Vitamin B2 (riboflavin) increases drought tolerance of Agaricus bisporus

Multi-scale characterisation of cold response reveals immediate and long-term impacts on cell physiology up to seed composition in sunflower

Early sowing can help summer crops escape drought and can mitigate the impacts of climate change on them. However, it exposes them to cold stress during initial developmental stages, which has both immediate and long-term effects on development and physiology. To understand how early night-chilling stress impacts plant development and yield, we studied the reference sunflower line XRQ under controlled, semi-controlled and field conditions. We performed high-throughput imaging of the whole plant parts and obtained physiological and transcriptomic data from leaves, hypocotyls and roots. We observed morphological reductions in early stages under field and controlled conditions, with a decrease in root development, an increase in reactive oxygen species content in leaves and changes in lipid composition in hypocotyls. A long-term increase in leaf chlorophyll suggests a stress memory mechanism that was supported by transcriptomic induction of histone coding genes. We highlighted DEGs related to cold acclimation such as chaperone, heat shock and late embryogenesis abundant proteins. We identified genes in hypocotyls involved in lipid, cutin, suberin and phenylalanine ammonia lyase biosynthesis and ROS scavenging. This comprehensive study describes new phenotyping methods and candidate genes to understand phenotypic plasticity better in response to chilling and study stress memory in sunflower.

Dipterocarpoidae genomics reveal their demography and adaptations to Asian rainforests

Dipterocarpoideae species form the emergent layer of Asian rainforests. They are the indicator species for Asian rainforest distribution, but they are severely threatened. Here, to understand their adaptation and population decline, we assemble high-quality genomes of seven Dipterocarpoideae species including two autotetraploid species. We estimate the divergence time between Dipterocarpoideae and Malvaceae and within Dipterocarpoideae to be 108.2 (97.8‒118.2) and 88.4 (77.7‒102.9) million years ago, and we identify a whole genome duplication event preceding dipterocarp lineage diversification. We find several genes that showed a signature of selection, likely associated with the adaptation to Asian rainforests. By resequencing of two endangered species, we detect an expansion of effective population size after the last glacial period and a recent sharp decline coinciding with the history of local human activities. Our findings contribute to understanding the diversification and adaptation of dipterocarps and highlight anthropogenic disturbances as a major factor in their endangered status.

The chromosome-level genome assembly of an endangered herb Bergenia scopulosa provides insights into local adaptation and genomic vulnerability under climate change

BACKGROUND

Global climate change poses severe threats to biodiversity and ecosystem stability. Rapid climate oscillations potentially lead to species geographic range shifts, population declines, and even extinctions. The rare and endangered species, being critical components of regional biodiversity, hold the key to understanding local adaptation and evolutionary processes shaping species distributions. Therefore, assessing the evolutionary mechanisms of local adaptation and population vulnerability under climate change is crucial for developing conservation strategies of endangered species.

RESULTS

In this study, we assembled a high-quality, chromosome-level genome of the rare and endangered herb Bergenia scopulosa in the Qinling Mountains in East Asia and resequenced 37 individual genomes spanning its entire geographic distributional ranges. By integrating population genetics, landscape genomics, and climate datasets, a substantial number of adaptive single-nucleotide polymorphism loci associated with climate variables were identified. The genotype-environment association analysis showed that some cold-tolerant genes have played pivotal roles in cold environmental adaptation of B. scopulosa. These findings are further corroborated through evolutionary analysis of gene family and quantitative PCR validation. Population genomic analysis revealed 2 distinct genetic lineages in B. scopulosa. The western lineage showed higher genomic vulnerability and more rare cold-tolerance alleles, suggesting its heightened sensitivity to impending climate shifts, and should be given priority conservation in the management practices.

CONCLUSIONS

These findings provide novel insights into local adaptation and genomic vulnerability of B. scopulosa under climate change in the Qinling Mountains in East Asia. Additionally, the study also offers valuable guidance for formulating conservation strategies for the rare and endangered plants.

Biochar Enhances the Resistance of Legumes and Soil Microbes to Extreme Short-Term Drought

Short-term drought events occur more frequently and more intensively under global climate change. Biochar amendment has been documented to ameliorate the negative effects of water deficits on plant performance. Moreover, biochar can alter the soil microbial community, soil properties and soil metabolome, resulting in changes in soil functioning. We aim to reveal the extent of biochar addition on soil nutrients and the soil microbial community structure and how this improves the tolerance of legume crops (peanuts) to short-term extreme drought. We measured plant performances under different contents of biochar, set as a gradient of 2%, 3% and 4%, after an extreme experimental drought. In addition, we investigated how soil bacteria and fungi respond to biochar additions and how the soil metabolome changes in response to biochar amendments, with combined growth experiments, high-throughput sequencing and soil omics. The results indicated that biochar increased nitrites and available phosphorus. Biochar was found to influence the soil bacterial community structure more intensively than the soil fungal community. Additionally, the fungal community showed a higher randomness under biochar addition when experiencing short-term extreme drought compared to the bacterial community. Soil bacteria may be more strongly related to soil nutrient cycling in peanut agricultural systems. Although the soil metabolome has been documented to be influenced by biochar addition independent of soil moisture, we found more differential metabolites with a higher biochar content. We suggest that biochar enhances the resistance of plants and soil microbes to short-term extreme drought by indirectly modifying soil functioning probably due to direct changes in soil moisture and soil pH.

Rebalancing Nutrients, Reinforcing Antioxidant and Osmoregulatory Capacity, and Improving Yield Quality in Drought-Stressed Phaseolus vulgaris by Foliar Application of a Bee-Honey Solution

Bee-honey solution (BHS) is considered a plant growth multi-biostimulator because it is rich in osmoprotectants, antioxidants, vitamins, and mineral nutrients that can promote drought stress (DtS) resistance in common bean plants. As a novel strategy, BHS has been used in a few studies, which shows that the application of BHS can overcome the stress effects on plant productivity and can contribute significantly to bridging the gap between agricultural production and the steady increase in population under climate changes. Under sufficient watering (SW (100% of crop evapotranspiration; ETc) and DtS (60% of ETc)), the enhancing impacts of foliar application with BHS (0%, 0.5%, 1.0%, and 1.5%) on growth, productivity, yield quality, physiological-biochemical indices, antioxidative defense ingredients, and nutrient status were examined in common bean plants (cultivar Bronco). DtS considerably decreased growth and yield traits, green pod quality, and water use efficiency (WUE); however, application of BHS at all concentrations significantly increased all of these parameters under normal or DtS conditions. Membrane stability index, relative water content, nutrient contents, SPAD (chlorophyll content), and PSII efficiency (Fv/Fm, photochemical activity, and performance index) were markedly reduced under DtS; however, they increased significantly under normal or DtS conditions by foliar spraying of BHS at all concentrations. The negative impacts of DtS were due to increased oxidants [hydrogen peroxide (H₂O₂) and superoxide (O₂^•-)], electrolyte leakage (EL), and malondialdehyde (MDA). As a result, the activity of the antioxidant system (ascorbate peroxidase, glutathione reductase, catalase, superoxide dismutase, α-tocopherol, glutathione, and ascorbate) and levels of osmoprotectants (soluble protein, soluble sugars, glycine betaine, and proline) were increased. However, all BHS concentrations further increased osmoprotectant and antioxidant capacity, along with decreased MDA and EL under DtS. What is interesting in this study was that a BHS concentration of 1.0% gave the best results under SW, while a BHS concentration of 1.5% gave the best results under DtS. Therefore, a BHS concentration of 1.5% could be a viable strategy to mitigate the DtS impairment in common beans to achieve satisfactory growth, productivity, and green pod quality under DtS.

Transcriptome Analysis of Persian Oak (Quercus brantii L.) Decline Using RNA-seq Technology

Since the late 1980s, the oak decline has affected the Zagros oak forests in western Iran. Persian oak (Quercus brantii L.) the most important tree species of these forests has been damaged more than any other plant species. In the present study, the RNA sequencing technique was used for the first time to identify key genes and molecular mechanisms involved in Persian oak decline. The RNA was extracted from the leaves of healthy and declined oak trees, and sequenced using the Illumina HiSeq 2500 platform (2 × 150 bp paired-end reads). De novo transcriptome assembly of Persian oak revealed 56,743 unigenes and 6049 differentially expressed genes (DEGs) between declined and control samples. The results of gene ontology analysis showed that most of the DEGs involved in oak decline belong to the group of stress-responsive genes. In general, oak decline samples showed significant reductions in gene expression associated with "photosynthesis and storage of sugar" and "protein synthesis and related processes." Additionally, DEGs related to the starch degradation pathway were up-regulated, whereas DEGs associated with acetate-mevalonate (MVA), biosynthesis of lignin, and lignases pathways were down-regulated. The present study's findings can be an effective step in identifying the genes involved in oak decline and deciphering the relationship between this phenomenon and biotic and abiotic stresses.

Fungal Priming: Prepare or Perish

Priming (also referred to as acclimation, acquired stress resistance, adaptive response, or cross-protection) is defined as an exposure of an organism to mild stress that leads to the development of a subsequent stronger and more protective response. This memory of a previously encountered stress likely provides a strong survival advantage in a rapidly shifting environment. Priming has been identified in animals, plants, fungi, and bacteria. Examples include innate immune priming and transgenerational epigenetic inheritance in animals and biotic and abiotic stress priming in plants, fungi, and bacteria. Priming mechanisms are diverse and include alterations in the levels of specific mRNAs, proteins, metabolites, and epigenetic changes such as DNA methylation and histone acetylation of target genes.

Root exudation of contrasting drought-stressed pearl millet genotypes conveys varying biological nitrification inhibition (BNI) activity

Roots secrete a vast array of low molecular weight compounds into the soil broadly referred to as root exudates. It is a key mechanism by which plants and soil microbes interact in the rhizosphere. The effect of drought stress on the exudation process and composition is rarely studied, especially in cereal crops. This study focuses on comparative metabolic profiling of the exudates from sensitive and tolerant genotypes of pearl millet after a period of drought stress. We employed a combined platform of gas and liquid chromatography coupled to mass spectrometry to cover both primary and secondary metabolites. The results obtained demonstrate that both genotype and drought stress have a significant impact on the concentration and composition of root exudates. The complexity and function of these differential root exudates are discussed. To reveal the potential effect of root exudates on the soil microbial community after a period of drought stress, we also tested for biological nitrification inhibition (BNI) activity. The analysis revealed a genotype-dependent enhancement of BNI activity after a defined period of drought stress. In parallel, we observed a genotype-specific relation of elongated root growth and root exudation under drought stress. These data suggest that the drought stress-dependent change in root exudation can manipulate the microbial soil communities to adapt and survive under harsh conditions.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s00374-021-01578-w.

Colors of life: a review on fungal pigments

Colorants find social and commercial applications in cosmetics, food, pharmaceuticals, textiles, and other industrial sectors. Among the available options, chemically synthesized colorants are popular due to their low-cost and flexible production modes, but health and environmental concerns have encouraged the valorization of biopigments that are natural and ecofriendly. Among natural biopigment producers, microorganisms are noteworthy for their all-seasonal production of stable and low-cost pigments with high-yield titers. Fungi are paramount sources of natural pigments. They occupy diverse ecological niches with adaptive metabolisms and biocatalytic pathways, making them entities with an industrial interest. Industrially important biopigments like carotenoids, melanins, riboflavins, azaphilones, and quinones produced by filamentous fungi are described within the context of this review. Most recent information about fungal pigment characteristics, biochemical production routes and pathways, potential applications, limitations, and future research perspectives are described.

Stress priming affects fungal competition - evidence from a combined experimental and modelling study

Priming, an inducible stress defence strategy that prepares an organism for an impending stress event, is common in microbes and has been studied mostly in isolated organisms or populations. How the benefits of priming change in the microbial community context and, vice versa, whether priming influences competition between organisms, remain largely unknown. In this study, we grew different isolates of soil fungi that experienced heat stress in isolation and pairwise competition experiments and assessed colony extension rate as a measure of fitness under priming and non-priming conditions. Based on this data, we developed a cellular automaton model simulating the growth of the ascomycete Chaetomium angustispirale competing against other fungi and systematically varied fungal response traits to explain similarities and differences observed in the experimental data. We showed that competition changes the priming benefit compared with isolated growth and that it can even be reversed depending on the competitor's traits such as growth rate, primeability and stress susceptibility. With this study, we transfer insights on priming from studies in isolation to competition between species. This is an important step towards understanding the role of inducible defences in microbial community assembly and composition.

Drought-Induced Stress Priming in Two Distinct Filamentous Saprotrophic Fungi

Sessile organisms constantly face environmental fluctuations and especially drought is a common stressor. One adaptive mechanism is "stress priming," the ability to cope with a severe stress ("triggering") by retaining information from a previous mild stress event ("priming"). While plants have been extensively investigated for drought-induced stress priming, no information is available for saprotrophic filamentous fungi, which are highly important for nutrient cycles. Here, we investigated the potential for drought-induced stress priming of one strain each of two ubiquitous species, Neurospora crassa and Penicillium chrysogenum. A batch experiment with 4 treatments was conducted on a sandy soil: exposure to priming and/or triggering as well as non-stressed controls. A priming stress was caused by desiccation to pF 4. The samples were then rewetted and after 1-, 7-, or 14-days of recovery triggered (pF 6). After triggering, fungal biomass, respiration, and β-glucosidase activity were quantified. P. chrysogenum showed positive stress priming effects. After 1 day of recovery, biomass as well as β-glucosidase activity and respiration were 0.5 to 5 times higher during triggering. Effects on biomass and activity decreased with prolonged recovery but lasted for 7 days and minor effects were still detectable after 14 days. Without triggering, stress priming had a temporary negative impact on biomass but this reversed after 14 days. For N. crassa, no stress priming effect was observed on the tested variables. The potential for drought-induced stress priming seems to be species specific with potentially high impact on composition and activity of fungal communities considering the expected increase of drought events.

Metabolic profiles of moso bamboo in response to drought stress in a field investigation

An increasing number of moso bamboo habitats are suffering severe drought events. The improvement in our understanding of the mechanisms of drought-resistance in moso bamboo benefits their genetic improvement and maintenance of forest sustainability. Here, we investigated the metabolic changes across the annual growth cycle of moso bamboo in the field under drought stress using liquid chromatography coupled to mass spectrometry (LC-MS) based on untargeted metabolomic profiling. Our results showed that the metabolic profiles induced by drought stress were relatively consistent among the three growth stages. Specifically, most responsive metabolites exhibited enhanced accumulation under drought stress, including anthocyanins, glycosides, organic acids, amino acids, and sugars and sugar alcohols. The potential metabolism pathways involved in the response to drought stress were mainly included into amino acid metabolism and sugar metabolism pathways. Five common responsive metabolic pathways were found among three growth stages, including linoleic acid metabolism, ubiquinone and other terpenoid-quinone biosynthesis, tyrosine metabolism, starch and sucrose metabolism and isoquinoline alkaloid biosynthesis. Overall, our findings provide new insights into the responsive mechanisms of the moso bamboo under drought stress in terms of metabolic profiles.