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RNA-viromics reveals diverse communities of soil RNA viruses with the potential to affect grassland ecosystems across multiple trophic levels
Get PDFThe distribution and diversity of RNA viruses in soil ecosystems are largely unknown, despite their significant impact on public health, ecosystem functions, and food security. Here, we characterise soil RNA viral communities along an altitudinal productivity gradient of peat, managed grassland and coastal soils. We identified 3462 viral contigs in RNA viromes from purified virus-like-particles in five soil-types and assessed their spatial distribution, phylogenetic diversity and potential host ranges. Soil types exhibited minimal similarity in viral community composition, but with >10-fold more viral contigs shared between managed grassland soils when compared with peat or coastal soils. Phylogenetic analyses predicted soil RNA viral communities are formed from viruses of bacteria, plants, fungi, vertebrates and invertebrates, with only 12% of viral contigs belonging to the bacteria-infecting Leviviricetes class. 11% of viral contigs were found to be most closely related to members of the Ourmiavirus genus, suggesting that members of this clade of plant viruses may be far more widely distributed and diverse than previously thought. These results contrast with soil DNA viromes which are typically dominated by bacteriophages. RNA viral communities, therefore, have the potential to exert influence on inter-kingdom interactions across terrestrial biomes
Clay-hydrochar composites return to cadmium contaminated paddy soil: Reduced Cd accumulation in rice seed and affected soil microbiome
No full textExcess cadmium (Cd) in rice precipitated by Cd contamination in paddy soils is a global human health threat and rational response is urgently needed. In this study, attapulgite-modified hydrochar (CA) and the montmorillonite-modified hydrochar (CM) were utilized in Cd-contaminated paddy soils at 0.5% (w/w) and 1% (w/w) application rates to investigate the effects of these clay-hydrochar composites on rice growth and soil Cd availability. The results show that the utility of CA and CM resulted in a significant increase in rice yield, especially at 1% application rate, which extended rice yield by 46.7–50.0% compared to 0.5% application rate. This is related to the Cd fixation and nutrient sequestration of the acidic functional groups on the surface of CA and CM. Additionally, CA-1% and CM-1% reduced the Cd concentration in rice seeds by 26.9–28.1% relative to the control. Notably, CA-1% showed the capacity to passivate Cd at the early stage of rice transplanting, lowering the proportion of Cd in the ion exchange state by 41.6% compared to the control, and this passivation effect persisted until the late stage of transplanted rice. The soil microbial community consequences showed that CA and CM did not significantly change the horizontal composition of the soil bacterial phylum and species diversity, indicating that CA and CM had excessive soil microbial adaptability. Moreover, results of correlation and Canonical Correspondence Analysis confirm that microbial genera responded significantly to the soil Cd morphologies, revealing the importance of CA and CM in the remediation of Cd-contaminated soils by influencing microorganisms. Our findings provide clay-hydrochar composites as a low-cost approach to effectively mitigate soil Cd contamination and improve the security and quality of rice
Exploring sex differences in fetal programming for childhood emotional disorders
No full textIn examining maternal depression, placental 11β-HSD2 mRNA expression and offspring cortisol regulation as a potential fetal programming pathway in relation to later child emotional disorders, it has become clear that sex differences may be important to consider. This study reports on data obtained from 209 participants in the Mercy Pregnancy and Emotional Wellbeing Study (MPEWS) recruited before 20 weeks of pregnancy. Maternal depressive disorders were diagnosed using the SCID-IV and maternal childhood trauma using the Childhood Trauma Questionnaire. Placental 11β-HSD2 mRNA was measured using qRT-PCR. For assessment of stress-induced cortisol reactivity, salivary cortisol samples were taken at 12 months of age. At 4 years of age, measurement of Childhood Emotional Disorders (depression and anxiety) was based on maternal report using the Preschool Age Psychiatric Assessment (PAPA) and internalizing symptoms using the Child Behavior Checklist (CBCL). Maternal depression in pregnancy and postpartum, and infant cortisol reactivity, was associated with internalizing symptoms for females only. For female offspring only, increased 12-month cortisol reactivity was also associated with increased emotional disorders at 4 years of age; however, there was no association with placental 11β-HSD2 mRNA expression. In females only, the combination of lower placental 11β-HSD2 mRNA expression and higher cortisol reactivity at 12 months of age predicted increased internalising problems. These findings suggest there may be sex differences in prenatal predictors and pathways for early childhood depression and anxiety symptoms and disorder
Agronomic performance of chickpea affected by drought stress at different growth stages
Get PDFSusceptibility to drought stress has restrained chickpea productivity at a global level, and the development of drought-tolerant varieties is essential to maintain its productivity. Therefore, the present study was conducted to evaluate genetic divergence in selected genotypes of chickpea and their morpho-physiological responses under irrigated and stressed conditions to identify the traits that account for the better performance of these genotypes under stressed conditions, as well as genotypes with improved drought tolerance. The genotypes were evaluated for two years under irrigated and drought stressed conditions, and significant variation was found amongst the genotypes for different morpho-physiological and yield traits. The maximum reduction was observed for plant yield (33.23%) under stressed conditions. Principle component analysis (PCA)-based biplots and correlation studies established its strong positive correlation with relative water content (RWC), membrane stability index (MSI), chlorophyll index (CI), secondary branches (SB) and yield traits and negative correlations with drought susceptibility index (DSI), days to maturity (DM) and 100 seed weight (100 SW) under drought stress, suggesting their use in selecting drought-tolerant germplasm. Ten genotypes with high values of RWC, MSI, CI, SB, yield traits and lower DSI were identified as drought-tolerant and might serve as ideal donors in the forthcoming breeding of elite chickpea cultivars. The seed-filling stage began earlier in these genotypes, with significantly reduced days to maturity under stressed conditions. Our results indicate selection for earliness offers a promising strategy for the development of drought-tolerant chickpea cultivars
Molecular and brain volume changes following aerobic exercise, cognitive and combined training in physically inactive healthy Late-Middle-Aged Adults: The Projecte Moviment Randomized Controlled Trial
Get PDFBehavioral interventions have shown promising neuroprotective effects, but the cascade of molecular, brain and behavioral changes involved in these benefits remains poorly understood. Projecte Moviment is a 12-week (5 days per week—45 min per day) multi-domain, single-blind, proof-of-concept randomized controlled trial examining the cognitive effect and underlying mechanisms of an aerobic exercise (AE), computerized cognitive training (CCT) and a combined (COMB) groups compared to a waitlist control group. Adherence was > 80% for 82/109 participants recruited (62% female; age = 58.38 ± 5.47). In this study we report intervention-related changes in plasma biomarkers (BDNF, TNF-α, HGF, ICAM-1, SDF1-α) and structural-MRI (brain volume) and how they related to changes in physical activity and individual variables (age and sex) and their potential role as mediators in the cognitive changes. Our results show that although there were no significant changes in molecular biomarker concentrations in any intervention group, changes in ICAM-1 and SDF1-α were negatively associated with changes in physical activity outcomes in AE and COMB groups. Brain volume changes were found in the CCT showing a significant increase in precuneus volume. Sex moderated the brain volume change in the AE and COMB groups, suggesting that men may benefit more than women. Changes in molecular biomarkers and brain volumes did not significantly mediate the cognitive-related benefits found previously for any group. This study shows crucial initial molecular and brain volume changes related to lifestyle interventions at early stages and highlights the value of examining activity parameters, individual difference characteristics and using a multi-level analysis approach to address these questions
Pride, belonging and community: What does this mean if you are Aboriginal and LGBT+ and living in Western Australia?
No full textThe lived experience of being LGBT+ and an Aboriginal person was a major focus of the mixed methods Breaking the Silence research project led by Aboriginal LGBT+ researchers. Aboriginal LGBT+ participants were invited to respond to a survey that canvassed how they were included and accepted within their own families, on social media, dating apps and the wider community. The analysis and discussion of the findings from the survey examine the issues of discrimination, racism, homophobia and what belonging to a community means for intersectional identities. The findings show that while participants do experience microaggressions and queer-phobia, they also describe agency and positive experiences. The question is how these instances of resistance and disruption can be enabled to proliferate and (if appropriate) be supported collectively, to enable Aboriginal LGBT+ individuals to experience a sense of pride and belonging to communities at times and in spaces of their own choosing
Biological control potential of trichoderma species and bacterial antagonists against Sclerotinia sclerotiorum on canola in Western Australia
Get PDFFifteen fungal and three bacterial biological control agents (F-BCA and B-BCA, respectively) were isolated from the canola production areas of Western Australia to investigate their potential for controlling sclerotinia stem rot (SSR) caused by Sclerotinia sclerotiorum under in vitro and field conditions. The capacity of these isolates to inhibit mycelial growth and sclerotia formation by S. sclerotiorum was assessed in dual culture tests in Petri dishes. Using Sanger Sequencing of the ITS regions, the F-BCAs were identified as Trichoderma atroviride (four isolates), T. gamsii (three isolates), T. koningiopsis (two isolates), T. longibrachiatum (two isolates), T. paraviridescens (two isolates), T. pseudokoningii (one isolate) and T. viridescens (one isolate). Four of the seven Trichoderma species (T. koningiopsis, T. gamsii, T. atroviride and T. viridescens) are reported for the first time from Western Australia. 16S rRNA sequencing identified B-BCA1 and B-BCA2 as Serratia proteamaculans and B-BCA3 as Ochrobactrum anthropi. There were significant differences among F-BCAs (P≤0.001) in their effect on radial mycelial growth (40–60% inhibition) and sclerotia formation (65–100% inhibition). Two isolates of T. atroviride (F-BCA12 and F-BCA15) completely blocked sclerotial formation of the pathogen on Potato dextrose agar + 10 ppm/L Aureomycin (PDAA). Incubation of sclerotia in soil inoculated with F-BCA indicated that sclerotia were colonized by the conidia of each F-BCA, and all sclerotia in the presence of F-BCAs failed to germinate on PDAA. The B-BCAs reduced radial mycelial growth by 57–59% and formation of sclerotia by 89–95%. Selected isolates of F-BCAs (T. koningiopsis and T. atroviride) and B-BCAs (O. anthropi and S. proteamaculans) significantly reduced disease incidence of S. sclerotiorum under glasshouse and field conditions. Field efficacy of tested BCAs was similar or better than the commercial fungicide Prosaro®
Induction of compression wood inhibits development of spiral grain in radiata pine
No full textSpiral grain refers to the helical patterns formed by the wood grain in the trunks of many tree species. In most gymnosperms, grain near the pith is vertical but wood formed after several years of growth has a slight to pronounced left-handed twist. Grain changes presumably involve the slow rotation of cells within the vascular cambium, but the mechanisms that allow this reorientation to occur remain unclear. Understanding this process is, however, important as the presence of strong spiral grain within the corewood of gymnosperms is a major wood quality issue devaluing cut timber. In this study, we measured wood grain in stems of Pinus radiata (radiata pine) saplings through reconstructions of resin canals that follow the grain, visualised by serial sectioning and scanning with circularly polarised light, and through X-ray computed microtomography (μCT) and image analysis in ImageJ. Vertical trees retained a symmetrical grain pattern that was weakly right-handed near the pith, but which became progressively more left-handed during the first eight months of growth. In tilted trees, however, the development of left-handed grain was inhibited by the formation of compression wood on the lower side of the tree whereas the wood on the upper side of the tree developed increasingly more left-handed grain as in the vertical controls. These results demonstrate that a previously unidentified link exists between compression wood formation and the inhibition of grain development
Machine learning-based detection of freezing events using infrared thermography
No full textFrost can cause irreversible damage to plant tissue and can significantly reduce yields and quality. A thorough understanding of the freezing dynamics is crucial to developing strategies for frost protection and the prevention of freezing damage. This study investigated artificial intelligence machine learning (ML) models to capture the thermodynamic patterns of freezing based on infrared thermography (IRT) imagery, which would help to automate the image analysis process in real-time or post frost events. A small-scale dataset of IRT images was collected to capture the freezing process from sample droplets containing ice-nucleating bacterium. We performed several ML experiments on the data to detect the transitions in temperatures from the images. We evaluated five popular ML models, namely support vector machines, random forest (RF), extreme gradient boosting (XGBoost), multi-layer perceptron, and convolutional neural networks. We analysed the dataset to classify adjacent temperature transitions. The results show that ML models can consistently capture the thermodynamics of frost events, i.e., ice-nucleation and freezing points on typical freezing curves. Amongst the ML models, RF and XGBoost achieved the best results, both with an average accuracy of 87–88% in classifying the temperatures. With 0.25 °C temperature transitions, RF model identified the ice nucleation and freezing points at around −2.25 °C to −2.75 °C and −4.25 °C to −4.75 °C, respectively. RF and XGBoost took about 7.3 ms and 5.5 ms time per image respectively, which indicates that these models can be used in real-time applications. Our study shows that ML models using IRT imagery can be used as an automatic real-time tool to accurately detect the critical temperatures for frost formation
