Transcriptome analysis of Arabidopsis reveals freezing-tolerance related genes induced by root endophytic fungus Piriformospora indica

Symbiont effector-guided mapping of proteins in plant networks to improve crop climate stress resilience: Symbiont effectors inform highly interconnected plant protein networks and provide an untapped resource for crop climate resilience strategies

There is an urgent need for novel protection strategies to sustainably secure crop production under changing climates. Studying microbial effectors, defined as microbe-derived proteins that alter signalling inside plant cells, has advanced our understanding of plant immunity and microbial plant colonisation strategies. Our understanding of effectors in the establishment and beneficial outcome of plant symbioses is less well known. Combining functional and comparative interaction assays uncovered specific symbiont effector targets in highly interconnected plant signalling networks and revealed the potential of effectors in beneficially modulating plant traits. The diverse functionality of symbiont effectors differs from the paradigmatic immuno-suppressive function of pathogen effectors. These effectors provide solutions for improving crop resilience against climate stress by their evolution-driven specification in host protein targeting and modulation. Symbiont effectors represent stringent tools not only to identify genetic targets for crop breeding, but to serve as applicable agents in crop management strategies under changing environments.

Nutrient and mycoremediation of a global menace 'arsenic': exploring the prospects of phosphorus and Serendipita indica-based mitigation strategies in rice and other crops

KEY MESSAGE

Serendipita indica induced metabolic reprogramming in colonized plants complements phosphorus-management in improving their tolerance to arsenic stress on multifaceted biological fronts. Restoration of the anthropic damage done to our environment is inextricably linked to devising strategies that are not only economically sound but are self-renewing and ecologically conscious. The dilemma of heavy metal (HM) dietary ingestion, especially arsenic (As), faced by humans and animals alike, necessitates the exploitation of such technologies and the cultivation of healthy and abundant crops. The remarkable symbiotic alliance between plants and 'mycorrhizas' has evolved across eons, benefiting growth/yield aspects as well as imparting abiotic/biotic stress tolerance. The intricate interdependence of Serendipita indica (S. indica) and rice plant reportedly reduce As accumulation, accentuating the interest of microbiologists, agriculturists, and ecotoxicological scientists apropos of the remediation mechanisms of As in the soil-AMF-rice system. Nutrient management, particularly of phosphorus (P), is also praised for mitigating As phytotoxicity by deterring the uptake of As molecules due to the rhizospheric cationic competition. Taking into consideration the reasonable prospects of success in minimizing As acquisition by rice plants, this review focuses on the physiological, metabolic, and transcriptional alterations underlying S. indica symbiosis, recuperation of As stress together with nutritional management of P by gathering case studies and presenting successful paradigms. Weaving together a volume of literature, we assess the chemical forms of As and related transport pathways, discuss As-P-rice interaction and the significance of fungi in As toxicity mitigation, predominantly the role of mycorrhiza, as well as survey of the multifaceted impacts of S. indica on plants. A potential strategy for simultaneous S. indica + P administration in paddy fields is proposed, followed by future research orientation to expand theoretic comprehension and encourage field-based implementation.

Fungal Endophytes as Mitigators against Biotic and Abiotic Stresses in Crop Plants

The escalating global food demand driven by a gradually expanding human population necessitates strategies to improve agricultural productivity favorably and mitigate crop yield loss caused by various stressors (biotic and abiotic). Biotic stresses are caused by phytopathogens, pests, and nematodes, along with abiotic stresses like salt, heat, drought, and heavy metals, which pose serious risks to food security and agricultural productivity. Presently, the traditional methods relying on synthetic chemicals have led to ecological damage through unintended impacts on non-target organisms and the emergence of microbes that are resistant to them. Therefore, addressing these challenges is essential for economic, environmental, and public health concerns. The present review supports sustainable alternatives, emphasizing the possible application of fungal endophytes as innovative and eco-friendly tools in plant stress management. Fungal endophytes demonstrate capabilities for managing plants against biotic and abiotic stresses via the direct or indirect enhancement of plants' innate immunity. Moreover, they contribute to elevated photosynthesis rates, stimulate plant growth, facilitate nutrient mineralization, and produce bioactive compounds, hormones, and enzymes, ultimately improving overall productivity and plant stress resistance. In conclusion, harnessing the potentiality of fungal endophytes represents a promising approach toward the sustainability of agricultural practices, offering effective alternative solutions to reduce reliance on chemical treatments and address the challenges posed by biotic and abiotic stresses. This approach ensures long-term food security and promotes environmental health and economic viability in agriculture.

Cactus Endophytic Fungi and Bioprospecting for their Enzymes and Bioactive Molecules: A Systematic Review

Endophytic fungi are associated with plant health and represent a remarkable source of potential of enzymes and bioactive compounds, but the diversity of endophytes remains uncertain and poorly explored, especially in Cactaceae, one of the most species-rich families adapted to growing in arid and semi-arid regions. The aim of this study was to conduct a systematic review on the diversity and bioprospecting of endophytic fungi from Cactaceae. We analysed peer-reviewed articles from seven databases using PRISMA guidelines. The results showed that the Cactaceae family is a source of new taxa, but the diversity of endophytic fungi of Cactaceae is little explored, mainly the diversity among tissues and by metagenomics. Bioprospecting studies have shown that these microorganisms can be used in the production of enzymes and larvicidal and antifungal compounds. Our results are relevant as a starting point for researchers to develop studies that expand the knowledge of plant mycobiota in arid and semi-arid ecosystems, as well as comprising a remarkable source of fungal compounds with several biotechnological applications.

Symbiont-host interactome mapping reveals effector-targeted modulation of hormone networks and activation of growth promotion

Plants have benefited from interactions with symbionts for coping with challenging environments since the colonisation of land. The mechanisms of symbiont-mediated beneficial effects and similarities and differences to pathogen strategies are mostly unknown. Here, we use 106 (effector-) proteins, secreted by the symbiont Serendipita indica (Si) to modulate host physiology, to map interactions with Arabidopsis thaliana host proteins. Using integrative network analysis, we show significant convergence on target-proteins shared with pathogens and exclusive targeting of Arabidopsis proteins in the phytohormone signalling network. Functional in planta screening and phenotyping of Si effectors and interacting proteins reveals previously unknown hormone functions of Arabidopsis proteins and direct beneficial activities mediated by effectors in Arabidopsis. Thus, symbionts and pathogens target a shared molecular microbe-host interface. At the same time Si effectors specifically target the plant hormone network and constitute a powerful resource for elucidating the signalling network function and boosting plant productivity.

Serendipita indica-A Review from Agricultural Point of View

Fulfilling the food demand of a fast-growing population is a global concern, resulting in increased dependence of the agricultural sector on various chemical formulations for enhancing crop production. This leads to an overuse of chemicals, which is not only harmful to human and animal health, but also to the environment and the global economy. Environmental safety and sustainable production are major responsibilities of the agricultural sector, which is inherently linked to the conservation of the biodiversity, the economy, and human and animal health. Scientists, therefore, across the globe are seeking to develop eco-friendly and cost-effective strategies to mitigate these issues by putting more emphasis on the use of beneficial microorganisms. Here, we review the literature on Serendipita indica, a beneficial endophytic fungus, to bring to the fore its properties of cultivation, the ability to enhance plant growth, improve the quality of produced crops, mitigate various plant stresses, as well as protect the environment. The major points in this review are as follows: (1) Although various plant growth promoting microorganisms are available, the distinguishing character of S. indica being axenically cultivable with a wide range of hosts makes it more interesting for research. (2) S. indica has numerous functions, ranging from promoting plant growth and quality to alleviating abiotic and biotic stresses, suggesting the use of this fungus as a biofertiliser. It also improves the soil quality by limiting the movement of heavy metals in the soil, thus, protecting the environment. (3) S. indica's modes of action are due to interactions with phytohormones, metabolites, photosynthates, and gene regulation, in addition to enhancing nutrient and water absorption. (4) Combined application of S. indica and nanoparticles showed synergistic promotion in crop growth, but the beneficial effects of these interactions require further investigation. This review concluded that S. indica has a great potential to be used as a plant growth promoter or biofertiliser, ensuring sustainable crop production and a healthy environment.

Minimizing the deleterious effects of endophytes in plant shoot tip cryopreservation

Plant cryopreservation technologies are used within gene banks for the long-term preservation of vegetatively propagated collections. Surface-sterilized plant tissues grown in the field, greenhouse/screenhouse, growth chamber, or in vitro are the source of shoot tips subjected to vitrification-based cryopreservation methods. Here, we describe the methods used to minimize microbial contamination during the tissue culture initiation process. We also discuss the occurrence and possible elimination of endophytes after extended in vitro culture and during recovery after liquid nitrogen exposure. We describe two case studies in which bacterial endophytes were observed in Citrus gene bank accessions during recovery after cryopreservation. These were identified using the MinION Oxford Nanopore system and Kirby-Bauer disc diffusion assays to examine the bacterial responses to antibiotic exposure. The methods used in this case study could be applied to identify endophytes to better target antimicrobial treatments of plant tissue collections.

High Ambient Temperature Regulated the Plant Systemic Response to the Beneficial Endophytic Fungus Serendipita indica

Most plants in nature establish symbiotic associations with endophytic fungi in soil. Beneficial endophytic fungi induce a systemic response in the aboveground parts of the host plant, thus promoting the growth and fitness of host plants. Meanwhile, temperature elevation from climate change widely affects global plant biodiversity as well as crop quality and yield. Over the past decades, great progresses have been made in the response of plants to high ambient temperature and to symbiosis with endophytic fungi. However, little is known about their synergistic effect on host plants. The endophytic fungus Serendipita indica colonizes the roots of a wide range of plants, including Arabidopsis. Based on the Arabidopsis-S. indica symbiosis experimental system, we analyzed the synergistic effect of high ambient temperature and endophytic fungal symbiosis on host plants. By transcriptome analysis, we found that DNA replication-related genes were significantly upregulated during the systemic response of Arabidopsis aboveground parts to S. indica colonization. Plant hormones, such as jasmonic acid (JA) and ethylene (ET), play important roles in plant growth and systemic responses. We found that high ambient temperature repressed the JA and ET signaling pathways of Arabidopsis aboveground parts during the systemic response to S. indica colonization in roots. Meanwhile, PIF4 is the central hub transcription factor controlling plant thermosensory growth under high ambient temperature in Arabidopsis. PIF4 is also involving JA and/or ET signaling pathway. We found that PIF4 target genes overlapped with many differentially expressed genes (DEGs) during the systemic response, and further showed that the growth promotion efficiency of S. indica on the pif4 mutant was higher than that on the wild-type plants. In short, our data showed that high ambient temperature strengthened the growth promotion effect of S. indica fungi on the aboveground parts of the host plant Arabidopsis, and the growth promotion effect of the systemic response under high ambient temperature was regulated by PIF4.

Dynamics of Etiolation Monitored by Seedling Morphology, Carotenoid Composition, Antioxidant Level, and Photoactivity of Protochlorophyllide in Arabidopsis thaliana

Although etiolated Arabidopsis thaliana seedlings are widely used as a model to study the de-etiolation process, the etiolation itself at the molecular level still needs elucidation. Here, we monitored the etiolation dynamics for wild type A. thaliana seedlings and lutein-deficient (lut2) mutant between 2 and 12 days of their growth in the absence of light. We analyzed the shape of the apex, the growth rate, the carotenoids and protochlorophyllide (Pchlide) accumulation, and the light-dependent protochlorophyllide oxidoreductase (LPOR) transcripts. Differences concerning the apical hook curvature and cotyledon opening among seedlings of the same age were observed, mostly after day 6 of the culture. We categorized the observed apex shapes and presented quantitatively how distribution among the categories changed during 12 days of seedling growth. The Pchlide₆₅₄/Pchlide₆₃₃ ratio, corresponding to the amount of the photoactive Pchlide, was the highest in the youngest seedlings, and decreased with their age. LPORA, LPORB, and LPORC transcripts were detected in etiolated seedlings, and their content decreased during seedling growth. Expression of SAG12 or SAG13 senescence markers, depletion in antioxidants, and excess ion leakage were not observed during the etiolation. Lack of lutein in the lut2 mutant resulted in slow Pchlide accumulation and affected other xanthophyll composition.

Unravelling the Role of Piriformospora indica in Combating Water Deficiency by Modulating Physiological Performance and Chlorophyll Metabolism-Related Genes in Cucumis sativus

Water stress is the most critical aspect restricting the development of agriculture in regions with scarce water resources, which requires enhancing irrigation water-saving strategies. The current work discusses the potential application of the plant-strengthening root endophyte Piriformospora indica against moderate (25% less irrigation water) and severe (50% less irrigation water) water stress in comparison to the optimum irrigation conditions of greenhouse cucumbers. P. indica improved growth, nutrient content, and photosynthesis apparatus under normal or water-stress conditions. On the other hand, moderate and severe water stress reduced yield up to 47% and 83%, respectively, in non-colonized cucumber plants, while up to 28 and 78%, respectively, in P. indica-colonized plants. In terms of water-use efficiency (WUE), P. indica improved the WUE of colonized cucumber plants grown under moderate (26 L/kg) or severe stress (73 L/kg) by supporting colonized plants in producing higher yield per unit volume of water consumed by the crop in comparison to non-colonized plants under the same level of moderate (43 L/kg) or severe (81 L/kg) water stress. Furthermore, P. indica increased the indole-3-acetic acid (IAA) content, activity levels of catalase (CAT) and peroxidase (POD) with an apparent clear reduction in the abscisic acid (ABA), ethylene, malondialdehyde (MDA), proline contents and stomatal closure compared to non-stressed plants under both water-stress levels. In addition, chlorophyll a, b, a + b contents were increased in the leaves of the colonized plants under water-stress conditions. This improvement in chlorophyll content could be correlated with a significant increment in the transcripts of chlorophyll biosynthesis genes (protochlorophyllide oxidoreductase [POR], chlorophyll a oxygenase [CAO]) and a reduction in the chlorophyll degradation genes (PPH, pheophorbide a oxygenase [PAO], and red chlorophyll catabolite reductase [RCCR]). In conclusion, P. indica has the potential to enhance the cucumber yield grown under moderate water stress rather than severe water stress by improving WUE and altering the activity levels of antioxidant enzymes and chlorophyll metabolism-related genes.

Conservation and divergence of the TaSOS1 gene family in salt stress response in wheat (Triticum aestivum L.)

Salinity is one of the most important problems that adversely affect crops growth, productivity and quality worldwide. Salt Overly Sensitive 1 (SOS1) gene family plays vital roles in plant response to salt stress. Herein, we report the identification of the SOS family in wheat and the exploration of the expression profiles of SOSs under salt stress. Complete genome sequences of T. aestivum were downloaded from Ensembl plant database. Conservation and divergence of TaSOS1 family were conducted by using phylogenetic tree, gene structure and synteny distribution analysis. Expression profiles of TaSOS1s were obtained based on transcriptome and qRT-PCR analysis. Totally, 119 TaSOS1 proteins in wheat were identified at the genome-wide level and classified into three groups. Six motifs were conserved in TaSOS1 gene family. Moreover, 25 TaSOS1 genes had three copies distributing in three sub-genomes (A, B and D). A total of 32, 28 and 29 TaSOS1 genes were located on the sub-genomes A, B and D, respectively. Moreover, there were 19, 12, 6, 7, 28, 5 and 12 genes located on the three homologous of chromosomes 1, 2, 3, 4, 5, 6 and 7, respectively. Two genes were mapped to unattributed scaffolds. The duplication events analysis indicated that tandem repeats contributed to the expansion of the SOS1 family in wheat. Collinearity analysis demonstrated that segmental duplications play an important role in the expansion of SOS1 members. Chromosome 7, 5, 3, and 2 showed collinear relationship. Tissue specific expression pattern analysis revealed that 41 TaSOS1 genes expressed in various tissues, such as root, shoot, leaf, spike and grain. Transcriptomic analysis revealed that 28 and 26 genes were up- and down-regulated under salinity stress, respectively, of which 18 genes were further confirmed by RT-qPCR. The plants with high expression level of these genes displayed higher tolerance to salinity stress, stronger root system, higher Fv/Fm value and water potential. The results could be helpful for further elucidating the molecular mechanism of TaSOS1 related to salt tolerance in wheat and provide a toolkit for improving the salinity tolerance of wheat.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01009-y.