30 interacting proteins. In addition to ubiquitination and immunology related processes, they also participate in Hippo signaling, insulin signaling, EMT, histone methylation and phosphorylation kinase binding. Our study for the first time analyzed the expression of OTUD5 in cervical cancer and its relationship with clinicopathology and provided new insights for further study of its regulatory mechanism in tumors.
Bai et al. (2020) Analysis of deubiquitinase OTUD5 as a biomarker and therapeutic target for cervical cancer by bioinformatic analysis. PeerJ 8:e9146 https://doi.org/10.7717/peerj.9146
Microbial community analysis in the gills of abalones suggested possible dominance of epsilonproteobacterium in Haliotis gigantea
Gills are important organs for aquatic invertebrates because they harbor chemosynthetic bacteria, which fix inorganic carbon and/or nitrogen and provide their hosts with organic compounds. Nevertheless, in contrast to the intensive researches related to the gut microbiota, much is still needed to further understand the microbiota within the gills of invertebrates. Using abalones as a model, we investigated the community structure of microbes associated with the gills of these invertebrates using next-generation sequencing. Molecular identification of representative bacterial sequences was performed using cloning, nested PCR and fluorescence in situ hybridization (FISH) analysis with specific primers or probes. We examined three abalone species, namely Haliotis gigantea, H. discus and H. diversicolor using seawater and stones as controls. Microbiome analysis suggested that the gills of all three abalones had the unclassified Spirochaetaceae (one OTU, 15.7 ± 0.04%) and Mycoplasma sp. (one OTU, 9.1 ± 0.03%) as the core microbes. In most libraries from the gills of H. gigantea, however, a previously unknown epsilonproteobacterium species (one OTU) was considered as the dominant bacterium, which accounted for 62.2% of the relative abundance. The epsilonproteobacterium was only detected in the gills of H. diversicolor at 0.2% and not in H. discus suggesting that it may be unique to H. gigantea. Phylogenetic analysis performed using a near full-length 16S rRNA gene placed the uncultured epsilonproteobacterium species at the root of the family Helicobacteraceae. Interestingly, the uncultured epsilonproteobacterium was commonly detected from gill tissue rather than from the gut and foot tissues using a nested PCR assay with uncultured epsilonproteobacterium-specific primers. FISH analysis with the uncultured epsilonproteobacterium-specific probe revealed that probe-reactive cells in H. gigantea had a coccus-like morphology and formed microcolonies on gill tissue. This is the first report to show that epsilonproteobacterium has the potential to be a dominant species in the gills of the coastal gastropod, H. gigantea.
Mizutani et al. (2020) Microbial community analysis in the gills of abalones suggested possible dominance of epsilonproteobacterium in Haliotis gigantea. PeerJ 8:e9326 https://doi.org/10.7717/peerj.9326
Multi-predator assemblages, dive type, bathymetry and sex influence foraging success and efficiency in African penguins
Marine predators adapt their hunting techniques to locate and capture prey in response to their surrounding environment. However, little is known about how certain strategies influence foraging success and efficiency. Due to the miniaturisation of animal tracking technologies, a single individual can be equipped with multiple data loggers to obtain multi-scale tracking information. With the addition of animal-borne video data loggers, it is possible to provide context-specific information for movement data obtained over the video recording periods. Through a combination of video data loggers, accelerometers, GPS and depth recorders, this study investigated the influence of habitat, sex and the presence of other predators on the foraging success and efficiency of the endangered African penguin, Spheniscus demersus, from two colonies in Algoa Bay, South Africa. Due to limitations in the battery life of video data loggers, a machine learning model was developed to detect prey captures across full foraging trips. The model was validated using prey capture signals detected in concurrently recording accelerometers and animal-borne cameras and was then applied to detect prey captures throughout the full foraging trip of each individual. Using GPS and bathymetry information to inform the position of dives, individuals were observed to perform both pelagic and benthic diving behaviour. Females were generally more successful on pelagic dives than males, suggesting a trade-off between manoeuvrability and physiological diving capacity. By contrast, males were more successful in benthic dives, at least for Bird Island (BI) birds, possibly due to their larger size compared to females, allowing them to exploit habitat deeper and for longer durations. Both males at BI and both sexes at St Croix (SC) exhibited similar benthic success rates. This may be due to the comparatively shallower seafloor around SC, which could increase the likelihood of females capturing prey on benthic dives. Observation of camera data indicated individuals regularly foraged with a range of other predators including penguins and other seabirds, predatory fish (sharks and tuna) and whales. The presence of other seabirds increased individual foraging success, while predatory fish reduced it, indicating competitive exclusion by larger heterospecifics. This study highlights novel benthic foraging strategies in African penguins and suggests that individuals could buffer the effects of changes to prey availability in response to climate change. Furthermore, although group foraging was prevalent in the present study, its influence on foraging success depends largely on the type of heterospecifics present.
Sutton et al. (2020) Multi-predator assemblages, dive type, bathymetry and sex influence foraging success and efficiency in African penguins. PeerJ 8:e9380 https://doi.org/10.7717/peerj.9380
Microenvironment-related gene TNFSF13B predicts poor prognosis in kidney renal clear cell carcinoma
Background Kidney renal clear cell carcinoma (KIRC) affects the genitourinary system. Although treatment of KIRC in early stages can be highly successful, this type of cancer is difficult to detect until later stages of disease that are less easily treatable. Previous studies have focused on tumor cells, but have ignored the contributions of the tumor microenvironment. Methods We analyzed KIRC gene expression data from The Cancer Genome Atlas with the ESTIMATE algorithm to identify differentially expressed genes. Through protein–protein interaction network analysis, we identified clusters and picked genes from the clusters for further analysis. Differential expression, Kaplan–Meier, and univariate Cox analyses were used to select prognostic biomarkers. Gene Set Enrichment Analysis (GSEA) and Tumor Immune Estimation Resource (TIMER) analysis were used to explore the immune characteristics of these genes as biomarkers. Results Through the ESTIMATE algorithm and other system biology tools, TNFSF13B was identified as a prognostic biomarker. TNFSF13B is highly expressed in tumors, and high expression of TNFSF13B leads to poor prognosis. Further GSEA and TIMER analysis revealed that the expression of TNFSF13B was related to the immune signaling pathway and lymphocyte infiltration. Our findings strongly suggest that TNFSF13B may be a potential biomarker or target related to the tumor microenvironment for KIRC.
Jiang et al. (2020) Microenvironment-related gene TNFSF13B predicts poor prognosis in kidney renal clear cell carcinoma. PeerJ 8:e9453 https://doi.org/10.7717/peerj.9453