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A major trade-off between growth and defense in Arabidopsis thaliana can vanish in field conditions
Get PDFWhen wild plants defend themselves from pathogens, this often comes with a trade-off: the same genes that protect a plant from disease can also reduce its growth and fecundity in the absence of pathogens. One protein implicated in a major growth-defense trade-off is ACCELERATED CELL DEATH 6 (ACD6), an ion channel that modulates salicylic acid (SA) synthesis to potentiate a wide range of defenses. Wild Arabidopsis thaliana populations maintain significant functional variation at the ACD6 locus, with some alleles making the protein hyperactive. In the greenhouse, plants with hyperactive ACD6 alleles are resistant to diverse pathogens, yet they are of smaller stature, their leaves senesce earlier, and they set fewer seeds compared to plants with the standard allele. We hypothesized that ACD6 hyperactivity would not only affect the growth of microbial pathogens but also more generally change leaf microbiome assembly. To test this in an ecologically meaningful context, we compared plants with hyperactive, standard, and defective ACD6 alleles in the same field-collected soil, both outdoors and in naturally lit and climate-controlled indoor conditions, taking advantage of near-isogenic lines as well as a natural accession and a CRISPR-edited derivative. We surveyed visual phenotypes, gene expression, hormone levels, seed production, and the microbiome in each environment. The genetic precision of CRISPR-edited plants allowed us to conclude that ACD6 genotype had no effect on mature field plants in our setting, despite reproducibly dramatic effects on greenhouse plants. We conclude that additional abiotic and/or microbial signals present outdoors-but not in the greenhouse-greatly modulate ACD6 activity. This raises the possibility that the fitness costs of other commonly studied immune system genes may be grossly misjudged without field studies
Genome editing for sustainable agriculture in Peru: advances, potential applications and regulation
Get PDFPeruvian agriculture is characterize by crops such as potato, maize, rice, asparagus, mango, banana, avocado, cassava, onion, oil palm, chili, papikra, blueberry, coffee, cacao, grapes, quinoa, olive, citrus and others. All of them have challenges in production in their specific agroecosystems under stress due to pests, diseases, salinity, drought, cold among others. Gene editing through CRISPR/Cas is a key tool for addressing critical challenges in agriculture by improving resilience to biotic and abiotic stress, increasing yield and enhancing the nutritional value of the crops. This approach allows precise mutation on site-specific gene at the DNA level, obtaining desirable traits when its function is altered. The CRISPR/Cas system could be used as a transgene-free genome editing tool when the ribonucleoprotein (RNP) acts as a carrier to delivered the CRISPR/Cas components into the plant cell protoplasts, or when the tRNA-like sequence (TLS) motifs are fused to single-guide RNA (sgRNA) and Cas mRNA sequence and expressed in transgenic plants rootstock to produce "mobile" CRISPR/Cas components to upper tissue (scion). Those innovations could be a potential approach to strengthen the Peruvian agriculture, food security and gricultural economy, especially in the tropical, Andean and coastal regions. This review article examines the advances and strategies of gene editing, focusing on transgene-free methodologies that could be adopted for research, development and use, and also identifies potential applications in key crops for Peru and analyzes their impact in the productivity and reduction of agrochemicals dependence. Finally, this review highlights the need to establish regulatory policies that strengthen the use of biotechnological precise innovations, ensuring the conservation and valorization of agrobiodiversity for the benefit of Peruvian farmers
Predicting gene distribution in ammonia-oxidizing archaea using phylogenetic signals
Get PDFPhylogenetic conservatism of microbial traits has paved the way for phylogeny-based predictions, allowing us to move from descriptive to predictive functional microbial ecology. Here, we applied phylogenetic eigenvector mapping to predict the presence of genes indicating potential functions of ammonia-oxidizing archaea (AOA), which are important players in nitrogen cycling. Using 160 nearly complete AOA genomes and metagenome assembled genomes from public databases, we predicted the distribution of 18 ecologically relevant genes across an updated amoA gene phylogeny, including a novel variant of an ammonia transporter found in this study. All selected genes displayed a significant phylogenetic signal and gene presence was predicted with an average of >88% accuracy, >85% sensitivity, and >80% specificity. The phylogenetic eigenvector approach performed equally well as ancestral state reconstruction of gene presence. We implemented the predictive models on an amoA sequencing dataset of AOA soil communities and showed key ecological predictions, e.g. that AOA communities in nitrogen-rich soils were predicted to have capacity for ureolytic metabolism while those adapted to low-pH soils were predicted to have the high-affinity ammonia transporter (amt2). Predicting gene presence can shed light on the potential functions that microorganisms perform in the environment, further contributing to a better mechanistic understanding of their community assembly
Recent advances and future directions on GLA-producing organisms
Get PDFGamma-linolenic acid (GLA) is a biologically active omega-6 fatty acid with anti-inflammatory, immunomodulatory, and cardiovascular protective effects. It is a vital constituent of human health and is finding more widespread applications in nutritional supplements, medications, and functional foods. GLA can be derived from many different natural sources, including plants, fungi, and microorganisms. This review paper presents an overview of the current advances in the discovery, metabolic engineering, and GLA-producing organism optimization. We further present a discussion on new biotechnological approaches-such as culture medium optimization, genetic engineering, and genome editing-that can be employed to enhance GLA production. The paper also presents new trends and directions in the commercial exploitation of GLA-containing products, unveiling new, health-oriented applications
The Arabidopsis thaliana core splicing factor PORCUPINE/SmE1 requires intron-mediated expression
Get PDFPlants are prone to genome duplications and tend to preserve multiple gene copies. This is also the case for the genes encoding the Sm proteins of Arabidopsis thaliana (L). The Sm proteins are best known for their roles in RNA processing such as pre-mRNA splicing and nonsense-mediated mRNA decay. In this study, we have taken a closer look at the phylogeny and differential regulation of the SmE-coding genes found in A. thaliana, PCP/SmE1, best known for its cold-sensitive phenotype, and its paralog, PCPL/SmE2. The phylogeny of the PCP homologs in the green lineage shows that SmE duplications happened multiple times independently in different plant clades and that the duplication that gave rise to PCP and PCPL occurred only in the Brassicaceae family. Our analysis revealed that A. thaliana PCP and PCPL proteins, which only differ in two amino acids, exhibit a very high level of functional conservation and can perform the same function in the cell. However, our results indicate that PCP is the prevailing copy of the two SmE genes in A. thaliana as it is more highly expressed and that the main difference between PCP and PCPL resides in their transcriptional regulation, which is strongly linked to intronic sequences. Our results provide insight into the complex mechanisms that underlie the differentiation of the paralogous gene expression as an adaptation to stress
Vulnerability and fascination with wildlife encounters and psychological restoration in local natural settings
Get PDFPeople often visit natural settings for recreation and psychological restoration. This study aims to improve understanding of how exposure to and experiences of mammalian wildlife in local natural settings can permit and promote recreation and restoration. Randomly sampled residents in three regions of Sweden (N = 303) with varying presence of fear-relevant species (wolf, wild boar) and fear-irrelevant species (roe deer, squirrel) completed a questionnaire. Squirrel and roe deer were rated significantly higher than wolf and wild boar for anticipated positive feelings and restoration outcomes, and significantly lower for negative feelings and avoidance of natural settings. The possibility of exposure explained little of the variation in the restoration variables, whereas the experiences anticipated with an animal encounter contributed substantially to explanation. Vulnerability seems to counteract the restorative benefit of fascination. Wildlife conservation efforts and public health initiatives may find practical utility in distinguishing between potential exposure and anticipated experience when designing interventions
Seasonal dynamics of biotoxins and potentially toxic phytoplankton in three Baltic Sea blue mussel farms
Get PDFCyanobacterial blooms are common in the Baltic Sea during summer, and even though several cyanobacteria are toxin producers, many organisms still ingest them as feed. These and other phytoplankton toxins can be detected in blue mussels accumulating over the season, which represents a potential health hazard for shellfish consumers. On a global scale, biotoxins therefore need to be quantified in shellfish before human consumption. We monitored 11 different groups of biotoxins in three blue mussel farms and the composition of 23 potentially toxin producing phytoplankton taxa from March to November 2022. None of the biotoxins were above available health guideline values nor regulated levels. However, the well-known cyanobacterial toxin in the Baltic Sea, nodularin, produced by Nodularia spumigena, was detected in net- and rope-farmed mussels throughout the summer, with the highest concentration of 47 mu g kg-1. In contrast, the less studied toxin cylindrospermopsin was only present in mussels in early spring and late fall (surface water temperature approx. 2-10 degrees C), with the maximum concentration of 19.7 mu g kg-1 in April, where Aphanizomenon is a potential producer, but yet not confirmed. Further, Dinophysis acuminata, a potential producer of Diarrhetic Shellfish Toxins (DSTs), was observed above warning levels at two sites with up to 2 400 individuals L-1, although the found concentration of 73 mu g kg-1 is below the regulated level for DST group (160 mu g kg-1). Altogether emphasizing that high species abundance does not necessarily result in a high toxin accumulation. On the other hand, mussels can serve effectively as indicator species, detecting the presence of novel toxins when producer abundance is low. As no period of the year was completely toxin-free, quantitative analysis is recommended when mussels are to be harvested
Tree rows and grass-strips increase water availability in fruit tree-crop agroforestry systems on sloping land
Get PDFSoil water conservation in upland areas characterised by slopes is extremely challenging. Information about soil water availability and variability, which can guide appropriate soil water management, is often lacking, including for agroforestry (AF) which is considered a sustainable farming practice in these regions. This study aims to describe how soil water is distributed and how it impacts crop growth and yield in an agroforestry system. Investigations were carried out in 2022–2023, in year 6 and 7 of an experiment wherein a fruit tree (mango and longan)-maize-grass treatment was compared to sole-maize in four replicates. Nine slope positions in each AF-plot were defined based on their distance from the tree rows, whilst three positions along the slope were selected in the sole-maize. Available soil water content (ASWC) down to 60 cm depth varied between 14 and 141 mm and was up to 28 mm higher in the AF system than the sole-maize following rain events. Generally, the ASWC was lower downslope than upslope of the tree rows and declined more rapidly after rain events. During the early dry season, ASWC was higher in mango-AF but lower in longan-AF compared to sole-maize, whereas the opposite was true late in the dry season. Maize grain yield was consistently lower in the zone immediately downslope (1.0 ton ha− 1 ) than upslope (3.2 ton ha− 1 ) of tree rows, but the yield-reducing effect downslope decreased with increasing distance from the tree rows and grass-strips. Water was generally not limiting maize yields. To conclude, ASWC was higher in AF than in sole-maize and increased more upslope than downslope of tree rows and grass strips immediately after rain events. The choice of tree species influenced ASWC in the dry season
Resistance and resilience of co-occurring nitrifying microbial guilds to drying-rewetting stress in soil
Get PDFNitrification, the oxidation of ammonia via nitrite to nitrate, contributes to nitrogen losses in agricultural soils. When nitrification is a two-step process, it depends on the successful metabolic interaction between ammonia oxidising archaea (AOA) and bacteria (AOB), and nitrite oxidising bacteria primarily within Nitrobacter (NIB) and Nitrospira (NIS). However, consequences of dry spells caused by climate change on the composition and co-associations of these microbial guilds and the fate of nitrogen remain unclear. Here we subject four distinct soils to either one long or two shorter drought periods (7-11 % water holding capacity) followed by rewetting in a microcosm experiment to evaluate the hypothesis that drying-rewetting stress triggers distinct responses in the functional guilds due to differences in environmental preferences and adaptation strategies. While AOB were highly resistant, AOA were the most sensitive to drying among the four guilds and decreased in relative abundance. This coincided with reduced ammonia oxidation rates in three soils by on average 27 % compared to the control. However, we observed almost full recovery of AOA one week after rewetting. NIS, but not NIB, were strongly affected by rewetting with no recovery during the experiment, showing shifts in community composition and relative abundance with up to 30 % affected ASVs. Network analysis revealed that drying-rewetting affected co-occurrences between ammonia and nitrite oxidisers in a soil-dependant manner, possibly indicating a destabilisation of their metabolic interaction. Overall, this study emphasises the importance to consider weather extremes like drought on soil nitrifier community dynamics and the fate of nitrogen in soils
Identification of lncRNAs involved in the hair follicle cycle transition of cashmere goats in response to photoperiod change
Get PDFBackgroundCashmere goats, as one of the important domesticated animal species, are known for their high-quality fiber. The growth of cashmere has seasonal variations caused by photoperiodic changes, but the molecular genetic mechanisms underlying this phenotype including the functional role of long non-coding RNAs (lncRNA) is still poorly understood.ResultsIn this study, we analyzed the RNA-seq dataset of 39 Cashmere goat skin samples including all different growth stages and identified 1591 lncRNAs. These lncRNAs exhibited growth stage-specific expression patterns. Combining shortened light and hair follicle growth cycles, we found that 68% of differentially photo-responsive lncRNAs showed similar expression trends during transition phase I (early anagen to anagen phase). This suggests that the mechanism of light-controlled induction of hair follicles from early anagen to anagen is similar to that of transition phase I. According to weighted gene co-expression network analyses (WGCNA) analysis, it was found that two gene clusters and 10 hub lncRNAs participated in the transformation of hair follicle cycle, inducing hair follicles to enter the full growth phase in advance. These hub lncRNAs may regulate the development cycle of hair follicles through cis- or trans-regulation on clock genes, SLC superfamily genes, fibroblast growth factor genes.ConclusionsThis study identified the key lncRNAs and target genes probably participating in the transformation of hair follicle cycle. This study will help further elucidate the role of lncRNAs in the hair follicle cycle and development