Immediate impacts of soybean cover crop on bacterial community composition and diversity in soil under long-term Saccharum monoculture
Saccharum yield decline results from long-term monoculture practices. Changes in cropping management can improve soil health and productivity. Below-ground bacterial community diversity and composition across soybean (Glycine max (L.) Merr) cover crop, Saccharum monoculture (30+ year) and fallowed soil were determined. Near full length (~1,400 base pairs) of 16S rRNA gene sequences were extracted from the rhizospheres of sugarcane and soybean and fallowed soil were compared. Higher soil bacterial diversity was observed in the soybean cover crop than sugarcane monoculture across all measured indices (observed operationational taxonomic units, Chao1, Shannon, reciprocal Simpson and Jackknife). Acidocateria, Proteobacteria, Bacteroidetes and Planctomycetes were the most abundant bacterial phyla across the treatments. Indicator species analysis identified nine indicator phyla. Planctomycetes, Armatimonadetes and candidate phylum FBP were associated with soybean; Proteobacteria and Firmicutes were linked with sugarcane and Gemmatimonadetes, Nitrospirae, Rokubacteria and unclassified bacteria were associated with fallowed soil. Non-metric multidimensional scaling analysis showed distinct groupings of bacterial operational taxonomic units (97% identity) according to management system (soybean, sugarcane or fallow) indicating compositional differences among treatments. This is confirmed by the results of the multi-response permutation procedures (A = 0.541, p = 0.00045716). No correlation between soil parameters and bacterial community structure was observed according to Mantel test (r = 211865, p = 0.14). Use of soybean cover-crop fostered bacterial diversity and altered community structure. This indicates cover crops could have a restorative effect and potentially promote sustainability in long-term Saccharum production systems.
Mula-Michel et al. (2023) Immediate impacts of soybean cover crop on bacterial community composition and diversity in soil under long-term Saccharum monoculture. PeerJ 11:e15754 https://doi.org/10.7717/peerj.15754
Comparative analysis of the fecal microbiota of healthy and injured common kestrel (Falco tinnunculus) from the Beijing Raptor Rescue Center
The gut microbiota is a complex ecosystem that interacts with many other factors to affect the health and disease states of the host. The common kestrel (Falco tinnunculus) is protected at the national level in China. However, the available sequencing data of the gut microbiota from the feces of wild common kestrels, especially for being rescued individuals by professional organization, remains limited. In the present study, we characterized the fecal bacterial communities of healthy and injured common kestrels, and compared the structure of their fecal microbiota by analyzing the V3–V4 region of the 16S rRNA gene using high-throughput sequencing technology with the Illumina MiSeq platform. We found that Firmicutes, Proteobacteria and Actinobacteria were the most predominant phyla in common kestrels. Further, the beta diversity analysis showed that changes in gut microbes were associated with injuries to the common kestrel. The Bacteroides/Firmicutes ratio was significantly lower in the injured group. At the genus level, Glutamicibacter showed significant difference in the two groups. The aim of our current study was to characterize the basic bacterial composition and community structure in the feces of healthy common kestrels, and then compare the differences in the fecal microbiota between healthy and injured individuals. Patescibacteria, Spirochaetes, and Glutamicibacter may be studied as potential biomarkers for certain diseases in raptors. The results could provide the basic data for additional research on the fecal microbiota of common kestrels and contribute to the rescue of wild raptors in the future.
Guan et al. (2023) Comparative analysis of the fecal microbiota of healthy and injured common kestrel (Falco tinnunculus) from the Beijing Raptor Rescue Center. PeerJ 11:e15789 https://doi.org/10.7717/peerj.15789
The experiences of COVID-19 preprint authors: a survey of researchers about publishing and receiving feedback on their work during the pandemic
The COVID-19 pandemic caused a rise in preprinting, triggered by the need for open and rapid dissemination of research outputs. We surveyed authors of COVID-19 preprints to learn about their experiences with preprinting their work and also with publishing their work in a peer-reviewed journal. Our research had the following objectives: 1. to learn about authors’ experiences with preprinting, their motivations, and future intentions; 2. to consider preprints in terms of their effectiveness in enabling authors to receive feedback on their work; 3. to compare the impact of feedback on preprints with the impact of comments of editors and reviewers on papers submitted to journals. In our survey, 78% of the new adopters of preprinting reported the intention to also preprint their future work. The boost in preprinting may therefore have a structural effect that will last after the pandemic, although future developments will also depend on other factors, including the broader growth in the adoption of open science practices. A total of 53% of the respondents reported that they had received feedback on their preprints. However, more than half of the feedback was received through “closed” channels–privately to the authors. This means that preprinting was a useful way to receive feedback on research, but the value of feedback could be increased further by facilitating and promoting “open” channels for preprint feedback. Almost a quarter of the feedback received by respondents consisted of detailed comments, showing the potential of preprint feedback to provide valuable comments on research. Respondents also reported that, compared to preprint feedback, journal peer review was more likely to lead to major changes to their work, suggesting that journal peer review provides significant added value compared to feedback received on preprints.
Rzayeva et al. (2023) The experiences of COVID-19 preprint authors: a survey of researchers about publishing and receiving feedback on their work during the pandemic. PeerJ 11:e15864 https://doi.org/10.7717/peerj.15864
Water lettuce (Pistia stratiotes L.) increases biogas effluent pollutant removal efficacy and proves a positive substrate for renewable energy production
Background Aquatic plants play a crucial role in nature-based wastewater treatment and provide a promising substrate for renewable energy production using anaerobic digestion (AD) technology. This study aimed to examine the contaminant removal from AD effluent by water lettuce (WL) and produce biogas from WL biomass co-digested with pig dung (PD) in a farm-scale biogas digester. Methods The first experiment used styrofoam boxes containing husbandry AD effluent. WLs were initially arranged in 50%, 25%, 12.5%, and 0% surface coverage. Each treatment was conducted in five replicates under natural conditions. In the second experiment, WL biomass was co-digested with PD into an existing anaerobic digester to examine biogas production on a farm scale. Results Over 30 days, the treatment efficiency of TSS, BOD5, COD, TKN, and TP in the effluent was 93.75–97.66%, 76.63–82.56%, 76.78–82.89%, 61.75–63.75%, and 89.00–89.57%, respectively. Higher WL coverage increased the pollutant elimination potential. The WL biomass doubled after 12 days for all treatments. In the farm-scale biogas production, the biogas yield varied between 190.6 and 292.9 L kg VSadded−1. The methane content reached over 54%. Conclusions WL removed AD effluent nutrients effectively through a phytoremediation system and generated significant biomass for renewable energy production in a farm-scale model.
Environmental Contamination and Remediation
Nguyen Vo Chau et al. (2023) Water lettuce (Pistia stratiotes L.) increases biogas effluent pollutant removal efficacy and proves a positive substrate for renewable energy production. PeerJ 11:e15879 https://doi.org/10.7717/peerj.15879
Exogenous glutathione maintains the postharvest quality of mango fruit by modulating the ascorbate-glutathione cycle
Background Mango fruit is prone to decay after harvest and premature senescence, which significantly lowers its quality and commercial value. Methods The mango fruit (Mangifera indica L.cv. Guixiang) was treated with 0 (control), 2, 5, and 8 mM of reduced glutathione (GSH) after harvest. The fruit was stored at 25 ± 1 °C for 12 days to observe the changes in the antioxidant capacity and postharvest quality. Results Compared with the control, the 5 mM GSH treatment significantly decreased the weight loss by 44.0% and 24.4%, total soluble solids content by 25.1% and 4.5%, and soluble sugar content by 19.0% and 27.0%. Conversely, the 5 mM GSH treatment increased the firmness by 25.9% and 30.7% on days 4 and 8, respectively, and the titratable acidity content by 115.1% on day 8. Additionally, the 5 mM GSH treatment decreased the malondialdehyde and hydrogen peroxide contents and improved the antioxidant capacity of mango fruit by increasing the superoxide dismutase and peroxidase activities and upregulating the expression of the encoding genes. Meanwhile, the higher levels of monodehydroascorbate reductase, dehydroascorbate reductase, and glutathione reductase enzyme activities and gene expressions accelerated the AsA-GSH cycle, thereby increasing the accumulation of AsA and GSH and maintaining the redox balance. Conclusions Overall, the experimental results suggest that 5 mM GSH maintains high antioxidant capacity and postharvest quality of mangoes and can use as an effective preservation technique for postharvest mangoes.
Zhou et al. (2023) Exogenous glutathione maintains the postharvest quality of mango fruit by modulating the ascorbate-glutathione cycle. PeerJ 11:e15902 https://doi.org/10.7717/peerj.15902
Icariin activates far upstream element binding protein 1 to regulate hypoxia-inducible factor-1α and hypoxia-inducible factor-2α signaling and benefits chondrocytes
Icariin (ICA) is a typical flavonoid glycoside derived from epimedium plants. It has both anabolic and anti-catabolic effects to improve bone mineral density and reduce bone microstructural degradation. However, the effect and underlying mechanism of ICA on the proliferation and metabolism of chondrocyte and synthesis of extracellular matrix are still unclear. This study aimed to investigate the role and regulation of far upstream element binding protein 1 (FUBP1) in chondrocytes treated with ICA to maintain homeostasis and suppress inflammatory responses. In the study, the effect of ICA on chondrocytes with overexpressed or silenced FUBP1 was detected by the MTS and single-cell cloning methods. The expression of hypoxia-inducible factor-1/2α (HIF-1/2α), FUBP1, matrix metalloproteinase (MMP)9, SRY-box transcription factor 9 (SOX9), and type II collagen (Col2α) in ATDC5 cells, a mouse chondrogenic cell line, treated with ICA was evaluated by immunoblotting. Western blotting revealed 1 µM ICA to have the most significant effect on chondrocytes. Alcian blue staining and colony formation assays showed that the promoting effect of ICA was insignificant in FUBP1-knockdown cells (P > 0.05) but significantly enhanced in FUBP1-overexpressed cells (P < 0.05). Western blot results from FUBP1-knockdown cells treated with or without ICA showed no significant difference in the expression of FUBP1, HIF-1/2α, MMP9, SOX9, and Col2α proteins, whereas the same proteins showed increased expression in FUBP1-overexpressed chondrocytes; moreover, HIF-2α and MMP9 expression was significantly inhibited in FUBP1-knockdown chondrocytes (P < 0.05). In conclusion, as a bioactive monomer of traditional Chinese medicine, ICA is beneficial to chondrocytes.
Wang et al. (2023) Icariin activates far upstream element binding protein 1 to regulate hypoxia-inducible factor-1α and hypoxia-inducible factor-2α signaling and benefits chondrocytes. PeerJ 11:e15917 https://doi.org/10.7717/peerj.15917
Skeletal anatomy of the early Permian parareptile Delorhynchus with new information provided by neutron tomography
Detailed description of the holotype skeleton of Delorhynchus cifellii, made possible through the use of neutron tomography, has yielded important new information about the cranial and postcranial anatomy of this early Permian acleistorhinid parareptile. Hitherto unknown features of the skull include a sphenethmoid, paired epipterygoids and a complete neurocranium. In addition, the stapes has been exposed in three dimensions for the first time in an early parareptile. Postcranial material found in articulation with the skull in this holotype allows for the first detailed description of vertebrae, ribs, shoulder girdle and humerus of an acleistorhinid parareptile, allowing for a reevaluation of the phylogenetic relationships of this taxon with other acleistorhinids, and more broadly among parareptiles. Results show that Delorhynchus is recovered as the sister taxon of Colobomycter, and ‘acleistorhinids’ now include Lanthanosuchus.
Rowe et al. (2023) Skeletal anatomy of the early Permian parareptile Delorhynchus with new information provided by neutron tomography. PeerJ 11:e15935 https://doi.org/10.7717/peerj.15935
Crown-of-thorns starfish spines secrete defence proteins
Background The crown-of-thorns starfish (COTS; Acanthaster species) is a slow-moving corallivore protected by an extensive array of long, sharp toxic spines. Envenomation can result in nausea, numbness, vomiting, joint aches and sometimes paralysis. Small molecule saponins and the plancitoxin proteins have been implicated in COTS toxicity. Methods Brine shrimp lethality assays were used to confirm the secretion of spine toxin biomolecules. Histological analysis, followed by spine-derived proteomics helped to explain the source and identity of proteins, while quantitative RNA-sequencing and phylogeny confirmed target gene expression and relative conservation, respectively. Results We demonstrate the lethality of COTS spine secreted biomolecules on brine shrimp, including significant toxicity using aboral spine semi-purifications of >10 kDa (p > 0.05, 9.82 µg/ml), supporting the presence of secreted proteins as toxins. Ultrastructure observations of the COTS aboral spine showed the presence of pores that could facilitate the distribution of secreted proteins. Subsequent purification and mass spectrometry analysis of spine-derived proteins identified numerous secretory proteins, including plancitoxins, as well as those with relatively high gene expression in spines, including phospholipase A2, protease inhibitor 16-like protein, ependymin-related proteins and those uncharacterized. Some secretory proteins (e.g., vitellogenin and deleted in malignant brain tumor protein 1) were not highly expressed in spine tissue, yet the spine may serve as a storage or release site. This study contributes to our understanding of the COTS through functional, ultrastructural and proteomic analysis of aboral spines.
Hillberg et al. (2023) Crown-of-thorns starfish spines secrete defence proteins. PeerJ 11:e15689 https://doi.org/10.7717/peerj.15689
Elevational surveys of Sulawesi herpetofauna 1: Gunung Galang, Gunung Dako Nature Reserve
The Indonesian island of Sulawesi has a unique geology and geography, which have produced an astoundingly diverse and endemic flora and fauna and a fascinating biogeographic history. Much biodiversity research has focused on the regional endemism in the island’s Central Core and on its four peninsulas, but the biodiversity of the island’s many upland regions is still poorly understood for most taxa, including amphibians and reptiles. Here, we report the first of several planned full-mountain checklists from a series of herpetological surveys of Sulawesi’s mountains conducted by our team. In more than 3 weeks of work on Gunung Galang, a 2,254 m peak west of the city of Tolitoli, Sulawesi Tengah Province, on Sulawesi’s Northern Peninsula, we recovered nearly fifty species of reptiles and amphibians, more than a dozen of which are either new to science or known but undescribed. The incompleteness of our sampling suggests that many more species remain to be discovered on and around this mountain.
Karin et al. (2023) Elevational surveys of Sulawesi herpetofauna 1: Gunung Galang, Gunung Dako Nature Reserve. PeerJ 11:e15766 https://doi.org/10.7717/peerj.15766
Acute effect of combined exercise with aerobic and resistance exercises on executive function
Objective Recent studies indicate that acute exercise, whether aerobic exercise (AE) or resistance exercise (RE), improves cognitive function. However, the effects on cognitive function of combined exercise (CE), involving both AE and RE in an exercise session, remain unknown. The aim of this study was to investigate the effects of acute CE on cognitive function. Design Within-subject design with counterbalancing. Methods Fifteen healthy men with a sedentary lifestyle in the previous three months were recruited. The participants were assessed for muscular fitness after performing four upper body exercises for a 10-repetition maximum and underwent a submaximal aerobic fitness assessment for V̇O2peak and corresponding workload (watts). They were then assigned to a CE, RE, or sitting control (SC) session in counterbalanced order and were assessed with the Stroop Color and Word Test (SCWT) after each session. Results Acute CE led to a significantly shorter response time compared to SC (p < .05) in the SCWT, wherein there were no significant differences between acute CE and RE (p = 1.00). Additionally, no significant differences in the accuracy rate were observed across the different sessions (ps > .05). Conclusion A single session of moderate-intensity CE improved response time in the SCWT, comparable to RE. CE shows promise for enhancing cognitive function, warranting further research on its benefits and other exercise modalities.
Chen et al. (2023) Acute effect of combined exercise with aerobic and resistance exercises on executive function. PeerJ 11:e15768 https://doi.org/10.7717/peerj.15768